Smg9 MGI Mouse Gene Detail - MGI:1919247 - SMG9 nonsense mediated mRNA decay factor

Symbol

Smg9
Name

SMG9 nonsense mediated mRNA decay factor
Synonyms

1500002O20Rik, N28092, smg-9 homolog, nonsense mediated mRNA decay factor (C. elegans)

Feature Type

protein coding gene
IDs

MGI:1919247
NCBI Gene: 71997
Alliance

gene page
Transcription Start Sites

9 TSS

Sequence Map

Chr7:24099044-24122203 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 7, 10.54 cM
Mapping Data

2 experiments

SNPs within 2kb

270 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1919247	protein coding gene	Chr7:24096176-24122203 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0031827	protein coding gene	Chr7:22719476-22743654 (+)
A/J	MGP_AJ_G0031806	protein coding gene	Chr7:22198535-22225155 (+)
AKR/J	MGP_AKRJ_G0031735	protein coding gene	Chr7:22698031-22725149 (+)
BALB/cJ	MGP_BALBcJ_G0031812	protein coding gene	Chr7:22408817-22431921 (+)
C3H/HeJ	MGP_C3HHeJ_G0031532	protein coding gene	Chr7:23109393-23133176 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0032275	protein coding gene	Chr7:23465811-23488928 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0029333	protein coding gene	Chr7:23672371-23695646 (+)
CAST/EiJ	MGP_CASTEiJ_G0030873	protein coding gene	Chr7:16571955-16596540 (+)
CBA/J	MGP_CBAJ_G0031497	protein coding gene	Chr7:24347434-24373100 (+)
DBA/2J	MGP_DBA2J_G0031651	protein coding gene	Chr7:22115551-22138750 (+)
FVB/NJ	MGP_FVBNJ_G0031604	protein coding gene	Chr7:22070814-22095184 (+)
LP/J	MGP_LPJ_G0031730	protein coding gene	Chr7:23071423-23094644 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0031641	protein coding gene	Chr7:24127364-24151376 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0032307	protein coding gene	Chr7:22413903-22437650 (+)
PWK/PhJ	MGP_PWKPhJ_G0030597	protein coding gene	Chr7:17003590-17026560 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0030427	protein coding gene	Chr7:13747889-13770626 (+)
WSB/EiJ	MGP_WSBEiJ_G0030976	protein coding gene	Chr7:22536220-22559242 (+)

Human Ortholog

SMG9, SMG9 nonsense mediated mRNA decay factor

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SMG9, SMG9 nonsense mediated mRNA decay factor
Synonyms

C19orf61, F17127_1, HBMS, NEDITPO
Links

HGNC:25763

NCBI Gene ID: 56006

neXtProt AC: NX_Q9H0W8

UniProt: Q9H0W8
Chr Location

19q13.31; chr19:43727992-43754990 (-) GRCh38.p7

Alliance of Genome Resources

Smg9 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SMG9
Gene Tree

Smg9

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Phenotype Summary

74 phenotypes from 2 alleles in 3 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	immune system	integument	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	neoplasm	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	vision/eye

Click cells to view annotations.

All Mutations and Alleles

20
Endonuclease-mediated

2
Gene trapped

15
Targeted

3
Incidental Mutations

APF
Find Mice (IMSR)

33 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a severe hypomorphic allele exhibit edema, hemorrhage, exencephaly, preaxial polydactyly, reduced size and growth, decreased mid- and hindrain size, microphthalmia, thin myocardium and atrioventricular septal defect.

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All GO Annotations

7
GO References

4

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	establishment of localization	homeostatic process	immune system process	lipid metabolic process	nucleic acid-templated transcription	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	non-membrane-bounded 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

56

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase smg9

ZFIN smg9

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Smg9 interacts with 62 markers (Mir23b, Mir93, Mir122, ...) View All

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All Sequences

52
RefSeq

8
UniProt

3
CCDS

CCDS20949.1

Ensembl

ENSMUSG00000002210 (Evidence)
NCBI Gene

71997

			Length	Strain/Species	Flank
genomic	ENSMUSG00000002210	Ensembl Gene Model \| MGI Sequence Detail	23160	C57BL/6J	± kb
transcript	ENSMUST00000002280	Ensembl \| MGI Sequence Detail	2242	Not Applicable
polypeptide	ENSMUSP00000002280	Ensembl \| MGI Sequence Detail	520	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000030999 nonsense-mediated mRNA decay factor SMG9

(term hierarchy)
InterPro Domains

IPR019354 Nonsense-mediated mRNA decay factor SMG8/SMG9

IPR039177 Nonsense-mediated mRNA decay factor SMG9

IPR027417 P-loop containing nucleoside triphosphate hydrolase

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All nucleic 56

cDNA 56

Microarray probesets 3

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MGI:2141954, MGI:2142378

Summaries

All 37

Gene Ontology 4

Phenotypes 15
Earliest

J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
Latest

J:301232 Butterfield NC, et al., Accelerating functional gene discovery in osteoarthritis. Nat Commun. 2021 Jan 20;12(1):467

TSS for Smg9:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr64959	Chr7:24099031-24099098 (+)	21 bp
Tssr64960	Chr7:24099099-24099152 (+)	82 bp
Tssr64961	Chr7:24099238-24099243 (+)	197 bp
Tssr64962	Chr7:24099384-24099400 (+)	348 bp
Tssr64963	Chr7:24099402-24099436 (+)	375 bp
Tssr64964	Chr7:24099438-24099455 (+)	403 bp
Tssr64965	Chr7:24102286-24102298 (+)	3,248 bp
Tssr64966	Chr7:24102451-24102470 (+)	3,417 bp
Tssr64967	Chr7:24106660-24106685 (+)	7,629 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)
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