Setx (senataxin) - Rat Genome Database

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Gene: Setx (senataxin) Rattus norvegicus
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Symbol: Setx
Name: senataxin
RGD ID: 1565575
Description: Predicted to enable RNA binding activity; identical protein binding activity; and transcription termination site sequence-specific DNA binding activity. Predicted to be involved in several processes, including intracellular signaling cassette; nucleic acid metabolic process; and positive regulation of RNA metabolic process. Predicted to act upstream of or within circadian rhythm. Predicted to be located in several cellular components, including growth cone; intercellular bridge; and nuclear lumen. Predicted to be active in nuclear body. Human ortholog(s) of this gene implicated in amyotrophic lateral sclerosis type 4 and spinocerebellar ataxia with axonal neuropathy 2. Orthologous to human SETX (senataxin); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DEAxQ-box helicase; LOC362096; probable helicase senataxin; RGD1565575; similar to senataxin; tRNA splicing endonuclease regulator 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8332,825,771 - 32,878,740 (+)NCBIGRCr8
mRatBN7.2312,428,091 - 12,480,801 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl312,427,635 - 12,480,803 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.037,680,430 - 7,731,815 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,686,503 - 7,730,539 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0313,029,002 - 13,080,379 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.438,113,749 - 8,156,463 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera37,210,020 - 7,259,874 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:15106121   PMID:17562789   PMID:19515850   PMID:21576111   PMID:21700224   PMID:22767893   PMID:24105744   PMID:24244371   PMID:26700805  


Genomics

Comparative Map Data
Setx
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8332,825,771 - 32,878,740 (+)NCBIGRCr8
mRatBN7.2312,428,091 - 12,480,801 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl312,427,635 - 12,480,803 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.037,680,430 - 7,731,815 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl37,686,503 - 7,730,539 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0313,029,002 - 13,080,379 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.438,113,749 - 8,156,463 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera37,210,020 - 7,259,874 (+)NCBICelera
Cytogenetic Map3p12NCBI
SETX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389132,261,356 - 132,356,744 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9132,261,356 - 132,354,986 (-)EnsemblGRCh38hg38GRCh38
GRCh379135,136,743 - 135,230,373 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369134,126,648 - 134,220,193 (-)NCBINCBI36Build 36hg18NCBI36
Build 349132,168,836 - 132,259,926NCBI
Celera9105,678,763 - 105,772,221 (-)NCBICelera
Cytogenetic Map9q34.13NCBI
HuRef9104,630,757 - 104,723,804 (-)NCBIHuRef
CHM1_19135,286,879 - 135,380,398 (-)NCBICHM1_1
T2T-CHM13v2.09144,475,833 - 144,571,334 (-)NCBIT2T-CHM13v2.0
Setx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39229,013,600 - 29,072,483 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl229,014,193 - 29,072,483 (+)EnsemblGRCm39 Ensembl
GRCm38229,123,588 - 29,182,471 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl229,124,181 - 29,182,471 (+)EnsemblGRCm38mm10GRCm38
MGSCv37228,980,512 - 29,037,991 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36228,976,093 - 29,004,480 (+)NCBIMGSCv36mm8
Celera228,830,977 - 28,888,543 (+)NCBICelera
Cytogenetic Map2A3- BNCBI
cM Map219.45NCBI
Setx
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555131,718,377 - 1,777,021 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555131,718,432 - 1,776,133 (-)NCBIChiLan1.0ChiLan1.0
SETX
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2116,999,456 - 7,095,610 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan197,000,759 - 7,097,946 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09103,381,356 - 103,474,902 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19132,016,513 - 132,109,665 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9132,016,767 - 132,109,665 (-)Ensemblpanpan1.1panPan2
SETX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1951,900,004 - 51,980,694 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl951,901,233 - 51,978,833 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha951,164,800 - 51,245,022 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0952,793,044 - 52,873,500 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl952,793,516 - 52,871,521 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1951,573,459 - 51,653,339 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0951,897,710 - 51,978,318 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0951,983,718 - 52,064,342 (+)NCBIUU_Cfam_GSD_1.0
Setx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947199,087,545 - 199,175,658 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648718,855,744 - 18,944,158 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648718,858,384 - 18,945,253 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SETX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1272,095,358 - 272,170,747 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11272,093,449 - 272,170,857 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21306,152,306 - 306,230,231 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SETX
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1125,773,122 - 5,872,372 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl125,773,165 - 5,875,481 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660799,727,751 - 9,825,267 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Setx
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247603,955,494 - 4,007,610 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247603,932,213 - 4,007,290 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Setx
229 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:136
Count of miRNA genes:115
Interacting mature miRNAs:120
Transcripts:ENSRNOT00000017984
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 32 30 14 19 14 8 8 74 28 41 11 8
Low 1 11 27 27 27 3 7
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000017984   ⟹   ENSRNOP00000017984
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl312,430,334 - 12,480,803 (+)Ensembl
Rnor_6.0 Ensembl37,686,503 - 7,730,539 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101235   ⟹   ENSRNOP00000082851
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl312,427,635 - 12,480,803 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000110450   ⟹   ENSRNOP00000083466
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl312,430,334 - 12,480,803 (+)Ensembl
RefSeq Acc Id: NM_001427280   ⟹   NP_001414209
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,828,412 - 32,878,740 (+)NCBI
RefSeq Acc Id: XM_006233886   ⟹   XP_006233948
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,828,233 - 32,878,740 (+)NCBI
mRatBN7.2312,430,332 - 12,480,801 (+)NCBI
Rnor_6.037,681,338 - 7,731,815 (+)NCBI
Rnor_5.0313,029,002 - 13,080,379 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006233887   ⟹   XP_006233949
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,825,771 - 32,878,740 (+)NCBI
mRatBN7.2312,428,091 - 12,480,801 (+)NCBI
Rnor_6.037,680,430 - 7,731,815 (+)NCBI
Rnor_5.0313,029,002 - 13,080,379 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039106152   ⟹   XP_038962080
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,825,771 - 32,868,205 (+)NCBI
mRatBN7.2312,428,091 - 12,470,235 (+)NCBI
RefSeq Acc Id: XR_005502066
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8332,825,771 - 32,864,433 (+)NCBI
mRatBN7.2312,428,091 - 12,466,493 (+)NCBI
RefSeq Acc Id: XP_006233949   ⟸   XM_006233887
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZYQ6 (UniProtKB/TrEMBL),   A0A8I5ZVF7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233948   ⟸   XM_006233886
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZYQ6 (UniProtKB/TrEMBL),   A0A8I5ZVF7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000017984   ⟸   ENSRNOT00000017984
RefSeq Acc Id: XP_038962080   ⟸   XM_039106152
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZVF7 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000083466   ⟸   ENSRNOT00000110450
RefSeq Acc Id: ENSRNOP00000082851   ⟸   ENSRNOT00000101235
RefSeq Acc Id: NP_001414209   ⟸   NM_001427280
- UniProtKB: A0A8I5ZVF7 (UniProtKB/TrEMBL),   D4AEB3 (UniProtKB/TrEMBL)
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AEB3-F1-model_v2 AlphaFold D4AEB3 1-2647 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565575 AgrOrtholog
BioCyc Gene G2FUF-50261 BioCyc
Ensembl Genes ENSRNOG00000013491 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017984.6 UniProtKB/TrEMBL
  ENSRNOT00000101235.1 UniProtKB/TrEMBL
  ENSRNOT00000110450.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro DNA2/NAM7-like UniProtKB/TrEMBL
  DNA2/NAM7_AAA_11 UniProtKB/TrEMBL
  DNA2/NAM7_like_AAA_12 UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  SF1_C_Upf1 UniProtKB/TrEMBL
KEGG Report rno:362096 UniProtKB/TrEMBL
NCBI Gene 362096 ENTREZGENE
PANTHER HELICASE SENATAXIN-RELATED UniProtKB/TrEMBL
  PTHR10887 UniProtKB/TrEMBL
Pfam AAA_11 UniProtKB/TrEMBL
  AAA_12 UniProtKB/TrEMBL
PhenoGen Setx PhenoGen
RatGTEx ENSRNOG00000013491 RatGTEx
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A0A8I5ZVF7 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I5ZYQ6 ENTREZGENE, UniProtKB/TrEMBL
  D4AEB3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Setx  senataxin  RGD1565575_predicted  similar to senataxin; DEAxQ-box helicase; tRNA splicing endonuclease regulator 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565575_predicted  similar to senataxin; DEAxQ-box helicase; tRNA splicing endonuclease regulator 1 (predicted)  LOC362096  similar to senataxin; DEAxQ-box helicase; tRNA splicing endonuclease regulator 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC362096  similar to senataxin; DEAxQ-box helicase; tRNA splicing endonuclease regulator 1      Symbol and Name status set to provisional 70820 PROVISIONAL