Human Gene STAMBP (ENST00000394070.7_9) from GENCODE V47lift37
  Description: STAM binding protein, transcript variant 3 (from RefSeq NM_213622.4)
Gencode Transcript: ENST00000394070.7_9
Gencode Gene: ENSG00000124356.17_15
Transcript (Including UTRs)
   Position: hg19 chr2:74,056,088-74,094,295 Size: 38,208 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr2:74,057,984-74,089,386 Size: 31,403 Coding Exon Count: 9 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:74,056,088-74,094,295)mRNA (may differ from genome)Protein (424 aa)
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UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: STABP_HUMAN
DESCRIPTION: RecName: Full=STAM-binding protein; EC=3.4.19.-; AltName: Full=Associated molecule with the SH3 domain of STAM; AltName: Full=Endosome-associated ubiquitin isopeptidase;
FUNCTION: Zinc metalloprotease that specifically cleaves 'Lys-63'- linked polyubiquitin chains. Does not cleave 'Lys-48'-linked polyubiquitin chains (By similarity). Functions at the endosome and is able to oppose the ubiquitin-dependent sorting of receptors to lysosomes. Plays a role in signal transduction for cell growth and MYC induction mediated by IL-2 and GM-CSF. Potentiates BMP (bone morphogenetic protein) signaling by antagonizing the inhibitory action of SMAD6 and SMAD7.
COFACTOR: Binds 2 zinc ions per subunit (By similarity).
ENZYME REGULATION: Inhibited by N-ethylmaleimide.
SUBUNIT: Interacts with STAM1. Interacts with SMAD6 and SMAD7. Interacts with CHMP3; the interaction appears to relieve the autoinhibition of CHMP3. Interacts with SMURF2 and RNF11; this interaction promotes ubiquitination.
INTERACTION: Q9HD42:CHMP1A; NbExp=3; IntAct=EBI-396676, EBI-1057156; Q7LBR1:CHMP1B; NbExp=5; IntAct=EBI-396676, EBI-2118090; Q9Y3E7:CHMP3; NbExp=5; IntAct=EBI-396676, EBI-2118119; Q9NZZ3:CHMP5; NbExp=2; IntAct=EBI-396676, EBI-751303; P62993:GRB2; NbExp=3; IntAct=EBI-396676, EBI-401755; Q9Y3C5:RNF11; NbExp=2; IntAct=EBI-396676, EBI-396669; O43541-2:SMAD6; NbExp=2; IntAct=EBI-396676, EBI-4324970; Q92783:STAM; NbExp=3; IntAct=EBI-396676, EBI-752333; O75886:STAM2; NbExp=3; IntAct=EBI-396676, EBI-373258;
SUBCELLULAR LOCATION: Nucleus. Membrane; Peripheral membrane protein. Cytoplasm. Early endosome.
TISSUE SPECIFICITY: Ubiquitously expressed.
DOMAIN: The JAMM motif is essential for the protease activity (By similarity).
PTM: Phosphorylated after BMP type I receptor activation.
PTM: Ubiquitinated by SMURF2 in the presence of RNF11.
MISCELLANEOUS: X-ray crystallography studies of STAMBPL1, another member of the peptidase M67C family, has shown that Glu-280 binds zinc indirectly via a water molecule. Nevertheless, this residue is essential for catalytic activity.
SIMILARITY: Belongs to the peptidase M67C family.
SIMILARITY: Contains 1 MPN (JAB/Mov34) domain.

-  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: STAMBP
Diseases sorted by gene-association score: microcephaly-capillary malformation syndrome* (1690), capillary disease (7), microcephaly (5), acrofacial dysostosis 1, nager type (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 9.80 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 255.83 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -221.90562-0.395 Picture PostScript Text
3' UTR -1424.504909-0.290 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
IPR000555 - JAB1_Mov34_MPN_PAD1

Pfam Domains:
PF01398 - JAB1/Mov34/MPN/PAD-1 ubiquitin protease
PF08969 - USP8 dimerisation domain
PF14464 - Prokaryotic homologs of the JAB domain

SCOP Domains:
140856 - USP8 N-terminal domain-like
116846 - MIT domain
52540 - P-loop containing nucleoside triphosphate hydrolases
102712 - JAB1/MPN domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2XZE - X-ray 3RZU - X-ray MuPIT 3RZV - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O95630
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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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004843 thiol-dependent ubiquitin-specific protease activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008237 metallopeptidase activity
GO:0016787 hydrolase activity
GO:0019904 protein domain specific binding
GO:0046872 metal ion binding

Biological Process:
GO:0000281 mitotic cytokinesis
GO:0006508 proteolysis
GO:0007259 JAK-STAT cascade
GO:0008284 positive regulation of cell proliferation
GO:0014067 negative regulation of phosphatidylinositol 3-kinase signaling
GO:0016579 protein deubiquitination
GO:0043524 negative regulation of neuron apoptotic process
GO:0046580 negative regulation of Ras protein signal transduction

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0032154 cleavage furrow
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  HM005594 - Homo sapiens clone HTL-S-54 testicular secretory protein Li 54 mRNA, complete cds.
BC065574 - Homo sapiens STAM binding protein, mRNA (cDNA clone MGC:74767 IMAGE:6170296), complete cds.
JD196569 - Sequence 177593 from Patent EP1572962.
AF052135 - Homo sapiens clone 23625 mRNA sequence.
BC101467 - Homo sapiens STAM binding protein, transcript variant 1, mRNA (cDNA clone MGC:126516 IMAGE:8068973), complete cds.
BC101469 - Homo sapiens STAM binding protein, mRNA (cDNA clone MGC:126518 IMAGE:8068975), complete cds.
JD306640 - Sequence 287664 from Patent EP1572962.
BC007682 - Homo sapiens STAM binding protein, mRNA (cDNA clone MGC:3546 IMAGE:3619837), complete cds.
U73522 - Homo sapiens AMSH mRNA, complete cds.
CU675757 - Synthetic construct Homo sapiens gateway clone IMAGE:100019337 5' read STAMBP mRNA.
CU688078 - Synthetic construct Homo sapiens gateway clone IMAGE:100021728 5' read STAMBP mRNA.
DQ892616 - Synthetic construct clone IMAGE:100005246; FLH188347.01X; RZPDo839B0573D STAM binding protein (STAMBP) gene, encodes complete protein.
DQ895856 - Synthetic construct Homo sapiens clone IMAGE:100010316; FLH188343.01L; RZPDo839B0563D STAM binding protein (STAMBP) gene, encodes complete protein.
KJ893091 - Synthetic construct Homo sapiens clone ccsbBroadEn_02485 STAMBP gene, encodes complete protein.
KJ898258 - Synthetic construct Homo sapiens clone ccsbBroadEn_07652 STAMBP gene, encodes complete protein.
EU927390 - Homo sapiens STAM binding protein (STAMBP) mRNA, partial cds, alternatively spliced.
JD429081 - Sequence 410105 from Patent EP1572962.
JD440304 - Sequence 421328 from Patent EP1572962.
JD237492 - Sequence 218516 from Patent EP1572962.
JD225270 - Sequence 206294 from Patent EP1572962.
JD082982 - Sequence 64006 from Patent EP1572962.
JD055977 - Sequence 37001 from Patent EP1572962.
JD414434 - Sequence 395458 from Patent EP1572962.
JD530947 - Sequence 511971 from Patent EP1572962.
JD286250 - Sequence 267274 from Patent EP1572962.
JD301110 - Sequence 282134 from Patent EP1572962.
JD093351 - Sequence 74375 from Patent EP1572962.
AK023768 - Homo sapiens cDNA FLJ13706 fis, clone PLACE2000317.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O95630 (Reactome details) participates in the following event(s):

R-HSA-5693061 STAMBP binds STAM
R-HSA-5689901 Metalloprotease DUBs
R-HSA-5688426 Deubiquitination
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: AMSH , B5M0B6, D6W5H7, ENST00000394070.1, ENST00000394070.2, ENST00000394070.3, ENST00000394070.4, ENST00000394070.5, ENST00000394070.6, NM_213622, O95630, Q3MJE7, STABP_HUMAN, uc318wit.1, uc318wit.2
UCSC ID: ENST00000394070.7_9
RefSeq Accession: NM_213622.4
Protein: O95630 (aka STABP_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene STAMBP:
miccap-ms (Microcephaly-Capillary Malformation Syndrome)

-  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.