Thsd1 (thrombospondin type 1 domain containing 1) - Rat Genome Database

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Gene: Thsd1 (thrombospondin type 1 domain containing 1) Rattus norvegicus
Analyze
Symbol: Thsd1
Name: thrombospondin type 1 domain containing 1
RGD ID: 1306998
Description: Predicted to enable extracellular matrix binding activity. Predicted to be involved in focal adhesion assembly. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be located in cell surface; endosome; and focal adhesion. Predicted to be active in cell periphery. Human ortholog(s) of this gene implicated in hereditary lymphedema and intracranial berry aneurysm 12. Orthologous to human THSD1 (thrombospondin type 1 domain containing 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC364630; thrombospondin type-1 domain-containing protein 1; thrombospondin, type I, domain 1; thrombospondin, type I, domain containing 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81676,473,026 - 76,507,404 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1676,473,859 - 76,503,951 (-)EnsemblGRCr8
mRatBN7.21669,771,408 - 69,804,844 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1669,771,408 - 69,801,504 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1675,045,087 - 75,075,180 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01678,482,659 - 78,513,813 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01673,731,938 - 73,763,094 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01674,680,621 - 74,712,368 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1674,680,621 - 74,710,704 (-)Ensemblrn6Rnor6.0
Rnor_5.01674,316,449 - 74,346,278 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41674,423,526 - 74,453,530 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1667,660,826 - 67,690,866 (-)NCBICelera
RGSC_v3.11674,425,343 - 74,443,897 (-)NCBI
Cytogenetic Map16q12.5NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cell periphery  (IBA,ISO)
cell surface  (ISO)
cytoplasm  (IEA,ISO)
cytosol  (ISO)
endosome  (ISO)
focal adhesion  (ISO)

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. 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
Additional References at PubMed
PMID:12477932   PMID:16455951   PMID:19143766  


Genomics

Comparative Map Data
Thsd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81676,473,026 - 76,507,404 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1676,473,859 - 76,503,951 (-)EnsemblGRCr8
mRatBN7.21669,771,408 - 69,804,844 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1669,771,408 - 69,801,504 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1675,045,087 - 75,075,180 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01678,482,659 - 78,513,813 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01673,731,938 - 73,763,094 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01674,680,621 - 74,712,368 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1674,680,621 - 74,710,704 (-)Ensemblrn6Rnor6.0
Rnor_5.01674,316,449 - 74,346,278 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41674,423,526 - 74,453,530 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1667,660,826 - 67,690,866 (-)NCBICelera
RGSC_v3.11674,425,343 - 74,443,897 (-)NCBI
Cytogenetic Map16q12.5NCBI
THSD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381352,377,167 - 52,406,172 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1352,377,163 - 52,416,373 (-)Ensemblhg38GRCh38
GRCh371352,951,302 - 52,980,307 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361351,849,303 - 51,878,321 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341351,849,304 - 51,878,321NCBI
Celera1334,016,568 - 34,045,895 (+)NCBICelera
Cytogenetic Map13q14.3NCBI
HuRef1333,689,629 - 33,718,949 (-)NCBIHuRef
CHM1_11352,919,377 - 52,948,686 (-)NCBICHM1_1
T2T-CHM13v2.01351,591,989 - 51,620,993 (-)NCBIT2T-CHM13v2.0
Thsd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39822,711,623 - 22,752,973 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl822,717,329 - 22,751,350 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38822,220,938 - 22,262,957 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl822,227,313 - 22,261,334 (+)Ensemblmm10GRCm38
MGSCv37823,348,972 - 23,370,361 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36823,704,045 - 23,725,434 (+)NCBIMGSCv36mm8
Celera823,731,367 - 23,752,587 (+)NCBICelera
Cytogenetic Map8A2NCBI
cM Map811.16NCBI
Thsd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554315,472,287 - 5,495,995 (+)Ensembl
ChiLan1.0NW_0049554315,472,209 - 5,495,937 (+)NCBIChiLan1.0ChiLan1.0
THSD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21453,746,186 - 53,775,503 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11352,390,647 - 52,421,953 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01333,442,480 - 33,472,259 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11352,301,206 - 52,330,504 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1352,301,206 - 52,330,504 (-)EnsemblpanPan2panpan1.1
THSD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.125197,294 - 223,804 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl25201,301 - 223,560 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha25317,148 - 342,957 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.025300,765 - 326,595 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl25300,762 - 326,593 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.125181,718 - 207,474 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.025196,312 - 222,144 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.025264,131 - 289,945 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Thsd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945161,441,192 - 161,467,900 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365654,925,237 - 4,954,054 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365654,925,400 - 4,952,210 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
THSD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1115,668,813 - 15,697,872 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11115,668,435 - 15,698,031 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21116,006,405 - 16,035,636 (+)NCBISscrofa10.2Sscrofa10.2susScr3
THSD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1330,152,706 - 30,180,223 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl330,153,364 - 30,183,302 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605713,630,583 - 13,660,217 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Thsd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247481,846,249 - 1,875,156 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247481,843,361 - 1,875,748 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Thsd1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11364,179,257 - 64,215,666 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Thsd1
150 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:914
Count of miRNA genes:321
Interacting mature miRNAs:427
Transcripts:ENSRNOT00000016859
Prediction methods:Microtar, Miranda, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164445512389455123Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165942871491442908Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)163439829479398294Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)163692878281928782Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)163188527176885271Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)164199206486992064Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164445512389455123Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165942871491442908Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165942871491442908Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164909919691442908Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)167523528581732231Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)163236104377361043Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 86 59 6 350 186 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000016859   ⟹   ENSRNOP00000016859
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1676,473,859 - 76,503,951 (-)Ensembl
mRatBN7.2 Ensembl1669,771,408 - 69,801,504 (-)Ensembl
Rnor_6.0 Ensembl1674,680,621 - 74,710,704 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000081297   ⟹   ENSRNOP00000073040
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1676,475,229 - 76,494,062 (-)Ensembl
mRatBN7.2 Ensembl1669,772,779 - 69,791,614 (-)Ensembl
Rnor_6.0 Ensembl1674,681,991 - 74,700,815 (-)Ensembl
RefSeq Acc Id: NM_001108878   ⟹   NP_001102348
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81676,473,859 - 76,503,951 (-)NCBI
mRatBN7.21669,771,408 - 69,801,504 (-)NCBI
Rnor_6.01674,680,621 - 74,710,704 (-)NCBI
Rnor_5.01674,316,449 - 74,346,278 (-)NCBI
RGSC_v3.41674,423,526 - 74,453,530 (-)RGD
Celera1667,660,826 - 67,690,866 (-)RGD
Sequence:
RefSeq Acc Id: XM_006253357   ⟹   XP_006253419
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81676,473,026 - 76,507,404 (-)NCBI
mRatBN7.21669,772,772 - 69,804,844 (-)NCBI
Rnor_6.01674,681,522 - 74,712,368 (-)NCBI
Rnor_5.01674,316,449 - 74,346,278 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001102348   ⟸   NM_001108878
- Peptide Label: precursor
- UniProtKB: D3ZW62 (UniProtKB/TrEMBL),   A6IW78 (UniProtKB/TrEMBL),   A6IW79 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253419   ⟸   XM_006253357
- Peptide Label: isoform X1
- UniProtKB: B1WC79 (UniProtKB/TrEMBL),   A0A0G2K4H0 (UniProtKB/TrEMBL),   A6IW79 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000016859   ⟸   ENSRNOT00000016859
Ensembl Acc Id: ENSRNOP00000073040   ⟸   ENSRNOT00000081297
Protein Domains
THSD1 N-terminal   THSD1 second Ig-like   THSD1 third Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZW62-F1-model_v2 AlphaFold D3ZW62 1-850 view protein structure

Transcriptome

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

Promoters
RGD ID:13700191
Promoter ID:EPDNEW_R10715
Type:multiple initiation site
Name:Thsd1_1
Description:thrombospondin type 1 domain containing 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_6.01674,710,666 - 74,710,726EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306998 AgrOrtholog
BioCyc Gene G2FUF-10864 BioCyc
Ensembl Genes ENSRNOG00000012108 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016859 ENTREZGENE
  ENSRNOT00000016859.7 UniProtKB/TrEMBL
  ENSRNOT00000081297 ENTREZGENE
  ENSRNOT00000081297.3 UniProtKB/TrEMBL
Gene3D-CATH 2.20.100.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7097232 IMAGE-MGC_LOAD
InterPro Thrombospondin_1_rpt UniProtKB/TrEMBL
  THSD1 UniProtKB/TrEMBL
  THSD1_D2 UniProtKB/TrEMBL
  THSD1_D3 UniProtKB/TrEMBL
  THSD1_N UniProtKB/TrEMBL
  TSP1_rpt_sf UniProtKB/TrEMBL
KEGG Report rno:364630 UniProtKB/TrEMBL
MGC_CLONE MGC:187951 IMAGE-MGC_LOAD
NCBI Gene 364630 ENTREZGENE
PANTHER PTHR16311 UniProtKB/TrEMBL
  THROMBOSPONDIN TYPE-1 DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
Pfam THSD1_D2 UniProtKB/TrEMBL
  THSD1_D3 UniProtKB/TrEMBL
  THSD1_N UniProtKB/TrEMBL
  TSP_1 UniProtKB/TrEMBL
PhenoGen Thsd1 PhenoGen
PROSITE TSP1 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012108 RatGTEx
SMART TSP1 UniProtKB/TrEMBL
Superfamily-SCOP TSP1 UniProtKB/TrEMBL
UniProt A0A0G2K4H0 ENTREZGENE, UniProtKB/TrEMBL
  A6IW78 ENTREZGENE, UniProtKB/TrEMBL
  A6IW79 ENTREZGENE, UniProtKB/TrEMBL
  B1WC79 ENTREZGENE, UniProtKB/TrEMBL
  D3ZW62 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-20 Thsd1  thrombospondin type 1 domain containing 1  Thsd1  thrombospondin, type I, domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-23 Thsd1  thrombospondin, type I, domain containing 1  Thsd1  thrombospondin, type I, domain 1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Thsd1  thrombospondin, type I, domain 1   Thsd1_predicted  thrombospondin, type I, domain 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Thsd1_predicted  thrombospondin, type I, domain 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED