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    SDF4 stromal cell derived factor 4 [ Homo sapiens (human) ]

    Gene ID: 51150, updated on 7-Oct-2018

    Summary

    Official Symbol
    SDF4provided by HGNC
    Official Full Name
    stromal cell derived factor 4provided by HGNC
    Primary source
    HGNC:HGNC:24188
    See related
    Ensembl:ENSG00000078808 MIM:614282; Vega:OTTHUMG00000001812
    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
    Cab45; SDF-4
    Summary
    This gene encodes a stromal cell derived factor that is a member of the CREC protein family. The encoded protein contains six EF-hand motifs and calcium-binding motifs. This protein localizes to the Golgi lumen and may be involved in regulating calcium dependent cellular activities. [provided by RefSeq, Sep 2011]
    Expression
    Ubiquitous expression in colon (RPKM 31.3), kidney (RPKM 26.5) and 25 other tissues See more
    Orthologs

    Genomic context

    See SDF4 in Genome Data Viewer
    Location:
    1p36.33
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (1216908..1232067, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1152288..1167447, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene TNF receptor superfamily member 18 Neighboring gene TNF receptor superfamily member 4 Neighboring gene beta-1,3-galactosyltransferase 6 Neighboring gene C1q and TNF related 12

    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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of stromal cell derived factor 4 (SDF4) 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 HIV-1 gp120 is identified to have a physical interaction with stromal cell derived factor 4 (SDF4) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    calcium ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    identical protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    Process Evidence Code Pubs
    UV protection ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    calcium ion regulated exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    calcium ion regulated exocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    cerebellum development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    fat cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    response to ethanol ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    zymogen granule exocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    Component Evidence Code Pubs
    Golgi apparatus IDA
    Inferred from Direct Assay
    more info
     
    Golgi lumen ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    bleb IEA
    Inferred from Electronic Annotation
    more info
     
    cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    extracellular exosome HDA PubMed 
    late endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    membrane HDA PubMed 
    colocalizes_with plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 

    General protein information

    Preferred Names
    45 kDa calcium-binding protein

    NCBI Reference Sequences (RefSeq)

    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_030007.1 RefSeqGene

      Range
      5001..20160
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_016176.3NP_057260.2  45 kDa calcium-binding protein isoform 2 precursor

      See identical proteins and their annotated locations for NP_057260.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses a different splice site in the 3' coding region, compared to variant 1, that results in a frameshift. It encodes isoform 2, which has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL162741, BC022375, DC405714
      Consensus CDS
      CCDS30553.1
      UniProtKB/Swiss-Prot
      Q9BRK5
      UniProtKB/TrEMBL
      A0A024R084
      Related
      ENSP00000353094.6, OTTHUMP00000001752, ENST00000360001.10, OTTHUMT00000005064
      Conserved Domains (1) summary
      cd16225
      Location:67347
      EFh_CREC_cab45; EF-hand, calcium binding motif, found in 45 kDa calcium-binding protein (Cab45)
    2. NM_016547.2NP_057631.1  45 kDa calcium-binding protein isoform 1 precursor

      See identical proteins and their annotated locations for NP_057631.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript yet it encodes the shorter protein (isoform 1).
      Source sequence(s)
      AF178986, AL162741, BC022375, DC405714
      Consensus CDS
      CCDS12.1
      UniProtKB/Swiss-Prot
      Q9BRK5
      UniProtKB/TrEMBL
      A0A024R0A9
      Related
      ENSP00000263741.7, OTTHUMP00000001755, ENST00000263741.11, OTTHUMT00000005070
      Conserved Domains (3) summary
      cd00051
      Location:102161
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam13499
      Location:103163
      EF-hand_7; EF-hand domain pair
      cl08302
      Location:216261
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

      Range
      1216908..1232067 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024447473.1XP_024303241.1  45 kDa calcium-binding protein isoform X1

      Conserved Domains (1) summary
      cd16225
      Location:67392
      EFh_CREC_cab45; EF-hand, calcium binding motif, found in 45 kDa calcium-binding protein (Cab45)
    2. XM_011541556.1XP_011539858.1  45 kDa calcium-binding protein isoform X2

      See identical proteins and their annotated locations for XP_011539858.1

      UniProtKB/Swiss-Prot
      Q9BRK5
      Conserved Domains (2) summary
      cd00051
      Location:102161
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
      pfam13499
      Location:103163
      EF-hand_7; EF-hand domain pair
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