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

Gene ID: 30471, updated on 18-Sep-2024

Summary

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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

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See qkia in Genome Data Viewer
Location:
chromosome: 17
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 17 NC_007128.7 (27723458..27810687)
105 previous assembly GRCz10 (GCF_000002035.5) 17 NC_007128.6 (27706468..27792115)

Chromosome 17 - NC_007128.7Genomic Context describing neighboring genes Neighboring gene cathepsin L.1 Neighboring gene PARK2 co-regulated Neighboring gene uncharacterized LOC137488107 Neighboring gene platelet-activating factor receptor

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages 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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Related articles in PubMed

  1. Cloning and expression of the quaking gene in the zebrafish embryo. Tanaka H, et al. Mech Dev, 1997 Dec. PMID 9486543
  2. Quaking RNA-Binding Proteins Control Early Myofibril Formation by Modulating Tropomyosin. Bonnet A, et al. Dev Cell, 2017 Sep 11. PMID 28867488
  3. Characterization and Expression of the Zebrafish qki Paralogs. Radomska KJ, et al. PLoS One, 2016. PMID 26727370, Free PMC Article
  4. Fine-tuning of Hh signaling by the RNA-binding protein Quaking to control muscle development. Lobbardi R, et al. Development, 2011 May. PMID 21447554
  5. Expression screening and annotation of a zebrafish myoblast cDNA library. Baxendale S, et al. Gene Expr Patterns, 2009 Feb. PMID 19007914

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. This work uncovers a Quaking/Tpm3 pathway controlling de novo myofibril assembly.
    Title: Quaking RNA-Binding Proteins Control Early Myofibril Formation by Modulating Tropomyosin.
  2. 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.
  3. 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

Homology

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 
involved_in spliceosome-depend formation of circular RNA ISS
Inferred from Sequence or Structural Similarity
more info
  
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)

  1. 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: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007128.7 Reference GRCz11 Primary Assembly

    Range
    27723458..27810687
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009293119.4 → 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

  2. XM_009293118.4 → 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

  3. XM_009293120.4 → 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
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6P0D0.2 GenPept UniProtKB/Swiss-Prot:Q6P0D0

Gene LinkOut

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