Smg5 SMG5 nonsense mediated mRNA decay factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Smg5provided by RGD
Official Full Name: SMG5 nonsense mediated mRNA decay factorprovided by RGD
Primary source: RGD:1584731
See related: EnsemblRapid:ENSRNOG00000019590 AllianceGenome:RGD:1584731
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable enzyme binding activity and nucleic acid binding activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay; regulation of dephosphorylation; and regulation of telomere maintenance. Predicted to be located in cytoplasm and nucleus. Predicted to be part of telomerase holoenzyme complex. Orthologous to human SMG5 (SMG5 nonsense mediated mRNA decay factor). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 138.5), Spleen (RPKM 134.2) and 9 other tissues See more
Orthologs: human mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 2q34

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (176102812..176129925)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (173804987..173832102)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (187708247..187735355)

Chromosome 2 - NC_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

Go to the top of the page Help

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables protein phosphatase 2A binding	ISO Inferred from Sequence Orthology more info
enables telomerase RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables telomerase RNA binding	ISO Inferred from Sequence Orthology more info
enables telomeric DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables telomeric DNA binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of dephosphorylation	ISO Inferred from Sequence Orthology more info
involved_in regulation of telomere maintenance	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of telomerase holoenzyme complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

Go to the top of the page Help

Preferred Names: nonsense-mediated mRNA decay factor SMG5

Names: Smg-5 homolog, nonsense mediated mRNA decay factor; protein SMG5

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001427645.1 → NP_001414574.1 nonsense-mediated mRNA decay factor SMG5

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/TrEMBL

E9PU03

Related

ENSRNOP00000026514.7, ENSRNOT00000026514.10

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_086020.1 Reference GRCr8

Range

176102812..176129925

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039103754.2 → XP_038959682.1 nonsense-mediated mRNA decay factor SMG5 isoform X2

Conserved Domains (3) summary

pfam10373
Location:198 → 412

EST1_DNA_bind; Est1 DNA/RNA binding domain

pfam10374
Location:78 → 189

EST1; Telomerase activating protein Est1

NF033845
Location:470 → 573

MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
XM_039103751.2 → XP_038959679.1 nonsense-mediated mRNA decay factor SMG5 isoform X1

UniProtKB/TrEMBL

A6J668

Conserved Domains (4) summary

cd09884
Location:857 → 1015

PIN_Smg5-like; VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs

pfam10373
Location:198 → 412

EST1_DNA_bind; Est1 DNA/RNA binding domain

pfam10374
Location:78 → 189

EST1; Telomerase activating protein Est1

NF033845
Location:470 → 573

MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB