Prpf6 pre-mRNA processing factor 6 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Prpf6provided by RGD
Official Full Name: pre-mRNA processing factor 6provided by RGD
Primary source: RGD:1307103
See related: EnsemblRapid:ENSRNOG00000051498 AllianceGenome:RGD:1307103
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1307103
Summary: Predicted to enable several functions, including identical protein binding activity; protein-macromolecule adaptor activity; and ribonucleoprotein complex binding activity. Predicted to be involved in spliceosomal tri-snRNP complex assembly. Predicted to act upstream of or within RNA localization and positive regulation of transcription by RNA polymerase II. Predicted to be located in nuclear speck. Predicted to be part of nucleus. Human ortholog(s) of this gene implicated in retinitis pigmentosa 60. Orthologous to human PRPF6 (pre-mRNA processing factor 6). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Biased expression in Thymus (RPKM 190.7), Adrenal (RPKM 184.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q43

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (189084465..189148705)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (168706952..168771191)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (177098137..177162937)

Chromosome 3 - NC_086021.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Prpf6 (e-PCR), detects polymorphism
- UniSTS:478980

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein-macromolecule adaptor activity	IEA Inferred from Electronic Annotation more info
enables protein-macromolecule adaptor activity	ISO Inferred from Sequence Orthology more info
enables protein-macromolecule adaptor activity	ISS Inferred from Sequence or Structural Similarity more info
enables ribonucleoprotein complex binding	IEA Inferred from Electronic Annotation more info
enables ribonucleoprotein complex binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in RNA localization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within RNA localization	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in mRNA splicing, via spliceosome	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in spliceosomal tri-snRNP complex assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in spliceosomal tri-snRNP complex assembly	IEA Inferred from Electronic Annotation more info
involved_in spliceosomal tri-snRNP complex assembly	ISO Inferred from Sequence Orthology more info
involved_in spliceosomal tri-snRNP complex assembly	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of U2-type precatalytic spliceosome	IEA Inferred from Electronic Annotation more info
part_of U2-type precatalytic spliceosome	ISO Inferred from Sequence Orthology more info
part_of U2-type precatalytic spliceosome	ISS Inferred from Sequence or Structural Similarity more info
part_of U4/U6 x U5 tri-snRNP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of U4/U6 x U5 tri-snRNP complex	IEA Inferred from Electronic Annotation more info
part_of U4/U6 x U5 tri-snRNP complex	ISO Inferred from Sequence Orthology more info
part_of U5 snRNP	IEA Inferred from Electronic Annotation more info
part_of U5 snRNP	ISO Inferred from Sequence Orthology more info
part_of catalytic step 2 spliceosome	IBA Inferred from Biological aspect of Ancestor more info
part_of catalytic step 2 spliceosome	IEA Inferred from Electronic Annotation more info
part_of catalytic step 2 spliceosome	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: pre-mRNA-processing factor 6

Names: PRP6 homolog; PRP6 pre-mRNA processing factor 6 homolog; PRP6 pre-mRNA splicing factor 6 homolog; U5 snRNP-associated 102 kDa protein; U5-102 kDa protein

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_001079766.1 → NP_001073234.1 pre-mRNA-processing factor 6

See identical proteins and their annotated locations for NP_001073234.1

Status: PROVISIONAL

Source sequence(s)

BC128779

UniProtKB/Swiss-Prot

A1A5S1

UniProtKB/TrEMBL

A0A8I6AVE4

Related

ENSRNOP00000073536.2, ENSRNOT00000083423.3

Conserved Domains (3) summary

TIGR02917
Location:290 → 806

PEP_TPR_lipo; putative PEP-CTERM system TPR-repeat lipoprotein

sd00006
Location:708 → 738

TPR; TPR repeat [structural motif]

pfam06424
Location:13 → 169

PRP1_N; PRP1 splicing factor, N-terminal