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Aliases for SDF4 Gene

Aliases for SDF4 Gene

  • Stromal Cell Derived Factor 4 2 3 5
  • Cab45 3 4
  • SDF-4 3 4
  • 45 KDa Calcium-Binding Protein 3
  • Stromal Cell-Derived Factor 4 4
  • 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 Cardiomyopathy, Dilated, 1P. Gene Ontology (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

Additional gene information for SDF4 Gene

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

Genomics for SDF4 Gene

GeneHancer (GH) Regulatory Elements for SDF4 Gene

Promoters and enhancers for SDF4 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I001229 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 561.6 +0.7 745 3.5 SMAD1 ZFP64 ARID4B SIN3A DMAP1 YY1 POLR2B ZNF766 E2F8 ZNF207 B3GALT6 SDF4 CCNL2 ENSG00000240731 LOC100288379 INTS11 ATAD3B ENSG00000234396 LINC00115 FAM87B
GH01I001775 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 24 -547.5 -547459 8.6 HDGF PKNOX1 FOXA2 SMAD1 ARNT ZFP64 ARID4B SIN3A DMAP1 IRF4 NADK INTS11 ENSG00000240731 CCNL2 CDK11A LOC100288379 LOC105378949 SDF4 ENSG00000230092 ATAD3B
GH01I001745 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 22.4 -514.0 -514034 2.2 PKNOX1 CLOCK ARNT ARID4B SIN3A DMAP1 ZNF766 E2F8 ZNF207 ZNF143 SLC35E2 LOC100288379 CCNL2 ENSG00000230092 RER1 SDF4 CDK11A INTS11 LOC100129381 MXRA8
GH01I001373 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 23.3 -143.1 -143056 3.9 CLOCK MLX ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF213 E2F8 AURKAIP1 GC01M001374 CDK11A ENSG00000230092 ATAD3B LOC100288379 ENSG00000237094 LINC01786 LOC100288069 CCNL2
GH01I001269 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 20.3 -40.4 -40425 5.5 PKNOX1 CLOCK ARID4B SIN3A ZNF2 ZBTB7B YY1 SLC30A9 POLR2B ZNF207 UBE2J2 LINC01786 ENSG00000230092 CDK11A ENSG00000237094 INTS11 LOC100288069 LOC100288379 ATAD3B CDK11B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SDF4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SDF4 gene promoter:

Genomic Locations for SDF4 Gene

Genomic Locations for SDF4 Gene
15,160 bases
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:
    Recommended name:
    45 kDa calcium-binding protein
    Protein Accession:
    Secondary Accessions:
    • B1AME5
    • B1AME6
    • B2RDF1
    • B4DSM1
    • Q53G52
    • Q53HQ9
    • Q8NBQ3
    • Q96AA1
    • Q9NZP7
    • Q9UN53

    Protein attributes for SDF4 Gene

    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.
    • 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 isoforms=3, 4, 685 and posLast=350350
  • Glycosylation at isoforms=3, 4, 640, posLast=108108, posLast=343343, isoforms=2, 5347, posLast=349349, and isoforms=2, 5357
  • Modification sites at PhosphoSitePlus

Other Protein References for SDF4 Gene

No data available for DME Specific Peptides for SDF4 Gene

Domains & Families for SDF4 Gene

Gene Families for SDF4 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted secreted proteins
  • Transporters

Protein Domains for SDF4 Gene

Suggested Antigen Peptide Sequences for SDF4 Gene

Graphical View of Domain Structure for InterPro Entry



  • Binds calcium via its EF-hands (By similarity). Isoform 5 binds calcium.
  • Belongs to the CREC family.
  • Binds calcium via its EF-hands (By similarity). Isoform 5 binds calcium.
  • 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.

Phenotypes From GWAS Catalog for SDF4 Gene

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
GO:0046872 metal ion binding IEA --
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

Clone 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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SDF4 gene
Compartment Confidence
extracellular 5
golgi apparatus 5
plasma membrane 4
endoplasmic reticulum 3
endosome 3
cytoskeleton 2
mitochondrion 2
nucleus 2
cytosol 2
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SDF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm ISS,IEA 17442889
GO:0005770 late endosome ISS --
GO:0005794 Golgi apparatus IDA,IEA --
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

No Data Available

Gene Ontology (GO) - Biological Process for SDF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006887 exocytosis IEA --
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 --
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 Approved 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:

Clone 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: - - -
SP8: - -
SP9: - -

Relevant External Links for SDF4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SDF4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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:


SOURCE GeneReport for Unigene cluster for SDF4 Gene:


mRNA Expression by UniProt/SwissProt for SDF4 Gene:

Tissue specificity: Ubiquitous. Isoform 5 is expressed in pancreas.

Evidence on tissue expression from TISSUES for SDF4 Gene

  • Nervous system(5)
  • Pancreas(4.7)
  • Liver(4.5)
  • Skin(4.4)
  • Lung(4.1)
  • Bone(4)
  • Intestine(4)
  • Kidney(3.7)
  • Eye(3.5)
  • Muscle(2.7)
  • Heart(2.4)
  • Adrenal gland(2.2)
  • Blood(2.2)
  • Thyroid gland(2.2)
  • Stomach(2)
genes like me logo Genes that share expression patterns with SDF4: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
(Bos Taurus)
Mammalia SDF4 33 34
  • 84.6 (n)
(Canis familiaris)
Mammalia SDF4 33 34
  • 84.04 (n)
(Mus musculus)
Mammalia Sdf4 33 16 34
  • 83.01 (n)
(Rattus norvegicus)
Mammalia Sdf4 33
  • 82.46 (n)
(Monodelphis domestica)
Mammalia SDF4 34
  • 79 (a)
(Ornithorhynchus anatinus)
Mammalia SDF4 34
  • 69 (a)
(Gallus gallus)
Aves SDF4 33 34
  • 73.21 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia sdf4 33
  • 70.23 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.6490 33
(Danio rerio)
Actinopterygii sdf4 33 34
  • 71.21 (n)
wufb66d06 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10046 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002810 33
  • 49.27 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG31475 33 34
  • 48.63 (n)
(Caenorhabditis elegans)
Secernentea C56C10.9 33 34
  • 43.94 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 33 (a)
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

Gene Tree for SDF4 (if available)
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 Variation AA Info Type
rs397514717 pathogenic, Spondyloepimetaphyseal dysplasia with joint laxity 1,232,972(-) C/G/T upstream_transcript_variant
rs397514718 pathogenic, Spondyloepimetaphyseal dysplasia with joint laxity 1,232,744(-) G/A upstream_transcript_variant
rs397514719 pathogenic, Spondyloepimetaphyseal dysplasia with joint laxity 1,232,471(-) A/G upstream_transcript_variant
rs397514720 pathogenic, Spondyloepimetaphyseal dysplasia with joint laxity 1,232,478(-) C/T upstream_transcript_variant
rs397514721 pathogenic, Ehlers-Danlos syndrome, progeroid type, 2 1,233,203(-) T/A upstream_transcript_variant

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)

Additional Variant Information for SDF4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for SDF4 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
bladder squamous cell carcinoma
  • epidermoid carcinoma of the urinary bladder
cardiomyopathy, dilated, 1p
  • cmd1p
myopathy, tubular aggregate, 1
  • tam1
- elite association - COSMIC cancer census association via MalaCards
Search SDF4 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SDF4

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 VM (DNA sequence : the journal of DNA sequencing and mapping 1997) 2 3 4 58
  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 SD … DREAM investigators (Diabetes care 2010) 3 44 58
  3. Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity. (PMID: 19773279) Hosgood HD … Lan Q (Occupational and environmental medicine 2009) 3 44 58
  4. A cytosolic splice variant of Cab45 interacts with Munc18b and impacts on amylase secretion by pancreatic acini. (PMID: 17442889) Lam PP … Olkkonen VM (Molecular biology of the cell 2007) 3 4 58
  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 research : an international journal for rapid publication of reports on genes and genomes 2005) 3 4 58

Products for SDF4 Gene

Sources for SDF4 Gene

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