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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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