FlyBase Gene Report: Dmel\sqz

General Information

Symbol

Dmel\sqz

Species

D. melanogaster

Name

squeeze

Annotation Symbol

CG5557

Feature Type

protein_coding_gene

FlyBase ID

FBgn0010768

Gene Model Status

Current

Stock Availability

14 publicly available

Gene Summary

squeeze (sqz) encodes a transcription factor that regulates neuropeptidergic cellular identity and axon/dendrite pathfinding. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)

All Summaries

Gene Snapshot
Alliance
Auto summary
Gene Group
UniProtKB
Interactive Fly

Also Known As

l(3)02102

Key Links

Genomic Location

Cytogenetic map

91F4-91F4

Sequence location

3R:19,164,211..19,170,576 [+]

Recombination map

3-66

RefSeq locus

NT_033777 REGION:19164211..19170576

Sequence

Get Decorated FASTA

Genomic Maps

JBrowse GBrowse

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Other Genome Views

The following external sites may use different assemblies or annotations than FlyBase.

Function

GO Summary Ribbons

Gene Ontology (GO) Annotations (6 terms)

Molecular Function (2 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (2 terms)

CV Term

Evidence

References

enables DNA-binding transcription factor activity, RNA polymerase II-specific

inferred from biological aspect of ancestor with PANTHER:PTN004701291

(assigned by GO_Central )

(Gaudet et al., 2011)

enables RNA polymerase II transcription regulatory region sequence-specific DNA binding

inferred from biological aspect of ancestor with PANTHER:PTN004701291

(assigned by GO_Central )

(Gaudet et al., 2011)

Biological Process (4 terms)

Terms Based on Experimental Evidence (3 terms)

CV Term

Evidence

References

involved_in dendrite guidance

inferred from mutant phenotype

(Komiyama and Luo, 2007)

involved_in neuroblast development

inferred from mutant phenotype

(Tsuji et al., 2008)

involved_in neuron development

inferred from mutant phenotype

(Félix et al., 2007)

Terms Based on Predictions or Assertions (1 term)

CV Term

Evidence

References

involved_in regulation of transcription by RNA polymerase II

inferred from biological aspect of ancestor with PANTHER:PTN004701291

(assigned by GO_Central )

(Gaudet et al., 2011)

Cellular Component (0 terms)

Terms Based on Experimental Evidence (0 terms)

Terms Based on Predictions or Assertions (0 terms)

Gene Group (FlyBase)

C2H2 ZINC FINGER TRANSCRIPTION FACTORS

Protein Family (UniProt)

Belongs to the krueppel C2H2-type zinc-finger protein family. (Q9VDZ3)

Protein Signatures (InterPro)

Summaries

Gene Snapshot

squeeze (sqz) encodes a transcription factor that regulates neuropeptidergic cellular identity and axon/dendrite pathfinding. [Date last reviewed: 2019-03-14]

Gene Group (FlyBase)

C2H2 ZINC FINGER TRANSCRIPTION FACTORS -: Zinc finger C2H2 transcription factors are sequence-specific DNA binding proteins that regulate transcription. They possess DNA-binding domains that are formed from repeated Cys₂His₂ zinc finger motifs. (Adapted from PMID:1835093, FBrf0220103 and FBrf0155739).

Protein Function (UniProtKB)

Transcription factor involved in neuronal fate specification. First required in embryonic CNS development to define the number of cells that express apterous (ap) in the ap thoracic cluster of interneurons. Later on, it plays a central role in the combinatorial code of transcription factors that specifies the fate of the Tv neuron in the ap cluster by participating in the transcription regulation of FMRFa in Tv cells. Also required for projection neuron dendritic targeting.

(UniProt, Q9VDZ3)

Summary (Interactive Fly)

zinc finger transcription factor - regulates neuropeptidergic cellular identity and FMRFamide expression

Interactive Fly

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\sqz for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)

Isoform displayed:

Pfam protein domains

InterPro name

classification

start

end

Protein Domains (via SMART)

Isoform displayed:

SMART protein domains

InterPro name

classification

start

end

Structure New Section

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry Q9VDZ3)

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Model Confidence:

Very high (pLDDT > 90)
Confident (90 > pLDDT > 70)
Low (70 > pLDDT > 50)
Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Comments on Gene Model

Gene model reviewed during 5.54

Sequence Ontology: Class of Gene

nuclear_gene

protein_coding_gene

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

sqz-RA

FBtr0083733

NM_079679

3258

535

Additional Transcript Data and Comments

Reported size (kB)

Comments

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kDa)

Length (aa)

Theoretical pI

UniProt

RefSeq ID

GenBank

sqz-PA

FBpp0083147

59.5

535

8.75

Q9VDZ3

NP_524403

AAF55644

Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments

Reported size (kDa)

Comments

External Data

Subunit Structure (UniProtKB)

Interacts with nab; which acts as a coactivator. Interacts with ap.

(UniProt, Q9VDZ3)

Crossreferences

InterPro - A database of protein families, domains and functional sites

Linkouts

Sequences Consistent with the Gene Model

Nucleotide / Polypeptide Records

UniProt

Q9VDZ3

Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\sqz using the Feature Mapper tool.

External Data

Crossreferences

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

sqz_1

Linkouts

Expression Data

Expression Summary Ribbons

Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:

low

high

Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.

Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.

Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:

low

high

as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.

Transcript Expression

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

ventral midline of embryo

(Wheeler et al., 2009)

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 10 -- 11

ventral nerve cord primordium | segmentally repeated | subset

(Berman et al., 2004)

embryonic stage 11 -- 12

central nervous system

Comment: subsets of neurons

(Allan et al., 2003)

central brain primordium

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 12 -- first instar larval stage

embryonic/larval central nervous system

(Allan et al., 2003)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

Additional Descriptive Data

sqz transcript is expressed in a subset of neurons in the embryonic and first instar larval central nervous system. Scer\GAL4^sqz-GAL4-driven expression reveals that this subset is a population of lateral interneurons that primarily project axons in the anterior and posterior commisures of the ventral nerve cord.

(Allan et al., 2003)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

immunolocalization

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage 13

EL neuron | subset of embryonic abdomen

(Tsuji et al., 2008)

embryonic stage 13 -- second instar larval stage

EL neuron | subset of thorax

(Tsuji et al., 2008)

embryonic stage 16

apterous-expressing neuron of the lateral cluster of the thorax

(Losada-Pérez et al., 2013)

larval stage

apterous-expressing neuron of the lateral cluster of the thorax Ap4

(Baumgardt et al., 2007)

Additional Descriptive Data

sqz is expressed in the fifth born EL neuron.

(Tsuji et al., 2008)

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

Reporter: P{GawB}sqz^GAL4

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

Leucokinin neuron

(Herrero et al., 2007)

larval stage

larval abdominal ganglion Leucokinin neuron

(Herrero et al., 2007)

larval lateral horn Leucokinin neuron

Comment: gone by wandering stage

(Herrero et al., 2007)

larval subesophageal Leucokinin neuron

(Herrero et al., 2007)

larval ipc-1 neuron

(Herrero et al., 2007)

embryonic stage 17

apterous-expressing neuron of the lateral cluster of the thorax Ap4 | subset

(Allan et al., 2003)

Reporter: P{PZ}sqz⁰²¹⁰²

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage -- adult stage

Leucokinin neuron

(Herrero et al., 2007)

embryonic stage 16 -- first instar larval stage

neuron | subset of embryonic/larval central nervous system

(Allan et al., 2003)

larval stage

larval abdominal ganglion Leucokinin neuron

(Herrero et al., 2007)

larval lateral horn Leucokinin neuron

(Herrero et al., 2007)

larval subesophageal Leucokinin neuron

(Herrero et al., 2007)

larval ipc-1 neuron

(Herrero et al., 2007)

wandering third instar larval stage

imaginal disc