Human Gene PTBP1 (ENST00000356948.11_10) from GENCODE V47lift37
  Description: polypyrimidine tract binding protein 1, transcript variant 1 (from RefSeq NM_002819.5)
Gencode Transcript: ENST00000356948.11_10
Gencode Gene: ENSG00000011304.22_17
Transcript (Including UTRs)
   Position: hg19 chr19:797,452-812,312 Size: 14,861 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr19:797,498-810,826 Size: 13,329 Coding Exon Count: 15 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:797,452-812,312)mRNA (may differ from genome)Protein (557 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PTBP1_HUMAN
DESCRIPTION: RecName: Full=Polypyrimidine tract-binding protein 1; Short=PTB; AltName: Full=57 kDa RNA-binding protein PPTB-1; AltName: Full=Heterogeneous nuclear ribonucleoprotein I; Short=hnRNP I;
FUNCTION: Plays a role in pre-mRNA splicing and in the regulation of alternative splicing events. Activates exon skipping of its own pre-mRNA during muscle cell differentiation. Binds to the polypyrimidine tract of introns. May promote RNA looping when bound to two separate polypyrimidine tracts in the same pre-mRNA. May promote the binding of U2 snRNP to pre-mRNA. Cooperates with RAVER1 to modulate switching between mutually exclusive exons during maturation of the TPM1 pre-mRNA. Represses the splicing of MAPT/Tau exon 10.
SUBUNIT: Monomer. Part of a ternary complex containing KHSRP, PTBP1, PTBP2 and HNRPH1. Interacts with RAVER1 and SFPQ.
INTERACTION: Q7ZYE9:hnrnpab (xeno); NbExp=4; IntAct=EBI-350540, EBI-1086317; Q15365:PCBP1; NbExp=2; IntAct=EBI-350540, EBI-946095; Q96PU8:QKI; NbExp=2; IntAct=EBI-350540, EBI-945792; P23246:SFPQ; NbExp=2; IntAct=EBI-350540, EBI-355453;
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Contains 4 RRM (RNA recognition motif) 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: PTBP1
Diseases sorted by gene-association score: human t-cell leukemia virus type 2 (18), conventional angiosarcoma (7), mouth disease (1), congenital myasthenic syndrome (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D003300 Copper
  • D013749 Tetrachlorodibenzodioxin
  • C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone
  • C023514 2,6-dinitrotoluene
  • C049584 2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine
  • C009505 4,4'-diaminodiphenylmethane
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D015127 9,10-Dimethyl-1,2-benzanthracene
  • C103505 AM 251
  • D000082 Acetaminophen
          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: 92.48 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2320.81 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 -10.3046-0.224 Picture PostScript Text
3' UTR -554.101486-0.373 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
IPR006536 - HnRNP-L_PTB
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF11835 - RRM-like domain
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
53383 - PLP-dependent transferases
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1QM9 - NMR MuPIT 1SJQ - NMR MuPIT 1SJR - NMR MuPIT 2AD9 - NMR MuPIT 2ADB - NMR MuPIT 2ADC - NMR MuPIT 2EVZ - NMR MuPIT 3ZZY - X-ray MuPIT 3ZZZ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P26599
FrontTopSide
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 SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008187 poly-pyrimidine tract binding
GO:0036002 pre-mRNA binding

Biological Process:
GO:0000381 regulation of alternative mRNA splicing, via spliceosome
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0008543 fibroblast growth factor receptor signaling pathway
GO:0016070 RNA metabolic process
GO:0033119 negative regulation of RNA splicing
GO:0035307 positive regulation of protein dephosphorylation
GO:0048025 negative regulation of mRNA splicing, via spliceosome
GO:0051148 negative regulation of muscle cell differentiation
GO:0070886 positive regulation of calcineurin-NFAT signaling cascade
GO:0075522 IRES-dependent viral translational initiation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0016020 membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  HZ489601 - JP 2016020328-A/1: ANTICANCER AGENT.
X66975 - H.sapiens mRNA for heterogeneous nuclear ribonucleoprotein.
BC002397 - Homo sapiens polypyrimidine tract binding protein 1, mRNA (cDNA clone MGC:8461 IMAGE:2821531), complete cds.
BC023219 - Homo sapiens polypyrimidine tract binding protein 1, mRNA (cDNA clone IMAGE:4939047).
AB208910 - Homo sapiens mRNA for polypyrimidine tract-binding protein 1 isoform c variant protein.
X62006 - H.sapiens PTB-1 gene for polypirimidine tract binding protein.
X65371 - H.sapiens PTB-2 gene for polypirimidine tract binding protein.
X65372 - H.sapiens PTB-4 gene for polypirimidine tract binding protein.
X60648 - Human polypyrimidine tract-binding (PTB) mRNA for polypyrimidine tract-binding protein (pPTB).
BC013694 - Homo sapiens polypyrimidine tract binding protein 1, mRNA (cDNA clone MGC:9838 IMAGE:3863892), complete cds.
BC004383 - Homo sapiens polypyrimidine tract binding protein 1, mRNA (cDNA clone MGC:10830 IMAGE:3615251), complete cds.
CU678698 - Synthetic construct Homo sapiens gateway clone IMAGE:100017392 5' read PTBP1 mRNA.
AB528745 - Synthetic construct DNA, clone: pF1KB9975, Homo sapiens PTBP1 gene for polypyrimidine tract binding protein 1, without stop codon, in Flexi system.
KJ891935 - Synthetic construct Homo sapiens clone ccsbBroadEn_01329 PTBP1 gene, encodes complete protein.
KJ897415 - Synthetic construct Homo sapiens clone ccsbBroadEn_06809 PTBP1 gene, encodes complete protein.
BT006819 - Homo sapiens polypyrimidine tract binding protein 1 mRNA, complete cds.
LF209676 - JP 2014500723-A/17179: Polycomb-Associated Non-Coding RNAs.
HZ489603 - JP 2016020328-A/3: ANTICANCER AGENT.
HZ489604 - JP 2016020328-A/4: ANTICANCER AGENT.
DQ579473 - Homo sapiens piRNA piR-47585, complete sequence.
LF330725 - JP 2014500723-A/138228: Polycomb-Associated Non-Coding RNAs.
HZ489605 - JP 2016020328-A/5: ANTICANCER AGENT.
LF330724 - JP 2014500723-A/138227: Polycomb-Associated Non-Coding RNAs.
LF330723 - JP 2014500723-A/138226: Polycomb-Associated Non-Coding RNAs.
LF330722 - JP 2014500723-A/138225: Polycomb-Associated Non-Coding RNAs.
LF330721 - JP 2014500723-A/138224: Polycomb-Associated Non-Coding RNAs.
JD516848 - Sequence 497872 from Patent EP1572962.
HZ489606 - JP 2016020328-A/6: ANTICANCER AGENT.
JD305709 - Sequence 286733 from Patent EP1572962.
JD221497 - Sequence 202521 from Patent EP1572962.
JD484635 - Sequence 465659 from Patent EP1572962.
JD209703 - Sequence 190727 from Patent EP1572962.
JD217237 - Sequence 198261 from Patent EP1572962.
JD477311 - Sequence 458335 from Patent EP1572962.
JD399844 - Sequence 380868 from Patent EP1572962.
JD195376 - Sequence 176400 from Patent EP1572962.
JD476275 - Sequence 457299 from Patent EP1572962.
JD395182 - Sequence 376206 from Patent EP1572962.
JD479825 - Sequence 460849 from Patent EP1572962.
JD393909 - Sequence 374933 from Patent EP1572962.
JD408597 - Sequence 389621 from Patent EP1572962.
JD338815 - Sequence 319839 from Patent EP1572962.
JD564970 - Sequence 545994 from Patent EP1572962.
HZ489607 - JP 2016020328-A/7: ANTICANCER AGENT.
HZ489608 - JP 2016020328-A/8: ANTICANCER AGENT.
JD503913 - Sequence 484937 from Patent EP1572962.
JD442266 - Sequence 423290 from Patent EP1572962.
JD177175 - Sequence 158199 from Patent EP1572962.
JD458323 - Sequence 439347 from Patent EP1572962.
JD406237 - Sequence 387261 from Patent EP1572962.
JD039981 - Sequence 21005 from Patent EP1572962.
JD491415 - Sequence 472439 from Patent EP1572962.
JD489936 - Sequence 470960 from Patent EP1572962.
MA566302 - JP 2018138019-A/138228: Polycomb-Associated Non-Coding RNAs.
MA566301 - JP 2018138019-A/138227: Polycomb-Associated Non-Coding RNAs.
MA566300 - JP 2018138019-A/138226: Polycomb-Associated Non-Coding RNAs.
MA566299 - JP 2018138019-A/138225: Polycomb-Associated Non-Coding RNAs.
MA566298 - JP 2018138019-A/138224: Polycomb-Associated Non-Coding RNAs.
MA445253 - JP 2018138019-A/17179: Polycomb-Associated Non-Coding RNAs.

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

Protein P26599 (Reactome details) participates in the following event(s):

R-HSA-72103 Formation of pre-mRNPs
R-HSA-6803523 PTB and hnRNPA1 bind FGFR2 pre-mRNA to repress IIIb splicing and promote formation of FGFR2c mRNA
R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-6803529 FGFR2 alternative splicing
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-8953854 Metabolism of RNA
R-HSA-5654738 Signaling by FGFR2
R-HSA-72172 mRNA Splicing
R-HSA-190236 Signaling by FGFR
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000356948.1, ENST00000356948.10, ENST00000356948.2, ENST00000356948.3, ENST00000356948.4, ENST00000356948.5, ENST00000356948.6, ENST00000356948.7, ENST00000356948.8, ENST00000356948.9, NM_002819, P26599, PTB, PTBP1_HUMAN, Q9BUQ0, uc317zup.1, uc317zup.2
UCSC ID: ENST00000356948.11_10
RefSeq Accession: NM_002819.5
Protein: P26599 (aka PTBP1_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.