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

    Gene ID: 51150, updated on 6-Oct-2024

    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; AllianceGenome:HGNC:24188
    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
    NEW
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    Genomic context

    See SDF4 in Genome Data Viewer
    Location:
    1p36.33
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (1216931..1232001, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (645388..660462, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (1152311..1167381, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak6 silencer Neighboring gene TNF receptor superfamily member 18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1143552-1144431 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 47 Neighboring gene TNF receptor superfamily member 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1167335-1168016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1168017-1168698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:1169483-1169984 Neighboring gene beta-1,3-galactosyltransferase 6 Neighboring gene C1q and TNF related 12 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:1182045-1182826

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What'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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables calcium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables calcium ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables identical protein binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in UV protection ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in calcium-ion regulated exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in calcium-ion regulated exocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in cerebellum development ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in fat cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in maintenance of synapse structure IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in response to ethanol ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in zymogen granule exocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi lumen ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in bleb IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in late endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in 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)

    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_030007.1 RefSeqGene

      Range
      5067..20137
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_016176.6NP_057260.3  45 kDa calcium-binding protein isoform 2 precursor

      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
      Consensus CDS
      CCDS30553.2
      UniProtKB/TrEMBL
      A0A5F9UP49
      Related
      ENSP00000353094.7, ENST00000360001.12
      Conserved Domains (1) summary
      cd16225
      Location:60340
      EFh_CREC_cab45; EF-hand, calcium binding motif, found in 45 kDa calcium-binding protein (Cab45)
    2. NM_016547.3NP_057631.2  45 kDa calcium-binding protein isoform 1 precursor

      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, R15491
      Consensus CDS
      CCDS12.2
      UniProtKB/TrEMBL
      A0A5F9UJX7
      Related
      ENSP00000263741.8, ENST00000263741.12
      Conserved Domains (1) summary
      cd16225
      Location:60297
      EFh_CREC_cab45; EF-hand, calcium binding motif, found in 45 kDa calcium-binding protein (Cab45)

    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
      1216931..1232001 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422111.1XP_047278067.1  45 kDa calcium-binding protein isoform X1

      UniProtKB/Swiss-Prot
      B1AME5, B1AME6, B2RDF1, B4DSM1, Q53G52, Q53HQ9, Q8NBQ3, Q96AA1, Q9BRK5, Q9NZP7, Q9UN53
    2. XM_047422112.1XP_047278068.1  45 kDa calcium-binding protein isoform X2

    3. XM_011541556.2XP_011539858.1  45 kDa calcium-binding protein isoform X3

      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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      645388..660462 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336904.1XP_054192879.1  45 kDa calcium-binding protein isoform X1

      UniProtKB/Swiss-Prot
      B1AME5, B1AME6, B2RDF1, B4DSM1, Q53G52, Q53HQ9, Q8NBQ3, Q96AA1, Q9BRK5, Q9NZP7, Q9UN53
    2. XM_054336905.1XP_054192880.1  45 kDa calcium-binding protein isoform X2

    3. XM_054336906.1XP_054192881.1  45 kDa calcium-binding protein isoform X3