qkia QKI, KH domain containing, RNA binding a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: qkiaprovided by ZNC
Official Full Name: QKI, KH domain containing, RNA binding aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-990415-230
See related: Ensembl:ENSDARG00000097478 AllianceGenome:ZFIN:ZDB-GENE-990415-230
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: qk; qk1; qkA; zqk; zqk1; cb344; zqk-1; fb44d06; fc32f06; wu:fb44d06; wu:fc32f06
Summary: Predicted to enable mRNA binding activity. Acts upstream of or within several processes, including 3'-UTR-mediated mRNA stabilization; regulation of smoothened signaling pathway; and skeletal myofibril assembly. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Is expressed in several structures, including heart tube; mesoderm; musculature system; nervous system; and solid lens vesicle. Orthologous to human QKI (QKI, KH domain containing RNA binding). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 17

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	17	NC_007128.7 (27723435..27813509)
105	previous assembly	GRCz10 (GCF_000002035.5)	17	NC_007128.6 (27706468..27792115)

Chromosome 17 - NC_007128.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

This work uncovers a Quaking/Tpm3 pathway controlling de novo myofibril assembly.
Title: Quaking RNA-Binding Proteins Control Early Myofibril Formation by Modulating Tropomyosin.
qkia is an ancestral paralog of the single tetrapod Qk gene that was likely lost during the fin-to-limb transition. qkia is not expressed in the progenitor domains of the central nervous system.
Title: Characterization and Expression of the Zebrafish qki Paralogs.
Fine-tuning of Hh signaling by the RNA-binding protein Quaking to control muscle development.
Title: Fine-tuning of Hh signaling by the RNA-binding protein Quaking to control muscle development.

Submit: New GeneRIF Correction

General gene information

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Markers

G47329 (e-PCR)
- UniSTS:108110

fb44d06.x1 (e-PCR)
- UniSTS:190589

fb44d06.x1 (e-PCR)
- UniSTS:190590

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables SH3 domain binding	IEA Inferred from Electronic Annotation more info
enables mRNA 3'-UTR binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within 3'-UTR-mediated mRNA stabilization	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within RNA splicing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of macrophage differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of astrocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of smoothened signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of translation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within skeletal muscle tissue development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within skeletal myofibril assembly	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protein quaking-A

Names: quaking; quaking a

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_131224.1 → NP_571299.1 protein quaking-A

See identical proteins and their annotated locations for NP_571299.1

Status: PROVISIONAL

Source sequence(s)

U62134

UniProtKB/Swiss-Prot

O42476, Q6P0D0, Q6PHD0

UniProtKB/TrEMBL

A9JTF1

Related

ENSDARP00000140694.1, ENSDART00000169708.2

Conserved Domains (3) summary

cd02395
Location:84 → 206

SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...

pfam16544
Location:11 → 69

STAR_dimer; Homodimerization region of STAR domain protein

pfam16551
Location:356 → 383

Quaking_NLS; Putative nuclear localization signal of quaking

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007128.7 Reference GRCz11 Primary Assembly

Range

27723435..27813509

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009293118.3 → XP_009291393.1 protein quaking-A isoform X1

UniProtKB/Swiss-Prot

O42476, Q6P0D0, Q6PHD0

UniProtKB/TrEMBL

A0A8M3ARG3

Conserved Domains (3) summary

cd02395
Location:84 → 206

SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...

pfam16544
Location:11 → 69

STAR_dimer; Homodimerization region of STAR domain protein

pfam16551
Location:348 → 375

Quaking_NLS; Putative nuclear localization signal of quaking
XM_009293120.3 → XP_009291395.1 protein quaking-A isoform X3

UniProtKB/Swiss-Prot

O42476, Q6P0D0, Q6PHD0

UniProtKB/TrEMBL

A0A8M3B2H4, F6NV62

Related

ENSDARP00000105382.3, ENSDART00000123588.5

Conserved Domains (3) summary

cd02395
Location:84 → 206

SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...

pfam16544
Location:11 → 69

STAR_dimer; Homodimerization region of STAR domain protein

pfam16551
Location:307 → 334

Quaking_NLS; Putative nuclear localization signal of quaking
XM_009293119.3 → XP_009291394.1 protein quaking-A isoform X2

UniProtKB/Swiss-Prot

O42476, Q6P0D0, Q6PHD0

UniProtKB/TrEMBL

A0A0R4IA73, A0A8M3AJ30

Related

ENSDARP00000131081.1, ENSDART00000170462.2

Conserved Domains (3) summary

cd02395
Location:84 → 206

SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...

pfam16544
Location:11 → 69

STAR_dimer; Homodimerization region of STAR domain protein

pfam16551
Location:315 → 342

Quaking_NLS; Putative nuclear localization signal of quaking