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Result Summary
| Number of genes | 26 | |
| Export | ||
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Ventral localization Posterior localization Dorsal localization Anterior localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Localized Posterior localization Embryonic localization patterns Ventral localization Dorsal localization Anterior localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Localized Embryonic localization patterns Ventral localization Posterior localization Germ band localization Dorsal localization Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Malpighian tubules Head Head epidermis Ectoderm Anal pad |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal Localized Subcellular localization patterns Cytoplasmic foci |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Weak expression (>41ms exp) Localized Subcellular localization patterns Ventral localization Exclusionary patterns Pole cell exclusion Apical exclusion Cytoplasmic foci Embryonic localization patterns Degraded Degraded partially stage 5 |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in mesoderm Expression in API Anterior blastoderm nuclei Localized Embryonic localization patterns Ventral localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in neuroblasts Expression in mesoderm Anterior blastoderm nuclei Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Ventral localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Salivary glands Muscles-embryo Muscles - subregion Midgut Blastoderm nuclei Localized Subcellular localization patterns Foci Small Foci Small Foci in muscle cells |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| The probe looks good on gel. |
| It is expressed on the ventral side of the developing embryo, it accumulates in the cytoplasm. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Zygotic Zygotic starting stage 3 Cortical nuclei All cortical nuclei Ubiquitous Localized Subcellular localization patterns Nuclei associated localization Cytoplasmic foci |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Yolk nuclei Subset yolk nuclei Random yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Dorsal blastoderm nuclei All blastoderm nuclei Transiently widespread Ubiquitous Localized Subcellular localization patterns Yolk plasm localization Ventral localization Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around yolk nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation in subset nuclei Exclusionary patterns Pole cell exclusion Dorsal localization Cytoplasmic foci |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in mesoderm Expression in ectoderm Expression in API All blastoderm nuclei Ubiquitous Localized Subcellular localization patterns Nuclei-associated localization Cytoplasmic foci |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in mesoderm Expression in ectoderm Expression in API All blastoderm nuclei Transiently widespread Ubiquitous Localized Subcellular localization patterns Cytoplasmic foci Germ cell localization Germ cell enrichment Degraded Degraded partially stage 9 |
| stage 10-17 |
|
Stage 10-17 Non-Expressed |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -probes were designed against RA isoform |
| -tested using HCR-FISH probes (3 probe sets) |
| -expression pattern aligns well with modENCODE RNA-seq data -observed possible early lateral or dorsal-ventral localization of early ectoderm |
| -bright foci is mostly background |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Posterior blastoderm nuclei Localized Subcellular localization patterns Ventral localization Exclusionary patterns Pole cell exclusion Degraded Degraded partially stage 5 Degraded partially stage 4 |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in mesoderm Localized Subcellular localization patterns Exclusionary patterns Embryonic localization patterns Ventral localization Exclusionary patterns Pole cell exclusion |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Yolk nuclei Subset yolk nuclei Random yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Anterior blastoderm nuclei |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Blastoderm nuclei |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| Low probe on gel... still, good in situ. |
| Salivary glands, midgut and other expression. |
| Zygotic expression at the anterior and posterior midgut nuclei and other cells. Dynamic expression. |
Probe CR46003-RC Links: Permalink
Genes: CR46003
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
Stage 1-3 Non-Expressed |
|
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Dorsal blastoderm nuclei Localized Subcellular localization patterns Ventral localization Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation nuclear subregion Accumulation in subset nuclei Dorsal localization Cytoplasmic foci Basal localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in ectoderm Dorsal blastoderm nuclei Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Ventral localization Dorsal localization Degraded Degraded partially stage 7 |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in ectoderm Localized Subcellular localization patterns Nuclei-associated localization Cytoplasmic foci Embryonic localization patterns Ventral localization Degraded Degraded partially stage 8 Degraded completely stage 9 |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Segmented pattern Neuroblasts Polarized Neuroblasts Head Head epidermis Ectoderm Polarized Ectoderm CNS Ventral nerve cord Perinuclear VNC Nuclear - VNC Foci - VNC Polarized CNS Brain Localized Subcellular localization patterns Perinuclear localization Perinuclear around CNS nuclei Nuclei-associated localization Nuclear in CNS Foci Small Foci Small Foci in CNS Small Foci in Brain Basal enrichment Basal (outside) in CNS Basal (outside) in brain |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RC isoform transcript |
| -the gene is a lncRNA with quite interesting patterns in the CNS (brain and VNC) |
| -seems to be expressed in the anterior transverse furrow, shown in stage 6-7 images |
Probe CR46452-RA Links: Permalink
Genes: CR46452
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
Stage 1-3 Non-Expressed |
|
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Pair-rule pattern Dorsal blastoderm nuclei Ubiquitous Localized Subcellular localization patterns Ventral localization Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Exclusionary patterns Pole cell exclusion Apical exclusion Dorsal localization Cytoplasmic foci Basal localization Basal enrichment |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Pair-rule pattern Ubiquitous Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Cytoplasmic foci Embryonic localization patterns Ventral localization Degraded Degraded partially stage 6 |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in mesoderm Expression in ectoderm Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Germ band localization Degraded Degraded partially stage 8 Degraded completely stage 9 |
| stage 10-17 |
Stage 10-17 Non-Expressed |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
| -interesting 7-stripe pattern observed in the blastoderm/epidermis |
Probe E-spl-malpha-BFM-RA Links: Permalink
Genes: E(spl)malpha-BFM
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Localized Subcellular localization patterns Ventral localization Basal localization Basal enrichment |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Dorsal blastoderm nuclei |
| stage 8-9 |
|
Stage 8-9 Expressed Ubiquitous Localized Embryonic localization patterns Ventral localization Germ band localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Muscles-embryo Visceral mesoderm Head Head epidermis Ectoderm |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -Our experiment did not observe the same late stage patterns observed by BDGP (i.e. dorsal vessel, tracheal system, certain epidermal signals) |
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
Probe Hsromega-ex Links: Permalink
Genes: Hsr-omega
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Yolk nuclei Subset yolk nuclei Ventral yolk nuclei Posterior yolk nuclei Anterior yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Posterior blastoderm nuclei Anterior blastoderm nuclei Strong expression (1-20ms exp) Localized Subcellular localization patterns Ventral localization Posterior localization Exclusionary patterns Pole cell exclusion Basal localization Anterior localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Posterior blastoderm nuclei Anterior blastoderm nuclei Localized Posterior localization Embryonic localization patterns Ventral localization Anterior localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Segment polarity pattern Expression in ectoderm Strong expression (1-20ms exp) Localized Embryonic localization patterns Germ band localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Yolk nuclei Midgut Head Head epidermis Ectoderm CNS Ventral nerve cord Brain Amnioserosa Ubiquitous |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting common exons |
| -lcnRNA |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Strong expression (1-20ms exp) Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Strong expression (1-20ms exp) Maternal Localized Subcellular localization patterns Ventral localization Posterior localization Exclusionary patterns Basal localization Basal enrichment Apical localization Apical enrichment Diffuse apical localization Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Strong expression (1-20ms exp) Maternal Localized Subcellular localization patterns Other subcellular pattern Exclusionary patterns Cytoplasmic foci Apical localization Apical enrichment Diffuse apical localization Embryonic localization patterns Degraded Degraded partially stage 7 Degradation maternal transcripts |
| stage 8-9 |
|
Stage 8-9 Expressed Strong expression (1-20ms exp) Localized Subcellular localization patterns Other subcellular pattern Exclusionary patterns Apical localization Apical enrichment Diffuse apical localization Apical Localization Neuroblasts Embryonic localization patterns Ventral localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Segmented pattern Neuroblasts CNS Localized |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| Ventral nerve cord, midgut, muscles, etc. |
| Posterior gradient, enriched ventrally. Strong expression. |
| Good probe on gel. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Maternal Localized Subcellular localization patterns Ventral localization Other subcellular pattern Exclusionary patterns Pole cell exclusion Apical exclusion |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Maternal Localized Embryonic localization patterns Ventral localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in neuroblasts Expression in mesoderm Maternal Localized Subcellular localization patterns Perinuclear localization Embryonic localization patterns Ventral localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic CNS Ventral nerve cord Brain Localized Subcellular localization patterns |
Larva
| Area | Images | Terms |
|---|---|---|
| fat body |
|
3rd Instar Larval Tissues Fat body Subcellular Localization - Fat body Fat body - Nuclear localization Fat body - Subnuclear localization Nascent transcript in fat body Expressed in fat body Fat body allover - Ubiquitous |
| intestine |
|
3rd Instar Larval Tissues Intestine Expressed in midgut Subcellular localization in midgut Midgut - foci Midgut - Few foci Expressed in hindgut Subcellular localization in hindgut Nuclear in hindgut Hindgut - subnuclear localization Hindgut foci Expressed in gastric caeca Gastric caeca allover |
| salivary gland |
|
3rd Instar Larval Tissues Salivary gland Subcellular localization in salivary gland Salivary gland - apical Salivary gland - lumen Expressed in salivary glands Salivary glands allover |
Adult
| Area | Images | Terms |
|---|
Comments
| Probe on gel a bit low. Good in situ! |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Dorsal blastoderm nuclei Anterior blastoderm nuclei Weak expression (>41ms exp) Localized Subcellular localization patterns Ventral localization Other subcellular pattern Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation nuclear subregion Exclusionary patterns Pole cell exclusion Dorsal localization Cell division apparatus Other cell division pattern Basal localization Basal enrichment Apical localization Apical enrichment Diffuse apical localization Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Weak expression (>41ms exp) Localized Subcellular localization patterns Other subcellular pattern Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation nuclear subregion Exclusionary patterns Cell division apparatus Apical localization Apical enrichment Discrete apical foci Apical clusters Embryonic localization patterns Ventral localization Exclusionary patterns Pole cell exclusion Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in neuroblasts Expression in amnioserosa Weak expression (>41ms exp) Localized Subcellular localization patterns Perinuclear localization Nuclei-associated localization Cytoplasmic foci Apical localization Apical enrichment Diffuse apical localization Apical Localization Neuroblasts Embryonic localization patterns Ventral localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic PNS Fat body Fat body- specific region Fat body polarized Dorsal vessel Dorsal vessel specific pattern CNS Ventral nerve cord Polarized VNC Perinuclear VNC Polarized CNS Brain Blastoderm nuclei Amnioserosa Localized Subcellular localization patterns Perinuclear localization Perinuclear polarized Perinuclear around fat body nuclei Perinuclear around CNS nuclei Membrane associated Foci Small Foci Small Foci in fat body Small Foci in dorsal vessel |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Ventral localization Posterior localization Dorsal localization Anterior localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Posterior localization Embryonic localization patterns Ventral localization Dorsal localization Anterior localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Embryonic localization patterns Ventral localization Posterior localization Dorsal localization Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Posterior spiracles Muscles-embryo Muscles - subregion Maxillary complex Head Head epidermis Ectoderm Brain |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
| -There is no entry for this gene on BDGP, and modENCODE RNAseq data on FlyBase indicates that it is not expressed in the embryo. However, we observed obvious patterns during embryogenesis. Additionally, FlyBase does not have any in-depth characterizations of this gene. |
| -Osi21 does not overlap with any other genes, ruling out the possibility of the targeting of alternative transcripts. BLAST also confirms the specificity of our probes to Osi21. Additionally, no other genes for which probes were designed for on this plate show patterns such as those observed here, ruling out the possibility of cross-contamination during probe preparation. |
| -This may be a result of Osi21's poor characterization or incorrect RNAseq data |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Yolk nuclei All yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Medium expression (21-40ms exp) Localized Subcellular localization patterns Ventral localization Exclusionary patterns Pole cell exclusion Basal localization Basal enrichment Apical localization Apical enrichment Diffuse apical localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Yolk nuclei Weak expression (>41ms exp) Localized Subcellular localization patterns Perinuclear localization Perinuclear around yolk nuclei Other subcellular pattern |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Ubiquitous Localized Subcellular localization patterns Ventral localization Dorsal localization Cytoplasmic foci |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Ventral localization Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Ventral localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Head Head epidermis Ectoderm CNS Ventral nerve cord Foci - VNC Brain Localized Subcellular localization patterns Foci Small Foci Small Foci in CNS Small Foci in Brain |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Ventral localization Posterior localization Dorsal localization Anterior localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Posterior localization Embryonic localization patterns Ventral localization Dorsal localization Anterior localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Embryonic localization patterns Ventral localization Posterior localization Germ band localization Dorsal localization Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Head Head epidermis Ectoderm |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Yolk nuclei Subset yolk nuclei Random yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Terminal-gene pattern Gap-gene pattern Localized Subcellular localization patterns Ventral localization Posterior localization Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around yolk nuclei Membrane associated Exclusionary patterns Pole cell exclusion Apical localization Apical enrichment Diffuse apical localization Anterior localization Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Yolk Nuclei Subset yolk nuclei Random yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around yolk nuclei Exclusionary patterns Apical localization Apical enrichment Diffuse apical localization Embryonic localization patterns Exclusionary patterns Pole cell exclusion |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Expression in neuroblasts Expression in ectoderm Localized Subcellular localization patterns Perinuclear localization Perinuclear around blastoderm nuclei Other subcellular pattern Nuclei-associated localization Intranuclear accumulation |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Segmented pattern Ring gland Proventriculus PNS Neuroblasts Polarized Neuroblasts Muscles-embryo Visceral mesoderm Specific visceral mesoderm pattern Muscles - subregion Midgut Midgut subset Midgut ICPs Hindgut Head Fat body Ectoderm Polarized Ectoderm CNS Ventral nerve cord Nuclear - VNC Axons Brain Blastoderm nuclei Atrium Anal pad Localized Subcellular localization patterns Perinuclear localization Nuclei-associated localization Nuclear in PNS Nuclear in CNS Accumulation nuclear subregion Accumulation entire nucleus Cell extensions or 'podia' Apical enrichment Apical enriched midgut Apical enriched hindgut |
Larva
| Area | Images | Terms |
|---|---|---|
| fat body |
|
3rd Instar Larval Tissues Fat body Subcellular Localization - Fat body Cytoplasmic foci-fat body Expressed in fat body Fat body allover - Ubiquitous |
| intestine |
|
3rd Instar Larval Tissues Intestine Not expressed in the intestine |
| imaginal discs |
|
3rd Instar Larval Tissues Imaginal discs Not expressed in imaginal discs |
| salivary gland |
|
3rd Instar Larval Tissues Salivary gland Not expressed in salivary glands |
Adult
| Area | Images | Terms |
|---|
Comments
| Good probe on gel Maybe some small foci. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal Localized Subcellular localization patterns Cytoplasmic foci |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Localized Subcellular localization patterns Ventral localization Basal localization Basal enrichment Degraded Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in ectoderm Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Basal localization Embryonic localization patterns Ventral localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Pair-rule pattern Expression in neuroblasts Expression in ectoderm Dorsal blastoderm nuclei Anterior blastoderm nuclei Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Posterior localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system PNS Neuroblasts Polarized Neuroblasts Head Head epidermis Ectoderm CNS Ventral nerve cord Polarized VNC Perinuclear VNC Brain Localized Subcellular localization patterns Foci Small Foci Small Foci in ectoderm |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA transcript isoform |
| -neat marker for neural precursor formation, appears to not be expressed past stage 13-14 except for 4 small points near the dorsal-posterior region of the ectoderm (possibly tip cells of the Malpighian tubules); clear stomatogastric nervous system primordium expression |
| -images are from two separate experiments under identical conditions for better coverage |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed Expressed Ubiquitous |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Subcellular localization patterns Ventral localization Dorsal localization Cytoplasmic foci |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Embryonic localization patterns Ventral localization Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Localized Embryonic localization patterns Ventral localization Germ band localization Dorsal localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Segmented pattern Hindgut Ectoderm Polarized Ectoderm CNS Ventral nerve cord Polarized VNC Brain |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Gap-gene pattern Strong expression (1-20ms exp) Localized Subcellular localization patterns Yolk plasm localization Ventral localization Dorsal localization Cytoplasmic foci Anterior localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Gap-gene pattern Expression in ectoderm Strong expression (1-20ms exp) Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Ventral localization Anterior localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in ectoderm Strong expression (1-20ms exp) Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Germ band localization Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Hindgut Specific hindgut area or cells Head Head epidermis Ectoderm Anal pad Ring around anal pad Strong expression (1-20ms exp) |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting common exons |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Strong expression (1-20ms exp) Localized Subcellular localization patterns Ventral localization Exclusionary patterns Pole cell exclusion Dorsal localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Pair-rule pattern Expression in ectoderm Strong expression (1-20ms exp) Localized Embryonic localization patterns Ventral localization Exclusionary patterns Pole cell exclusion Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Strong expression (1-20ms exp) Localized Embryonic localization patterns Ventral localization Germ band localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Segmented pattern PNS Optic lobes primordium Head Head epidermis Ectoderm CNS Brain Strong expression (1-20ms exp) |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Medium expression (21-40ms exp) Maternal Localized Subcellular localization patterns Posterior localization RNA islands Pole plasm Pole buds Anterior localization Embryonic localization patterns |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei All blastoderm nuclei Maternal Localized Subcellular localization patterns Ventral localization Exclusionary patterns Pole cell exclusion Anterior localization Embryonic localization patterns Degraded Degraded partially stage 4 Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern All blastoderm nuclei Localized Embryonic localization patterns Ventral localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Anterior blastoderm nuclei |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Single stripe Segmented pattern Segment polarity pattern Pair-rule pattern Dorsal blastoderm nuclei Anterior blastoderm nuclei Localized Subcellular localization patterns Ventral localization Nuclei-associated localization Intranuclear accumulation Accumulation in subset nuclei Dorsal localization Cytoplasmic foci Apical localization Apical enrichment |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Segment polarity pattern Posterior blastoderm nuclei Expression in ectoderm Dorsal blastoderm nuclei Localized Subcellular localization patterns Cytoplasmic foci Apical localization Apical enrichment Posterior localization Embryonic localization patterns Ventral localization Dorsal localization Degraded Degraded partially stage 7 |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Zygotic starting stage 9 Zygotic starting stage 8 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Segment polarity pattern Expression in ectoderm Dorsal blastoderm nuclei Degraded Degraded partially stage 8 |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system PNS Maxillary complex Head Head epidermis Clypeo-labral bud Localized Subcellular localization patterns Perinuclear localization Perinuclear around PNS nuclei |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA isoform transcript |
| -retested recently for late stage coverage (2025); appears to be expressed in a different program in the gnathal elements and sensory regions in late stages |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Localized Subcellular localization patterns Ventral localization Exclusionary patterns Pole cell exclusion Apical localization Apical enrichment Degraded Degraded partially stage 5 Degraded partially stage 4 |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Localized Embryonic localization patterns Ventral localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in neuroblasts Localized Embryonic localization patterns Ventral localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system PNS Head CNS Brain Localized Subcellular localization patterns Perinuclear localization Perinuclear around PNS nuclei |
Larva
| Area | Images | Terms |
|---|---|---|
| intestine |
|
3rd Instar Larval Tissues Intestine Not expressed in the intestine |
| imaginal discs |
|
3rd Instar Larval Tissues Imaginal discs Not expressed in imaginal discs |
| nervous system |
|
3rd Instar Larval Tissues Nervous system Expressed in brain lobes Brain lobes - Significant area Brain lobes - Foci or dots |
| salivary gland |
|
3rd Instar Larval Tissues Salivary gland Not expressed in salivary glands |
| ovary and testis |
|
3rd Instar Larval Tissues Larval Ovary and Testis-Larva Not expressed in larval testis |
Adult
| Area | Images | Terms |
|---|
Comments
| Good probe on gel. |
| Interesting expression and localization patterns. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 5 Localized Subcellular localization patterns Ventral localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Localized Embryonic localization patterns Ventral localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in mesoderm Expression in ectoderm Localized Embryonic localization patterns Germ band localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Muscles-embryo Visceral mesoderm Hindgut Esophagus |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting common exons |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Non-Expressed |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Zygotic starting stage 4 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Posterior blastoderm nuclei Anterior blastoderm nuclei Localized Subcellular localization patterns Ventral localization Posterior localization Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Exclusionary patterns Yolk plasm exclusion Pole cell exclusion Cytoplasmic foci Basal localization Basal enrichment Apical localization Apical enrichment Diffuse apical localization Anterior localization |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in mesoderm Expression in ectoderm Anterior blastoderm nuclei Localized Yolk cortex localization Yolk cortex enrichment Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Exclusionary patterns Yolk cortex exclusion Basal localization Basal enrichment Apical localization Apical enrichment Diffuse apical localization Posterior localization Embryonic localization patterns Anterior localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Pair-rule pattern Expression in mesoderm Expression in ectoderm Expression in API Localized Subcellular localization patterns Perinuclear localization Perinuclear around blastoderm nuclei Cytoplasmic foci Basal localization Basal enrichment Embryonic localization patterns Ventral localization Germ band localization Dorsal localization Anterior localization Degraded Degraded partially stage 9 |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Muscles-embryo Visceral mesoderm Specific visceral mesoderm pattern Muscles - subregion Hindgut Head Foregut Esophagus Ectoderm Localized Subcellular localization patterns Perinuclear localization Perinuclear around muscle nuclei |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -retested using HCR-FISH 2025 for full coverage of late stage expression patterns |
| -performed using 3 probe pairs (HCR-FISH) against the RB isoform |
| -really interesting patterns! |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Zygotic Zygotic starting stage 3 Ubiquitous Localized Subcellular localization patterns Nuclei associated localization Intranuclear accumulation Accumulation in subset nuclei Cytoplasmic foci |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Pole cell nuclei Subset pole cell nuclei Blastoderm nuclei Subset blastoderm nuclei Posterior blastoderm nuclei Dorsal blastoderm nuclei Anterior blastoderm nuclei Localized Subcellular localization patterns Yolk cortex localization Yolk cortex enrichment Ventral localization Posterior localization Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Exclusionary patterns Yolk plasm exclusion Yolk cortex exclusion Basal localization Apical localization Apical enrichment Anterior localization Embryonic localization patterns |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Pole cell nuclei Subset pole cell nuclei Blastoderm nuclei Subset blastoderm nuclei Expression in ectoderm Expression in API Dorsal blastoderm nuclei Localized Yolk cortex localization Yolk cortex enrichment Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around pole cell nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation in subset nuclei Exclusionary patterns Yolk plasm exclusion Yolk cortex exclusion Cytoplasmic foci Pole cell localization Pole cell enrichment Embryonic localization patterns Dorsal localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Germ cell nuclei Subset pole cell nuclei Blastoderm nuclei Subset blastoderm nuclei Expression in ectoderm Expression in API Expression in amnioserosa Dorsal blastoderm nuclei Localized Yolk cortex localization Yolk cortex enrichment Subcellular localization patterns Perinuclear localization Perinuclear around pole cell nuclei Exclusionary patterns Yolk plasm exclusion Yolk cortex exclusion Cytoplasmic foci Basal localization Germ cell localization Germ cell enrichment Embryonic localization patterns Dorsal localization Degraded Degraded partially stage 9 |
| stage 10-17 |
Stage 10-17 Non-Expressed |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA transcript isoform |
| -neat expression patterns in early embryos and early germ band elongation stages; expression is no longer detectable after stage 9-10 (fits modENCODE RNA-seq data well) |