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PTBP3 polypyrimidine tract binding protein 3 [ Homo sapiens (human) ]

Gene ID: 9991, updated on 1-Jun-2020

Summary

Official Symbol
PTBP3provided by HGNC
Official Full Name
polypyrimidine tract binding protein 3provided by HGNC
Primary source
HGNC:HGNC:10253
See related
Ensembl:ENSG00000119314 MIM:607527
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
ROD1
Summary
The protein encoded by this gene binds RNA and is a regulator of cell differentiation. The encoded protein preferentially binds to poly(G) and poly(U) sequences in vitro. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
Expression
Ubiquitous expression in appendix (RPKM 17.8), lymph node (RPKM 17.7) and 25 other tissues See more
Orthologs

Genomic context

See PTBP3 in Genome Data Viewer
Location:
9q32
Exon count:
16
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (112217715..112333669, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (114979995..115095944, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene sushi domain containing 1 Neighboring gene RNA, U6 small nuclear 855, pseudogene Neighboring gene ribosomal protein L29 pseudogene 20 Neighboring gene RNA, 7SL, cytoplasmic 57, pseudogene Neighboring gene RNA, 5S ribosomal pseudogene 295 Neighboring gene RNA, 7SL, cytoplasmic 430, pseudogene Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 28 Neighboring gene HNF4 motif-containing MPRA enhancer 25 Neighboring gene ribosomal protein L32 pseudogene 22

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp781I1117

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
RNA splicing IEA
Inferred from Electronic Annotation
more info
 
anatomical structure morphogenesis TAS
Traceable Author Statement
more info
PubMed 
erythrocyte maturation IEA
Inferred from Electronic Annotation
more info
 
mRNA processing IEA
Inferred from Electronic Annotation
more info
 
negative regulation of RNA splicing IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of RNA splicing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of cell differentiation IEA
Inferred from Electronic Annotation
more info
 
regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
polypyrimidine tract-binding protein 3
Names
ROD1 regulator of differentiation 1
fission yeast differentiation regulator
regulator of differentiation 1

NCBI Reference Sequences (RefSeq)

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)

  1. NM_001163788.4NP_001157260.1  polypyrimidine tract-binding protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001157260.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 6. The resulting isoform (2) is shorter at the N-terminus and contains an alternate short internal segment compared to isoform 6.
    Source sequence(s)
    AK302558, AL158824, CN371677
    Consensus CDS
    CCDS55332.1
    UniProtKB/Swiss-Prot
    O95758
    Related
    ENSP00000363375.1, ENST00000374257.5
    Conserved Domains (1) summary
    TIGR01649
    Location:29524
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
  2. NM_001163790.2NP_001157262.1  polypyrimidine tract-binding protein 3 isoform 3

    See identical proteins and their annotated locations for NP_001157262.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 6. The resulting isoform (3) has a shorter and distinct N-terminus and contains an alternate short internal segment compared to isoform 6.
    Source sequence(s)
    AL158824, AL359073, BX097575, CN371677
    Consensus CDS
    CCDS55333.1
    UniProtKB/Swiss-Prot
    O95758
    Related
    ENSP00000334499.6, ENST00000334318.10
    Conserved Domains (1) summary
    TIGR01649
    Location:60555
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
  3. NM_001244896.2NP_001231825.1  polypyrimidine tract-binding protein 3 isoform 4

    See identical proteins and their annotated locations for NP_001231825.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence, uses an alternate in-frame splice junction at the 3' end of an exon, and lacks an alternate coding exon compared to variant 6. The resulting isoform (4) has a shorter and distinct N-terminus compared to isoform 6.
    Source sequence(s)
    AK001685, AL158824, BX097575, CN371677
    Consensus CDS
    CCDS59140.1
    UniProtKB/Swiss-Prot
    O95758
    Related
    ENSP00000340705.2, ENST00000343327.6
    Conserved Domains (1) summary
    TIGR01649
    Location:1457
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
  4. NM_001244897.2NP_001231826.1  polypyrimidine tract-binding protein 3 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence, uses an alternate in-frame splice junction at the 3' end of an exon, and uses an alternate splice junction at the 5' end of the last exon, that causes a frameshift, compared to variant 6. The resulting isoform (5) is shorter at the N-terminus, contains a short alternate internal segment, and has a shorter and distinct C-terminus compared to isoform 6.
    Source sequence(s)
    AL158824, BC039896, BX097575
    UniProtKB/Swiss-Prot
    O95758
    Conserved Domains (5) summary
    COG0724
    Location:329471
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12693
    Location:151246
    RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins
    cd12779
    Location:26115
    RRM1_ROD1; RNA recognition motif 1 in vertebrate regulator of differentiation 1 (Rod1)
    TIGR01661
    Location:38398
    ELAV_HUD_SF; ELAV/HuD family splicing factor
    cl17169
    Location:331423
    RRM_SF; RNA recognition motif (RRM) superfamily
  5. NM_001244898.1NP_001231827.1  polypyrimidine tract-binding protein 3 isoform 6

    See identical proteins and their annotated locations for NP_001231827.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) encodes the longest isoform (6).
    Source sequence(s)
    AL158824, BC044585, BX097575
    Consensus CDS
    CCDS59141.1
    UniProtKB/Swiss-Prot
    O95758
    Related
    ENSP00000414921.1, ENST00000458258.5
    Conserved Domains (1) summary
    TIGR01649
    Location:63558
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
  6. NM_001375918.1NP_001362847.1  polypyrimidine tract-binding protein 3 isoform 7

    Status: REVIEWED

    Source sequence(s)
    AB023967, AL158824, AL359073
  7. NM_001375920.1NP_001362849.1  polypyrimidine tract-binding protein 3 isoform 8

    Status: REVIEWED

    Source sequence(s)
    AL158824, AL359073
  8. NM_005156.7NP_005147.3  polypyrimidine tract-binding protein 3 isoform 1

    See identical proteins and their annotated locations for NP_005147.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence compared to variant 6. The resulting isoform (1) has a shorter and distinct N-terminus compared to isoform 6.
    Source sequence(s)
    AL158824, AL359073, BX097575, CN371677
    Consensus CDS
    CCDS6784.1
    UniProtKB/Swiss-Prot
    O95758
    UniProtKB/TrEMBL
    A0A024R163
    Related
    ENSP00000363373.2, ENST00000374255.6
    Conserved Domains (1) summary
    TIGR01649
    Location:57552
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    112217715..112333669 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447722.1XP_024303490.1  polypyrimidine tract-binding protein 3 isoform X3

    Conserved Domains (1) summary
    TIGR01649
    Location:1457
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
  2. XM_011519265.1XP_011517567.1  polypyrimidine tract-binding protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011517567.1

    Conserved Domains (5) summary
    cd12693
    Location:188283
    RRM2_PTBP1_like; RNA recognition motif 2 in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins
    cd12703
    Location:481561
    RRM4_ROD1; RNA recognition motif 4 in vertebrate regulator of differentiation 1 (Rod1)
    cd12779
    Location:63152
    RRM1_ROD1; RNA recognition motif 1 in vertebrate regulator of differentiation 1 (Rod1)
    TIGR01649
    Location:66561
    hnRNP-L_PTB; hnRNP-L/PTB/hephaestus splicing factor family
    cl17169
    Location:368460
    RRM_SF; RNA recognition motif (RRM) superfamily
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