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Stage 6-7 / Expressed / Localized / Subcellular localization patterns / Exclusionary patterns / Yolk cortex exclusion

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Result Summary

Number of genes	10
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Probe LD47289 Links: Permalink

Genes: CG16742

Embryo

Area	Images	Terms
stage 1-3		Stage 1-3 Expressed Ubiquitous Medium expression (21-40ms exp) Maternal
stage 4-5		Stage 4-5 Expressed Maternal Localized Subcellular localization patterns Yolk plasm localization Yolk plasm enrichment Exclusionary patterns Yolk cortex exclusion Pole cell exclusion Apical exclusion Embryonic localization patterns
stage 6-7		Stage 6-7 Expressed Maternal Localized Yolk plasm localization Yolk plasm enrichment Subcellular localization patterns Exclusionary patterns Yolk cortex exclusion Apical exclusion Embryonic localization patterns Exclusionary patterns Pole cell exclusion
stage 8-9		Stage 8-9 Expressed Weak expression (>41ms exp) Maternal Localized Subcellular localization patterns Cytoplasmic foci Basal localization Basal enrichment Embryonic localization patterns Degraded Degraded partially stage 8 Degradation maternal transcripts

Larva

Area	Images	Terms

Adult

Area	Images	Terms

Comments

Re-annotated

Small, clear foci or puncta.

Probe GH13213 Links: Permalink

Genes: CG32392

Embryo

Area	Images	Terms
stage 1-3		Stage 1-3 Expressed Zygotic Zygotic starting stage 3 Cortical nuclei Subset cortical nuclei Random cortical nuclei Weak expression (>41ms exp) Maternal Localized Subcellular localization patterns Embryonic localization patterns Yolk plasm localization Yolk plasm enrichment Exclusionary patterns Yolk cortex exclusion
stage 4-5		Stage 4-5 Expressed Weak expression (>41ms exp) Maternal Localized Subcellular localization patterns Yolk plasm localization Yolk plasm enrichment Exclusionary patterns Yolk cortex exclusion Pole cell exclusion Basal exclusion Apical exclusion Embryonic localization patterns
stage 6-7		Stage 6-7 Expressed Weak expression (>41ms exp) Maternal Localized Subcellular localization patterns Exclusionary patterns Yolk cortex exclusion Apical exclusion Basal localization Basal enrichment Embryonic localization patterns Exclusionary patterns Pole cell exclusion
stage 8-9		Stage 8-9 Expressed Weak expression (>41ms exp) Localized Subcellular localization patterns Basal localization Basal enrichment Embryonic localization patterns
stage 10-17		Stage 10-17 Expressed Zygotic Tracheal system Tracheal lumen Sensory system Salivary glands Salivary glands lumen Bolwig's organ Blastoderm nuclei Localized

Larva

Area	Images	Terms

Adult

Area	Images	Terms

Comments

Good probe on gel.

Probe RE72980 Links: Permalink

Genes: CG8696

Embryo

Area	Images	Terms
stage 1-3		Stage 1-3 Expressed Ubiquitous Medium expression (21-40ms exp) Maternal
stage 4-5		Stage 4-5 Expressed Medium expression (21-40ms exp) Maternal Localized Subcellular localization patterns Exclusionary patterns Yolk cortex exclusion Basal exclusion Apical exclusion Embryonic localization patterns
stage 6-7		Stage 6-7 Expressed Medium expression (21-40ms exp) Maternal Localized Subcellular localization patterns Exclusionary patterns Yolk cortex exclusion Apical exclusion Embryonic localization patterns
stage 8-9		Stage 8-9 Expressed Weak expression (>41ms exp) Ubiquitous Maternal

Larva

Area	Images	Terms

Adult

Area	Images	Terms

Comments

Probe RE54049 Links: Permalink

Genes: Reg-5

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 Embryonic localization patterns
stage 6-7		Stage 6-7 Expressed Weak expression (>41ms exp) Maternal Localized Yolk plasm localization Yolk plasm enrichment Subcellular localization patterns Other subcellular pattern Nuclei-associated localization Intranuclear accumulation Accumulation nuclear subregion Accumulation in subset nuclei Exclusionary patterns Yolk cortex exclusion Apical exclusion Embryonic localization patterns Exclusionary patterns Pole cell exclusion
stage 8-9		Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Random blastoderm nuclei Expression in amnioserosa Weak expression (>41ms exp) Localized
stage 10-17		Stage 10-17 Expressed Zygotic Tracheal system Salivary glands Posterior spiracles Midgut Fat body Ectoderm Localized

Larva

Area	Images	Terms

Adult

Area	Images	Terms

Comments

Ring gland (I think)

Good probe on gel.

Probe RE44641 Links: Permalink

Genes: alphaTub67C

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 Maternal Localized Subcellular localization patterns Exclusionary patterns Yolk cortex exclusion Pole cell exclusion Apical exclusion Embryonic localization patterns Degraded Degraded partially stage 4 Degradation maternal transcripts
stage 6-7		Stage 6-7 Expressed Maternal Localized Subcellular localization patterns Exclusionary patterns Yolk cortex exclusion Apical exclusion Embryonic localization patterns Exclusionary patterns Pole cell exclusion Degraded Degraded partially stage 6 Degradation maternal transcripts
stage 8-9		Stage 8-9 Non-Expressed Degraded Degraded completely stage 8 Degradation maternal transcripts

Larva

Area	Images	Terms

Adult

Area	Images	Terms

Comments

Probe LD43519 Links: Permalink

Genes: bc10

Embryo

Area	Images	Terms
stage 4-5		Stage 4-5 Expressed Maternal Localized Subcellular localization patterns Exclusionary patterns Pole cell exclusion Basal exclusion Apical exclusion Embryonic localization patterns
stage 6-7		Stage 6-7 Expressed Maternal Localized Subcellular localization patterns Exclusionary patterns Yolk cortex exclusion Apical exclusion Basal localization Embryonic localization patterns

Larva

Area	Images	Terms

Adult

Area	Images	Terms

Comments

Probe LP02621 Links: Permalink

Genes: btsz

Embryo

Area	Images	Terms
stage 1-3		Stage 1-3 Expressed Zygotic Zygotic starting stage 3 Cortical nuclei All cortical nuclei Weak expression (>41ms exp) Localized Subcellular localization patterns Cell division apparatus Spindle midzone localization Other cell division pattern Embryonic localization patterns Exclusionary patterns Pole plasm excluded
stage 4-5		Stage 4-5 Expressed Zygotic Yolk nuclei Subset yolk nuclei Random yolk nuclei Blastoderm nuclei Subset blastoderm nuclei Dorsal blastoderm nuclei All blastoderm nuclei Weak expression (>41ms exp) Localized Subcellular localization patterns Other subcellular pattern Exclusionary patterns Pole cell exclusion Dorsal localization Cell division apparatus Spindle midzone localization Apical localization Apical enrichment Diffuse apical localization Embryonic localization patterns
stage 6-7		Stage 6-7 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Dorsal blastoderm nuclei Weak expression (>41ms exp) Localized Subcellular localization patterns Exclusionary patterns Yolk cortex exclusion Cytoplasmic foci Apical localization Apical enrichment Diffuse apical localization Pole cell localization Embryonic localization patterns Exclusionary patterns Pole cell exclusion Dorsal localization
stage 8-9		Stage 8-9 Expressed Zygotic Blastoderm nuclei Subset blastoderm nuclei Expression in API Expression in amnioserosa Weak expression (>41ms exp) Localized Subcellular localization patterns Apical localization Apical enrichment Diffuse apical localization Embryonic localization patterns
stage 10-17		Stage 10-17 Expressed Zygotic Salivary glands PNS Hindgut Ectoderm Blastoderm nuclei Localized

Larva

Area	Images	Terms

Adult

Area	Images	Terms

Comments

Good probe on gel.

Probe LD29455 Links: Permalink

Genes: kel

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 Segmented pattern Gap-gene pattern Weak expression (>41ms exp) Localized Subcellular localization patterns Exclusionary patterns Pole cell exclusion Apical localization Apical enrichment Embryonic localization patterns
stage 6-7		Stage 6-7 Expressed Zygotic Zygotic starting stage 6 Blastoderm nuclei Subset blastoderm nuclei Segmented pattern Gap-gene pattern Weak expression (>41ms exp) Localized Subcellular localization patterns Exclusionary patterns Yolk cortex exclusion Basal localization Basal enrichment Apical localization Apical enrichment Diffuse apical localization
stage 8-9		Stage 8-9 Expressed Ubiquitous
stage 10-17		Stage 10-17 Expressed Zygotic Salivary glands Salivary glands lumen

Larva

Area	Images	Terms

Adult

Area	Images	Terms

Comments

Good probe.

Probe twi-RB Links: Permalink

Genes: twi

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!

Probe zen-RA Links: Permalink

Genes: zen

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)