Human Gene FAP (ENST00000188790.9_9) from GENCODE V47lift37
  Description: fibroblast activation protein alpha, transcript variant 1 (from RefSeq NM_004460.5)
Gencode Transcript: ENST00000188790.9_9
Gencode Gene: ENSG00000078098.15_17
Transcript (Including UTRs)
   Position: hg19 chr2:163,027,194-163,099,955 Size: 72,762 Total Exon Count: 26 Strand: -
Coding Region
   Position: hg19 chr2:163,027,489-163,099,837 Size: 72,349 Coding Exon Count: 26 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:163,027,194-163,099,955)mRNA (may differ from genome)Protein (760 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SEPR_HUMAN
DESCRIPTION: RecName: Full=Seprase; EC=3.4.21.-; AltName: Full=170 kDa melanoma membrane-bound gelatinase; AltName: Full=Fibroblast activation protein alpha; AltName: Full=Integral membrane serine protease;
FUNCTION: In association with DPP4 is involved in the pericellular proteolysis of the extracellular matrix (ECM), the migration and invasion of endothelial cells into the ECM. May have a role in tissue remodeling during development and wound healing, and may contribute to invasiveness in malignant cancers.
CATALYTIC ACTIVITY: Degrades gelatin and heat-denatured type I and type IV collagen, but not native type I or type IV collagen. Does not cleave laminin, fibronectin, fibrin or casein.
SUBUNIT: Homodimer, or heterodimer with DPP4. The monomer is inactive.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type II membrane protein. Cell projection, lamellipodium membrane; Single-pass type II membrane protein. Cell projection, invadopodium membrane; Single-pass type II membrane protein. Note=Found in cell surface lamellipodia, invadopodia and on shed vesicles. Colocalized with DPP4 in invadopodia and lamellipodia of migratory activated endothelial cells in collagenous matrix. Colocalized with DPP4 on endothelial cells of capillary-like microvessels but not large vessels within invasive breast ductal carcinoma.
TISSUE SPECIFICITY: Fibroblast specific.
INDUCTION: In fibroblasts at times and sites of tissue remodeling during development, tissue repair, and carcinogenesis.
PTM: N-glycosylated.
PTM: The N-terminus may be blocked.
SIMILARITY: Belongs to the peptidase S9B family.

-  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: FAP
Diseases sorted by gene-association score: infiltrative basal cell carcinoma (10), hemophagocytic lymphohistiocytosis, familial, 5 (8), breast ductal carcinoma (8), melanoma (6), glioma (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 48.55 RPKM in Cells - Cultured fibroblasts
Total median expression: 147.70 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
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -15.00118-0.127 Picture PostScript Text
3' UTR -54.60295-0.185 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
IPR002471 - Pept_S9_AS
IPR001375 - Peptidase_S9
IPR002469 - Peptidase_S9B

Pfam Domains:
PF00326 - Prolyl oligopeptidase family
PF00930 - Dipeptidyl peptidase IV (DPP IV) N-terminal region
PF03583 - Secretory lipase

SCOP Domains:
117281 - Kelch motif
50952 - Soluble quinoprotein glucose dehydrogenase
50956 - Thermostable phytase (3-phytase)
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
117289 - Nucleoporin domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50978 - WD40 repeat-like
50993 - Peptidase/esterase 'gauge' domain
69322 - Tricorn protease domain 2
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like
53474 - alpha/beta-Hydrolases

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1Z68 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q12884
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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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0002020 protease binding
GO:0004175 endopeptidase activity
GO:0004222 metalloendopeptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008236 serine-type peptidase activity
GO:0008239 dipeptidyl-peptidase activity
GO:0016787 hydrolase activity
GO:0042803 protein homodimerization activity
GO:0046983 protein dimerization activity

Biological Process:
GO:0001525 angiogenesis
GO:0006508 proteolysis
GO:0006915 apoptotic process
GO:0007155 cell adhesion
GO:0010710 regulation of collagen catabolic process
GO:0010716 negative regulation of extracellular matrix disassembly
GO:0043542 endothelial cell migration
GO:0051603 proteolysis involved in cellular protein catabolic process
GO:0051917 regulation of fibrinolysis
GO:0060244 negative regulation of cell proliferation involved in contact inhibition
GO:0071158 positive regulation of cell cycle arrest
GO:0071850 mitotic cell cycle arrest
GO:0097325 melanocyte proliferation
GO:1900119 positive regulation of execution phase of apoptosis
GO:1902362 melanocyte apoptotic process
GO:1903054 negative regulation of extracellular matrix organization

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030027 lamellipodium
GO:0030054 cell junction
GO:0031258 lamellipodium membrane
GO:0032587 ruffle membrane
GO:0042995 cell projection
GO:0045177 apical part of cell
GO:0045178 basal part of cell
GO:0071438 invadopodium membrane


-  Descriptions from all associated GenBank mRNAs
  AL832166 - Homo sapiens mRNA; cDNA DKFZp686G13158 (from clone DKFZp686G13158).
AK310293 - Homo sapiens cDNA, FLJ17335.
BC026250 - Homo sapiens fibroblast activation protein, alpha, mRNA (cDNA clone MGC:22451 IMAGE:4731931), complete cds.
U09278 - Human fibroblast activation protein mRNA, complete cds.
AK297118 - Homo sapiens cDNA FLJ60298 complete cds, highly similar to Seprase (EC 3.4.21.-).
AF007822 - Homo sapiens cytoplasmic Seprase truncated isoform mRNA, complete cds.
U76833 - Human integral membrane serine protease Seprase mRNA, complete cds.
AK315448 - Homo sapiens cDNA, FLJ96506, highly similar to Homo sapiens fibroblast activation protein, alpha (FAP), mRNA.
DQ891423 - Synthetic construct clone IMAGE:100004053; FLH176795.01X; RZPDo839H05122D fibroblast activation protein, alpha (FAP) gene, encodes complete protein.
DQ894597 - Synthetic construct Homo sapiens clone IMAGE:100009057; FLH176791.01L; RZPDo839H05121D fibroblast activation protein, alpha (FAP) gene, encodes complete protein.
KU257678 - Homo sapiens fibroblast activation protein mRNA, partial cds.
AB529180 - Synthetic construct DNA, clone: pF1KB5768, Homo sapiens FAP gene for fibroblast activation protein, alpha, without stop codon, in Flexi system.
AK055327 - Homo sapiens cDNA FLJ30765 fis, clone FEBRA2000659, highly similar to Human fibroblast activation protein mRNA.
JD436224 - Sequence 417248 from Patent EP1572962.
JD235253 - Sequence 216277 from Patent EP1572962.
AK309260 - Homo sapiens cDNA, FLJ99301.
CU693176 - Synthetic construct Homo sapiens gateway clone IMAGE:100022017 5' read FAP mRNA.
JD154913 - Sequence 135937 from Patent EP1572962.
JD140545 - Sequence 121569 from Patent EP1572962.
JD163247 - Sequence 144271 from Patent EP1572962.
JD514658 - Sequence 495682 from Patent EP1572962.
JD036445 - Sequence 17469 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000188790.1, ENST00000188790.2, ENST00000188790.3, ENST00000188790.4, ENST00000188790.5, ENST00000188790.6, ENST00000188790.7, ENST00000188790.8, FAP , NM_004460, O00199, Q12884, Q53TP5, Q86Z29, Q99998, Q9UID4, SEPR_HUMAN, uc317cfy.1, uc317cfy.2
UCSC ID: ENST00000188790.9_9
RefSeq Accession: NM_004460.5
Protein: Q12884 (aka SEPR_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.