Human Gene S100A4 (ENST00000368716.9_7) from GENCODE V47lift37

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Description: S100 calcium binding protein A4, transcript variant 1 (from RefSeq NM_002961.3)
Gencode Transcript: ENST00000368716.9_7
Gencode Gene: ENSG00000196154.12_10
Transcript (Including UTRs)
Position: hg19 chr1:153,516,097-153,518,282 Size: 2,186 Total Exon Count: 3 Strand: -
Coding Region
Position: hg19 chr1:153,516,235-153,517,270 Size: 1,036 Coding Exon Count: 2

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr1:153,516,097-153,518,282)			mRNA (may differ from genome)		Protein (101 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	UniProtKB
Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: S10A4_HUMAN DESCRIPTION: RecName: Full=Protein S100-A4; AltName: Full=Calvasculin; AltName: Full=Metastasin; AltName: Full=Placental calcium-binding protein; AltName: Full=Protein Mts1; AltName: Full=S100 calcium-binding protein A4; SUBUNIT: Homodimer. Interacts with PPFIBP1 in a calcium-dependent mode. TISSUE SPECIFICITY: Ubiquitously expressed. SIMILARITY: Belongs to the S-100 family. SIMILARITY: Contains 2 EF-hand domains.

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: S100A4 Diseases sorted by gene-association score: bile duct adenocarcinoma (4), pancreatic cancer (4), colorectal cancer (2), breast cancer (2), osteosarcoma, somatic (1), lipid-rich carcinoma (1)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D013749 Tetrachlorodibenzodioxin D016572 Cyclosporine D004041 Dietary Fats D005492 Folic Acid D010126 Ozone C045621 miglitol C024709 2,6-di-tert-butyl-4-methylene-2,5-cyclohexadienone C029955 2-nitrotoluene C016583 4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 479.00 RPKM in Whole Blood Total median expression: 4355.02 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-4.40	69	-0.064	Picture	PostScript	Text
3' UTR	-40.60	138	-0.294	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR011992 - EF-hand-like_dom
IPR018247 - EF_Hand_1_Ca_BS
IPR018249 - EF_HAND_2
IPR001751 - S100/CaBP-9k_CS
IPR013787 - S100_Ca-bd_sub

Pfam Domains:
PF01023 - S-100/ICaBP type calcium binding domain
PF13833 - EF-hand domain pair

SCOP Domains:
47473 - EF-hand

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1M31 - NMR MuPIT

2LNK - NMR MuPIT

2Q91 - X-ray MuPIT

3C1V - X-ray MuPIT

3CGA - X-ray MuPIT

3KO0 - X-ray MuPIT

3M0W - X-ray MuPIT

3ZWH - X-ray MuPIT

4ETO - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on P26447


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0003723 RNA binding GO:0003779 actin binding GO:0005509 calcium ion binding GO:0005515 protein binding GO:0042802 identical protein binding GO:0046872 metal ion binding GO:0046914 transition metal ion binding GO:0048306 calcium-dependent protein binding GO:0050786 RAGE receptor binding Biological Process: GO:0001837 epithelial to mesenchymal transition GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling Cellular Component: GO:0005576 extracellular region GO:0005615 extracellular space GO:0005634 nucleus GO:0043005 neuron projection GO:0048471 perinuclear region of cytoplasm GO:0070062 extracellular exosome

Descriptions from all associated GenBank mRNAs


	AK292083 - Homo sapiens cDNA FLJ76571 complete cds, highly similar to Homo sapiens S100 calcium binding protein A4 (calcium protein, calvasculin, metastasin, murine placental homolog) (S100A4), transcript variant 1, mRNA. BC016300 - Homo sapiens S100 calcium binding protein A4, mRNA (cDNA clone MGC:13315 IMAGE:4247807), complete cds. BC000838 - Homo sapiens S100 calcium binding protein A4, mRNA (cDNA clone MGC:5193 IMAGE:3456833), complete cds. BC024974 - Homo sapiens S100 calcium binding protein A4, mRNA (cDNA clone IMAGE:4520588). M80563 - Human CAPL protein mRNA, complete cds. LF213867 - JP 2014500723-A/21370: Polycomb-Associated Non-Coding RNAs. AY762982 - Homo sapiens leukemia multidrug resistance associated protein mRNA, partial cds. LF352400 - JP 2014500723-A/159903: Polycomb-Associated Non-Coding RNAs. JD269890 - Sequence 250914 from Patent EP1572962. LF352399 - JP 2014500723-A/159902: Polycomb-Associated Non-Coding RNAs. JD369277 - Sequence 350301 from Patent EP1572962. KJ892080 - Synthetic construct Homo sapiens clone ccsbBroadEn_01474 S100A4 gene, encodes complete protein. DQ892788 - Synthetic construct clone IMAGE:100005418; FLH189735.01X; RZPDo839A0875D S100 calcium binding protein A4 (calcium protein, calvasculin, metastasin, murine placental homolog) (S100A4) gene, encodes complete protein. DQ896035 - Synthetic construct Homo sapiens clone IMAGE:100010495; FLH189731.01L; RZPDo839A0865D S100 calcium binding protein A4 (calcium protein, calvasculin, metastasin, murine placental homolog) (S100A4) gene, encodes complete protein. AB464697 - Synthetic construct DNA, clone: pF1KB8863, Homo sapiens S100A4 gene for S100 calcium binding protein A4, without stop codon, in Flexi system. CR450345 - Homo sapiens full open reading frame cDNA clone RZPDo834B127D for gene S100A4, S100 calcium binding protein A4 (calcium protein, calvasculin, metastasin, murine placental homolog); complete cds; without stopcodon. CU677599 - Synthetic construct Homo sapiens gateway clone IMAGE:100017525 5' read S100A4 mRNA. LF352398 - JP 2014500723-A/159901: Polycomb-Associated Non-Coding RNAs. MA449444 - JP 2018138019-A/21370: Polycomb-Associated Non-Coding RNAs. MA587977 - JP 2018138019-A/159903: Polycomb-Associated Non-Coding RNAs. MA587976 - JP 2018138019-A/159902: Polycomb-Associated Non-Coding RNAs. MA587975 - JP 2018138019-A/159901: Polycomb-Associated Non-Coding RNAs.

Other Names for This Gene


	Alternate Gene Symbols: A8K7R8, CAPL, D3DV46, ENST00000368716.1, ENST00000368716.2, ENST00000368716.3, ENST00000368716.4, ENST00000368716.5, ENST00000368716.6, ENST00000368716.7, ENST00000368716.8, MTS1, NM_002961, P26447, Q6ICP8, S10A4_HUMAN, uc318gzq.1, uc318gzq.2 UCSC ID: ENST00000368716.9_7 RefSeq Accession: NM_002961.3 Protein: P26447 (aka S10A4_HUMAN or S104_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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