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KHDRBS2 KH RNA binding domain containing, signal transduction associated 2 [ Homo sapiens (human) ]

Gene ID: 202559, updated on 5-Mar-2024

Summary

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Official Symbol
KHDRBS2provided by HGNC
Official Full Name
KH RNA binding domain containing, signal transduction associated 2provided by HGNC
Primary source
HGNC:HGNC:18114
See related
Ensembl:ENSG00000112232 MIM:610487; AllianceGenome:HGNC:18114
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SLM1; SLM-1; KHDRBS2-OT; KHDRBS2-OT1
Summary
Predicted to enable mRNA binding activity and poly(A) binding activity. Predicted to be involved in regulation of alternative mRNA splicing, via spliceosome. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
6q11.1
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (61542670..62286225, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (62687495..63431119, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (62252575..62996130, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:57811262-57811857 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 41 Neighboring gene NANOG hESC enhancer GRCh37_chr6:57850183-57850684 Neighboring gene RBBP4 pseudogene 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:62043813-62044313 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:62043312-62043812 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:61904506-61905007 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:62315562-62316235 Neighboring gene Sharpr-MPRA regulatory region 774 Neighboring gene MT-RNR2 like 9 (pseudogene) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:62650913-62651412 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17306 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:63202223-63202723 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:63295707-63296254 Neighboring gene dihydrofolate reductase pseudogene 5 Neighboring gene NANOG hESC enhancer GRCh37_chr6:63614387-63614952 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:63708848-63710047 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:63762677-63763208 Neighboring gene NANOG hESC enhancer GRCh37_chr6:63790275-63790776 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:63796218-63796424 Neighboring gene keratin, type II pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. Cloning and characterization of a novel human STAR domain containing cDNA KHDRBS2. Wang L, et al. Mol Biol Rep, 2002 Dec. PMID 12549823
  2. Mapping of determinants involved in the stimulation of HIV-1 expression by Sam68. McLaren M, et al. Virology, 2009 Mar 1. PMID 19091369
  3. Inhibition of HIV-1 gene expression by Sam68 Delta C: multiple targets but a common mechanism? Cochrane A. Retrovirology, 2009 Mar 2. PMID 19254361, Free PMC Article
  4. p59(fyn)-mediated phosphorylation regulates the activity of the tissue-specific splicing factor rSLM-1. Stoss O, et al. Mol Cell Neurosci, 2004 Sep. PMID 15345239
  5. Sam68 RNA binding protein is an in vivo substrate for protein arginine N-methyltransferase 1. Côté J, et al. Mol Biol Cell, 2003 Jan. PMID 12529443, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. molecular cloning and characterization
    Title: Cloning and characterization of a novel human STAR domain containing cDNA KHDRBS2.
Submit: New GeneRIF Correction

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
A genome-wide association study identifies protein quantitative trait loci (pQTLs).
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Rev rev Overexpression of the two GSG family members, SLM1 and SLM2, enhance unspliced HIV RNA cleavage and expression PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ38664, MGC26664

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables SH2 domain binding IEA
Inferred from Electronic Annotation
more info
  
enables SH3 domain binding IEA
Inferred from Electronic Annotation
more info
  
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables poly(A) binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables poly(U) RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of alternative mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
KH domain-containing, RNA-binding, signal transduction-associated protein 2
Names
KH domain containing, RNA binding, signal transduction associated 2
KHDRBS2 3'UTR overlapping transcript 1
Sam68-like mammalian protein 1

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_001350622.2 → NP_001337551.1  KH domain-containing, RNA-binding, signal transduction-associated protein 2 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL049544, AL133459, AL138882, AL355347, AL360220, AL391644, Z93021
    UniProtKB/TrEMBL
    A0A6Q8PGH5
    Conserved Domains (3) summary
    cd02395
    Location:61 → 180
    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 ...
    pfam16274
    Location:6 → 57
    Qua1; Qua1 domain
    pfam16568
    Location:288 → 338
    Sam68-YY; Tyrosine-rich domain of Sam68

  2. NM_152688.4 → NP_689901.2  KH domain-containing, RNA-binding, signal transduction-associated protein 2 isoform 2

    See identical proteins and their annotated locations for NP_689901.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AK292043, AL049544, AY077838, BC034043, D60325, Z93021
    Consensus CDS
    CCDS4963.1
    UniProtKB/Swiss-Prot
    A8K7M8, Q5VWX1, Q8N4I4, Q8TCZ4
    UniProtKB/TrEMBL
    A0A6Q8PGH5
    Related
    ENSP00000281156.3, ENST00000281156.5
    Conserved Domains (3) summary
    cd02395
    Location:61 → 180
    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 ...
    pfam16274
    Location:5 → 57
    Qua1; Qua1 domain
    pfam16568
    Location:267 → 321
    Sam68-YY; Tyrosine-rich domain of Sam68

RNA

  1. NR_146870.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL049544, AL138882, AL355347, AL356135, AL360220, AL391644, Z93021

  2. NR_146871.3 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL049544, AL138882, AL355347, AL360220, AL391644, Z93021

  3. NR_146872.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL049544, AL138882, AL355347, AL360220, AL391644, Z93021
    Related
    ENST00000675091.1

  4. NR_146873.3 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL049544, AL138882, AL355347, AL360220, AL391644, Z93021

  5. NR_146874.3 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL049544, AL138882, AL355347, AL360220, AL391644, Z93021

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    61542670..62286225 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    62687495..63431119 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VWX1.1 GenPept UniProtKB/Swiss-Prot:Q5VWX1

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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