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

    Gene ID: 202559, updated on 2-Nov-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, Nov 2024]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See KHDRBS2 in Genome Data Viewer
    Location:
    6q11.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (61542670..62286225, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (62687495..63431119, complement)
    RS_2024_09 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 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. Characterization of Sam68-like mammalian proteins SLM-1 and SLM-2: SLM-1 is a Src substrate during mitosis. Di Fruscio M, et al. Proc Natl Acad Sci U S A, 1999 Mar 16. PMID 10077576, Free PMC Article

    See all (37) 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_2024_08

    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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