Smg5 MGI Mouse Gene Detail - MGI:2447364 - SMG5 nonsense mediated mRNA decay factor

Symbol

Smg5
Name

SMG5 nonsense mediated mRNA decay factor
Synonyms

MGC:30464, MGC:56792, mKIAA1089, Smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)

Feature Type

protein coding gene
IDs

MGI:2447364
NCBI Gene: 229512
Alliance

gene page
Transcription Start Sites

5 TSS

Sequence Map

Chr3:88243567-88269645 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 3, 38.80 cM
Mapping Data

1 experiment

SNPs within 2kb

612 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2447364	protein coding gene	Chr3:88242050-88269645 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0027391	protein coding gene	Chr3:88488879-88517403 (+)
A/J	MGP_AJ_G0027355	protein coding gene	Chr3:85493071-85519129 (+)
AKR/J	MGP_AKRJ_G0027321	protein coding gene	Chr3:87595765-87623733 (+)
BALB/cJ	MGP_BALBcJ_G0027364	protein coding gene	Chr3:85582532-85609397 (+)
C3H/HeJ	MGP_C3HHeJ_G0027107	protein coding gene	Chr3:87873994-87899871 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0027810	protein coding gene	Chr3:91746548-91776444 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025163	protein coding gene	Chr3:81111250-81138942 (+)
CAST/EiJ	MGP_CASTEiJ_G0026553	protein coding gene	Chr3:88084936-88115668 (+)
CBA/J	MGP_CBAJ_G0027082	protein coding gene	Chr3:94872177-94898164 (+)
DBA/2J	MGP_DBA2J_G0027218	protein coding gene	Chr3:84981772-85008437 (+)
FVB/NJ	MGP_FVBNJ_G0027187	protein coding gene	Chr3:83251321-83279092 (+)
LP/J	MGP_LPJ_G0027326	protein coding gene	Chr3:89482734-89511917 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0027206	protein coding gene	Chr3:101101786-101134417 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0027868	protein coding gene	Chr3:87350700-87379733 (+)
PWK/PhJ	MGP_PWKPhJ_G0026286	protein coding gene	Chr3:84779440-84807355 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0026104	protein coding gene	Chr3:86540883-86570148 (+)
WSB/EiJ	MGP_WSBEiJ_G0026633	protein coding gene	Chr3:87705602-87732372 (+)

Human Ortholog

SMG5, SMG5 nonsense mediated mRNA decay factor

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SMG5, SMG5 nonsense mediated mRNA decay factor
Synonyms

EST1B, LPTS-RP1, LPTSRP1, SMG-5
Links

HGNC:24644

NCBI Gene ID: 23381

neXtProt AC: NX_Q9UPR3

UniProt: Q9UPR3
Chr Location

1q22; chr1:156249224-156291516 (-) GRCh38

MGI Vertebrate Homology

Smg5 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SMG5
Gene Tree

Smg5

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References

1 with disease annotations

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Phenotype Summary

6 phenotypes from 2 alleles in 2 genetic backgrounds
15 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

47
Chemically induced (other)

1
Endonuclease-mediated

1
Gene trapped

40
Radiation induced

1
Targeted

4
Genomic Mutations

2 involving Smg5
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

57 strains or lines available

Homozygous knock-out embryos die before E13.5.

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All GO Annotations

23
GO References

5

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

706
cDNA Data

143

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase smg5

ZFIN smg5

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All Sequences

68
RefSeq

14
UniProt

4
CCDS

CCDS38480.1

Ensembl

ENSMUSG00000001415 (Evidence)
NCBI Gene

229512

			Length	Strain/Species	Flank
genomic	ENSMUSG00000001415	Ensembl Gene Model \| MGI Sequence Detail	26079	C57BL/6J	± kb
transcript	ENSMUST00000001451	Ensembl \| MGI Sequence Detail	4448	Not Applicable
polypeptide	ENSMUSP00000001451	Ensembl \| MGI Sequence Detail	1017	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000015284 nonsense-mediated mRNA decay factor SMG5

(term hierarchy)
InterPro Domains

IPR018834 DNA/RNA-binding domain, Est1-type

IPR045153 Est1/Ebs1-like

IPR002716 PIN domain

IPR019458 Telomerase activating protein Est1-like, N-terminal

IPR011990 Tetratricopeptide-like helical domain superfamily

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All nucleic 143

cDNA 143

Microarray probesets 5

Summaries

All 42

Diseases 1

Gene Ontology 5

Phenotypes 15
Earliest

J:70677 Cook SA, et al., Mouse paracentric inversion In(3)55Rk mutates the urate oxidase gene. Cytogenet Cell Genet. 2001;93(1-2):77-82
Latest

J:353570 Chen C, et al., RNA Surveillance Factor SMG5 Is Essential for Mouse Embryonic Stem Cell Differentiation. Biomolecules. 2024 Aug 17;14(8)

TSS for Smg5:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr29942	Chr3:88243563-88243611 (+)	20 bp
Tssr29943	Chr3:88245150-88245160 (+)	1,588 bp
Tssr29944	Chr3:88247584-88247588 (+)	4,019 bp
Tssr29945	Chr3:88258404-88258419 (+)	14,845 bp
Tssr29946	Chr3:88265589-88265602 (+)	22,029 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/19/2024 MGI 6.24