Tspan6 (tetraspanin 6) - Rat Genome Database

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Gene: Tspan6 (tetraspanin 6) Rattus norvegicus
Analyze
Symbol: Tspan6
Name: tetraspanin 6
RGD ID: 1560160
Description: Predicted to be involved in negative regulation of canonical NF-kappaB signal transduction and negative regulation of cytoplasmic pattern recognition receptor signaling pathway. Predicted to be located in membrane. Predicted to be active in plasma membrane. Orthologous to human TSPAN6 (tetraspanin 6); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC302313; similar to transmembrane 4 superfamily member 6; tetraspanin-6
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
GRCr8X101,385,686 - 101,395,371 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX101,385,694 - 101,392,627 (-)EnsemblGRCr8
mRatBN7.2X97,092,394 - 97,099,659 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX97,092,388 - 97,099,309 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX98,766,541 - 98,773,427 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X102,276,323 - 102,283,209 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X99,779,719 - 99,786,605 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X104,719,930 - 104,729,606 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX104,719,940 - 104,726,816 (-)Ensemblrn6Rnor6.0
Rnor_5.0X104,555,374 - 104,562,260 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X121,432,320 - 121,439,205 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX98,140,232 - 98,147,118 (-)NCBICelera
Cytogenetic MapXq32NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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. 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:12761501   PMID:19056867   PMID:19199708   PMID:22908223   PMID:23533145  


Genomics

Comparative Map Data
Tspan6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X101,385,686 - 101,395,371 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX101,385,694 - 101,392,627 (-)EnsemblGRCr8
mRatBN7.2X97,092,394 - 97,099,659 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX97,092,388 - 97,099,309 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX98,766,541 - 98,773,427 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X102,276,323 - 102,283,209 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X99,779,719 - 99,786,605 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X104,719,930 - 104,729,606 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX104,719,940 - 104,726,816 (-)Ensemblrn6Rnor6.0
Rnor_5.0X104,555,374 - 104,562,260 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X121,432,320 - 121,439,205 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX98,140,232 - 98,147,118 (-)NCBICelera
Cytogenetic MapXq32NCBI
TSPAN6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X100,627,108 - 100,637,104 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX100,627,108 - 100,639,991 (-)Ensemblhg38GRCh38
GRCh37X99,882,105 - 99,892,101 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X99,770,451 - 99,778,450 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34X99,689,939 - 99,697,939NCBI
CeleraX100,402,531 - 100,410,530 (-)NCBICelera
Cytogenetic MapXq22.1NCBI
HuRefX89,659,381 - 89,692,021 (-)NCBIHuRef
CHM1_1X99,774,986 - 99,784,982 (-)NCBICHM1_1
T2T-CHM13v2.0X99,069,540 - 99,081,815 (-)NCBIT2T-CHM13v2.0
Tspan6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X132,791,817 - 132,801,957 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX132,791,817 - 132,799,178 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X133,891,068 - 133,901,208 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX133,891,068 - 133,898,429 (-)Ensemblmm10GRCm38
MGSCv37X130,425,609 - 130,432,968 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X129,237,418 - 129,244,713 (-)NCBIMGSCv36mm8
CeleraX116,767,033 - 116,774,362 (-)NCBICelera
Cytogenetic MapXE3NCBI
cM MapX55.47NCBI
Tspan6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555036,779,377 - 6,789,142 (-)Ensembl
ChiLan1.0NW_0049555036,782,264 - 6,788,533 (-)NCBIChiLan1.0ChiLan1.0
TSPAN6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X100,236,835 - 100,247,796 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X100,241,107 - 100,251,401 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X89,840,067 - 89,848,114 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X99,979,128 - 99,987,520 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX99,979,171 - 99,987,402 (-)EnsemblpanPan2panpan1.1
TSPAN6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X74,499,684 - 74,510,079 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX74,499,686 - 74,505,683 (-)EnsemblcanFam3CanFam3.1
ROS_Cfam_1.0X75,909,342 - 75,919,721 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX75,909,344 - 75,915,137 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X73,471,844 - 73,482,187 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X75,142,139 - 75,152,488 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X74,903,105 - 74,913,506 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tspan6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X63,700,668 - 63,711,691 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365845,840,312 - 5,848,622 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365845,842,549 - 5,848,533 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TSPAN6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX82,323,624 - 82,328,903 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X82,323,634 - 82,328,919 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X90,165,047 - 90,174,442 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TSPAN6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X88,940,666 - 88,948,459 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX88,942,300 - 88,948,069 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606513,869,745 - 13,877,832 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tspan6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249021,978,467 - 1,986,303 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046249021,977,700 - 1,985,004 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Tspan6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X86,214,690 - 86,221,687 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tspan6
22 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:555
Count of miRNA genes:263
Interacting mature miRNAs:328
Transcripts:ENSRNOT00000005165
Prediction methods:Microtar, Miranda, Pita, 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
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X97528096142528096Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X80434318125434318Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX92979612117740458Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
2302047Pia34Pristane induced arthritis QTL 345.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1996916163141916163Rat

Markers in Region
RH139794  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X97,092,688 - 97,092,892 (+)MAPPERmRatBN7.2
Rnor_6.0X104,720,225 - 104,720,428NCBIRnor6.0
Rnor_5.0X104,555,669 - 104,555,872UniSTSRnor5.0
RGSC_v3.4X121,432,615 - 121,432,818UniSTSRGSC3.4
CeleraX98,140,527 - 98,140,730UniSTS
Cytogenetic MapXq34UniSTS
RH141922  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8X101,386,371 - 101,387,277 (+)Marker Load Pipeline
mRatBN7.2X97,093,079 - 97,093,985 (+)MAPPERmRatBN7.2
Rnor_6.0X104,720,616 - 104,721,521NCBIRnor6.0
Rnor_5.0X104,556,060 - 104,556,965UniSTSRnor5.0
RGSC_v3.4X121,433,006 - 121,433,911UniSTSRGSC3.4
CeleraX98,140,918 - 98,141,823UniSTS
Cytogenetic MapXq34UniSTS


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 67 165 91 90 59 86 59 6 350 186 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000005165   ⟹   ENSRNOP00000005165
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX101,385,694 - 101,392,572 (-)Ensembl
mRatBN7.2 EnsemblX97,092,388 - 97,099,277 (-)Ensembl
Rnor_6.0 EnsemblX104,719,940 - 104,726,816 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000119163   ⟹   ENSRNOP00000088359
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX101,387,271 - 101,392,627 (-)Ensembl
mRatBN7.2 EnsemblX97,092,400 - 97,099,309 (-)Ensembl
RefSeq Acc Id: NM_001100672   ⟹   NP_001094142
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,385,686 - 101,392,572 (-)NCBI
mRatBN7.2X97,092,394 - 97,099,280 (-)NCBI
Rnor_6.0X104,719,930 - 104,726,816 (-)NCBI
Rnor_5.0X104,555,374 - 104,562,260 (-)NCBI
RGSC_v3.4X121,432,320 - 121,439,205 (-)RGD
CeleraX98,140,232 - 98,147,118 (-)RGD
Sequence:
RefSeq Acc Id: XM_008773408   ⟹   XP_008771630
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,386,324 - 101,395,371 (-)NCBI
mRatBN7.2X97,093,030 - 97,099,659 (-)NCBI
Rnor_6.0X104,720,566 - 104,729,606 (-)NCBI
Sequence:
RefSeq Acc Id: XM_063279888   ⟹   XP_063135958
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,386,324 - 101,395,371 (-)NCBI
RefSeq Acc Id: NP_001094142   ⟸   NM_001100672
- UniProtKB: B0BN20 (UniProtKB/TrEMBL),   A0A8I6A7Q5 (UniProtKB/TrEMBL),   F7ESS4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771630   ⟸   XM_008773408
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000005165   ⟸   ENSRNOT00000005165
Ensembl Acc Id: ENSRNOP00000088359   ⟸   ENSRNOT00000119163
RefSeq Acc Id: XP_063135958   ⟸   XM_063279888
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A7Q5 (UniProtKB/TrEMBL),   B0BN20 (UniProtKB/TrEMBL),   F7ESS4 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B0BN20-F1-model_v2 AlphaFold B0BN20 1-245 view protein structure

Transcriptome

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

Promoters
RGD ID:13701926
Promoter ID:EPDNEW_R12450
Type:initiation region
Name:Tspan6_1
Description:tetraspanin 6
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_6.0X104,726,862 - 104,726,922EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560160 AgrOrtholog
BioCyc Gene G2FUF-1699 BioCyc
Ensembl Genes ENSRNOG00000003786 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005165 ENTREZGENE
  ENSRNOT00000005165.8 UniProtKB/TrEMBL
  ENSRNOT00000119163 ENTREZGENE
  ENSRNOT00000119163.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.1450.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7301508 IMAGE-MGC_LOAD
  IMAGE:8368067 IMAGE-MGC_LOAD
InterPro Tetraspanin UniProtKB/TrEMBL
  Tetraspanin_CS UniProtKB/TrEMBL
  Tetraspanin_EC2 UniProtKB/TrEMBL
  Tetraspanin_sub UniProtKB/TrEMBL
  TSN6/7_LEL UniProtKB/TrEMBL
KEGG Report rno:302313 UniProtKB/TrEMBL
MGC_CLONE MGC:105933 IMAGE-MGC_LOAD
  MGC:187634 IMAGE-MGC_LOAD
NCBI Gene 302313 ENTREZGENE
PANTHER PTHR19282 UniProtKB/TrEMBL
  TETRASPANIN-6 UniProtKB/TrEMBL
Pfam Tetraspannin UniProtKB/TrEMBL
PhenoGen Tspan6 PhenoGen
PIRSF Tetraspanin UniProtKB/TrEMBL
PRINTS TMFOUR UniProtKB/TrEMBL
PROSITE TM4_1 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000003786 RatGTEx
Superfamily-SCOP Tetraspanin UniProtKB/TrEMBL
UniProt A0A8I6A7Q5 ENTREZGENE, UniProtKB/TrEMBL
  B0BN20 ENTREZGENE, UniProtKB/TrEMBL
  F7ESS4 ENTREZGENE, UniProtKB/TrEMBL
  Q5RJZ3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Tspan6  tetraspanin 6  LOC302313  similar to transmembrane 4 superfamily member 6  Symbol and Name updated 1299863 APPROVED
2006-02-09 LOC302313  similar to transmembrane 4 superfamily member 6      Symbol and Name status set to provisional 70820 PROVISIONAL