Human Gene PTBP2 (ENST00000674951.1_6) from GENCODE V47lift37
  Description: polypyrimidine tract binding protein 2, transcript variant 6 (from RefSeq NM_021190.4)
Gencode Transcript: ENST00000674951.1_6
Gencode Gene: ENSG00000117569.20_15
Transcript (Including UTRs)
   Position: hg19 chr1:97,187,340-97,280,605 Size: 93,266 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg19 chr1:97,187,421-97,278,961 Size: 91,541 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:97,187,340-97,280,605)mRNA (may differ from genome)Protein (531 aa)
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-  Comments and Description Text from UniProtKB
  ID: PTBP2_HUMAN
DESCRIPTION: RecName: Full=Polypyrimidine tract-binding protein 2; AltName: Full=Neural polypyrimidine tract-binding protein; AltName: Full=Neurally-enriched homolog of PTB; AltName: Full=PTB-like protein;
FUNCTION: RNA-binding protein which binds to intronic polypyrimidine tracts and mediates negative regulation of exons splicing. May antagonize in a tissue-specific manner the ability of NOVA1 to activate exon selection. Beside its function in pre- mRNA splicing, plays also a role in the regulation of translation. Isoform 5 has a reduced affinity for RNA.
SUBUNIT: Monomer. Interacts with NOVA1; the interaction is direct. Interacts with NOVA2; the interaction is direct (By similarity). Identified in a mRNP complex, at least composed of DHX9, DDX3X, ELAVL1, HNRNPU, IGF2BP1, ILF3, PABPC1, PCBP2, PTBP2, STAU1, STAU2, SYNCRIP and YBX1. Part of a ternary complex containing KHSRP and HNRPH1.
SUBCELLULAR LOCATION: Nucleus (By similarity).
TISSUE SPECIFICITY: Mainly expressed in brain although also detected in other tissues like heart and skeletal muscle. Isoform 1 and isoform 2 are specifically expressed in neuronal tissues. Isoform 3 and isoform 4 are expressed in non-neuronal tissues. Isoform 5 and isoform 6 are truncated forms expressed in non- neuronal tissues.
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: PTBP2
Diseases sorted by gene-association score: lymph node tuberculosis (9), cancer-associated retinopathy (9), spinal cord glioma (8), pleural tuberculosis (5)

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

+  Common Gene Haplotype Alleles
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -31.0081-0.383 Picture PostScript Text
3' UTR -376.601644-0.229 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
53474 - alpha/beta-Hydrolases
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2CQ1 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9UKA9
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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:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding
GO:0036002 pre-mRNA binding

Biological Process:
GO:0006376 mRNA splice site selection
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0021510 spinal cord development
GO:0021549 cerebellum development
GO:0033119 negative regulation of RNA splicing
GO:2000177 regulation of neural precursor cell proliferation

Cellular Component:
GO:0005634 nucleus
GO:0005681 spliceosomal complex
GO:0030426 growth cone
GO:0043025 neuronal cell body


-  Descriptions from all associated GenBank mRNAs
  AK092216 - Homo sapiens cDNA FLJ34897 fis, clone NT2NE2018273, highly similar to Rattus rattus mRNA for PTB-like protein.
AB051232 - Homo sapiens PTBLP mRNA for PTB-like protein L, complete cds.
AK299755 - Homo sapiens cDNA FLJ60858 complete cds, highly similar to Polypyrimidine tract-binding protein 2.
AK299922 - Homo sapiens cDNA FLJ55583 complete cds, highly similar to Polypyrimidine tract-binding protein 2.
AF530580 - Homo sapiens non-neuronal splice variant nPTB3 (PTBP2) mRNA, complete cds; alternatively spliced.
AF530581 - Homo sapiens non-neuronal splice variant nPTB4 (PTBP2) mRNA, complete cds; alternatively spliced.
AF176085 - Homo sapiens neural polypyrimidine tract binding protein (PTB) mRNA, complete cds.
AK299897 - Homo sapiens cDNA FLJ55936 complete cds, highly similar to Polypyrimidine tract-binding protein 2.
BC016582 - Homo sapiens polypyrimidine tract binding protein 2, mRNA (cDNA clone MGC:9393 IMAGE:3872881), complete cds.
AB051233 - Homo sapiens PTBLP mRNA for PTB-like protein S, complete cds.
AK295384 - Homo sapiens cDNA FLJ55578 complete cds, highly similar to Polypyrimidine tract-binding protein 2.
EU176551 - Synthetic construct Homo sapiens clone IMAGE:100011367; FLH168632.01L; RZPDo839G09253D polypyrimidine tract binding protein 2 (PTBP2) gene, encodes complete protein.
DQ891027 - Synthetic construct clone IMAGE:100003657; FLH168633.01X; RZPDo839B0794D polypyrimidine tract binding protein 2 (PTBP2) gene, encodes complete protein.
KJ904843 - Synthetic construct Homo sapiens clone ccsbBroadEn_14237 PTBP2 gene, encodes complete protein.
AK022716 - Homo sapiens cDNA FLJ12654 fis, clone NT2RM4002093, highly similar to Homo sapiens neural polypyrimidine tract binding protein (PTB) mRNA.
AF530582 - Homo sapiens truncated non-neuronal splice variant nPTB5 (PTBP2) mRNA, partial cds; alternatively spliced.
AF530583 - Homo sapiens truncated non-neuronal splice variant nPTB6 (PTBP2) mRNA, partial cds; alternatively spliced.
AF530584 - Homo sapiens truncated non-neuronal splice variant nPTB7 (PTBP2) mRNA, partial cds; alternatively spliced.
AF530585 - Homo sapiens truncated non-neuronal splice variant nPTB8 (PTBP2) mRNA, partial cds; alternatively spliced.
AB209266 - Homo sapiens mRNA for polypyrimidine tract binding protein 2 variant protein.
AK025333 - Homo sapiens cDNA: FLJ21680 fis, clone COL09235, highly similar to AF176085 Homo sapiens neural polypyrimidine tract binding protein (PTB) mRNA.
JD321427 - Sequence 302451 from Patent EP1572962.
JD488837 - Sequence 469861 from Patent EP1572962.
JD145743 - Sequence 126767 from Patent EP1572962.
JD501164 - Sequence 482188 from Patent EP1572962.
JD359714 - Sequence 340738 from Patent EP1572962.
JD360825 - Sequence 341849 from Patent EP1572962.
JD309198 - Sequence 290222 from Patent EP1572962.
JD501420 - Sequence 482444 from Patent EP1572962.
JD305164 - Sequence 286188 from Patent EP1572962.
JD362983 - Sequence 344007 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_021190, NPTB, PTB, PTBLP, PTBP2 , PTBP2_HUMAN, Q8N0Z1, Q8N160, Q8NFB0, Q8NFB1, Q969N9, Q96Q76, Q9UKA9, uc329zaf.1, uc329zaf.2
UCSC ID: ENST00000674951.1_6
RefSeq Accession: NM_021190.4
Protein: Q9UKA9 (aka PTBP2_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.