Thoc2 (THO complex subunit 2) - Rat Genome Database

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Gene: Thoc2 (THO complex subunit 2) Rattus norvegicus
Analyze
Symbol: Thoc2
Name: THO complex subunit 2
RGD ID: 1561623
Description: Predicted to enable mRNA binding activity. Involved in negative regulation of neuron projection development. Predicted to be located in chromosome, telomeric region and nucleus. Predicted to be part of THO complex part of transcription export complex. Human ortholog(s) of this gene implicated in X-linked intellectual disability-short stature-overweight syndrome. Orthologous to human THOC2 (THO complex subunit 2); PARTICIPATES IN NXF1-NXT1 export pathway; RNA transport pathway; spliceosome pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC313308; RGD1561623; similar to THO complex 2; THO complex 2
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
GRCr8X125,500,549 - 125,615,139 (-)NCBIGRCr8
mRatBN7.2X120,634,966 - 120,749,569 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX120,634,968 - 120,749,513 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX122,744,669 - 122,859,251 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X126,266,121 - 126,380,689 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X123,861,559 - 123,976,122 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X128,153,824 - 128,268,327 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX128,161,895 - 128,268,322 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X128,246,548 - 128,361,045 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X3,196,205 - 3,310,749 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX119,751,149 - 119,864,843 (-)NCBICelera
Cytogenetic MapXq35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
17beta-estradiol  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3',4,4',5-Pentachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-methylcholine  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
alpha-pinene  (ISO)
aristolochic acid A  (ISO)
Aroclor 1254  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
caffeine  (ISO)
CGP 52608  (ISO)
chloroprene  (EXP)
coumarin  (ISO)
crocidolite asbestos  (ISO)
cyproconazole  (ISO)
decabromodiphenyl ether  (EXP,ISO)
dexamethasone  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
epoxiconazole  (ISO)
ethanol  (ISO)
fenvalerate  (EXP)
flutamide  (EXP)
folic acid  (ISO)
FR900359  (ISO)
genistein  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
miconazole  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenethyl isothiocyanate  (EXP)
phenobarbital  (ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
propiconazole  (ISO)
resveratrol  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
succimer  (ISO)
sunitinib  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichloroethene  (EXP)
triptonide  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function
mRNA binding  (IBA,ISO)
protein binding  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. A de novo X;8 translocation creates a PTK2-THOC2 gene fusion with THOC2 expression knockdown in a patient with psychomotor retardation and congenital cerebellar hypoplasia. Di Gregorio E, etal., J Med Genet. 2013 Aug;50(8):543-51. doi: 10.1136/jmedgenet-2013-101542. Epub 2013 Jun 7.
2. 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.
3. mRNA export and the TREX complex. Katahira J Biochim Biophys Acta. 2012 Jun;1819(6):507-13. doi: 10.1016/j.bbagrm.2011.12.001. Epub 2011 Dec 8.
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:15632090   PMID:15833825   PMID:15998806   PMID:17190602   PMID:18974867   PMID:22928037   PMID:24270157   PMID:24315442   PMID:26166480   PMID:31505169  


Genomics

Comparative Map Data
Thoc2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X125,500,549 - 125,615,139 (-)NCBIGRCr8
mRatBN7.2X120,634,966 - 120,749,569 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX120,634,968 - 120,749,513 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX122,744,669 - 122,859,251 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X126,266,121 - 126,380,689 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X123,861,559 - 123,976,122 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X128,153,824 - 128,268,327 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX128,161,895 - 128,268,322 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X128,246,548 - 128,361,045 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X3,196,205 - 3,310,749 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX119,751,149 - 119,864,843 (-)NCBICelera
Cytogenetic MapXq35NCBI
THOC2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X123,600,569 - 123,733,052 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX123,600,561 - 123,733,056 (-)EnsemblGRCh38hg38GRCh38
GRCh37X122,734,420 - 122,866,902 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X122,562,093 - 122,694,585 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X122,470,306 - 122,556,221NCBI
CeleraX123,120,365 - 123,252,932 (-)NCBICelera
Cytogenetic MapXq25NCBI
HuRefX112,121,467 - 112,254,690 (-)NCBIHuRef
CHM1_1X122,645,586 - 122,778,089 (-)NCBICHM1_1
T2T-CHM13v2.0X121,911,026 - 122,043,503 (-)NCBIT2T-CHM13v2.0
Thoc2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X40,883,869 - 41,000,878 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX40,883,868 - 41,009,551 (-)EnsemblGRCm39 Ensembl
GRCm38X41,794,992 - 41,911,937 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX41,794,991 - 41,920,674 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X39,148,171 - 39,265,078 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X38,039,624 - 38,156,528 (-)NCBIMGSCv36mm8
CeleraX29,379,665 - 29,496,534 (-)NCBICelera
Cytogenetic MapXA4NCBI
cM MapX23.19NCBI
Thoc2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547311,029,714 - 11,144,880 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495547311,029,860 - 11,143,493 (+)NCBIChiLan1.0ChiLan1.0
THOC2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X123,073,019 - 123,205,906 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X123,077,008 - 123,209,505 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X112,797,077 - 112,929,918 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X122,979,547 - 123,110,897 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX122,979,547 - 123,110,897 (-)Ensemblpanpan1.1panPan2
THOC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X95,087,209 - 95,217,450 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX95,095,711 - 95,199,747 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX81,155,235 - 81,285,078 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X96,857,397 - 96,987,320 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX96,865,923 - 96,970,059 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X94,303,965 - 94,433,814 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X96,060,074 - 96,189,923 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X95,849,520 - 95,979,385 (-)NCBIUU_Cfam_GSD_1.0
Thoc2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X94,015,239 - 94,132,114 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364796,855,411 - 6,972,256 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364796,855,405 - 6,972,256 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
THOC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX101,171,362 - 101,284,551 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X101,170,969 - 101,284,623 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X115,935,230 - 116,048,832 (-)NCBISscrofa10.2Sscrofa10.2susScr3
THOC2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366606536,312,625 - 36,442,756 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Thoc2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247972,299,694 - 2,411,269 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Thoc2
153 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1063
Count of miRNA genes:346
Interacting mature miRNAs:472
Transcripts:ENSRNOT00000009755
Prediction methods:Microtar, Miranda, Pita
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
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX112934952138400867Rat
5685004Bss104Bone structure and strength QTL 1043.9tibia area (VT:1000281)tibia area measurement (CMO:0001382)X113805422126975220Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat

Markers in Region
BE103656  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X120,674,843 - 120,675,033 (+)MAPPERmRatBN7.2
Rnor_6.0X128,193,647 - 128,193,836NCBIRnor6.0
Rnor_5.0X128,286,371 - 128,286,560UniSTSRnor5.0
RGSC_v3.4X3,270,684 - 3,270,873UniSTSRGSC3.4
CeleraX119,790,325 - 119,790,514UniSTS
RH 3.4 Map5717.1UniSTS
Cytogenetic MapXq11UniSTS
UniSTS:238018  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X120,636,361 - 120,636,680 (+)MAPPERmRatBN7.2
Rnor_6.0X128,155,220 - 128,155,538NCBIRnor6.0
Rnor_5.0X128,247,944 - 128,248,262UniSTSRnor5.0
RGSC_v3.4X3,309,037 - 3,309,355UniSTSRGSC3.4
CeleraX119,752,543 - 119,752,861UniSTS
Cytogenetic MapXq11UniSTS


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 3 34 43 27 19 27 8 8 74 35 36 11 8
Low 9 14 14 14 3 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009755   ⟹   ENSRNOP00000009755
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX120,643,457 - 120,749,513 (-)Ensembl
Rnor_6.0 EnsemblX128,161,895 - 128,268,285 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081880   ⟹   ENSRNOP00000074749
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX120,634,968 - 120,749,513 (-)Ensembl
Rnor_6.0 EnsemblX128,162,119 - 128,268,322 (-)Ensembl
RefSeq Acc Id: NM_001191756   ⟹   NP_001178685
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X125,500,549 - 125,615,087 (-)NCBI
mRatBN7.2X120,634,966 - 120,749,513 (-)NCBI
Rnor_6.0X128,153,826 - 128,268,315 (-)NCBI
Rnor_5.0X128,246,548 - 128,361,045 (-)NCBI
CeleraX119,751,149 - 119,864,843 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006257504   ⟹   XP_006257566
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X125,500,549 - 125,615,139 (-)NCBI
mRatBN7.2X120,634,966 - 120,749,569 (-)NCBI
Rnor_6.0X128,153,824 - 128,268,327 (-)NCBI
Rnor_5.0X128,246,548 - 128,361,045 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_001178685   ⟸   NM_001191756
- UniProtKB: F1M0V4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257566   ⟸   XM_006257504
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K8V3 (UniProtKB/TrEMBL),   F1M0V4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074749   ⟸   ENSRNOT00000081880
RefSeq Acc Id: ENSRNOP00000009755   ⟸   ENSRNOT00000009755
Protein Domains
THO complex subunit 2 N-terminal   THO complex subunitTHOC2 C-terminal   THO complex subunitTHOC2 N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K8V3-F1-model_v2 AlphaFold A0A0G2K8V3 1-1613 view protein structure

Transcriptome

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

Promoters
RGD ID:13702002
Promoter ID:EPDNEW_R12525
Type:multiple initiation site
Name:Thoc2_1
Description:THO complex 2
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_6.0X128,268,309 - 128,268,369EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561623 AgrOrtholog
BioCyc Gene G2FUF-1235 BioCyc
Ensembl Genes ENSRNOG00000007315 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009755 ENTREZGENE
  ENSRNOT00000009755.8 UniProtKB/TrEMBL
  ENSRNOT00000081880.2 UniProtKB/TrEMBL
InterPro Tho2 UniProtKB/TrEMBL
  THO_THOC2_C UniProtKB/TrEMBL
  THO_THOC2_N UniProtKB/TrEMBL
  THOC2_N UniProtKB/TrEMBL
NCBI Gene 313308 ENTREZGENE
PANTHER PTHR21597 UniProtKB/TrEMBL
  THO COMPLEX SUBUNIT 2 UniProtKB/TrEMBL
Pfam Tho2 UniProtKB/TrEMBL
  Thoc2 UniProtKB/TrEMBL
  THOC2_N UniProtKB/TrEMBL
PhenoGen Thoc2 PhenoGen
RatGTEx ENSRNOG00000007315 RatGTEx
UniProt A0A0G2K8V3 ENTREZGENE, UniProtKB/TrEMBL
  F1M0V4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-09-30 Thoc2  THO complex subunit 2  Thoc2  THO complex 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Thoc2  THO complex 2   Thoc2_predicted  THO complex 2 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Thoc2_predicted  THO complex 2 (predicted)  RGD1561623_predicted  similar to THO complex 2 (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1561623_predicted  similar to THO complex 2 (predicted)  LOC313308  similar to THO complex 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC313308  similar to THO complex 2      Symbol and Name status set to provisional 70820 PROVISIONAL