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; negative regulation of cytoplasmic pattern recognition receptor signaling pathway; and positive regulation of canonical NF-kappaB signal transduction. Predicted to be located in 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X101,385,686 - 101,395,371 (-)NCBIGRCr8
mRatBN7.2X97,092,394 - 97,099,659 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX97,092,388 - 97,099,309 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX98,766,541 - 98,773,427 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X102,276,323 - 102,283,209 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X99,779,719 - 99,786,605 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X104,719,930 - 104,729,606 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX104,719,940 - 104,726,816 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X104,555,374 - 104,562,260 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X121,432,320 - 121,439,205 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX98,140,232 - 98,147,118 (-)NCBICelera
Cytogenetic MapXq32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)

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 (-)NCBIGRCr8
mRatBN7.2X97,092,394 - 97,099,659 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX97,092,388 - 97,099,309 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX98,766,541 - 98,773,427 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X102,276,323 - 102,283,209 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X99,779,719 - 99,786,605 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X104,719,930 - 104,729,606 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX104,719,940 - 104,726,816 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X104,555,374 - 104,562,260 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X121,432,320 - 121,439,205 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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 (-)EnsemblGRCh38hg38GRCh38
GRCh37X99,882,105 - 99,892,101 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X99,770,451 - 99,778,450 (-)NCBINCBI36Build 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 Ensembl
GRCm38X133,891,068 - 133,901,208 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX133,891,068 - 133,898,429 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X130,425,609 - 130,432,968 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0X75,909,342 - 75,919,721 (-)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249021,977,700 - 1,985,004 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tspan6
12 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
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
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
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

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
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
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 46 38 11 38 3 3 74 35 41 11 3
Low 9 11 3 8 3 5 8 5
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000005165   ⟹   ENSRNOP00000005165
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX97,092,388 - 97,099,277 (-)Ensembl
Rnor_6.0 EnsemblX104,719,940 - 104,726,816 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000119163   ⟹   ENSRNOP00000088359
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
RefSeq Acc Id: ENSRNOP00000005165   ⟸   ENSRNOT00000005165
RefSeq Acc Id: ENSRNOP00000088359   ⟸   ENSRNOT00000119163
RefSeq Acc Id: XP_063135958   ⟸   XM_063279888
- Peptide Label: isoform X1

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 ENSRNOT00000005165.7 UniProtKB/TrEMBL
  ENSRNOT00000119163 ENTREZGENE
  ENSRNOT00000119163.1 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