QKI QKI, KH domain containing RNA binding [Homo sapiens (human)] - Gene

Summary

Official Symbol: QKIprovided by HGNC
Official Full Name: QKI, KH domain containing RNA bindingprovided by HGNC
Primary source: HGNC:HGNC:21100
See related: Ensembl:ENSG00000112531 MIM:609590; AllianceGenome:HGNC:21100
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: QK; Hqk; QK1; QK3; hqkI
Summary: The protein encoded by this gene is an RNA-binding protein that regulates pre-mRNA splicing, export of mRNAs from the nucleus, protein translation, and mRNA stability. The encoded protein is involved in myelinization and oligodendrocyte differentiation and may play a role in schizophrenia. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]
Expression: Broad expression in brain (RPKM 50.5), fat (RPKM 18.4) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6q26

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (163414718..163578592)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (164779884..164943697)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (163835750..163999624)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Isoform balance of the long noncoding RNA NEAT1 is regulated by the RNA-binding protein QKI, governs the glioma transcriptome, and impacts cell migration.
Title: Isoform balance of the long noncoding RNA NEAT1 is regulated by the RNA-binding protein QKI, governs the glioma transcriptome, and impacts cell migration.
Circular RNA Circ_0001322 inhibits gastric cancer progression by modulating the miR-1264/QKI axis and suppressing the Hedgehog pathway.
Title: Circular RNA Circ_0001322 inhibits gastric cancer progression by modulating the miR-1264/QKI axis and suppressing the Hedgehog pathway.
Involvement of circRNA Regulators MBNL1 and QKI in the Progression of Esophageal Squamous Cell Carcinoma.
Title: Involvement of circRNA Regulators MBNL1 and QKI in the Progression of Esophageal Squamous Cell Carcinoma.
Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing.
Title: Mature microRNA-binding protein QKI promotes microRNA-mediated gene silencing.
Non-adherent culture method affects the proliferation and apoptosis of mesenchymal stem cells through inhibiting LINC00707 to promote RNF6-mediated QKI ubiquitination.
Title: Non-adherent culture method affects the proliferation and apoptosis of mesenchymal stem cells through inhibiting LINC00707 to promote RNF6-mediated QKI ubiquitination.
RNA Binding Protein Quaking Promotes Hypoxia-induced Smooth Muscle Reprogramming in Pulmonary Hypertension.
Title: RNA Binding Protein Quaking Promotes Hypoxia-induced Smooth Muscle Reprogramming in Pulmonary Hypertension.
The possible molecular mechanism underlying the involvement of the variable shear factor QKI in the epithelial-mesenchymal transformation of oesophageal cancer.
Title: The possible molecular mechanism underlying the involvement of the variable shear factor QKI in the epithelial-mesenchymal transformation of oesophageal cancer.
microRNA-497 slows esophageal cancer development and reverses chemotherapy resistance through its target QKI.
Title: microRNA-497 slows esophageal cancer development and reverses chemotherapy resistance through its target QKI.
QKI deficiency in macrophages protects mice against JEV infection by regulating cell migration and antiviral response.
Title: QKI deficiency in macrophages protects mice against JEV infection by regulating cell migration and antiviral response.
Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate.
Title: Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate.

Submit: New GeneRIF Correction See all GeneRIFs (81)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association scan identifies candidate polymorphisms associated with differential response to anti-TNF treatment in rheumatoid arthritis. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
retropepsin	gag-pol	Positional proteomics analysis identifies the cleavage of human KH domain containing, RNA binding (QKI) at amino acid residues 163-164 by the HIV-1 protease	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6S1134E (e-PCR)
- UniSTS:7708

Qk (e-PCR), detects polymorphism
- UniSTS:462630

A007D02 (e-PCR)
- UniSTS:40747

WI-13590 (e-PCR)
- UniSTS:2861

Qk (e-PCR), detects polymorphism
- UniSTS:464688

D6S1171E (e-PCR)
- UniSTS:151092

WI-16266 (e-PCR)
- UniSTS:37712

RH35872 (e-PCR)
- UniSTS:72541

RH15845 (e-PCR)
- UniSTS:79721

RH41968 (e-PCR)
- UniSTS:6276

RH103867 (e-PCR)
- UniSTS:98192

D6S1930 (e-PCR)
- UniSTS:34704

G20830 (e-PCR)
- UniSTS:46253

A006I04 (e-PCR)
- UniSTS:46254

QKI (e-PCR)
- UniSTS:266175

Qk (e-PCR), detects polymorphism
- UniSTS:479216

RH92592 (e-PCR)
- UniSTS:91379

RH77886 (e-PCR)
- UniSTS:510

RH46662 (e-PCR)
- UniSTS:30975

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables SH3 domain binding	IEA Inferred from Electronic Annotation more info
enables internal N(7)-methylguanine-containing RNA reader activity	IDA Inferred from Direct Assay more info	PubMed
enables mRNA 3'-UTR binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA 3'-UTR binding	IEA Inferred from Electronic Annotation more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables miRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in intracellular mRNA localization	IDA Inferred from Direct Assay more info	PubMed
involved_in long-chain fatty acid biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in mRNA stabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA transport	IDA Inferred from Direct Assay more info	PubMed
involved_in microglia differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in myelination	IEA Inferred from Electronic Annotation more info
involved_in myofibroblast contraction	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of 3'-UTR-mediated mRNA stabilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of angiogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of macrophage differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of miRNA catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of translation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of translation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of translation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of type I interferon production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cholesterol biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of gene expression	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of myelination	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of oligodendrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in regulation of astrocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of epithelial to mesenchymal transition	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of mRNA splicing, via spliceosome	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of macrophage differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in spermatid development	IEA Inferred from Electronic Annotation more info
involved_in spliceosome-depend formation of circular RNA	IDA Inferred from Direct Assay more info	PubMed
involved_in vascular associated smooth muscle cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in vasculogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytoplasmic stress granule	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic stress granule	IEA Inferred from Electronic Annotation more info
is_active_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: KH domain-containing RNA-binding protein QKI

Names: QKI/LOC100132735 fusion; RNA binding protein HQK; homolog of mouse quaking QKI (KH domain RNA binding protein); quaking homolog, KH domain RNA binding

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.

Genomic

NG_029604.2 RefSeqGene

Range

5076..168950

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001301085.2 → NP_001288014.1 KH domain-containing RNA-binding protein QKI isoform 5

See identical proteins and their annotated locations for NP_001288014.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an in-frame segment in the 3' coding region, compared to variant 1. The resulting isoform (5) is shorter compared to isoform 1.

Source sequence(s)

AL031781, AL356119, AW131362, DQ323998

Consensus CDS

CCDS75546.1

UniProtKB/Swiss-Prot

Q96PU8

Related

ENSP00000354867.2, ENST00000361195.6

Conserved Domains (4) summary

PRK14950
Location:195 → 305

PRK14950; DNA polymerase III subunits gamma and tau; Provisional

pfam16544
Location:10 → 66

STAR_dimer; Homodimerization region of STAR domain protein

pfam16551
Location:304 → 333

Quaking_NLS; Putative nuclear localization signal of quaking

cd22465
Location:81 → 183

KH-I_Hqk; type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins
NM_006775.3 → NP_006766.1 KH domain-containing RNA-binding protein QKI isoform 1

See identical proteins and their annotated locations for NP_006766.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1; also known as HQK-5 and QKI-5).

Source sequence(s)

AB067798, AB067801, AF272349, AL031781, AW131362

Consensus CDS

CCDS5285.1

UniProtKB/Swiss-Prot

Q2I375, Q5MJQ1, Q969L9, Q96EJ3, Q96KA3, Q96PU6, Q96PU7, Q96PU8, Q9P0X6, Q9P0X7, Q9P0X8, Q9P0X9, Q9P0Y0, Q9P0Y1

Related

ENSP00000355094.3, ENST00000361752.8

Conserved Domains (4) summary

PHA03247
Location:211 → 314

PHA03247; large tegument protein UL36; Provisional

pfam16544
Location:10 → 66

STAR_dimer; Homodimerization region of STAR domain protein

pfam16551
Location:312 → 341

Quaking_NLS; Putative nuclear localization signal of quaking

cd22465
Location:81 → 183

KH-I_Hqk; type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins
NM_206853.3 → NP_996735.1 KH domain-containing RNA-binding protein QKI isoform 2

See identical proteins and their annotated locations for NP_996735.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' UTR and coding region compared to variant 1, which results in a frameshift. The resulting isoform (2; also known as HQK-6 and QKI-6) is shorter and has a distinct C-terminus compared to isoform 1. Isoforms 2 and 4 are the same length but have different C-termini.

Source sequence(s)

AB067799, AB067801, AF142422, AF272349, AL031781, AW131362

Consensus CDS

CCDS5286.1

UniProtKB/Swiss-Prot

Q96PU8

UniProtKB/TrEMBL

Q8WY44

Related

ENSP00000408775.2, ENST00000453779.6

Conserved Domains (3) summary

PRK14951
Location:210 → 281

PRK14951; DNA polymerase III subunits gamma and tau; Provisional

pfam16544
Location:10 → 66

STAR_dimer; Homodimerization region of STAR domain protein

cd22465
Location:81 → 183

KH-I_Hqk; type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins
NM_206854.3 → NP_996736.1 KH domain-containing RNA-binding protein QKI isoform 3

See identical proteins and their annotated locations for NP_996736.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 3' UTR and coding region compared to variant 1, which results in a frameshift. The resulting isoform (3; also known as HQK-7 and QKI-7) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AB067800, AB067801, AF272349, AL031781, AW131362

Consensus CDS

CCDS5287.1

UniProtKB/Swiss-Prot

Q96PU8

UniProtKB/TrEMBL

Q8WY44

Related

ENSP00000275262.7, ENST00000275262.11

Conserved Domains (3) summary

PRK14951
Location:210 → 281

PRK14951; DNA polymerase III subunits gamma and tau; Provisional

pfam16544
Location:10 → 66

STAR_dimer; Homodimerization region of STAR domain protein

cd22465
Location:81 → 183

KH-I_Hqk; type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins
NM_206855.3 → NP_996737.1 KH domain-containing RNA-binding protein QKI isoform 4

See identical proteins and their annotated locations for NP_996737.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 3' UTR and coding region compared to variant 1, which results in a frameshift. The resulting isoform (4; also known as HQK-7B and QKI-7b) is shorter and has a distinct C-terminus compared to isoform 1. Isoforms 2 and 4 are the same length but have different C-termini.

Source sequence(s)

AB067801, AF272349, AL031781, AW131362

Consensus CDS

CCDS43525.1

UniProtKB/Swiss-Prot

Q96PU8

UniProtKB/TrEMBL

Q8WY44

Related

ENSP00000375973.2, ENST00000392127.6

Conserved Domains (3) summary

cd02395
Location:83 → 205

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:10 → 68

STAR_dimer; Homodimerisation region of STAR domain protein

cl26386
Location:210 → 281

DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

163414718..163578592

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017011504.2 → XP_016866993.1 KH domain-containing RNA-binding protein QKI isoform X1

Conserved Domains (3) summary

PRK14971
Location:182 → 311

PRK14971; DNA polymerase III subunit gamma/tau

pfam16544
Location:10 → 66

STAR_dimer; Homodimerization region of STAR domain protein

cd22465
Location:81 → 183

KH-I_Hqk; type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins
XM_047419566.1 → XP_047275522.1 KH domain-containing RNA-binding protein QKI isoform X3
XM_011536260.3 → XP_011534562.1 KH domain-containing RNA-binding protein QKI isoform X2

Conserved Domains (3) summary

cd02395
Location:83 → 157

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:10 → 68

STAR_dimer; Homodimerization region of STAR domain protein

pfam16551
Location:266 → 293

Quaking_NLS; Putative nuclear localization signal of quaking
XM_011536261.2 → XP_011534563.1 KH domain-containing RNA-binding protein QKI isoform X4

Conserved Domains (2) summary

cd02395
Location:83 → 183

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:10 → 68

STAR_dimer; Homodimerization region of STAR domain protein

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

164779884..164943697

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054356831.1 → XP_054212806.1 KH domain-containing RNA-binding protein QKI isoform X1
XM_054356833.1 → XP_054212808.1 KH domain-containing RNA-binding protein QKI isoform X3
XM_054356832.1 → XP_054212807.1 KH domain-containing RNA-binding protein QKI isoform X2
XM_054356835.1 → XP_054212810.1 KH domain-containing RNA-binding protein QKI isoform X4
XM_054356834.1 → XP_054212809.1 KH domain-containing RNA-binding protein QKI isoform X5