Snrnp40 MGI Mouse Gene Detail - MGI:1913835 - small nuclear ribonucleoprotein 40 (U5)

Symbol

Snrnp40
Name

small nuclear ribonucleoprotein 40 (U5)
Synonyms

0610009C03Rik, Wdr57

Feature Type

protein coding gene
IDs

MGI:1913835
NCBI Gene: 66585
Alliance

gene page
Transcription Start Sites

2 TSS

Sequence Map

Chr4:130253925-130283819 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 4, 63.43 cM, cytoband D3
Mapping Data

2 experiments

SNPs within 2kb

392 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1913835	protein coding gene	Chr4:130253925-130283826 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0028851	protein coding gene	Chr4:132366081-132404094 (+)
A/J	MGP_AJ_G0028810	protein coding gene	Chr4:127053851-127084806 (+)
AKR/J	MGP_AKRJ_G0028763	protein coding gene	Chr4:130616998-130646868 (+)
BALB/cJ	MGP_BALBcJ_G0028833	protein coding gene	Chr4:127666639-127696539 (+)
C3H/HeJ	MGP_C3HHeJ_G0028547	protein coding gene	Chr4:130673216-130706371 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0029275	protein coding gene	Chr4:137317613-137357267 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0026547	protein coding gene	Chr4:120168630-120197280 (+)
CAST/EiJ	MGP_CASTEiJ_G0027980	protein coding gene	Chr4:128888013-128916522 (+)
CBA/J	MGP_CBAJ_G0028513	protein coding gene	Chr4:140820514-140854205 (+)
DBA/2J	MGP_DBA2J_G0028662	protein coding gene	Chr4:127488370-127518146 (+)
FVB/NJ	MGP_FVBNJ_G0028629	protein coding gene	Chr4:126280809-126313220 (+)
LP/J	MGP_LPJ_G0028763	protein coding gene	Chr4:132693850-132723876 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0028655	protein coding gene	Chr4:145517196-145550893 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0029313	protein coding gene	Chr4:130989143-131018025 (+)
PWK/PhJ	MGP_PWKPhJ_G0027701	protein coding gene	Chr4:124116860-124146589 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0027527	protein coding gene	Chr4:126854122-126884002 (+)
WSB/EiJ	MGP_WSBEiJ_G0028060	protein coding gene	Chr4:131134574-131165941 (+)

Human Ortholog

SNRNP40, small nuclear ribonucleoprotein U5 subunit 40

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SNRNP40, small nuclear ribonucleoprotein U5 subunit 40
Synonyms

40K, HPRP8BP, PRP8BP, PRPF8BP, SPF38, WDR57
Links

HGNC:30857

NCBI Gene ID: 9410

neXtProt AC: NX_Q96DI7

UniProt: Q96DI7
Chr Location

1p35.2; chr1:31259568-31296788 (-) GRCh38

MGI Vertebrate Homology

Snrnp40 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SNRNP40
Gene Tree

Snrnp40

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Phenotype Summary

44 phenotypes from 4 alleles in 7 genetic backgrounds
1 images
14 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

27
Chemically induced (other)

2
Endonuclease-mediated

3
Gene trapped

17
Radiation induced

1
Spontaneous

1
Targeted

3
Genomic Mutations

4 involving Snrnp40
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

52 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele show embryonic growth retardation, a small egg cylinder, disorganized extraembryonic tissue, failure to initiate gastrulation, and complete embryonic lethality by E9.5. Mice homozygous for a hypomorphic allelel exhibit reduced body weight, belly spotting, and immunodeficiency.

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All GO Annotations

14
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	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

716
Tissues

6
cDNA Data

11
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 snrnp40

ZFIN snrnp40

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All Sequences

44
RefSeq

2
UniProt

2
CCDS

CCDS38892.1

Ensembl

ENSMUSG00000074088 (Evidence)
NCBI Gene

66585

			Length	Strain/Species	Flank
genomic	ENSMUSG00000074088	Ensembl Gene Model \| MGI Sequence Detail	29895	C57BL/6J	± kb
transcript	ENSMUST00000105994	Ensembl \| MGI Sequence Detail	1584	Not Applicable
polypeptide	ENSMUSP00000101616	Ensembl \| MGI Sequence Detail	358	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000015336 U5 small nuclear ribonucleoprotein 40 kDa protein

(term hierarchy)
InterPro Domains

IPR020472 G-protein beta WD-40 repeat

IPR052234 U5 snRNP Complex Component

IPR001680 WD40 repeat

IPR019775 WD40 repeat, conserved site

IPR036322 WD40-repeat-containing domain superfamily

IPR015943 WD40/YVTN repeat-like-containing domain superfamily
GlyGen

Q6PE01 1 site, 1 N-linked glycan (1 site)

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All nucleic 11

cDNA 11

Microarray probesets 3

Summaries

All 37

Developmental Gene Expression 2

Gene Ontology 4

Phenotypes 14
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:313619 Bedogni F, et al., Cell-Type-Specific Gene Expression in Developing Mouse Neocortex: Intermediate Progenitors Implicated in Axon Development. Front Mol Neurosci. 2021;14:686034

TSS for Snrnp40:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr39236	Chr4:130253952-130254001 (+)	52 bp
Tssr39237	Chr4:130260651-130260658 (+)	6,730 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 10/29/2024 MGI 6.24