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    SPRTN SprT-like N-terminal domain [ Homo sapiens (human) ]

    Gene ID: 83932, updated on 8-Jul-2021

    Summary

    Official Symbol
    SPRTNprovided by HGNC
    Official Full Name
    SprT-like N-terminal domainprovided by HGNC
    Primary source
    HGNC:HGNC:25356
    See related
    Ensembl:ENSG00000010072 MIM:616086
    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
    DVC1; PRO4323; spartan; C1orf124
    Summary
    The protein encoded by this gene may play a role in DNA repair during replication of damaged DNA. This protein recruits valosin containing protein (p97) to stalled DNA replication forks where it may prevent excessive translesional DNA synthesis and limit the number of DNA-damage induced mutations. It may also be involved in replication-related G2/M-checkpoint regulation. Deficiency of a similar protein in mouse causes chromosomal instability and progeroid phenotypes. Mutations in this gene have been associated with Ruijs-Aalfs syndrome (RJALS). Alternatively spliced transcript variants have been identified. [provided by RefSeq, Mar 2015]
    Expression
    Broad expression in testis (RPKM 6.8), bone marrow (RPKM 3.1) and 24 other tissues See more
    Orthologs
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    Genomic context

    See SPRTN in Genome Data Viewer
    Location:
    1q42.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (231337980..231355023)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (231474039..231490769)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 80 Neighboring gene exocyst complex component 8 Neighboring gene uncharacterized LOC107985360 Neighboring gene egl-9 family hypoxia inducible factor 1 Neighboring gene small nuclear ribonucleoprotein D2 pseudogene 2

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • dJ876B10.3, DKFZp547N043

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables K63-linked polyubiquitin modification-dependent protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables metalloendopeptidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables polyubiquitin modification-dependent protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables single-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ubiquitin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in chromatin IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
     
    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
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    DNA-dependent metalloprotease SPRTN
    Names
    DNA damage protein targeting VCP
    DNA damage-targeting VCP (p97) adaptor
    zinc finger RAD18 domain-containing 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.

    Genomic

    1. NG_042052.1 RefSeqGene

      Range
      5358..22088
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001010984.4NP_001010984.1  DNA-dependent metalloprotease SPRTN isoform b

      See identical proteins and their annotated locations for NP_001010984.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an alternate segment in the 3' end which results in the introduction of an early stop codon, compared to variant 1. This variant encodes a protein (isoform B) with a shorter C-terminus which lacks a Rad18-like CCHC zinc finger domain, compared to isoform A.
      Source sequence(s)
      AL117352, AY358611, BC068478, BU630543
      Consensus CDS
      CCDS31054.1
      UniProtKB/Swiss-Prot
      Q9H040
      Related
      ENSP00000375731.4, ENST00000391858.8
      Conserved Domains (1) summary
      pfam10263
      Location:45213
      SprT-like; SprT-like family
    2. NM_001261462.3NP_001248391.1  DNA-dependent metalloprotease SPRTN isoform c

      See identical proteins and their annotated locations for NP_001248391.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks a coding exon and has an alternate segment in the 3' end which results in the introduction of an early stop codon, compared to variant 1. This variant encodes a protein (isoform C) with a shorter C-terminus which lacks a Rad18-like CCHC zinc finger domain, compared to isoform A.
      Source sequence(s)
      AL117352, AY358611, BC068478, BU630543
      Consensus CDS
      CCDS58066.1
      UniProtKB/Swiss-Prot
      Q9H040
      Related
      ENSP00000008440.9, ENST00000008440.9
      Conserved Domains (1) summary
      pfam10263
      Location:45170
      SprT-like; SprT-like family
    3. NM_032018.7NP_114407.3  DNA-dependent metalloprotease SPRTN isoform a

      See identical proteins and their annotated locations for NP_114407.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (A).
      Source sequence(s)
      AL117352, BC068478, BU630543
      Consensus CDS
      CCDS1594.1
      UniProtKB/Swiss-Prot
      Q9H040
      UniProtKB/TrEMBL
      A0A024R3U2
      Related
      ENSP00000295050.7, ENST00000295050.12
      Conserved Domains (2) summary
      smart00734
      Location:453476
      ZnF_Rad18; Rad18-like CCHC zinc finger
      pfam10263
      Location:45213
      SprT-like; SprT-like family

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

      Range
      231337980..231355023
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006711818.3XP_006711881.1  DNA-dependent metalloprotease SPRTN isoform X1

      Conserved Domains (2) summary
      smart00734
      Location:410433
      ZnF_Rad18; Rad18-like CCHC zinc finger
      smart00731
      Location:43169
      SprT; SprT homologues
    2. XM_011544289.2XP_011542591.1  DNA-dependent metalloprotease SPRTN isoform X2

      Conserved Domains (2) summary
      smart00734
      Location:325348
      ZnF_Rad18; Rad18-like CCHC zinc finger
      cl19237
      Location:2384
      DUF45; Protein of unknown function DUF45
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