Snrnp200 small nuclear ribonucleoprotein U5 subunit 200 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Snrnp200provided by RGD
Official Full Name: small nuclear ribonucleoprotein U5 subunit 200provided by RGD
Primary source: RGD:1561120
See related: EnsemblRapid:ENSRNOG00000012157 AllianceGenome:RGD:1561120
Gene type: protein coding
RefSeq status: INFERRED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Ascc3l1; U5-200KD
Summary: Predicted to enable RNA helicase activity and identical protein binding activity. Predicted to be involved in spliceosome conformational change to release U4 (or U4atac) and U1 (or U11). Predicted to be located in nucleoplasm. Predicted to be part of spliceosomal complex and spliceosomal snRNP complex. Human ortholog(s) of this gene implicated in retinitis pigmentosa and retinitis pigmentosa 33. Orthologous to human SNRNP200 (small nuclear ribonucleoprotein U5 subunit 200). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 408.0), Spleen (RPKM 346.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q36

Exon count:: 45

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (134882173..134911512)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (114428854..114458194)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (119640324..119669651)

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
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?

Submit: New GeneRIF Correction

General gene information

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Markers

BE119847 (e-PCR)
- UniSTS:249281

GDB:182527 (e-PCR)
- UniSTS:155386

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables RNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables helicase activity	ISO Inferred from Sequence Orthology more info
enables hydrolase activity	IEA Inferred from Electronic Annotation 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 nucleic acid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in biological_process	ND No biological Data available more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	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 spliceosome conformational change to release U4 (or U4atac) and U1 (or U11)	IBA Inferred from Biological aspect of Ancestor more info
involved_in spliceosome conformational change to release U4 (or U4atac) and U1 (or U11)	IEA Inferred from Electronic Annotation more info
involved_in spliceosome conformational change to release U4 (or U4atac) and U1 (or U11)	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of U2-type catalytic step 1 spliceosome	IEA Inferred from Electronic Annotation more info
part_of U2-type catalytic step 1 spliceosome	ISO Inferred from Sequence Orthology more info
part_of U2-type catalytic step 1 spliceosome	ISS Inferred from Sequence or Structural Similarity more info
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	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	IEA Inferred from Electronic Annotation more info
part_of catalytic step 2 spliceosome	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
part_of spliceosomal complex	IBA Inferred from Biological aspect of Ancestor more info
part_of spliceosomal complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: U5 small nuclear ribonucleoprotein 200 kDa helicase

Names: BRR2 homolog; U5 snRNP-specific 200 kDa protein; activating signal cointegrator 1 complex subunit 3-like 1; small nuclear ribonucleoprotein 200 (U5)

NP_001032855.2

EC 3.6.4.13

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_001037766.2 → NP_001032855.2 U5 small nuclear ribonucleoprotein 200 kDa helicase

See identical proteins and their annotated locations for NP_001032855.2

Status: INFERRED

Source sequence(s)

JAXUCZ010000003

UniProtKB/Swiss-Prot

F1LNJ2

UniProtKB/TrEMBL

M3ZCQ2

Related

ENSRNOP00000048598.4, ENSRNOT00000043895.6

Conserved Domains (5) summary

smart00611
Location:1809 → 2125

SEC63; Domain of unknown function in Sec63p, Brr2p and other proteins

COG1204
Location:452 → 1241

BRR2; Replicative superfamily II helicase [Replication, recombination and repair]

PRK00254
Location:1310 → 1897

PRK00254; ski2-like helicase; Provisional

cd18021
Location:1325 → 1515

DEXHc_Brr2_2; C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase

pfam18149
Location:254 → 363

Helicase_PWI; N-terminal helicase PWI domain