Setx MGI Mouse Gene Detail - MGI:2443480

Symbol

Setx
Name

senataxin
Synonyms

A930037J23Rik, Als4

Feature Type

protein coding gene
IDs

MGI:2443480
NCBI Gene: 269254
Gene Overview

MyGene.info: SETX
Alliance

gene page
Transcription Start Sites

8 TSS

Sequence Map

Chr2:29124181-29182471 bp, + strand
From Ensembl annotation of GRCm38

View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 19.45 cM
Mapping Data

2 experiments

SNPs within 2kb

170 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2443480	protein coding gene	Chr2:29123588-29182471 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0025537	protein coding gene	Chr2:27235105-27300398 (+)
A/J	MGP_AJ_G0025514	protein coding gene	Chr2:26192590-26251521 (+)
AKR/J	MGP_AKRJ_G0025484	protein coding gene	Chr2:27064124-27129574 (+)
BALB/cJ	MGP_BALBcJ_G0025510	protein coding gene	Chr2:26320740-26381021 (+)
C3H/HeJ	MGP_C3HHeJ_G0025271	protein coding gene	Chr2:26982534-27047909 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0025954	protein coding gene	Chr2:28129044-28194345 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023364	protein coding gene	Chr2:25001152-25058985 (+)
CAST/EiJ	MGP_CASTEiJ_G0024734	protein coding gene	Chr2:26886839-26951587 (+)
CBA/J	MGP_CBAJ_G0025249	protein coding gene	Chr2:29082601-29160697 (+)
DBA/2J	MGP_DBA2J_G0025382	protein coding gene	Chr2:25987517-26048531 (+)
FVB/NJ	MGP_FVBNJ_G0025344	protein coding gene	Chr2:25795061-25853632 (+)
LP/J	MGP_LPJ_G0025468	protein coding gene	Chr2:27167112-27232845 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0025375	protein coding gene	Chr2:29080860-29145188 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0026013	protein coding gene	Chr2:26975031-27038749 (+)
PWK/PhJ	MGP_PWKPhJ_G0024481	protein coding gene	Chr2:25802763-25862408 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0024281	protein coding gene	Chr2:27081897-27143483 (+)
WSB/EiJ	MGP_WSBEiJ_G0024803	protein coding gene	Chr2:27096831-27170556 (+)

Human Ortholog

SETX, senataxin

Vertebrate Orthologs

10

Human Ortholog

SETX, senataxin
Orthology source: HomoloGene, HGNC
Synonyms

ALS4, AOA2, bA479K20.2, SCAN2, SCAR1, Sen1
Links

HGNC:445

NCBI Gene ID: 23064

neXtProt AC: NX_Q7Z333

UniProt: Q7Z333
Chr Location

9q34.13; chr9:132261440-132356726 (-) GRCh38.p7

HomoloGene

Vertebrate Homology Class 41003
1 human;1 mouse;1 rat;1 chimpanzee;1 cattle;1 dog;1 chicken;1 zebrafish;1 frog, western clawed;1 macaque, rhesus
HCOP

human homology predictions: SETX
Gene Tree

Setx

Diseases

2 with human SETX associations

				Human Disease	Mouse Models
				amyotrophic lateral sclerosis type 4 IDs amyotrophic lateral sclerosis type 4 DOID:0060196 ICD10CM:G12.2 OMIM:602433 ORDO:357043
				ataxia with oculomotor apraxia type 2 IDs ataxia with oculomotor apraxia type 2 DOID:0050755 OMIM:606002

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

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Phenotype Summary

23 phenotypes from 2 alleles in 2 genetic backgrounds
3 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	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

61
Gene trapped

58
Targeted

3
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

101 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit male infertility due to arrested male meiosis and reduced female fertility.

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All GO Annotations

48
GO References

4

External Resources

FuncBase

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 death	cell differentiation	cell population proliferation	cellular component organization	establishment of localization	homeostatic process	immune system process	lipid metabolic process	nucleic acid-templated transcription	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	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

635
Tissues

1
cDNA Data

11
Literature Summary

1

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase setx

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Setx interacts with 348 markers (Mir7-1, Mir7-2, Mir7b, ...) View All

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All Sequences

56
RefSeq

11
UniProt

3
CCDS

CCDS38090.1

Ensembl

ENSMUSG00000043535 (Evidence)
NCBI Gene

269254

			Length	Strain/Species	Flank
genomic	ENSMUSG00000043535	Ensembl Gene Model \| MGI Sequence Detail	58291	C57BL/6J	± kb
transcript	ENSMUST00000061578	Ensembl \| MGI Sequence Detail	10970	Not Applicable
polypeptide	ENSMUSP00000051492	Ensembl \| MGI Sequence Detail	2646	Not Applicable

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UniProt

3 Sequences
EC

3.6.4.-
InterPro Domains

IPR041677 DNA2/NAM7 helicase, helicase domain

IPR041679 DNA2/NAM7 helicase-like, C-terminal

IPR027417 P-loop containing nucleoside triphosphate hydrolase

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All nucleic 12

cDNA 11

Primer pair 1

Microarray probesets 4

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MGI:2139292

Summaries

All 40

Developmental Gene Expression 1

Gene Ontology 4

Phenotypes 14
Earliest

J:80000 The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team, Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420:563-573
Latest

J:267571 Kannan A, et al., Combined deficiency of Senataxin and DNA-PKcs causes DNA damage accumulation and neurodegeneration in spinal muscular atrophy. Nucleic Acids Res. 2018 Sep 19;46(16):8326-8346

TSS for Setx:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr16989	Chr2:29124106-29124166 (+)	-45 bp
Tssr16990	Chr2:29124972-29125048 (+)	829 bp
Tssr16991	Chr2:29125143-29125178 (+)	980 bp
Tssr16992	Chr2:29125201-29125212 (+)	1,026 bp
Tssr16993	Chr2:29125216-29125238 (+)	1,046 bp
Tssr16994	Chr2:29125243-29125254 (+)	1,068 bp
Tssr16995	Chr2:29125316-29125327 (+)	1,141 bp
Tssr16996	Chr2:29125339-29125384 (+)	1,181 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 & Copyright Notice Send questions and comments to User Support.	last database update 10/13/2020 MGI 6.16