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Sdf4 stromal cell derived factor 4 [ Mus musculus (house mouse) ]

Gene ID: 20318, updated on 5-Mar-2024

Summary

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Official Symbol
Sdf4provided by MGI
Official Full Name
stromal cell derived factor 4provided by MGI
Primary source
MGI:MGI:108079
See related
Ensembl:ENSMUSG00000029076 AllianceGenome:MGI:108079
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Cab45
Summary
This gene encodes a member of the CREC family. The encoded protein contains multiple calcium-binding EF-hand motifs. This protein localizes to the Golgi lumen and may be involved in regulating calcium dependent cellular activities. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
Expression
Ubiquitous expression in frontal lobe adult (RPKM 24.3), genital fat pad adult (RPKM 24.0) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
4 E2; 4 87.66 cM
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (156077300..156098067)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (155992843..156013610)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene C1q and tumor necrosis factor related 12 Neighboring gene predicted gene, 42365 Neighboring gene STARR-seq mESC enhancer starr_12278 Neighboring gene STARR-seq mESC enhancer starr_12279 Neighboring gene UDP-Gal:betaGal beta 1,3-galactosyltransferase, polypeptide 6 Neighboring gene tumor necrosis factor receptor superfamily, member 4 Neighboring gene predicted gene 16008 Neighboring gene predicted gene, 25982 Neighboring gene tumor necrosis factor receptor superfamily, member 18

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. The ethanol response gene Cab45 can modulate the impairment elicited by ethanol and ultraviolet in PC12 cells. Zhu Y, et al. J Genet Genomics, 2008 Mar. PMID 18355758
  2. Cab45, a novel (Ca2+)-binding protein localized to the Golgi lumen. Scherer PE, et al. J Cell Biol, 1996 Apr. PMID 8609160, Free PMC Article
  3. Characterization of novel secreted and membrane proteins isolated by the signal sequence trap method. Shirozu M, et al. Genomics, 1996 Nov 1. PMID 8938438
  4. The antiobesity factor WDTC1 suppresses adipogenesis via the CRL4WDTC1 E3 ligase. Groh BS, et al. EMBO Rep, 2016 May. PMID 27113764, Free PMC Article
  5. Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy disease genes and pathways. Sang L, et al. Cell, 2011 May 13. PMID 21565611, Free PMC Article

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

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 ISO
Inferred from Sequence Orthology
more info
  
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in UV protection ISO
Inferred from Sequence Orthology
more info
  
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 ISO
Inferred from Sequence Orthology
more info
  
involved_in cerebellum development ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in fat cell differentiation IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in maintenance of synapse structure ISO
Inferred from Sequence Orthology
more info
  
involved_in response to ethanol ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in zymogen granule exocytosis ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
located_in Golgi lumen IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in late endosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in late endosome ISO
Inferred from Sequence Orthology
more info
  
colocalizes_with plasma membrane ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
45 kDa calcium-binding protein

NCBI Reference Sequences (RefSeq)

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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_001302467.1 → NP_001289396.1  45 kDa calcium-binding protein isoform 1 precursor

    See identical proteins and their annotated locations for NP_001289396.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    BC068152, BY226842, CJ253941
    Consensus CDS
    CCDS19054.1
    UniProtKB/Swiss-Prot
    Q3TK84, Q3TQP8, Q61112, Q61113
    Related
    ENSMUSP00000101204.2, ENSMUST00000105579.8
    Conserved Domains (2) summary
    pfam13499
    Location:102 → 162
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:101 → 160
    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 ...

  2. NM_001302468.1 → NP_001289397.1  45 kDa calcium-binding protein isoform 1 precursor

    See identical proteins and their annotated locations for NP_001289397.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AI226497, AK014418, AL627204, BC068152, CJ253941
    Consensus CDS
    CCDS19054.1
    UniProtKB/Swiss-Prot
    Q3TK84, Q3TQP8, Q61112, Q61113
    Related
    ENSMUSP00000101203.2, ENSMUST00000105578.2
    Conserved Domains (2) summary
    pfam13499
    Location:102 → 162
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:101 → 160
    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 ...

  3. NM_001302469.1 → NP_001289398.1  45 kDa calcium-binding protein isoform 2 precursor

    See identical proteins and their annotated locations for NP_001289398.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an upstream alternate 3' terminal exon compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AK163400, AL627204
    Consensus CDS
    CCDS80198.1
    UniProtKB/Swiss-Prot
    Q61112
    Related
    ENSMUSP00000095340.5, ENSMUST00000097734.11
    Conserved Domains (2) summary
    pfam13499
    Location:102 → 162
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:101 → 160
    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 ...

  4. NM_011341.5 → NP_035471.1  45 kDa calcium-binding protein isoform 1 precursor

    See identical proteins and their annotated locations for NP_035471.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    BC068152, CJ253941, DN176224
    Consensus CDS
    CCDS19054.1
    UniProtKB/Swiss-Prot
    Q3TK84, Q3TQP8, Q61112, Q61113
    Related
    ENSMUSP00000053175.7, ENSMUST00000050078.13
    Conserved Domains (2) summary
    pfam13499
    Location:102 → 162
    EF-hand_7; EF-hand domain pair
    cl08302
    Location:101 → 160
    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: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000070.7 Reference GRCm39 C57BL/6J

    Range
    156077300..156098067
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q61112.1 GenPept UniProtKB/Swiss-Prot:Q61112

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