ptbp1a polypyrimidine tract binding protein 1a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: ptbp1aprovided by ZNC
Official Full Name: polypyrimidine tract binding protein 1aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-050522-492
See related: Ensembl:ENSDARG00000019362 AllianceGenome:ZFIN:ZDB-GENE-050522-492
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: ptbp1; wu:fb99f12; zgc:110689
Summary: Predicted to enable mRNA binding activity. Acts upstream of or within several processes, including intestinal epithelial structure maintenance; negative regulation of Notch signaling pathway; and positive regulation of cortical granule exocytosis by positive regulation of cytosolic calcium ion concentration. Predicted to be active in nucleus. Orthologous to human PTBP1 (polypyrimidine tract binding protein 1). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 2

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	2	NC_007113.7 (26288344..26300617)
105	previous assembly	GRCz10 (GCF_000002035.5)	2	NC_007113.6 (26632673..26644878)

Chromosome 2 - NC_007113.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Data report on a zebrafish maternal-effect mutant, brom bones, which is defective in the cytosolic Ca(2+) rise and subsequent egg activation events, including cortical granule exocytosis and cytoplasmic segregation [brom bones].
Title: hnRNP I is required to generate the Ca2+ signal that causes egg activation in zebrafish.
Two stretches of polypyrimidine tracts designated PPT1 and PPT2 which influence the IRES activity of cx55.5 protein were identified; deletion of PPT1 results in an appreciable decrease of the IRES activity
Title: Characterization of the internal IRES element of the zebrafish connexin55.5 reveals functional implication of the polypyrimidine tract binding protein.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within RNA splicing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within dorsal/ventral pattern formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within intestinal epithelial structure maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of Notch signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of cortical granule exocytosis by positive regulation of cytosolic calcium ion concentration	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 cell differentiation	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: polypyrimidine tract-binding protein 1a

Names: brb; brom bones; hnRNP I; polypyrimidine tract binding protein 1

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_001020477.1 → NP_001018313.1 polypyrimidine tract-binding protein 1a

See identical proteins and their annotated locations for NP_001018313.1

Status: PROVISIONAL

Source sequence(s)

BC095372

UniProtKB/TrEMBL

A0A8M1N5N7, Q503D3

Related

ENSDARP00000011705.8, ENSDART00000017668.10

Conserved Domains (5) summary

cd12693
Location:191 → 286

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

cd12695
Location:381 → 473

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

cd12777
Location:74 → 154

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

TIGR01649
Location:72 → 574

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

cl17169
Location:494 → 574

RRM_SF; RNA recognition motif (RRM) superfamily

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007113.7 Reference GRCz11 Primary Assembly

Range

26288344..26300617

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021478816.2 → XP_021334491.1 polypyrimidine tract-binding protein 1a isoform X1

UniProtKB/TrEMBL

A0A8M9QFQ9

Conserved Domains (1) summary

TIGR01649
Location:71 → 573

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