PTBP1 polypyrimidine tract binding protein 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PTBP1provided by HGNC
Official Full Name: polypyrimidine tract binding protein 1provided by HGNC
Primary source: HGNC:HGNC:9583
See related: Ensembl:ENSG00000011304 MIM:600693; AllianceGenome:HGNC:9583
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PTB; PTB2; PTB3; PTB4; pPTB; HNRPI; PTB-1; PTB-T; HNRNPI; HNRNP-I
Summary: This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA-binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has four repeats of quasi-RNA recognition motif (RRM) domains that bind RNAs. This protein binds to the intronic polypyrimidine tracts that requires pre-mRNA splicing and acts via the protein degradation ubiquitin-proteasome pathway. It may also promote the binding of U2 snRNP to pre-mRNAs. This protein is localized in the nucleoplasm and it is also detected in the perinucleolar structure. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in placenta (RPKM 42.6), bone marrow (RPKM 39.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.3

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (797452..812312)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (751931..766786)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (797452..812312)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The leader RNA of SARS-CoV-2 sequesters polypyrimidine tract binding protein (PTBP1) and influences pre-mRNA splicing in infected cells.
Title: The leader RNA of SARS-CoV-2 sequesters polypyrimidine tract binding protein (PTBP1) and influences pre-mRNA splicing in infected cells.
RNA Binding Protein PTBP1 Promotes the Metastasis of Gastric Cancer by Stabilizing PGK1 mRNA.
Title: RNA Binding Protein PTBP1 Promotes the Metastasis of Gastric Cancer by Stabilizing PGK1 mRNA.
PTBP1 promotes the progression of hepatocellular carcinoma by enhancing the oncogenic splicing switch of FGFR2.
Title: PTBP1 promotes the progression of hepatocellular carcinoma by enhancing the oncogenic splicing switch of FGFR2.
LncRNA MIAT Modulates LPS-Induced Acute Kidney Injury via BECN1-Dependent Autophagy by Interacting with PTBP1.
Title: LncRNA MIAT Modulates LPS-Induced Acute Kidney Injury via BECN1-Dependent Autophagy by Interacting with PTBP1.
N4-acetylcytidine modification of lncRNA CTC-490G23.2 promotes cancer metastasis through interacting with PTBP1 to increase CD44 alternative splicing.
Title: N4-acetylcytidine modification of lncRNA CTC-490G23.2 promotes cancer metastasis through interacting with PTBP1 to increase CD44 alternative splicing.
The lncRNA MIR99AHG directs alternative splicing of SMARCA1 by PTBP1 to enable invadopodia formation in colorectal cancer cells.
Title: The lncRNA MIR99AHG directs alternative splicing of SMARCA1 by PTBP1 to enable invadopodia formation in colorectal cancer cells.
The role of RNA splicing factor PTBP1 in neuronal development.
Title: The role of RNA splicing factor PTBP1 in neuronal development.
PTBP1 regulates injury responses and sensory pathways in adult peripheral neurons.
Title: PTBP1 regulates injury responses and sensory pathways in adult peripheral neurons.
The Splicing Factor PTBP1 Represses TP63 gamma Isoform Production in Squamous Cell Carcinoma.
Title: The Splicing Factor PTBP1 Represses TP63 γ Isoform Production in Squamous Cell Carcinoma.
Polypyrimidine tract binding protein 1 (PTBP1) contains a novel regulatory sequence, the rBH3, that binds the prosurvival protein MCL1.
Title: Polypyrimidine tract binding protein 1 (PTBP1) contains a novel regulatory sequence, the rBH3, that binds the prosurvival protein MCL1.

Submit: New GeneRIF Correction See all GeneRIFs (156)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Rev	rev	hnRNP I binds to cis-acting repressive (CRS) sequences in HIV-1 RNA suggesting a role for this binding in influencing Rev function	PubMed
Tat	tat	Polypyrimidine tract binding protein 1 (PTBP1) is identified to interact with HIV-1 Tat mutant Nullbasic in HeLa cells by LC MS/MS	PubMed
	tat	Polypyrimidine tract-binding protein (PTB) stimulates the binding of RNA Polymerase II and TRP-185 to HIV-1 TAR RNA, suggesting an interaction between PTB and HIV-1 Tat	PubMed
retropepsin	gag-pol	Positional proteomics analysis identifies the cleavage of human polypyrimidine tract binding protein 1 (PTBP1) at amino acid residues 164-165 by the HIV-1 protease	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables poly-pyrimidine tract binding	TAS Traceable Author Statement more info	PubMed
enables pre-mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in IRES-dependent viral translational initiation	IDA Inferred from Direct Assay more info	PubMed
involved_in IRES-dependent viral translational initiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of RNA splicing	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of muscle cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of calcineurin-NFAT signaling cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein dephosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of RNA splicing	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of alternative mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of cell differentiation	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in extracellular exosome	HDA more info	PubMed
located_in membrane	HDA more info	PubMed
located_in nucleolus	TAS Traceable Author Statement more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: polypyrimidine tract-binding protein 1

Names: 57 kDa RNA-binding protein PPTB-1; RNA-binding protein; heterogeneous nuclear ribonucleoprotein I; heterogeneous nuclear ribonucleoprotein polypeptide I; hnRNP I; polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001411140.1 → NP_001398069.1 polypyrimidine tract-binding protein 1 isoform d

Status: REVIEWED

Source sequence(s)

AC006273

Consensus CDS

CCDS92475.1

UniProtKB/TrEMBL

A0A7I2V621

Related

ENSP00000504829.1, ENST00000679114.1
NM_002819.5 → NP_002810.1 polypyrimidine tract-binding protein 1 isoform a

See identical proteins and their annotated locations for NP_002810.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a).

Source sequence(s)

AC006273, BC002397, BQ068293

Consensus CDS

CCDS42456.1

UniProtKB/Swiss-Prot

P26599, Q9BUQ0

UniProtKB/TrEMBL

A0A0U1RRM4

Related

ENSP00000349428.4, ENST00000356948.11

Conserved Domains (1) summary

TIGR01649
Location:57 → 557

hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
NM_031990.4 → NP_114367.1 polypyrimidine tract-binding protein 1 isoform b

See identical proteins and their annotated locations for NP_114367.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternative splice site resulting in it lacking 21 nt in the coding region compared to variant 1. Thus isoform b is 7 aa shorter than isoform a, but it maintains the same reading frame.

Source sequence(s)

AC006273, BC002397, BQ068293, X65371

Consensus CDS

CCDS45892.1

UniProtKB/TrEMBL

A0A0U1RRM4

Related

ENSP00000408096.1, ENST00000394601.8

Conserved Domains (1) summary

TIGR01649
Location:57 → 550

hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
NM_031991.4 → NP_114368.1 polypyrimidine tract-binding protein 1 isoform c

See identical proteins and their annotated locations for NP_114368.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks 78 nt in the coding region compared to variant 1. Thus isoform c is 26 aa shorter than isoform a but it maintains the same reading frame.

Source sequence(s)

AC006273, BC002397, BQ068293, X60648

Consensus CDS

CCDS32859.1

UniProtKB/TrEMBL

A0A0U1RRM4

Related

ENSP00000014112.5, ENST00000349038.8

Conserved Domains (1) summary

TIGR01649
Location:57 → 531

hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

797452..812312

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005259598.3 → XP_005259655.1 polypyrimidine tract-binding protein 1 isoform X1

See identical proteins and their annotated locations for XP_005259655.1

UniProtKB/TrEMBL

A0A0U1RRM4

Conserved Domains (5) summary

cd12693
Location:183 → 278

RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins

cd12695
Location:340 → 432

RRM3_PTBP1; RNA recognition motif 3 in vertebrate polypyrimidine tract-binding protein 1 (PTB)

cd12777
Location:61 → 141

RRM1_PTBP1; RNA recognition motif 1 in vertebrate polypyrimidine tract-binding protein 1 (PTB)

TIGR01649
Location:59 → 533

hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

cl17169
Location:453 → 533

RRM_SF; RNA recognition motif (RRM) superfamily
XM_047439114.1 → XP_047295070.1 polypyrimidine tract-binding protein 1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

751931..766786

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054321515.1 → XP_054177490.1 polypyrimidine tract-binding protein 1 isoform X1
XM_054321516.1 → XP_054177491.1 polypyrimidine tract-binding protein 1 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_175847.2: Suppressed sequence

Description

NM_175847.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.