Thyn1 (thymocyte nuclear protein 1) - Rat Genome Database

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Gene: Thyn1 (thymocyte nuclear protein 1) Rattus norvegicus
Analyze
Symbol: Thyn1
Name: thymocyte nuclear protein 1
RGD ID: 1359525
Description: Predicted to be active in nucleus. Orthologous to human THYN1 (thymocyte nuclear protein 1); INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; 4,4'-diaminodiphenylmethane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: MGC72984; thymocyte protein thy28
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
mRatBN7.2825,406,563 - 25,415,444 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl825,406,500 - 25,415,445 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx829,448,526 - 29,457,408 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0827,742,824 - 27,751,706 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0825,622,821 - 25,631,701 (+)NCBIRnor_WKY
Rnor_6.0828,045,093 - 28,053,974 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl828,045,093 - 28,054,040 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0828,064,823 - 28,073,704 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera826,894,403 - 26,903,284 (+)NCBICelera
Cytogenetic Map8q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4-hydroxyphenyl retinamide  (ISO)
aflatoxin B1  (EXP,ISO)
anthracen-2-amine  (EXP)
aristolochic acid  (ISO)
arsenous acid  (ISO)
beauvericin  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chromium(6+)  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
enniatin  (ISO)
enzyme inhibitor  (ISO)
folic acid  (ISO)
furan  (EXP)
gentamycin  (EXP)
hydrogen peroxide  (ISO)
indometacin  (ISO)
ivermectin  (ISO)
lipopolysaccharide  (ISO)
N-nitrosodimethylamine  (EXP)
oxaliplatin  (EXP)
ozone  (ISO)
paracetamol  (ISO)
phenobarbital  (ISO)
potassium chromate  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
S-(1,2-dichlorovinyl)-L-cysteine  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sodium fluoride  (ISO)
tamoxifen  (ISO)
tetraphene  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IBA,ISO)

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:14601557   PMID:15489334   PMID:21630459  


Genomics

Comparative Map Data
Thyn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2825,406,563 - 25,415,444 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl825,406,500 - 25,415,445 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx829,448,526 - 29,457,408 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0827,742,824 - 27,751,706 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0825,622,821 - 25,631,701 (+)NCBIRnor_WKY
Rnor_6.0828,045,093 - 28,053,974 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl828,045,093 - 28,054,040 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0828,064,823 - 28,073,704 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera826,894,403 - 26,903,284 (+)NCBICelera
Cytogenetic Map8q13NCBI
THYN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811134,248,282 - 134,253,352 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl11134,248,279 - 134,253,370 (-)EnsemblGRCh38hg38GRCh38
GRCh3711134,118,176 - 134,123,246 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611133,623,383 - 133,628,470 (-)NCBINCBI36Build 36hg18NCBI36
Celera11131,291,036 - 131,296,123 (-)NCBICelera
Cytogenetic Map11q25NCBI
HuRef11130,072,934 - 130,078,021 (-)NCBIHuRef
CHM1_111134,004,909 - 134,009,996 (-)NCBICHM1_1
T2T-CHM13v2.011134,290,127 - 134,295,197 (-)NCBIT2T-CHM13v2.0
Thyn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39926,910,950 - 26,918,632 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl926,911,006 - 26,918,632 (+)EnsemblGRCm39 Ensembl
GRCm38926,999,642 - 27,007,336 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl926,999,710 - 27,007,336 (+)EnsemblGRCm38mm10GRCm38
MGSCv37926,807,262 - 26,814,919 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36926,749,168 - 26,756,780 (+)NCBIMGSCv36mm8
Celera924,257,858 - 24,265,515 (+)NCBICelera
Cytogenetic Map9A4NCBI
Thyn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541235,061,874 - 35,067,352 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541235,061,874 - 35,067,631 (-)NCBIChiLan1.0ChiLan1.0
THYN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111132,958,850 - 132,963,927 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11132,958,850 - 132,963,911 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v011129,101,422 - 129,106,521 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
THYN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.15992,126 - 999,609 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl5993,705 - 999,597 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha51,113,214 - 1,119,427 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.05949,494 - 955,705 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl5949,604 - 955,655 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.15982,706 - 988,908 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.05982,880 - 989,086 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.051,020,810 - 1,027,022 (+)NCBIUU_Cfam_GSD_1.0
Thyn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947116,001,021 - 116,011,924 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366841,591,270 - 1,597,609 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049366841,591,158 - 1,601,833 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
THYN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl960,802,928 - 60,807,409 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1960,802,925 - 60,807,404 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2967,487,439 - 67,490,210 (-)NCBISscrofa10.2Sscrofa10.2susScr3
THYN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11125,308,232 - 125,313,553 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666043731,010 - 736,452 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Thyn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248128,805,196 - 8,810,582 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248128,805,196 - 8,810,559 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Thyn1
25 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:104
Count of miRNA genes:88
Interacting mature miRNAs:93
Transcripts:ENSRNOT00000073373
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82266233067662330Rat

Markers in Region
RH134137  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2825,414,990 - 25,415,381 (+)MAPPERmRatBN7.2
Rnor_6.0828,053,521 - 28,053,911NCBIRnor6.0
Rnor_5.0828,073,251 - 28,073,641UniSTSRnor5.0
Celera826,902,831 - 26,903,221UniSTS
RH 3.4 Map8221.6UniSTS
Cytogenetic Map8q13UniSTS
RH134274  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2825,412,548 - 25,412,730 (+)MAPPERmRatBN7.2
Rnor_6.0828,051,079 - 28,051,260NCBIRnor6.0
Rnor_5.0828,070,809 - 28,070,990UniSTSRnor5.0
Celera826,900,389 - 26,900,570UniSTS
RH 3.4 Map8221.6UniSTS
Cytogenetic Map8q13UniSTS
RH140613  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2825,404,843 - 25,405,040 (+)MAPPERmRatBN7.2
Rnor_6.0828,043,374 - 28,043,570NCBIRnor6.0
Rnor_5.0828,063,104 - 28,063,300UniSTSRnor5.0
Celera826,892,684 - 26,892,880UniSTS
RH 3.4 Map8221.7UniSTS
Cytogenetic Map8q13UniSTS


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 43 53 37 19 37 7 10 74 35 41 11 7
Low 4 4 4 1 1 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000073373   ⟹   ENSRNOP00000067377
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl825,406,500 - 25,415,444 (+)Ensembl
Rnor_6.0 Ensembl828,045,093 - 28,053,974 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085997   ⟹   ENSRNOP00000073866
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl825,411,152 - 25,415,445 (+)Ensembl
Rnor_6.0 Ensembl828,045,288 - 28,054,040 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000107391   ⟹   ENSRNOP00000093977
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl825,411,096 - 25,415,444 (+)Ensembl
RefSeq Acc Id: NM_001007661   ⟹   NP_001007662
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2825,406,563 - 25,415,444 (+)NCBI
Rnor_6.0828,045,093 - 28,053,974 (+)NCBI
Rnor_5.0828,064,823 - 28,073,704 (+)NCBI
Celera826,894,403 - 26,903,284 (+)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001007662   ⟸   NM_001007661
- UniProtKB: Q6P3E0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000067377   ⟸   ENSRNOT00000073373
RefSeq Acc Id: ENSRNOP00000073866   ⟸   ENSRNOT00000085997
RefSeq Acc Id: ENSRNOP00000093977   ⟸   ENSRNOT00000107391
Protein Domains
EVE

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6P3E0-F1-model_v2 AlphaFold Q6P3E0 1-226 view protein structure

Transcriptome

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

Promoters
RGD ID:13695817
Promoter ID:EPDNEW_R6342
Type:initiation region
Name:Thyn1_1
Description:thymocyte nuclear protein 1
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_6.0828,045,098 - 28,045,158EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359525 AgrOrtholog
BioCyc Gene G2FUF-31307 BioCyc
Ensembl Genes ENSRNOG00000047053 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000067377.2 UniProtKB/TrEMBL
  ENSRNOP00000073866.2 UniProtKB/TrEMBL
  ENSRNOP00000093977.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073373.3 UniProtKB/TrEMBL
  ENSRNOT00000085997.2 UniProtKB/TrEMBL
  ENSRNOT00000107391.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6887845 IMAGE-MGC_LOAD
InterPro EVE_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PUA-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:300470 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72984 IMAGE-MGC_LOAD
NCBI Gene 300470 ENTREZGENE
Pfam EVE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Thyn1 PhenoGen
Superfamily-SCOP SSF88697 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AMV2_RAT UniProtKB/TrEMBL
  A0A8L2R049_RAT UniProtKB/TrEMBL
  A0A8L2R8I4_RAT UniProtKB/TrEMBL
  Q6P3E0 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Thyn1  thymocyte nuclear protein 1  MGC72984  thymocyte protein thy28  Symbol and Name updated 1299863 APPROVED
2005-07-29 MGC72984  thymocyte protein thy28      Symbol and Name status set to provisional 70820 PROVISIONAL