Smc5 MGI Mouse Gene Detail - MGI:2385088 - structural maintenance of chromosomes 5

Symbol

Smc5
Name

structural maintenance of chromosomes 5
Synonyms

MGC:7569, Smc5l1

Feature Type

protein coding gene
IDs

MGI:2385088
NCBI Gene: 226026
Alliance

gene page
Transcription Start Sites

6 TSS

Sequence Map

Chr19:23183815-23251261 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 19, 18.04 cM
Mapping Data

2 experiments

SNPs within 2kb

1804 from dbSNP Build 142
Strain Annotations

17

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2385088	protein coding gene	Chr19:23183815-23251286 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0024984	protein coding gene	Chr19:21340611-21415450 (-)
A/J	MGP_AJ_G0024961	protein coding gene	Chr19:20171887-20240749 (-)
AKR/J	MGP_AKRJ_G0024931	protein coding gene	Chr19:20945023-21019772 (-)
BALB/cJ	MGP_BALBcJ_G0024960	protein coding gene	Chr19:20215346-20285900 (-)
C3H/HeJ	MGP_C3HHeJ_G0024718	protein coding gene	Chr19:20907905-20985630 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0025402	protein coding gene	Chr19:22028092-22109490 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022821	protein coding gene	Chr19:20358714-20426979 (-)
CAST/EiJ	MGP_CASTEiJ_G0024186	protein coding gene	Chr19:20620162-20698522 (-)
CBA/J	MGP_CBAJ_G0024696	protein coding gene	Chr19:22960298-23046923 (-)
DBA/2J	MGP_DBA2J_G0024828	protein coding gene	Chr19:20190812-20261198 (-)
FVB/NJ	MGP_FVBNJ_G0024789	protein coding gene	Chr19:20041817-20115669 (-)
LP/J	MGP_LPJ_G0024912	protein coding gene	Chr19:21287566-21365167 (-)
NOD/ShiLtJ	no annotation
NZO/HlLtJ	MGP_NZOHlLtJ_G0025457	protein coding gene	Chr19:20938972-21014504 (-)
PWK/PhJ	MGP_PWKPhJ_G0023935	protein coding gene	Chr19:19761297-19836977 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0023740	protein coding gene	Chr19:20134688-20224055 (-)
WSB/EiJ	MGP_WSBEiJ_G0024254	protein coding gene	Chr19:20956501-21031498 (-)

Human Ortholog

SMC5, structural maintenance of chromosomes 5

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SMC5, structural maintenance of chromosomes 5
Synonyms

ATELS2, SMC5L1
Links

HGNC:20465

NCBI Gene ID: 23137

neXtProt AC: NX_Q8IY18

UniProt: Q8IY18
Chr Location

9q21.12; chr9:70258978-70354873 (+) GRCh38

MGI Vertebrate Homology

Smc5 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SMC5
Gene Tree

Smc5

Diseases

1 with human SMC5 associations

				Human Disease	Mouse Models
				mosaic variegated aneuploidy syndrome IDs mosaic variegated aneuploidy syndrome DOID:0080688 MESH:C536987 OMIM:PS257300 ORDO:1052

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

21 phenotypes from 3 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

12
Gene trapped

7
Targeted

5
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

42 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous knockout in embryonic stem cells causes abnormal mitosis, increased apoptosis and a shift from pluripotency to differentiation.

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All GO Annotations

50
GO References

9

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

711
Tissues

5
cDNA Data

133
Literature Summary

3

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase smc5

ZFIN smc5

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All Sequences

59
RefSeq

12
UniProt

2
CCDS

CCDS37936.1, CCDS89363.1, CCDS89364.1

Ensembl

ENSMUSG00000024943 (Evidence)
NCBI Gene

226026

			Length	Strain/Species	Flank
genomic	ENSMUSG00000024943	Ensembl Gene Model \| MGI Sequence Detail	67447	C57BL/6J	± kb
transcript	ENSMUST00000087556	Ensembl \| MGI Sequence Detail	5683	Not Applicable
polypeptide	ENSMUSP00000084837	Ensembl \| MGI Sequence Detail	1101	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000015274 structural maintenance of chromosomes protein 5

(term hierarchy)
InterPro Domains

IPR027417 P-loop containing nucleoside triphosphate hydrolase

IPR038729 Rad50/SbcC-type AAA domain

IPR003395 RecF/RecN/SMC, N-terminal

IPR027131 Structural maintenance of chromosomes protein 5

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All nucleic 135

cDNA 133

Primer pair 1

Other 1

Microarray probesets 3

Summaries

All 45

Developmental Gene Expression 3

Gene Ontology 9

Phenotypes 15
Earliest

J:162301 Taylor EM, et al., Characterization of a novel human SMC heterodimer homologous to the Schizosaccharomyces pombe Rad18/Spr18 complex. Mol Biol Cell. 2001 Jun;12(6):1583-94
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Smc5:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr158630	Chr19:23251257-23251282 (-)	-9 bp
Tssr158629	Chr19:23251228-23251248 (-)	23 bp
Tssr158628	Chr19:23251179-23251225 (-)	59 bp
Tssr158627	Chr19:23251153-23251160 (-)	104 bp
Tssr158626	Chr19:23224004-23224019 (-)	27,249 bp
Tssr158625	Chr19:23184890-23184914 (-)	66,359 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 11/12/2024 MGI 6.24