U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

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

    Summary

    Go to the top of the page Help
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Sdf4 in Genome Data Viewer
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    Alleles

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

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    45 kDa calcium-binding protein

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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.

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous