rbfox1 RNA binding fox-1 homolog 1 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: rbfox1provided by ZNC
Official Full Name: RNA binding fox-1 homolog 1provided by ZNC
Primary source: ZFIN:ZDB-GENE-040927-11
See related: Ensembl:ENSDARG00000014746 AllianceGenome:ZFIN:ZDB-GENE-040927-11
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: fox1; a2bp1; zgc:103635
Summary: Predicted to enable mRNA binding activity. Acts upstream of or within heart contraction; hypothalamus development; and regulation of alternative mRNA splicing, via spliceosome. Predicted to be active in cytoplasm and nucleus. Is expressed in digestive system; heart; nervous system; neural keel; and skeletal muscle. Orthologous to human RBFOX1 (RNA binding fox-1 homolog 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 3

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	3	NC_007114.7 (27984158..28428193, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	3	NC_007114.6 (27853320..28297356, complement)

Chromosome 3 - NC_007114.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Pleiotropic contribution of rbfox1 to psychiatric and neurodevelopmental phenotypes in two zebrafish models.
Title: Pleiotropic contribution of rbfox1 to psychiatric and neurodevelopmental phenotypes in two zebrafish models.
This study underlines that tightly regulated splicing is necessary for unconstrained cardiac function and renders the splicing regulator rbfox1 an interesting target for investigation in human heart failure and cardiomyopathy.
Title: RNA splicing regulated by RBFOX1 is essential for cardiac function in zebrafish.

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General gene information

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Markers

Z963 (e-PCR)
- UniSTS:10531

z963 (e-PCR), detects polymorphism
- UniSTS:238219

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 heart contraction	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hypothalamus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within left ventricular cardiac muscle tissue morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within nervous system development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of RNA splicing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of RNA splicing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of alternative mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of alternative mRNA splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of alternative mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within swimming behavior	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
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: RNA binding protein fox-1 homolog 1

Names: ataxin-2-binding protein 1; fox-1 homolog A

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_001005596.1 → NP_001005596.1 RNA binding protein fox-1 homolog 1

See identical proteins and their annotated locations for NP_001005596.1

Status: PROVISIONAL

Source sequence(s)

BC081500

UniProtKB/Swiss-Prot

Q642J5

Related

ENSDARP00000107099.2, ENSDART00000122037.4

Conserved Domains (3) summary

COG0724
Location:115 → 202

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12407
Location:119 → 194

RRM_FOX1_like; RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

pfam12414
Location:228 → 318

Fox-1_C; Calcitonin gene-related peptide regulator C terminal

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007114.7 Reference GRCz11 Primary Assembly

Range

27984158..28428193 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021470430.1 → XP_021326105.1 RNA binding protein fox-1 homolog 1 isoform X3

UniProtKB/TrEMBL

A0A8M9PY74

Related

ENSDARP00000155158.1, ENSDART00000191573.1

Conserved Domains (2) summary

cd12407
Location:137 → 212

RRM_FOX1_like; RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

pfam12414
Location:246 → 336

Fox-1_C; Calcitonin gene-related peptide regulator C terminal
XM_021470445.1 → XP_021326120.1 RNA binding protein fox-1 homolog 1 isoform X14

UniProtKB/TrEMBL

A0A8M9PY89

Conserved Domains (3) summary

cd12407
Location:137 → 212

RRM_FOX1_like; RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

pfam12414
Location:246 → 293

Fox-1_C; Calcitonin gene-related peptide regulator C terminal

pfam15961
Location:44 → 109

DUF4764; Domain of unknown function (DUF4764)
XM_021470439.1 → XP_021326114.1 RNA binding protein fox-1 homolog 1 isoform X12

UniProtKB/TrEMBL

A0A8M9PMK8

Conserved Domains (2) summary

cd12407
Location:137 → 212

RRM_FOX1_like; RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

pfam12414
Location:246 → 293

Fox-1_C; Calcitonin gene-related peptide regulator C terminal
XM_021470435.1 → XP_021326110.1 RNA binding protein fox-1 homolog 1 isoform X9

UniProtKB/TrEMBL

A0A8M9PY79

Conserved Domains (2) summary

cd12407
Location:137 → 212

RRM_FOX1_like; RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

pfam12414
Location:246 → 335

Fox-1_C; Calcitonin gene-related peptide regulator C terminal
XM_021470431.1 → XP_021326106.1 RNA binding protein fox-1 homolog 1 isoform X4

UniProtKB/TrEMBL

A0A8M9PUS3

Conserved Domains (2) summary

cd12407
Location:137 → 212

RRM_FOX1_like; RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

pfam12414
Location:246 → 336

Fox-1_C; Calcitonin gene-related peptide regulator C terminal
XM_021470437.1 → XP_021326112.1 RNA binding protein fox-1 homolog 1 isoform X11

UniProtKB/TrEMBL

A0A8M9P6C2

Conserved Domains (2) summary

pfam12414
Location:215 → 304

Fox-1_C; Calcitonin gene-related peptide regulator C terminal

cl17169
Location:137 → 176

RRM_SF; RNA recognition motif (RRM) superfamily
XM_021470436.1 → XP_021326111.1 RNA binding protein fox-1 homolog 1 isoform X10

UniProtKB/TrEMBL

A0A8M9PUS8

Conserved Domains (2) summary

cd12407
Location:137 → 212

RRM_FOX1_like; RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

pfam12414
Location:246 → 293

Fox-1_C; Calcitonin gene-related peptide regulator C terminal
XM_021470432.1 → XP_021326107.1 RNA binding protein fox-1 homolog 1 isoform X6

UniProtKB/TrEMBL

A0A8M9P6B9

Conserved Domains (2) summary

cd12407
Location:137 → 212

RRM_FOX1_like; RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

pfam12414
Location:246 → 293

Fox-1_C; Calcitonin gene-related peptide regulator C terminal
XM_017354041.2 → XP_017209530.1 RNA binding protein fox-1 homolog 1 isoform X1

UniProtKB/TrEMBL

A0A8M6YWH2
XM_021470425.1 → XP_021326100.1 RNA binding protein fox-1 homolog 1 isoform X2

UniProtKB/TrEMBL

A0A8M9PY70

Conserved Domains (3) summary

cd12407
Location:136 → 211

RRM_FOX1_like; RNA recognition motif in vertebrate RNA binding protein fox-1 homologs and similar proteins

pfam12414
Location:245 → 334

Fox-1_C; Calcitonin gene-related peptide regulator C terminal

pfam15961
Location:44 → 109

DUF4764; Domain of unknown function (DUF4764)
XM_017354044.2 → XP_017209533.1 RNA binding protein fox-1 homolog 1 isoform X7

UniProtKB/TrEMBL

A0A8M6Z4X9
XM_017354045.2 → XP_017209534.1 RNA binding protein fox-1 homolog 1 isoform X8

UniProtKB/TrEMBL

A0A8M6YVW0
XM_017354049.2 → XP_017209538.1 RNA binding protein fox-1 homolog 1 isoform X13

UniProtKB/TrEMBL

A0A8M6YWH6
XM_017354043.2 → XP_017209532.1 RNA binding protein fox-1 homolog 1 isoform X5

UniProtKB/TrEMBL

A0A8M6YYC7