Upf2 MGI Mouse Gene Detail - MGI:2449307 - UPF2 regulator of nonsense transcripts homolog (yeast)

Symbol

Upf2
Name

UPF2 regulator of nonsense transcripts homolog (yeast)

Feature Type

protein coding gene
IDs

MGI:2449307
NCBI Gene: 326622
Alliance

gene page
Transcription Start Sites

6 TSS

Sequence Map

Chr2:5956280-6061514 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 3.62 cM
Mapping Data

1 experiment

SNPs within 2kb

322 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2449307	protein coding gene	Chr2:5956218-6061514 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0025328	protein coding gene	Chr2:3092382-3206326 (+)
A/J	MGP_AJ_G0025305	protein coding gene	Chr2:2946697-3052795 (+)
AKR/J	MGP_AKRJ_G0025273	protein coding gene	Chr2:3029764-3143648 (+)
BALB/cJ	MGP_BALBcJ_G0025301	protein coding gene	Chr2:2922892-3036801 (+)
C3H/HeJ	MGP_C3HHeJ_G0025061	protein coding gene	Chr2:2985497-3091194 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0025743	protein coding gene	Chr2:3175240-3295743 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023157	protein coding gene	Chr2:2749765-2855383 (+)
CAST/EiJ	MGP_CASTEiJ_G0024524	protein coding gene	Chr2:3039692-3150339 (+)
CBA/J	MGP_CBAJ_G0025040	protein coding gene	Chr2:3317423-3445934 (+)
DBA/2J	MGP_DBA2J_G0025172	protein coding gene	Chr2:2891553-2998037 (+)
FVB/NJ	MGP_FVBNJ_G0025134	protein coding gene	Chr2:2886194-2992304 (+)
LP/J	MGP_LPJ_G0025258	protein coding gene	Chr2:3036451-3148464 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0025166	protein coding gene	Chr2:3151734-3274008 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0025801	protein coding gene	Chr2:3029004-3134418 (+)
PWK/PhJ	MGP_PWKPhJ_G0024275	protein coding gene	Chr2:2884211-2996305 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0024075	protein coding gene	Chr2:3003693-3112780 (+)
WSB/EiJ	MGP_WSBEiJ_G0024594	protein coding gene	Chr2:3067292-3181737 (+)

Human Ortholog

UPF2, UPF2 regulator of nonsense mediated mRNA decay

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

UPF2, UPF2 regulator of nonsense mediated mRNA decay
Synonyms

HUPF2, RENT2, smg-3
Links

HGNC:17854

NCBI Gene ID: 26019

neXtProt AC: NX_Q9HAU5

UniProt: Q9HAU5
Chr Location

10p14; chr10:11920022-12043170 (-) GRCh38

MGI Vertebrate Homology

Upf2 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: UPF2
Gene Tree

Upf2

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Phenotype Summary

27 phenotypes from 2 alleles in 3 genetic backgrounds
19 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

58
Endonuclease-mediated

1
Gene trapped

53
Targeted

4
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

62 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit early embryonic lethality.

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All GO Annotations

18
GO References

6

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	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

727
Tissues

12
cDNA Data

66
Literature Summary

2

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase upf2

ZFIN upf2

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All Sequences

51
RefSeq

11
UniProt

3
CCDS

CCDS38041.1

Ensembl

ENSMUSG00000043241 (Evidence)
NCBI Gene

326622

			Length	Strain/Species	Flank
genomic	ENSMUSG00000043241	Ensembl Gene Model \| MGI Sequence Detail	105235	C57BL/6J	± kb
transcript	ENSMUST00000060092	Ensembl \| MGI Sequence Detail	5174	Not Applicable
polypeptide	ENSMUSP00000058375	Ensembl \| MGI Sequence Detail	1269	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000017109 regulator of nonsense transcripts 2

(term hierarchy)
InterPro Domains

IPR016024 Armadillo-type fold

IPR003890 MIF4G-like, type 3

IPR039762 Nonsense-mediated mRNA decay protein Nmd2/UPF2

IPR007193 Up-frameshift suppressor 2, C-terminal

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All nucleic 67

cDNA 66

Primer pair 1

Microarray probesets 4

Summaries

All 45

Developmental Gene Expression 2

Gene Ontology 6

Phenotypes 19
Earliest

J:85162 Hansen J, et al., A large-scale, gene-driven mutagenesis approach for the functional analysis of the mouse genome. Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):9918-22
Latest

J:331055 Chousal JN, et al., Progression of the pluripotent epiblast depends upon the NMD factor UPF2. Development. 2022 Nov 1;149(21):dev200764

TSS for Upf2:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr16012	Chr2:5956251-5956279 (+)	-15 bp
Tssr16013	Chr2:5956291-5956347 (+)	39 bp
Tssr16014	Chr2:5956379-5956400 (+)	110 bp
Tssr16015	Chr2:5959392-5959432 (+)	3,132 bp
Tssr16016	Chr2:5962271-5962284 (+)	5,998 bp
Tssr16017	Chr2:5962408-5962431 (+)	6,140 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 04/23/2024 MGI 6.23