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Aliases for SDF4 Gene

Aliases for SDF4 Gene

  • Stromal Cell Derived Factor 4 2 3 5
  • Stromal Cell-Derived Factor 4 3 4
  • Cab45 3 4
  • SDF-4 3 4
  • 45 KDa Calcium-Binding Protein 3
  • Calcium Binding Protein 2

External Ids for SDF4 Gene

Previous GeneCards Identifiers for SDF4 Gene

  • GC01M001181
  • GC01M001143
  • GC01M000423
  • GC01M001152

Summaries for SDF4 Gene

Entrez Gene Summary for SDF4 Gene

  • 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]

GeneCards Summary for SDF4 Gene

SDF4 (Stromal Cell Derived Factor 4) is a Protein Coding gene. Diseases associated with SDF4 include Bladder Squamous Cell Carcinoma and Myopathy, Tubular Aggregate, 1. GO annotations related to this gene include calcium ion binding and identical protein binding. An important paralog of this gene is RCN1.

UniProtKB/Swiss-Prot for SDF4 Gene

  • May regulate calcium-dependent activities in the endoplasmic reticulum lumen or post-ER compartment.

  • Isoform 5 may be involved in the exocytosis of zymogens by pancreatic acini.

Gene Wiki entry for SDF4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SDF4 Gene

Genomics for SDF4 Gene

Regulatory Elements for SDF4 Gene

Enhancers for SDF4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
- Elite enhancer/Elite enhancer-gene association

Enhancers around SDF4 on UCSC Golden Path with GeneCards custom track

Promoters for SDF4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for SDF4 Gene

Chromosome:
1
Start:
1,216,908 bp from pter
End:
1,232,067 bp from pter
Size:
15,160 bases
Orientation:
Minus strand

Genomic View for SDF4 Gene

Genes around SDF4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SDF4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SDF4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SDF4 Gene

Proteins for SDF4 Gene

  • Protein details for SDF4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BRK5-CAB45_HUMAN
    Recommended name:
    45 kDa calcium-binding protein
    Protein Accession:
    Q9BRK5
    Secondary Accessions:
    • B1AME5
    • B1AME6
    • B2RDF1
    • B4DSM1
    • Q53G52
    • Q53HQ9
    • Q8NBQ3
    • Q96AA1
    • Q9NZP7
    • Q9UN53

    Protein attributes for SDF4 Gene

    Size:
    362 amino acids
    Molecular mass:
    41807 Da
    Quaternary structure:
    • Isoform 5 interacts with STXBP1; the interaction is enhanced in presence of calcium. Isoform 5 interacts with STX3.
    SequenceCaution:
    • Sequence=AAL75950.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305};

    Alternative splice isoforms for SDF4 Gene

neXtProt entry for SDF4 Gene

Post-translational modifications for SDF4 Gene

  • Ubiquitination at Lys 85 and Lys 350
  • Glycosylation at Asn 40, Ser 108, Ser 343, Thr 347, Ser 349, and Ser 357
  • Modification sites at PhosphoSitePlus

Other Protein References for SDF4 Gene

Antibody Products

  • Abcam antibodies for SDF4

No data available for DME Specific Peptides for SDF4 Gene

Domains & Families for SDF4 Gene

Gene Families for SDF4 Gene

Protein Domains for SDF4 Gene

Suggested Antigen Peptide Sequences for SDF4 Gene

Graphical View of Domain Structure for InterPro Entry

Q9BRK5

UniProtKB/Swiss-Prot:

CAB45_HUMAN :
  • Binds calcium via its EF-hands (By similarity). Isoform 5 binds calcium.
  • Belongs to the CREC family.
Domain:
  • Binds calcium via its EF-hands (By similarity). Isoform 5 binds calcium.
  • Contains 6 EF-hand domains.
Family:
  • Belongs to the CREC family.
genes like me logo Genes that share domains with SDF4: view

Function for SDF4 Gene

Molecular function for SDF4 Gene

UniProtKB/Swiss-Prot Function:
May regulate calcium-dependent activities in the endoplasmic reticulum lumen or post-ER compartment.
UniProtKB/Swiss-Prot Function:
Isoform 5 may be involved in the exocytosis of zymogens by pancreatic acini.

Gene Ontology (GO) - Molecular Function for SDF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding ISS --
GO:0042802 identical protein binding ISS 17442889
genes like me logo Genes that share ontologies with SDF4: view
genes like me logo Genes that share phenotypes with SDF4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SDF4 Gene

Localization for SDF4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SDF4 Gene

Isoform 1: Golgi apparatus lumen.
Isoform 5: Cytoplasm. Cell membrane. Cell projection, bleb. Note=Isoform 5 colocalizes with STX3 and STXBP1 isoform 2 at the plasma membrane and cell surface blebs. {ECO:0000269 PubMed:17442889}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SDF4 Gene COMPARTMENTS Subcellular localization image for SDF4 gene
Compartment Confidence
extracellular 5
golgi apparatus 5
plasma membrane 4
endoplasmic reticulum 3
endosome 3
cytoskeleton 2
cytosol 2
mitochondrion 2
nucleus 2
lysosome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for SDF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm ISS 17442889
GO:0005770 late endosome ISS --
GO:0005794 Golgi apparatus IDA --
GO:0005796 Golgi lumen ISS --
GO:0005886 colocalizes_with plasma membrane ISS 17442889
genes like me logo Genes that share ontologies with SDF4: view

Pathways & Interactions for SDF4 Gene

SuperPathways for SDF4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SDF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009650 UV protection ISS 18355758
GO:0017156 calcium ion regulated exocytosis ISS 17442889
GO:0021549 cerebellum development ISS 18355758
GO:0045444 fat cell differentiation ISS --
GO:0045471 response to ethanol ISS 18355758
genes like me logo Genes that share ontologies with SDF4: view

No data available for Pathways by source and SIGNOR curated interactions for SDF4 Gene

Drugs & Compounds for SDF4 Gene

(1) Drugs for SDF4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with SDF4: view

Transcripts for SDF4 Gene

Unigene Clusters for SDF4 Gene

Stromal cell derived factor 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SDF4 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b · 8c · 8d
SP1: - -
SP2: - - -
SP3: - - - - -
SP4: - - - - - - -
SP5: - - - -
SP6: - - -
SP7:
SP8: - -
SP9: - -

Relevant External Links for SDF4 Gene

GeneLoc Exon Structure for
SDF4
ECgene alternative splicing isoforms for
SDF4

Expression for SDF4 Gene

mRNA expression in normal human tissues for SDF4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SDF4 Gene

This gene is overexpressed in Amniocyte (18.9), Bone (11.1), and Vitreous humor (9.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SDF4 Gene



NURSA nuclear receptor signaling pathways regulating expression of SDF4 Gene:

SDF4

SOURCE GeneReport for Unigene cluster for SDF4 Gene:

Hs.42806

mRNA Expression by UniProt/SwissProt for SDF4 Gene:

Q9BRK5-CAB45_HUMAN
Tissue specificity: Ubiquitous. Isoform 5 is expressed in pancreas.
genes like me logo Genes that share expression patterns with SDF4: view

Primer Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for SDF4 Gene

Orthologs for SDF4 Gene

This gene was present in the common ancestor of animals.

Orthologs for SDF4 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia SDF4 34
  • 84.6 (n)
  • 84.51 (a)
SDF4 35
  • 83 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SDF4 34
  • 84.04 (n)
  • 86.76 (a)
SDF4 35
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sdf4 34
  • 83.01 (n)
  • 87.26 (a)
Sdf4 16
Sdf4 35
  • 86 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Sdf4 34
  • 82.46 (n)
  • 86.7 (a)
oppossum
(Monodelphis domestica)
Mammalia SDF4 35
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SDF4 35
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves SDF4 34
  • 73.21 (n)
  • 80.97 (a)
SDF4 35
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sdf4 34
  • 70.23 (n)
  • 75.49 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.6490 34
zebrafish
(Danio rerio)
Actinopterygii sdf4 34
  • 71.21 (n)
  • 75.07 (a)
wufb66d06 34
sdf4 35
  • 73 (a)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10046 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002810 34
  • 49.27 (n)
  • 38.25 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG31475 34
  • 48.63 (n)
  • 35.69 (a)
CG31475 35
  • 25 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea C56C10.9 34
  • 43.94 (n)
  • 30.87 (a)
C56C10.9 35
  • 28 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 33 (a)
OneToOne
Species where no ortholog for SDF4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chimpanzee (Pan troglodytes)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SDF4 Gene

ENSEMBL:
Gene Tree for SDF4 (if available)
TreeFam:
Gene Tree for SDF4 (if available)

Paralogs for SDF4 Gene

Paralogs for SDF4 Gene

genes like me logo Genes that share paralogs with SDF4: view

Variants for SDF4 Gene

Sequence variations from dbSNP and Humsavar for SDF4 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs766752243 A colorectal cancer sample 1,223,853(+) CACGG(C/T)GCGGA reference, missense
rs12745364 - 1,228,646(+) CCTGT(C/T)GGCTA reference, missense
rs11721 -- 1,217,251(-) ATCGT(A/C/G/T)GCATC utr-variant-3-prime
rs944369 -- 1,221,049(+) CAGGA(C/G)TTTGA intron-variant
rs1756271 -- 1,219,654(+) GCCCA(C/T)CCGGC intron-variant, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for SDF4 Gene

Variant ID Type Subtype PubMed ID
dgv2n67 CNV gain 20364138
esv3540788 CNV deletion 23714750
nsv1003578 CNV gain 25217958
nsv10161 CNV gain+loss 18304495
nsv1160644 CNV deletion 26073780
nsv1160772 CNV duplication 26073780
nsv159887 CNV deletion 16902084
nsv428334 CNV gain 18775914
nsv455661 CNV loss 19166990
nsv469848 CNV gain 16826518
nsv470680 CNV loss 18288195
nsv482937 CNV loss 15286789
nsv517709 CNV gain+loss 19592680
nsv544947 CNV loss 21841781
nsv544956 CNV loss 21841781
nsv544964 CNV loss 21841781
nsv544965 CNV loss 21841781
nsv821698 CNV gain 20364138
nsv950452 CNV deletion 24416366

Variation tolerance for SDF4 Gene

Residual Variation Intolerance Score: 78.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.27; 40.68% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SDF4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SDF4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SDF4 Gene

Disorders for SDF4 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SDF4 Gene - From: DISEASES

Disorder Aliases PubMed IDs
bladder squamous cell carcinoma
  • epidermoid carcinoma of the urinary bladder
myopathy, tubular aggregate, 1
  • myeloproliferative syndrome, transient
- elite association - COSMIC cancer census association via MalaCards
Search SDF4 in MalaCards View complete list of genes associated with diseases

Relevant External Links for SDF4

Genetic Association Database (GAD)
SDF4
Human Genome Epidemiology (HuGE) Navigator
SDF4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SDF4
genes like me logo Genes that share disorders with SDF4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SDF4 Gene

Publications for SDF4 Gene

  1. Sequence of a human cDNA encoding Cab45, a Ca2+-binding protein with six EF-hand motifs. (PMID: 9254016) Koivu T. … Olkkonen V.M. (DNA Seq. 1997) 2 3 4 65
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 65
  3. Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity. (PMID: 19773279) Hosgood H.D. … Lan Q. (Occup Environ Med 2009) 3 46 65
  4. A cytosolic splice variant of Cab45 interacts with Munc18b and impacts on amylase secretion by pancreatic acini. (PMID: 17442889) Lam P.P. … Olkkonen V.M. (Mol. Biol. Cell 2007) 3 4 65
  5. Signal sequence and keyword trap in silico for selection of full- length human cDNAs encoding secretion or membrane proteins from oligo- capped cDNA libraries. (PMID: 16303743) Otsuki T. … Isogai T. (DNA Res. 2005) 3 4 65

Products for SDF4 Gene

Sources for SDF4 Gene

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