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
Alliance

gene page
Transcription Start Sites

10 TSS

Sequence Map

Chr2:29014193-29072483 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 19.45 cM
Mapping Data

2 experiments

SNPs within 2kb

2077 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	Chr2:29013600-29072483 (+)
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

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SETX, senataxin
Synonyms

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

HGNC:445

NCBI Gene ID: 23064

UniProt: Q7Z333
Chr Location

9q34.13; chr9:132261356-132356744 (-) GRCh38

MGI Vertebrate Homology

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

vertebrate homology predictions: SETX
Gene Tree

Setx

Diseases

1 with Setx mouse models; 2 with human SETX associations

Human Disease

Mouse Models

amyotrophic lateral sclerosis type 4

IDs

View 1 model

spinocerebellar ataxia with axonal neuropathy 2

IDs

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

Mutations/Alleles

1 with disease annotations

References

1 with disease annotations

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Phenotype Summary

28 phenotypes from 3 alleles in 3 genetic backgrounds
3 images
24 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

49
Chemically induced (ENU)

1
Endonuclease-mediated

4
Gene trapped

40
Targeted

4
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

141 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

97
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

712
Tissues

3
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 setx

ZFIN setx

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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
Protein Ontology

PR:000031605 probable helicase senataxin

(term hierarchy)
EC

3.6.4.-
InterPro Domains

IPR041677 DNA2/NAM7 helicase, helicase domain

IPR041679 DNA2/NAM7 helicase-like, C-terminal

IPR045055 DNA2/NAM7-like helicase

IPR027417 P-loop containing nucleoside triphosphate hydrolase

IPR047187 Upf1-like, C-terminal helicase domain
GlyGen

A2AKX3 4 sites, 2 N-linked glycans (2 sites), 1 O-linked glycan (2 sites)

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All nucleic 12

cDNA 11

Primer pair 1

Microarray probesets 4

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MGI:2139292

Summaries

All 58

Developmental Gene Expression 2

Diseases 1

Gene Ontology 9

Phenotypes 24
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:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Setx:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr16989	Chr2:29014118-29014178 (+)	-45 bp
Tssr16990	Chr2:29014984-29015060 (+)	829 bp
Tssr16991	Chr2:29015155-29015190 (+)	980 bp
Tssr16992	Chr2:29015213-29015224 (+)	1,026 bp
Tssr16993	Chr2:29015228-29015250 (+)	1,046 bp
Tssr16994	Chr2:29015255-29015266 (+)	1,068 bp
Tssr16995	Chr2:29015328-29015339 (+)	1,141 bp
Tssr16996	Chr2:29015351-29015396 (+)	1,181 bp
Tssr16997	Chr2:29049927-29049931 (+)	35,736 bp
Tssr16998	Chr2:29071175-29071208 (+)	56,999 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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