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Result Summary
| Number of genes | 12 | |
| Export | ||
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
| stage 4-5 |
Stage 4-5 Expressed Weak expression (>41ms exp) Ubiquitous Maternal |
|
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Posterior spiracles Specific posterior spiracle pattern Maxillary complex Localized |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| Rays - posterior spiracles. |
| 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 Weak expression (>41ms exp) Maternal Localized Subcellular localization patterns Exclusionary patterns Pole cell exclusion Apical exclusion Cytoplasmic foci Embryonic localization patterns Degraded Degraded partially stage 5 Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Weak expression (>41ms exp) Ubiquitous |
| stage 8-9 |
|
Stage 8-9 Expressed Weak expression (>41ms exp) Ubiquitous Localized Subcellular localization patterns Cytoplasmic foci |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Pharynx Midgut Maxillary complex Malpighian tubules Hindgut Foregut Fat body Ectoderm CNS Brain Localized Subcellular localization patterns Foci Small Foci Small Foci in Pharynx Small Foci in midgut Small Foci in Malpighian tubules Small Foci in hindgut Small Foci in fat body Small Foci in ectoderm Small Foci in Brain Bigger Foci |
Larva
| Area | Images | Terms |
|---|---|---|
| fat body |
|
3rd Instar Larval Tissues Fat body Subcellular Localization - Fat body Cytoplasmic foci-fat body Nascent transcript in fat body |
| intestine |
|
3rd Instar Larval Tissues Intestine Expressed in proventriculus Subcellular localization in proventriculus Proventriculus foci Expressed in gastric caeca Subcellular localization in gastric caeca Gastric caeca foci |
| nervous system |
|
3rd Instar Larval Tissues Nervous system Expressed in brain lobes Brain lobes - Significant area |
| lymph glands and ring glands |
|
3rd Instar Larval Tissues Lymph Glands and Ring Glands Ring gland Expressed in ring gland Ring gland allover Lymph Glands Expressed in lymph glands |
Adult
| Area | Images | Terms |
|---|---|---|
| Male reproductive tissues |
|
Adult Tissues Male reproductive tissues Testis Testis Cell type and stage - TE Spermatogonium-TE Cytoplasmic in spermatogonium-TE Cytoplasmic foci in spermatogonium - TE Spermatocytes -TE Nuclear in Spermatocytes - TE Cytoplasmic in Spermatocytes - TE Cytoplasmic puncta in spermatocyte-TE Spermatids -TE Individualizing Spermatids - TE Cytoplasmic in individualizing spermatids - TE Elongating Spermatids - TE Cytoplasmic in elongating spermatids-TE Early elongating spermatids-TE Cytoplasmic in early elongating spermatids Cyst cells -TE Tail cyst cell - TE Individualizing Tail Cyst Cell - TE Individualizing Tail Cyst Cell Cytoplasm - TE Elongating Tail Cyst Cell - TE Elongating Tail Cyst Cell Cytoplasm - TE Cytoplasmic - Tail cyst cell Subcellularly localized - TE Nuclear Expression level-TE Expressed Medium - TE Distal tip region-TE Expressed in distal tip region - TE Specific tip region cells-TE Early cyst cell Cytoplasmic in early cyst cell Clusters in early cyst cell-TE Medium expression in tip region Cytoplasmic Seminal Vesicle Subcellularly localized - SV Lumenal-SV Scattered Foci - SV Expression level-SV Expressed Low - SV Cell type - SV Sperm Tail Decor - SV Ejaculatory Duct Subcellularly localized - ED Lumenal-ED ECM like pattern-ED Anterior ejaculatory duct papilla-ED Cytoplasmic in anterior ejaculatory papilla-ED Expression level-ED Expressed High - ED Cell type - ED Cytoplasmic-ED Membrane enriched - ED Cytoplasmic Foci - ED Apical Enrichment-ED Accessory Gland Subcellularly localized - AG Lumenal - AG Non-particulate - AG Expression level-AG Expressed Medium - AG Distal Enrichment - AG Cytoplasmic Cell type - AG Secondary cells - AG Cytoplasmic-SC Multivesicular bodies - SC Cytoplasmic foci-SC Main cells -AG Cytoplasmic-MC Cytoplasmic Foci - AG |
Comments
| Re-annotated by Ronit. Maybe some foci. |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Zygotic Ubiquitous Maternal Localized Subcellular localization patterns Cytoplasmic foci |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei All blastoderm nuclei Ubiquitous Degraded Degraded partially stage 5 Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Zygotic starting stage 6 Blastoderm nuclei Ubiquitous Degraded Degraded partially stage 7 |
| stage 8-9 |
|
Stage 8-9 Expressed |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Tracheal system Tracheal pits Salivary glands Pharynx Muscles-embryo Maxillary complex Hindgut Specific hindgut area or cells Head Head epidermis Ectoderm Anal pad Ring around anal pad Ubiquitous Localized Subcellular localization patterns Perinuclear localization Perinuclear around salivary gland nuclei Perinuclear around muscle nuclei Foci Small Foci Small Foci in tracheal cells Small Foci in head Small Foci in ectoderm |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RE transcript isoform |
| -very neat germ band stage and late stage patterns; salivary gland pattern may be real |
| -images are from two separate experiments under identical conditions for better coverage |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Yolk plasm localization |
| stage 4-5 |
|
Stage 4-5 Expressed Ubiquitous Maternal Localized Subcellular localization patterns Yolk cortex localization Exclusionary patterns Yolk plasm exclusion Degraded Degraded partially stage 4 |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Zygotic starting stage 6 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in ectoderm All blastoderm nuclei Transiently widespread Ubiquitous Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Expression in ectoderm All blastoderm nuclei Persistent widespread Ubiquitous Localized Subcellular localization patterns Nuclei-associated localization Accumulation in subset nuclei Cytoplasmic foci Embryonic localization patterns Ventral localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Segmented pattern PNS Maxillary complex Hindgut Germ cell nuclei Gonads CNS Ventral nerve cord Perinuclear VNC Axons Clypeo-labral bud Anal pad Ubiquitous Localized Subcellular localization patterns Perinuclear localization Perinuclear around ectoderm nuclei |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RB transcript isoform |
| -very diverse expression patterns in the late embryos; possibly expressed in the germ cell |
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 Blastoderm nuclei Subset blastoderm nuclei Single stripe Localized Subcellular localization patterns Cytoplasmic foci |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Single stripe Expression in ectoderm Localized Subcellular localization patterns Cytoplasmic foci |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Single stripe Expression in ectoderm Dorsal blastoderm nuclei Localized Subcellular localization patterns Perinuclear localization Perinuclear around blastoderm nuclei |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Segmented pattern Salivary glands Pharynx Maxillary complex Ectoderm CNS Ventral nerve cord Atrium Localized Subcellular localization patterns Perinuclear localization |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -tested via HCR-FISH using 3 probe sets |
| -probes designed to target the transcript isoform Scr-RF |
| -a classic homeobox gene |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
|
Stage 1-3 Expressed Ubiquitous Maternal Degraded Degraded partially stage 3 Degradation maternal transcripts |
| stage 4-5 |
|
Stage 4-5 Expressed Ubiquitous Maternal Degraded Degraded partially stage 4 Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Ubiquitous Maternal Degraded Degraded partially stage 7 Degradation maternal transcripts |
| stage 8-9 |
|
Stage 8-9 Expressed Ubiquitous Maternal Degraded Degraded partially stage 8 Degradation maternal transcripts |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system PNS Maxillary complex Malpighian tubules Fat body Localized Subcellular localization patterns Foci Small Foci Small Foci in PNS Small Foci in Malpighian tubules Small Foci in fat body |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RD isoform transcript |
| -maternal signal may not persist until stage 8-9 due to possible background (maternal signal may or may not be real but does align with RNAseq data) |
| -no midgut and dorsal vessel signal was observed under our experimental conditions but was reported by BDGP |
Embryo
| Area | Images | Terms |
|---|---|---|
| stage 1-3 |
Stage 1-3 Non-Expressed |
|
| stage 4-5 |
Stage 4-5 Non-Expressed |
|
| stage 6-7 |
Stage 6-7 Non-Expressed |
|
| stage 8-9 |
|
Stage 8-9 Non-Expressed |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system PNS Neuroblasts Maxillary complex Localized Subcellular localization patterns Foci Small Foci Small Foci in PNS |
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 Non-Expressed |
|
| stage 4-5 |
Stage 4-5 Non-Expressed |
|
| stage 6-7 |
Stage 6-7 Non-Expressed |
|
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in neuroblasts Expression in ectoderm Anterior blastoderm nuclei Localized Subcellular localization patterns Cytoplasmic foci Embryonic localization patterns Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Optic lobes primordium Muscles-embryo Visceral mesoderm Specific visceral mesoderm pattern Maxillary complex Hindgut Specific hindgut area or cells Esophagus CNS Ventral nerve cord Perinuclear VNC Foci - VNC Clypeo-labral bud Brain Localized Subcellular localization patterns Perinuclear localization Perinuclear around hindgut nuclei Perinuclear around esophagus nuclei Foci Small Foci Small Foci in hindgut Small Foci in CNS Small Foci in Brain |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed using HCR-FISH (3 probe sets) |
| -probes targeted dac-RB isoform of transcript |
| -very neat patterning in later stages; possibly visceral muscles of the hindgut |
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 Zygotic Zygotic starting stage 3 Yolk nuclei Subset yolk nuclei Random yolk nuclei Ubiquitous Localized Subcellular localization patterns Nuclei associated localization Intranuclear accumulation Accumulation in subset nuclei Cytoplasmic foci |
| stage 4-5 |
|
Stage 4-5 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Dorsal blastoderm nuclei Anterior blastoderm nuclei Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation in subset nuclei Exclusionary patterns Pole cell exclusion Apical exclusion Cytoplasmic foci Basal localization Basal enrichment Degraded Degraded partially stage 4 Degradation zygotic transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Segment polarity pattern Posterior blastoderm nuclei Expression in ectoderm Expression in API Dorsal blastoderm nuclei Anterior blastoderm nuclei Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation in subset nuclei Cytoplasmic foci Basal localization Basal enrichment Posterior localization Embryonic localization patterns Ventral localization Dorsal localization Anterior localization |
| stage 8-9 |
|
Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Segment polarity pattern Expression in neuroblasts 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 Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Sensory system Segmented pattern PNS Optic lobes primordium Neuroblasts Polarized Neuroblasts Midgut Maxillary complex Head Head epidermis CNS Ventral nerve cord Polarized VNC Perinuclear VNC Foci - VNC |
Larva
| Area | Images | Terms |
|---|
Adult
| Area | Images | Terms |
|---|
Comments
| -performed via HCR-FISH using 3 probe sets targeting the RA transcript isoform |
| -expression seen in the stomatogastric sensory primordium, and the anterior and posterior midgut primordium; forms a complex along with ac (CG3796) so should colocalize in neuronal regions |
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 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Dorsal blastoderm nuclei Anterior blastoderm nuclei All blastoderm nuclei Transiently widespread Ubiquitous Localized Subcellular localization patterns Yolk plasm localization Yolk cortex localization Nuclei-associated localization Intranuclear accumulation Exclusionary patterns Cytoplasmic foci Basal localization Basal enrichment Apical localization Apical enrichment Discrete apical foci Degraded Degradation maternal transcripts |
| stage 6-7 |
|
Stage 6-7 Expressed Zygotic Zygotic starting stage 7 Blastoderm nuclei Subset blastoderm nuclei Ventral blastoderm nuclei Segmented pattern Pair-rule pattern Expression in mesoderm Expression in ectoderm Expression in API Dorsal blastoderm nuclei Anterior blastoderm nuclei All blastoderm nuclei Transiently widespread Localized Subcellular localization patterns Nuclei-associated localization Perinuclear localization Perinuclear subset of nuclei Perinuclear around blastoderm nuclei Intranuclear accumulation Accumulation in subset nuclei 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 neuroblasts Expression in ectoderm Localized Subcellular localization patterns Perinuclear localization Perinuclear around blastoderm nuclei Nuclei-associated localization Accumulation in subset nuclei Cytoplasmic foci Embryonic localization patterns Ventral localization Posterior localization Germ band localization Dorsal localization Anterior localization |
| stage 10-17 |
|
Stage 10-17 Expressed Zygotic Segmented pattern Optic lobes primordium Neuroblasts Maxillary complex Head Head epidermis Ectoderm Dorsal vessel CNS Ventral nerve cord Perinuclear VNC Nuclear - VNC Foci - VNC Brain Localized Subcellular localization patterns Perinuclear localization Perinuclear around ectoderm nuclei Perinuclear around CNS nuclei Nuclei-associated localization Nuclear in ectoderm Nuclear in CNS Foci Small Foci Small Foci in head Small Foci in ectoderm 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 transcript isoform |
| -very diverse and neat patterns at all stages |