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Q9UKA9 (PTBP2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 121. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Polypyrimidine tract-binding protein 2
Alternative name(s):
Neural polypyrimidine tract-binding protein
Neurally-enriched homolog of PTB
PTB-like protein
Gene names
Name:PTBP2
Synonyms:NPTB, PTB, PTBLP
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length531 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.1 Ref.6

Subunit structure

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. Ref.1 Ref.8

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. Ref.1 Ref.3

Sequence similarities

Contains 4 RRM (RNA recognition motif) domains.

Alternative products

This entry describes 6 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9UKA9-1)

Also known as: nPTB1;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q9UKA9-2)

Also known as: nPTB2; PTBPLP-L;

The sequence of this isoform differs from the canonical sequence as follows:
     489-489: Q → QR
Isoform 3 (identifier: Q9UKA9-3)

Also known as: nPTB3; PTBPLP-L';

The sequence of this isoform differs from the canonical sequence as follows:
     302-302: A → GLPVAA
     489-489: Q → QR
Isoform 4 (identifier: Q9UKA9-4)

Also known as: nPTB4;

The sequence of this isoform differs from the canonical sequence as follows:
     302-302: A → GLPVAA
Isoform 5 (identifier: Q9UKA9-5)

Also known as: nPTB5; nPTB7; PTBPLP-S;

The sequence of this isoform differs from the canonical sequence as follows:
     349-356: MVTPQSLF → VFMEMCSV
     357-531: Missing.
Isoform 6 (identifier: Q9UKA9-6)

Also known as: nPTB6; nPTB8; PTBPLP-S';

The sequence of this isoform differs from the canonical sequence as follows:
     302-302: A → GLPVAA
     349-356: MVTPQSLF → VFMEMCSV
     357-531: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 531531Polypyrimidine tract-binding protein 2
PRO_0000232928

Regions

Domain59 – 13375RRM 1
Domain181 – 25777RRM 2
Domain338 – 41275RRM 3
Domain455 – 52975RRM 4
Compositional bias315 – 32410Poly-Ala

Amino acid modifications

Modified residue11N-acetylmethionine Ref.7 Ref.11
Modified residue3081Phosphoserine Ref.9

Natural variations

Alternative sequence3021A → GLPVAA in isoform 3, isoform 4 and isoform 6.
VSP_018015
Alternative sequence349 – 3568MVTPQSLF → VFMEMCSV in isoform 5 and isoform 6.
VSP_018016
Alternative sequence357 – 531175Missing in isoform 5 and isoform 6.
VSP_018017
Alternative sequence4891Q → QR in isoform 2 and isoform 3.
VSP_018018

Secondary structure

.................................................... 531
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (nPTB1) [UniParc].

Last modified May 1, 2000. Version 1.
Checksum: 57ADA23F422AE02A

FASTA53157,491
        10         20         30         40         50         60 
MDGIVTEVAV GVKRGSDELL SGSVLSSPNS NMSSMVVTAN GNDSKKFKGE DKMDGAPSRV 

        70         80         90        100        110        120 
LHIRKLPGEV TETEVIALGL PFGKVTNILM LKGKNQAFLE LATEEAAITM VNYYSAVTPH 

       130        140        150        160        170        180 
LRNQPIYIQY SNHKELKTDN TLNQRAQAVL QAVTAVQTAN TPLSGTTVSE SAVTPAQSPV 

       190        200        210        220        230        240 
LRIIIDNMYY PVTLDVLHQI FSKFGAVLKI ITFTKNNQFQ ALLQYGDPVN AQQAKLALDG 

       250        260        270        280        290        300 
QNIYNACCTL RIDFSKLVNL NVKYNNDKSR DYTRPDLPSG DGQPALDPAI AAAFAKETSL 

       310        320        330        340        350        360 
LAVPGALSPL AIPNAAAAAA AAAAGRVGMP GVSAGGNTVL LVSNLNEEMV TPQSLFTLFG 

       370        380        390        400        410        420 
VYGDVQRVKI LYNKKDSALI QMADGNQSQL AMNHLNGQKM YGKIIRVTLS KHQTVQLPRE 

       430        440        450        460        470        480 
GLDDQGLTKD FGNSPLHRFK KPGSKNFQNI FPPSATLHLS NIPPSVAEED LRTLFANTGG 

       490        500        510        520        530 
TVKAFKFFQD HKMALLQMAT VEEAIQALID LHNYNLGENH HLRVSFSKST I 

« Hide

Isoform 2 (nPTB2) (PTBPLP-L) [UniParc].

Checksum: A77702A0B7A84298
Show »

FASTA53257,647
Isoform 3 (nPTB3) (PTBPLP-L') [UniParc].

Checksum: 35F5BFD2614647B3
Show »

FASTA53758,084
Isoform 4 (nPTB4) [UniParc].

Checksum: 9510D0E9AC2FCBD6
Show »

FASTA53657,928
Isoform 5 (nPTB5) (nPTB7) (PTBPLP-S) [UniParc].

Checksum: C1D3D2E104207E27
Show »

FASTA35637,898
Isoform 6 (nPTB6) (nPTB8) (PTBPLP-S') [UniParc].

Checksum: C47DB1BA2B404A03
Show »

FASTA36138,336

References

« Hide 'large scale' references
[1]"Cooperative assembly of an hnRNP complex induced by a tissue-specific homolog of polypyrimidine tract binding protein."
Markovtsov V., Nikolic J.M., Goldman J.A., Turck C.W., Chou M.-Y., Black D.L.
Mol. Cell. Biol. 20:7463-7479(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PROTEIN SEQUENCE OF 55-65; 210-215; 216-235; 370-374; 404-411; 431-440 AND 487-492, FUNCTION, TISSUE SPECIFICITY, INTERACTION WITH HNRPH1 AND KHSRP.
Tissue: Retinoblastoma.
[2]"Molecular cloning and characterization of human PTB-like protein: a possible retinal autoantigen of cancer-associated retinopathy."
Tateiwa H., Gotoh N., Ichikawa M., Kikuchi T., Yoshimura N.
J. Neuroimmunol. 120:161-169(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 2 AND 5), ALTERNATIVE SPLICING (ISOFORMS 3 AND 6).
Tissue: Retina.
[3]"Alternative splicing of brain-specific PTB defines a tissue-specific isoform pattern that predicts distinct functional roles."
Rahman L., Bliskovski V., Reinhold W., Zajac-Kaye M.
Genomics 80:245-249(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 3 AND 4), NUCLEOTIDE SEQUENCE [MRNA] OF 282-531 (ISOFORMS 5 AND 6), ALTERNATIVE SPLICING (ISOFORM 2), TISSUE SPECIFICITY.
Tissue: Cervix carcinoma, Lung and Retinoblastoma.
[4]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Tissue: Eye.
[6]"The Apaf-1 internal ribosome entry segment attains the correct structural conformation for function via interactions with PTB and unr."
Mitchell S.A., Spriggs K.A., Coldwell M.J., Jackson R.J., Willis A.E.
Mol. Cell 11:757-771(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[7]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"Control of c-myc mRNA stability by IGF2BP1-associated cytoplasmic RNPs."
Weidensdorfer D., Stoehr N., Baude A., Lederer M., Koehn M., Schierhorn A., Buchmeier S., Wahle E., Huettelmaiery S.
RNA 15:104-115(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN A MRNP COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
[9]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-308, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[10]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"Solution structure of RNA-binding domain in PTB-like protein."
RIKEN structural genomics initiative (RSGI)
Submitted (NOV-2005) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 51-138.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF176085 mRNA. Translation: AAF14284.1.
AB051232 mRNA. Translation: BAB71742.1.
AB051233 mRNA. Translation: BAB71743.1.
AF530580 mRNA. Translation: AAM94624.1.
AF530581 mRNA. Translation: AAM94625.1.
AF530582 mRNA. Translation: AAM94626.1.
AF530583 mRNA. Translation: AAM94627.1.
BK000526 mRNA. Translation: DAA00060.1.
AL357150 Genomic DNA. Translation: CAH70266.1.
AL357150 Genomic DNA. Translation: CAH70267.1.
AL357150 Genomic DNA. Translation: CAH70268.1.
AL357150 Genomic DNA. Translation: CAH70269.1.
BC016582 mRNA. Translation: AAH16582.1.
CCDSCCDS754.1. [Q9UKA9-1]
RefSeqNP_067013.1. NM_021190.2. [Q9UKA9-1]
XP_005271141.1. XM_005271084.1. [Q9UKA9-3]
XP_005271142.1. XM_005271085.1. [Q9UKA9-4]
XP_005271143.1. XM_005271086.1. [Q9UKA9-2]
UniGeneHs.596061.
Hs.743449.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2CQ1NMR-A51-138[»]
2MJUNMR-A325-531[»]
4CQ1X-ray1.69A/B/C/D/E/F/G/H336-531[»]
ProteinModelPortalQ9UKA9.
SMRQ9UKA9. Positions 51-138, 177-281, 325-531.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid121796. 21 interactions.
IntActQ9UKA9. 19 interactions.
MINTMINT-1483252.
STRING9606.ENSP00000412788.

PTM databases

PhosphoSiteQ9UKA9.

Polymorphism databases

DMDM74761983.

2D gel databases

REPRODUCTION-2DPAGEIPI00647067.

Proteomic databases

MaxQBQ9UKA9.
PaxDbQ9UKA9.
PRIDEQ9UKA9.

Protocols and materials databases

DNASU58155.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000370197; ENSP00000359216; ENSG00000117569. [Q9UKA9-3]
ENST00000370198; ENSP00000359217; ENSG00000117569. [Q9UKA9-4]
ENST00000426398; ENSP00000412788; ENSG00000117569. [Q9UKA9-1]
ENST00000609116; ENSP00000477024; ENSG00000117569. [Q9UKA9-2]
GeneID58155.
KEGGhsa:58155.
UCSCuc001drn.2. human. [Q9UKA9-3]
uc001dro.2. human. [Q9UKA9-2]
uc001drq.3. human. [Q9UKA9-1]
uc001drr.3. human. [Q9UKA9-4]

Organism-specific databases

CTD58155.
GeneCardsGC01P097187.
HGNCHGNC:17662. PTBP2.
HPAHPA047420.
MIM608449. gene.
neXtProtNX_Q9UKA9.
PharmGKBPA33935.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG263741.
HOVERGENHBG069548.
KOK14948.
PhylomeDBQ9UKA9.
TreeFamTF319824.

Gene expression databases

ArrayExpressQ9UKA9.
BgeeQ9UKA9.
CleanExHS_PTBP2.
GenevestigatorQ9UKA9.

Family and domain databases

Gene3D3.30.70.330. 4 hits.
InterProIPR006536. HnRNP-L_PTB.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
SMARTSM00360. RRM. 4 hits.
[Graphical view]
TIGRFAMsTIGR01649. hnRNP-L_PTB. 1 hit.
PROSITEPS50102. RRM. 4 hits.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSPTBP2. human.
EvolutionaryTraceQ9UKA9.
GeneWikiPTBP2.
GenomeRNAi58155.
NextBio64859.
PROQ9UKA9.
SOURCESearch...

Entry information

Entry namePTBP2_HUMAN
AccessionPrimary (citable) accession number: Q9UKA9
Secondary accession number(s): Q8N0Z1 expand/collapse secondary AC list , Q8N160, Q8NFB0, Q8NFB1, Q969N9, Q96Q76
Entry history
Integrated into UniProtKB/Swiss-Prot: April 18, 2006
Last sequence update: May 1, 2000
Last modified: July 9, 2014
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM