Smg5 SMG5 nonsense mediated mRNA decay factor [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Smg5provided by MGI
Official Full Name: SMG5 nonsense mediated mRNA decay factorprovided by MGI
Primary source: MGI:MGI:2447364
See related: Ensembl:ENSMUSG00000001415 AllianceGenome:MGI:2447364
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: LPTS-RP1; mKIAA1089
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: Ubiquitous expression in testis adult (RPKM 31.0), thymus adult (RPKM 24.5) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 3 F1; 3 38.8 cM

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	3	NC_000069.7 (88242050..88269645)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	3	NC_000069.6 (88336259..88362338)

Chromosome 3 - NC_000069.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

RNA Surveillance Factor SMG5 Is Essential for Mouse Embryonic Stem Cell Differentiation.
Title: RNA Surveillance Factor SMG5 Is Essential for Mouse Embryonic Stem Cell Differentiation.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (2) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3Mit175 (e-PCR), detects polymorphism
- UniSTS:129592

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables histone deacetylase binding	IEA Inferred from Electronic Annotation more info
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables protein phosphatase 2A binding	ISO Inferred from Sequence Orthology more info
enables protein phosphatase 2A binding	ISS Inferred from Sequence or Structural Similarity more info
enables telomerase RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables telomerase RNA binding	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
enables telomeric DNA binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase binding	IEA Inferred from Electronic Annotation 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 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation more info
involved_in regulation of dephosphorylation	ISO Inferred from Sequence Orthology more info
involved_in regulation of dephosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of telomere maintenance	IEA Inferred from Electronic Annotation 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 cytoplasm	ISS Inferred from Sequence or Structural Similarity 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 telomerase holoenzyme complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: nonsense-mediated mRNA decay factor SMG5

Names: EST1-like protein B; LPTS-interacting protein; Smg-5 homolog, nonsense mediated mRNA decay factor; protein SMG5

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_178246.3 → NP_839977.2 nonsense-mediated mRNA decay factor SMG5

See identical proteins and their annotated locations for NP_839977.2

Status: VALIDATED

Source sequence(s)

AK133688, AK143911, AV146226, BB869373, BC066787

Consensus CDS

CCDS38480.1

UniProtKB/Swiss-Prot

Q497S2, Q6ZPY2, Q8R3S4

Related

ENSMUSP00000001451.6, ENSMUST00000001451.11

Conserved Domains (4) summary

sd00006
Location:172 → 206

TPR; TPR repeat [structural motif]

pfam10373
Location:197 → 411

EST1_DNA_bind; Est1 DNA/RNA binding domain

pfam10374
Location:77 → 187

EST1; Telomerase activating protein Est1

cl14812
Location:856 → 1014

PIN_SF; PIN (PilT N terminus) domain: Superfamily

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000069.7 Reference GRCm39 C57BL/6J

Range

88242050..88269645

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006501343.5 → XP_006501406.1 nonsense-mediated mRNA decay factor SMG5 isoform X1

Conserved Domains (3) summary

cd09884
Location:842 → 1000

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

pfam10373
Location:183 → 382

EST1_DNA_bind; Est1 DNA/RNA binding domain

pfam10374
Location:77 → 174

EST1; Telomerase activating protein Est1
XM_011240087.4 → XP_011238389.1 nonsense-mediated mRNA decay factor SMG5 isoform X2

Conserved Domains (3) summary

cd09884
Location:790 → 948

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

pfam10373
Location:131 → 330

EST1_DNA_bind; Est1 DNA/RNA binding domain

pfam10374
Location:11 → 122

EST1; Telomerase activating protein Est1
XM_036163050.1 → XP_036018943.1 nonsense-mediated mRNA decay factor SMG5 isoform X4

UniProtKB/TrEMBL

Q3UZS1

Conserved Domains (3) summary

cd09884
Location:595 → 753

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

pfam10373
Location:2 → 150

EST1_DNA_bind; Est1 DNA/RNA binding domain

NF033845
Location:208 → 311

MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
XM_006501345.4 → XP_006501408.1 nonsense-mediated mRNA decay factor SMG5 isoform X4

UniProtKB/TrEMBL

Q3UZS1

Conserved Domains (3) summary

cd09884
Location:595 → 753

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

pfam10373
Location:2 → 150

EST1_DNA_bind; Est1 DNA/RNA binding domain

NF033845
Location:208 → 311

MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB
XM_036163049.1 → XP_036018942.1 nonsense-mediated mRNA decay factor SMG5 isoform X3

Conserved Domains (4) summary

cd09884
Location:776 → 934

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

pfam10373
Location:117 → 331

EST1_DNA_bind; Est1 DNA/RNA binding domain

pfam10374
Location:11 → 108

EST1; Telomerase activating protein Est1

NF033845
Location:389 → 492

MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB

RNA

XR_004941306.1 RNA Sequence
XR_004941307.1 RNA Sequence

Related

ENSMUST00000192057.6

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_173188.1: Suppressed sequence

Description

NM_173188.1: This RefSeq was temporarily suppressed because the CDS was partial when compared to proteins in other species such as human.