Snrnp40 small nuclear ribonucleoprotein U5 subunit 40 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Snrnp40provided by RGD
Official Full Name: small nuclear ribonucleoprotein U5 subunit 40provided by RGD
Primary source: RGD:1309198
See related: EnsemblRapid:ENSRNOG00000012219 AllianceGenome:RGD:1309198
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: RGD1309198
Summary: Predicted to be located in cytosol and nuclear speck. Predicted to be part of U2-type catalytic step 2 spliceosome and U4/U6 x U5 tri-snRNP complex. Orthologous to human SNRNP40 (small nuclear ribonucleoprotein U5 subunit 40). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 201.5), Spleen (RPKM 150.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (147984758..148017932)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (142700632..142733776)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (148577498..148610658)

Chromosome 5 - NC_086023.1 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: 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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Gene Ontology Provided by RGD

Process	Evidence Code	Pubs
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of U2-type catalytic step 2 spliceosome	ISO Inferred from Sequence Orthology more info
part_of U4/U6 x U5 tri-snRNP complex	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	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	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

General protein information

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Preferred Names: U5 small nuclear ribonucleoprotein 40 kDa protein

Names: small nuclear ribonucleoprotein 40 (U5)

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_001134556.1 → NP_001128028.1 U5 small nuclear ribonucleoprotein 40 kDa protein

See identical proteins and their annotated locations for NP_001128028.1

Status: PROVISIONAL

Source sequence(s)

CH473968

UniProtKB/TrEMBL

A6ISP1, D4A944

Related

ENSRNOP00000016325.6, ENSRNOT00000016325.9

Conserved Domains (2) summary

cd00200
Location:63 → 352

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 ...

sd00039
Location:71 → 108

7WD40; WD40 repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

147984758..148017932

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063287574.1 → XP_063143644.1 U5 small nuclear ribonucleoprotein 40 kDa protein isoform X1

Related

ENSRNOP00000099467.1, ENSRNOT00000149523.1
XM_039109799.2 → XP_038965727.1 U5 small nuclear ribonucleoprotein 40 kDa protein isoform X2

Conserved Domains (2) summary

sd00039
Location:21 → 56

7WD40; WD40 repeat [structural motif]

cl29593
Location:2 → 176

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 ...