Tor4a (torsin family 4, member A) - Rat Genome Database

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Gene: Tor4a (torsin family 4, member A) Rattus norvegicus
Analyze
Symbol: Tor4a
Name: torsin family 4, member A
RGD ID: 1308019
Description: Predicted to enable ATP binding activity and ATP hydrolysis activity. Predicted to be located in membrane. Predicted to be active in endoplasmic reticulum lumen and nuclear envelope. Orthologous to human TOR4A (torsin family 4 member A); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC311795; LOC311795; RGD1308019; similar to hypothetical protein FLJ20245; torsin-4A; uncharacterized protein LOC311795
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,402,454 - 28,406,141 (-)NCBIGRCr8
mRatBN7.238,004,292 - 8,007,979 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,002,023 - 8,008,042 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,109,043 - 11,112,730 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0319,695,272 - 19,698,959 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0317,885,115 - 17,888,802 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,407,857 - 2,411,544 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,407,857 - 2,411,544 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,389,140 - 2,392,827 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,353,628 - 3,357,315 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,354,996 - 3,356,434 (-)NCBI
Celera32,831,136 - 2,834,823 (-)NCBICelera
Cytogenetic Map3p13NCBI
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Tor4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,402,454 - 28,406,141 (-)NCBIGRCr8
mRatBN7.238,004,292 - 8,007,979 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,002,023 - 8,008,042 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,109,043 - 11,112,730 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0319,695,272 - 19,698,959 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0317,885,115 - 17,888,802 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,407,857 - 2,411,544 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,407,857 - 2,411,544 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,389,140 - 2,392,827 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,353,628 - 3,357,315 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,354,996 - 3,356,434 (-)NCBI
Celera32,831,136 - 2,834,823 (-)NCBICelera
Cytogenetic Map3p13NCBI
TOR4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389137,277,726 - 137,282,641 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9137,277,726 - 137,282,641 (+)EnsemblGRCh38hg38GRCh38
GRCh379140,172,178 - 140,177,093 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,292,101 - 139,296,914 (+)NCBINCBI36Build 36hg18NCBI36
Celera9110,688,979 - 110,692,947 (+)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9109,631,637 - 109,636,404 (+)NCBIHuRef
CHM1_19140,320,857 - 140,325,670 (+)NCBICHM1_1
T2T-CHM13v2.09149,515,771 - 149,520,686 (+)NCBIT2T-CHM13v2.0
Tor4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,082,732 - 25,086,825 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,082,978 - 25,086,898 (-)EnsemblGRCm39 Ensembl
GRCm38225,192,720 - 25,196,813 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,192,966 - 25,196,886 (-)EnsemblGRCm38mm10GRCm38
MGSCv37225,048,240 - 25,052,333 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,014,729 - 25,018,622 (-)NCBIMGSCv36mm8
Celera224,920,489 - 24,924,582 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.06NCBI
Tor4a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555135,264,066 - 5,265,386 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555135,263,299 - 5,265,622 (+)NCBIChiLan1.0ChiLan1.0
TOR4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2112,116,706 - 2,121,932 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan192,119,039 - 2,124,266 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09108,337,814 - 108,342,723 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19137,307,611 - 137,311,577 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9137,307,626 - 137,310,283 (+)Ensemblpanpan1.1panPan2
TOR4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1948,405,017 - 48,411,583 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha947,591,577 - 47,597,042 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0949,266,440 - 49,271,907 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1948,042,857 - 48,048,329 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0948,341,602 - 48,347,076 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0948,388,507 - 48,393,992 (-)NCBIUU_Cfam_GSD_1.0
Tor4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947202,651,233 - 202,655,728 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936669721,349 - 722,620 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936669718,872 - 723,541 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TOR4A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa10.21314,112,192 - 314,114,924 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TOR4A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112908,956 - 911,198 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl12908,975 - 910,246 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660584,395,923 - 4,401,084 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tor4a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624760686,768 - 690,397 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624760686,754 - 692,557 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tor4a
11 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:383
Count of miRNA genes:212
Interacting mature miRNAs:247
Transcripts:ENSRNOT00000012406
Prediction methods:Microtar, Miranda
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
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3653764510778823Rat

Markers in Region
RH133027  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.238,004,503 - 8,004,697 (+)MAPPERmRatBN7.2
Rnor_6.032,408,069 - 2,408,262NCBIRnor6.0
Rnor_5.032,389,352 - 2,389,545UniSTSRnor5.0
RGSC_v3.433,353,840 - 3,354,033UniSTSRGSC3.4
Celera32,831,348 - 2,831,541UniSTS
Cytogenetic Map3p13UniSTS


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 3 14 10 3 5
Low 1 43 54 41 5 41 8 11 74 25 35 6 8
Below cutoff 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012406   ⟹   ENSRNOP00000012406
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl38,002,023 - 8,008,042 (-)Ensembl
Rnor_6.0 Ensembl32,407,857 - 2,411,544 (-)Ensembl
RefSeq Acc Id: NM_001107816   ⟹   NP_001101286
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8328,402,454 - 28,406,141 (-)NCBI
mRatBN7.238,004,292 - 8,007,979 (-)NCBI
Rnor_6.032,407,857 - 2,411,544 (-)NCBI
Rnor_5.032,389,140 - 2,392,827 (-)NCBI
RGSC_v3.433,353,628 - 3,357,315 (-)RGD
Celera32,831,136 - 2,834,823 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101286 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL93636 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000012406
  ENSRNOP00000012406.3
Reference Protein Sequences
RefSeq Acc Id: NP_001101286   ⟸   NM_001107816
- UniProtKB: D3ZG57 (UniProtKB/TrEMBL),   A6JT11 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012406   ⟸   ENSRNOT00000012406
Protein Domains
AAA+ ATPase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZG57-F1-model_v2 AlphaFold D3ZG57 1-434 view protein structure

Transcriptome

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

Promoters
RGD ID:13691859
Promoter ID:EPDNEW_R2383
Type:single initiation site
Name:Tor4a_1
Description:torsin family 4, member A
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.032,411,530 - 2,411,590EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308019 AgrOrtholog
BioCyc Gene G2FUF-50482 BioCyc
Ensembl Genes ENSRNOG00000009369 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012406 ENTREZGENE
  ENSRNOT00000012406.4 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro ATPase_AAA+_core UniProtKB/TrEMBL
  Chaprnin_clpA/B UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  Torsin UniProtKB/TrEMBL
KEGG Report rno:311795 UniProtKB/TrEMBL
NCBI Gene 311795 ENTREZGENE
PANTHER PTHR10760:SF1 UniProtKB/TrEMBL
  Torsin UniProtKB/TrEMBL
Pfam Torsin UniProtKB/TrEMBL
PhenoGen Tor4a PhenoGen
PRINTS CLPPROTEASEA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009369 RatGTEx
SMART AAA UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A6JT11 ENTREZGENE, UniProtKB/TrEMBL
  D3ZG57 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-10 Tor4a  torsin family 4, member A  RGD1308019  similar to hypothetical protein FLJ20245  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1308019  similar to hypothetical protein FLJ20245   RGD1308019_predicted  similar to hypothetical protein FLJ20245 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1308019_predicted  similar to hypothetical protein FLJ20245 (predicted)  LOC311795_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC311795_predicted  similar to hypothetical protein FLJ20245 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL