cpsf6 cleavage and polyadenylation specific factor 6 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: cpsf6provided by ZNC
Official Full Name: cleavage and polyadenylation specific factor 6provided by ZNC
Primary source: ZFIN:ZDB-GENE-030131-5277
See related: Ensembl:ENSDARG00000018618 AllianceGenome:ZFIN:ZDB-GENE-030131-5277
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: zgc:85819; wu:fa22f12
Summary: Predicted to enable mRNA binding activity. Predicted to be involved in several processes, including mRNA alternative polyadenylation; pre-mRNA cleavage required for polyadenylation; and protein-containing complex assembly. Predicted to act upstream of or within mRNA processing. Is active in paraspeckles. Is expressed in several structures, including blastomere; central nervous system; digestive system; eye; and yolk. Orthologous to human CPSF6 (cleavage and polyadenylation specific factor 6). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 4

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	4	NC_007115.7 (2043989..2059268, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	4	NC_007115.6 (2195798..2209984, complement)

Chromosome 4 - NC_007115.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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 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?

Expression of zebrafish cpsf6 in embryogenesis and role of protein domains on subcellular localization.
Title: Expression of zebrafish cpsf6 in embryogenesis and role of protein domains on subcellular localization.

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 mRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA alternative polyadenylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA alternative polyadenylation	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of RNA export from nucleus	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein heterotetramerization	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in interchromatin granule	ISS Inferred from Sequence or Structural Similarity more info
part_of mRNA cleavage and polyadenylation specificity factor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of mRNA cleavage factor complex	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear speck	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
is_active_in paraspeckles	IDA Inferred from Direct Assay more info	PubMed
located_in paraspeckles	ISS Inferred from Sequence or Structural Similarity more info
located_in perichromatin fibrils	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: cleavage and polyadenylation specificity factor subunit 6

Names: cleavage and polyadenylation specific factor 6, 68kDa

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_001017993.1 → NP_001017993.1 cleavage and polyadenylation specificity factor subunit 6

See identical proteins and their annotated locations for NP_001017993.1

Status: PROVISIONAL

Source sequence(s)

AY398330

UniProtKB/Swiss-Prot

Q6NWC6

Related

ENSDARP00000076726.4, ENSDART00000082289.6

Conserved Domains (1) summary

cd12643
Location:82 → 158

RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

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_007115.7 Reference GRCz11 Primary Assembly

Range

2043989..2059268 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005164453.5 → XP_005164510.1 cleavage and polyadenylation specificity factor subunit 6 isoform X3

See identical proteins and their annotated locations for XP_005164510.1

UniProtKB/Swiss-Prot

Q6NWC6, Q6TH26

Related

ENSDARP00000110285.2, ENSDART00000129521.4

Conserved Domains (1) summary

cd12643
Location:82 → 158

RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins
XM_005164452.5 → XP_005164509.1 cleavage and polyadenylation specificity factor subunit 6 isoform X2

UniProtKB/TrEMBL

A0A8M2BBP6

Conserved Domains (2) summary

cd12643
Location:82 → 158

RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

pfam16294
Location:492 → 526

RSB_motif; RNSP1-SAP18 binding (RSB) motif
XM_005164451.5 → XP_005164508.1 cleavage and polyadenylation specificity factor subunit 6 isoform X1

UniProtKB/TrEMBL

A0A2R8RIN6, A0A8M2BBU1

Related

ENSDARP00000145832.1, ENSDART00000188177.1

Conserved Domains (2) summary

cd12643
Location:82 → 158

RRM_CFIm68; RNA recognition motif of pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins

pfam16294
Location:505 → 539

RSB_motif; RNSP1-SAP18 binding (RSB) motif