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    KHDRBS1 KH RNA binding domain containing, signal transduction associated 1 [ Homo sapiens (human) ]

    Gene ID: 10657, updated on 9-Dec-2024

    Summary

    Official Symbol
    KHDRBS1provided by HGNC
    Official Full Name
    KH RNA binding domain containing, signal transduction associated 1provided by HGNC
    Primary source
    HGNC:HGNC:18116
    See related
    Ensembl:ENSG00000121774 MIM:602489; AllianceGenome:HGNC:18116
    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
    p62; p68; Sam68
    Summary
    This gene encodes a member of the K homology domain-containing, RNA-binding, signal transduction-associated protein family. The encoded protein appears to have many functions and may be involved in a variety of cellular processes, including alternative splicing, cell cycle regulation, RNA 3'-end formation, tumorigenesis, and regulation of human immunodeficiency virus gene expression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]
    Expression
    Ubiquitous expression in ovary (RPKM 44.4), endometrium (RPKM 41.0) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See KHDRBS1 in Genome Data Viewer
    Location:
    1p35.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (32013868..32060850)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31871794..31918779)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32479469..32526451)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene SPOC domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 579 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32303933-32304116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 655 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 657 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 658 Neighboring gene uncharacterized LOC128031832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32389035-32389578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 660 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32403472-32403643 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 581 Neighboring gene protein tyrosine phosphatase 4A2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 661 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32409768-32410302 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32419864-32420642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32420643-32421419 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32421420-32422197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 667 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:32473819-32474378 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32479704-32480274 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 583 Neighboring gene VISTA enhancer hs645 Neighboring gene NANOG hESC enhancer GRCh37_chr1:32526442-32527054 Neighboring gene Sharpr-MPRA regulatory region 15509 Neighboring gene Sharpr-MPRA regulatory region 7843 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32532900-32533694 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32537939-32538544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32557367-32557892 Neighboring gene transmembrane protein 39B Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32573351-32573869 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32573870-32574387 Neighboring gene microRNA 5585 Neighboring gene Sharpr-MPRA regulatory region 5670 Neighboring gene karyopherin subunit alpha 6

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of KH domain containing, RNA binding, signal transduction associated 1 (KHDRBS1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Sam68deltaC inhibits HIV-1 gp120 protein synthesis by altering the association of Rev-dependent RNA with PABP. N-terminal (residues 1-28) and C-terminal (residues 262-300) domain of Sam68deltaC are required for the inhibition PubMed
    Envelope surface glycoprotein gp160, precursor env Sam68deltaC inhibits HIV-1 gp160 protein synthesis by altering the association of Rev-dependent RNA with PABP. N-terminal (residues 1-28) and C-terminal (residues 262-300) domain of Sam68deltaC are required for the inhibition PubMed
    Nef nef Suppression of HIV-1 Nef expression by Sam68 mutant (delta410) requires the Sam68 domain between amino acids 269 and 321. Sam68 mutant delta410 interacts with the nef mRNA 3'UTR in stress granules PubMed
    Rev rev In stable Sam68 knockdown HeLa cells, HIV-1 Rev activation of RRE-mediated gene expression and HIV-1 production are inhibited due to the failure of exporting unspliced HIV-1 mRNAs to the cytoplasm, indicating Rev requires Sam68 for proper function PubMed
    rev Amino acid residues 269-321 of Sam68 are required for inhibition of HIV-1 Rev function and viral replication by Sam68 dominant negative mutants lacking the nuclear localization signals PubMed
    rev The GSG domain (amino acids 97-255) of Sam68 is sufficient to enhance HIV-1 3' end cleavage and gene expression. The GSG domain-mediated effects requires HIV-1 Rev and RRE PubMed
    rev down-modulation of Sam68 causes nuclear retention and co-localization of Rev and CRM1, suggesting Sam68 is directly involved in the CRM1-mediated Rev nuclear export pathway and is required for Rev function PubMed
    rev Sam68 dominant negative mutants inhibit Rev function resulting in sequestration of unspliced HIV-1 mRNA at perinuclear bundles PubMed
    rev Sam68 promotes Rev-mediated nuclear export of HIV-1 mRNA and synergizes with Rev during this function PubMed
    rev amino acids 321-410 of Sam68 are directly involved in the binding of Sam68 to the Rev nuclear export signal (NES, amino acids 75-83) PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ34027

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables RNA binding EXP
    Inferred from Experiment
    more info
    PubMed 
    enables RNA binding HDA PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables SH2 domain binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables SH3 domain binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables molecular function inhibitor activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables poly(A) binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables poly(A) binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables poly(U) RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein tyrosine kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-containing complex binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables signaling adaptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in G1/S transition of mitotic cell cycle TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in G2/M transition of mitotic cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in T cell receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of RNA export from nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of translational initiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of RNA export from nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of RNA splicing IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of alternative mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of alternative mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT involved_in regulation of protein stability IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of Grb2-Sos complex IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in membrane HDA PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    KH domain-containing, RNA-binding, signal transduction-associated protein 1
    Names
    GAP-associated tyrosine phosphoprotein p62 (Sam68)
    KH domain containing, RNA binding, signal transduction associated 1
    p21 Ras GTPase-activating protein-associated p62
    src-associated in mitosis 68 kDa protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001271878.2NP_001258807.1  KH domain-containing, RNA-binding, signal transduction-associated protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001258807.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2, also known as SAM68DeltaKH) is shorter, compared to isoform 1. This isoform (with a truncated KH domain) is specifically expressed in growth-arrested cells and has an antagonistic role in cell cycle progression (PMID:9013542).
      Source sequence(s)
      CA442272, CN345570, M88108, U78971
      Consensus CDS
      CCDS60067.1
      UniProtKB/TrEMBL
      B2R7B5
      Related
      ENSP00000417731.1, ENST00000492989.1
      Conserved Domains (3) summary
      pfam16274
      Location:102153
      Qua1; Qua1 domain
      pfam16568
      Location:327376
      Sam68-YY; Tyrosine-rich domain of Sam68
      cl00098
      Location:152218
      KH-I; K homology (KH) RNA-binding domain, type I
    2. NM_006559.3NP_006550.1  KH domain-containing, RNA-binding, signal transduction-associated protein 1 isoform 1

      See identical proteins and their annotated locations for NP_006550.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      CA442272, CN345570, M88108
      Consensus CDS
      CCDS350.1
      UniProtKB/Swiss-Prot
      D3DPP3, Q07666, Q6PJX7, Q8NB97, Q99760
      UniProtKB/TrEMBL
      B2R7B5
      Related
      ENSP00000313829.7, ENST00000327300.12
      Conserved Domains (3) summary
      pfam16274
      Location:102153
      Qua1; Qua1 domain
      pfam16568
      Location:366415
      Sam68-YY; Tyrosine-rich domain of Sam68
      cd22468
      Location:152257
      KH-I_KHDRBS1; type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 1 (KHDRBS1) and similar proteins

    RNA

    1. NR_073498.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC010132, CA442272, CN345570
      Related
      ENST00000307714.12
    2. NR_073499.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK091346, CN345570, DB365017, M88108
      Related
      ENST00000484270.2

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      32013868..32060850
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_007066502.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      31871794..31918779
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_008485875.1 RNA Sequence

    2. XR_008485874.1 RNA Sequence