rbb4l retinoblastoma binding protein 4, like [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: rbb4lprovided by ZNC
Official Full Name: retinoblastoma binding protein 4, likeprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-848
See related: Ensembl:ENSDARG00000015208 AllianceGenome:ZFIN:ZDB-GENE-030131-848
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: Caf1; rbbp7; zgc:56477; zgc:85617; wu:fa13g08; wu:fb50h10; wu:fc29d09
Summary: Predicted to enable histone binding activity. Acts upstream of or within fin regeneration and hematopoietic progenitor cell differentiation. Predicted to be part of ESC/E(Z) complex and NuRD complex. Predicted to be active in nucleus. Is expressed in mesoderm. Orthologous to several human genes including RBBP7 (RB binding protein 7, chromatin remodeling factor). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 11

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	11	NC_007122.7 (12744636..12768626)
105	previous assembly	GRCz10 (GCF_000002035.5)	11	NC_007122.6 (12686957..12710967)

Chromosome 11 - NC_007122.7 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?

Rbb4l acts as an enhancer of Nodal/Smad2/3 signaling during embryogene-sis, and depends on the existence of Nodal signaling
Title: [Rbb4l enhances TGF-β/Nodal signaling and promotes zebrafish embryonic dorsolization].
CAF-1 activity is essential for differentiation in several organs, including the retina, optic tectum, pectoral fins, and head skeleton
Title: Mutation of zebrafish caf-1b results in S phase arrest, defective differentiation, and p53-mediated apoptosis during organogenesis.

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General gene information

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Markers

fc29d09.x1 (e-PCR)
- UniSTS:187916

fa13g08.s1 (e-PCR)
- UniSTS:202368

AI477243 (e-PCR)
- UniSTS:206503

fb50h10.x1 (e-PCR)
- UniSTS:190646

fk21d03.y1 (e-PCR)
- UniSTS:200652

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA replication	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within fin regeneration	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within hematopoietic progenitor cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of ESC/E(Z) complex	IBA Inferred from Biological aspect of Ancestor more info
part_of ESC/E(Z) complex	ISS Inferred from Sequence or Structural Similarity more info
part_of NuRD complex	IBA Inferred from Biological aspect of Ancestor more info
part_of NuRD complex	ISS Inferred from Sequence or Structural Similarity 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
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: histone-binding protein RBBP7

Names: RBBP-7; retinoblastoma-binding protein 7

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_212610.1 → NP_997775.1 histone-binding protein RBBP7

See identical proteins and their annotated locations for NP_997775.1

Status: PROVISIONAL

Source sequence(s)

BC052110

UniProtKB/Swiss-Prot

Q6NWL5, Q6P3H7, Q6TLG5, Q7ZTY4, Q7ZW28

Related

ENSDARP00000108096.1, ENSDART00000131059.4

Conserved Domains (4) summary

COG2319
Location:162 → 408

WD40; WD40 repeat [General function prediction only]

pfam12265
Location:18 → 86

CAF1C_H4-bd; Histone-binding protein RBBP4 or subunit C of CAF1 complex

sd00039
Location:128 → 175

7WD40; WD40 repeat [structural motif]

cl02567
Location:172 → 403

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

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_007122.7 Reference GRCz11 Primary Assembly

Range

12744636..12768626

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009305881.3 → XP_009304156.1 histone-binding protein RBBP7 isoform X1

UniProtKB/TrEMBL

A0A8M3AXF6

Conserved Domains (3) summary

COG2319
Location:70 → 316

WD40; WD40 repeat [General function prediction only]

sd00039
Location:36 → 83

7WD40; WD40 repeat [structural motif]

cl02567
Location:31 → 312

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...