sqd squid [Drosophila melanogaster (fruit fly)] - Gene

Summary

Official Symbol: sqdprovided by FlyBase
Official Full Name: squidprovided by FlyBase
Primary source: FLYBASE:FBgn0263396
Locus tag: Dmel_CG16901
See related: AllianceGenome:FB:FBgn0263396
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Drosophila melanogaster
Lineage: Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as: BcDNA:GM03761; CG16901; CG17791; CR33328; Dmel\CG16901; fs(3)00048; hnRNP 1; hnRNP A; Hrb87; Hrb87Fb; hrp40; Hrp40; HRP40; l(3)EP3631; l(3)j4B4; l(3)j6E3; l(3)j8E7; Rbp3; rrm3; RRM3; Sqd; SQD; Squid
Old locus tag: Dmel_CR33328
Summary: Predicted to enable RNA binding activity. Involved in negative regulation of RNA splicing and oogenesis. Located in chromatin; omega speckle; and polytene chromosome puff. Part of catalytic step 2 spliceosome and precatalytic spliceosome. Is expressed in several structures, including Y chromosome loop; adult brain cell body rind; adult head; adult heart; and germline cell. Human ortholog(s) of this gene implicated in autosomal dominant limb-girdle muscular dystrophy type 3 and hepatocellular carcinoma. Orthologous to several human genes including HNRNPD (heterogeneous nuclear ribonucleoprotein D). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 87F5-87F6; 3-54 cM

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
Release 6.54	current	Release 6 plus ISO1 MT (GCF_000001215.4)	3R	NT_033777.3 (13634862..13646304, complement)
Release 5.57	previous assembly	Release 5 (GCF_000001215.2)	3R	NT_033777.2 (9460584..9472026, complement)

Chromosome 3R - NT_033777.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Novel roles for RNA binding proteins squid, hephaesteus, and Hrb27C in Drosophila oogenesis.
Title: Novel roles for RNA binding proteins squid, hephaesteus, and Hrb27C in Drosophila oogenesis.
Rbf physically and genetically interacts with Sqd.
Title: Sqd interacts with the Drosophila retinoblastoma tumor suppressor Rbf.
Data suggest that that Squid interacts with gurken mRNA in the nurse cell nuclei and, together with other factors, maintains gurken in a translationally silent state during its transport to the dorsal anterior region of the oocyte.
Title: Translational repression of gurken mRNA in the Drosophila oocyte requires the hnRNP Squid in the nurse cells.
sqd, cup, and PABP55B function together to regulate gurken translation.
Title: Squid, Cup, and PABP55B function together to regulate gurken translation in Drosophila.
Squid is required for the dynamic conversion of transport particles to sponge bodies.
Title: Drosophila Squid/hnRNP helps Dynein switch from a gurken mRNA transport motor to an ultrastructural static anchor in sponge bodies.
Loss of Sqd does not affect polarity in follicle cells, wings or eyes, indicating a specific role in the determination of MT polarity within the germline.
Title: The RNA-binding protein Squid is required for the establishment of anteroposterior polarity in the Drosophila oocyte.
Data show that Squid (Sqd) interacts with Hrb27C, and that Ovarian tumor (Otu) cooperates with Hrb27C and Sqd in the oocyte to mediate proper gurken (grk) localization.
Title: Hrb27C, Sqd and Otu cooperatively regulate gurken RNA localization and mediate nurse cell chromosome dispersion in Drosophila oogenesis.

Submit: New GeneRIF Correction

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by FlyBase

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables mRNA 3'-UTR binding	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA export from nucleus	TAS Traceable Author Statement more info	PubMed
involved_in dorsal/ventral axis specification, ovarian follicular epithelium	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in dorsal/ventral pattern formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in dorsal/ventral pattern formation	TAS Traceable Author Statement more info	PubMed
involved_in follicle cell of egg chamber migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in germarium-derived egg chamber formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular mRNA localization	NAS Non-traceable Author Statement more info	PubMed
involved_in intracellular mRNA localization	TAS Traceable Author Statement more info	PubMed
involved_in mRNA export from nucleus	NAS Non-traceable Author Statement more info	PubMed
involved_in mRNA splicing, via spliceosome	IC Inferred by Curator more info	PubMed
involved_in negative regulation of RNA splicing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of translation	TAS Traceable Author Statement more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	TAS Traceable Author Statement more info	PubMed
involved_in oocyte anterior/posterior axis specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in oocyte localization involved in germarium-derived egg chamber formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in oocyte microtubule cytoskeleton organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in oogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in oogenesis	TAS Traceable Author Statement more info	PubMed
involved_in pole plasm mRNA localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in pole plasm oskar mRNA localization	IEP Inferred from Expression Pattern more info	PubMed
involved_in regulation of alternative mRNA splicing, via spliceosome	HMP more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of catalytic step 2 spliceosome	HDA more info	PubMed
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	HDA more info	PubMed
located_in nucleus	IC Inferred by Curator more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	TAS Traceable Author Statement more info	PubMed
located_in omega speckle	IDA Inferred from Direct Assay more info	PubMed
located_in polytene chromosome puff	IDA Inferred from Direct Assay more info	PubMed
part_of precatalytic spliceosome	HDA more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: squid

Names: CG16901-PA; CG16901-PB; CG16901-PC; CG16901-PD; CG16901-PE; RNA-binding protein 3; heterogeneous-nuclear-ribonucleoprotein-87Fb; lethal (3) j4B4; sqd-PA; sqd-PB; sqd-PC; sqd-PD; sqd-PE

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NT_033777.3 Reference assembly

Range

13634862..13646304 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001260159.2 → NP_001247088.1 squid, isoform E [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001247088.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A0B4K6U6

Conserved Domains (2) summary

cd12329
Location:137 → 211

RRM2_hnRNPD_like; RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

cl17169
Location:58 → 129

RRM_SF; RNA recognition motif (RRM) superfamily
NM_143952.2 → NP_652209.1 squid, isoform C [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_652209.1

Status: REVIEWED

UniProtKB/TrEMBL

A0A0B4K6U6

Related

FBpp0082321

Conserved Domains (2) summary

cd12329
Location:137 → 211

RRM2_hnRNPD_like; RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

cl17169
Location:58 → 129

RRM_SF; RNA recognition motif (RRM) superfamily
NM_169528.2 → NP_731825.1 squid, isoform B [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_731825.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q08473, Q26273, Q3ZAN7, Q8IH71, Q8INH1, Q8MSY1, Q9VFT5, Q9VFT6

Related

FBpp0082320

Conserved Domains (2) summary

cd12329
Location:137 → 211

RRM2_hnRNPD_like; RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

cl17169
Location:58 → 129

RRM_SF; RNA recognition motif (RRM) superfamily
NM_206481.2 → NP_996203.1 squid, isoform D [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_996203.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q08473

Conserved Domains (1) summary

cl17169
Location:1 → 45

RRM_SF; RNA recognition motif (RRM) superfamily
NM_169529.3 → NP_731826.1 squid, isoform A [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_731826.1

Status: REVIEWED

UniProtKB/Swiss-Prot

Q08473

Related

FBpp0082319

Conserved Domains (2) summary

cd12329
Location:137 → 211

RRM2_hnRNPD_like; RNA recognition motif 2 in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins

cl17169
Location:58 → 129

RRM_SF; RNA recognition motif (RRM) superfamily