Tm9sf2 (transmembrane 9 superfamily member 2) - Rat Genome Database

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Gene: Tm9sf2 (transmembrane 9 superfamily member 2) Rattus norvegicus
Analyze
Symbol: Tm9sf2
Name: transmembrane 9 superfamily member 2
RGD ID: 1359230
Description: Predicted to be involved in protein localization to membrane; regulation of heparan sulfate proteoglycan biosynthetic process; and sphingolipid metabolic process. Predicted to be located in Golgi apparatus. Predicted to be active in membrane. Orthologous to human TM9SF2 (transmembrane 9 superfamily member 2); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC93724
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
GRCr815105,606,082 - 105,660,715 (+)NCBIGRCr8
mRatBN7.21599,201,556 - 99,254,054 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1599,201,489 - 99,254,049 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx15103,134,961 - 103,187,448 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.015104,227,449 - 104,279,876 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.015101,154,683 - 101,207,116 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.015108,526,341 - 108,579,268 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15108,526,014 - 108,579,256 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015111,911,685 - 111,967,206 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415107,228,796 - 107,281,296 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.115107,244,575 - 107,297,076 (+)NCBI
Celera1597,974,851 - 98,027,262 (+)NCBICelera
Cytogenetic Map15q25NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. A novel Rab9 effector required for endosome-to-TGN transport. Diaz E, etal., J Cell Biol 1997 Jul 28;138(2):283-90.
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
7. Classification of pediatric acute lymphoblastic leukemia by gene expression profiling. Ross ME, etal., Blood. 2003 Oct 15;102(8):2951-9. Epub 2003 May 1.
8. 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:15489334   PMID:19199708  


Genomics

Comparative Map Data
Tm9sf2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr815105,606,082 - 105,660,715 (+)NCBIGRCr8
mRatBN7.21599,201,556 - 99,254,054 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1599,201,489 - 99,254,049 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx15103,134,961 - 103,187,448 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.015104,227,449 - 104,279,876 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.015101,154,683 - 101,207,116 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.015108,526,341 - 108,579,268 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15108,526,014 - 108,579,256 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015111,911,685 - 111,967,206 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.415107,228,796 - 107,281,296 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.115107,244,575 - 107,297,076 (+)NCBI
Celera1597,974,851 - 98,027,262 (+)NCBICelera
Cytogenetic Map15q25NCBI
TM9SF2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381399,501,472 - 99,564,048 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1399,446,311 - 99,564,048 (+)EnsemblGRCh38hg38GRCh38
GRCh3713100,153,726 - 100,216,302 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361398,951,729 - 99,013,279 (+)NCBINCBI36Build 36hg18NCBI36
Build 341398,951,728 - 99,013,277NCBI
Celera1380,998,257 - 81,059,812 (+)NCBICelera
Cytogenetic Map13q32.3NCBI
HuRef1380,748,449 - 80,811,058 (+)NCBIHuRef
CHM1_113100,123,519 - 100,186,222 (+)NCBICHM1_1
T2T-CHM13v2.01398,712,365 - 98,774,941 (+)NCBIT2T-CHM13v2.0
Tm9sf2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914122,342,290 - 122,397,015 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14122,344,450 - 122,397,016 (+)EnsemblGRCm39 Ensembl
GRCm3814122,107,082 - 122,159,603 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14122,107,038 - 122,159,604 (+)EnsemblGRCm38mm10GRCm38
MGSCv3714122,506,304 - 122,558,825 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614121,242,262 - 121,294,783 (+)NCBIMGSCv36mm8
Celera14120,669,650 - 120,722,278 (+)NCBICelera
Cytogenetic Map14E5NCBI
cM Map1465.86NCBI
Tm9sf2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540411,069,843 - 11,129,056 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540411,071,716 - 11,128,758 (-)NCBIChiLan1.0ChiLan1.0
TM9SF2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v214101,025,667 - 101,088,026 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11399,695,871 - 99,758,225 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01380,669,277 - 80,731,340 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11399,806,942 - 99,869,456 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1399,807,555 - 99,869,456 (+)Ensemblpanpan1.1panPan2
TM9SF2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12249,515,350 - 49,578,519 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2249,515,382 - 49,577,905 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2249,296,268 - 49,359,483 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02249,957,024 - 50,020,235 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2249,957,036 - 50,020,235 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12249,607,692 - 49,671,749 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02249,642,267 - 49,704,740 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02249,678,708 - 49,741,653 (+)NCBIUU_Cfam_GSD_1.0
Tm9sf2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945184,945,849 - 185,005,895 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647210,945,906 - 11,006,324 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647210,946,263 - 11,006,311 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TM9SF2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1168,404,975 - 68,469,953 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11168,407,834 - 68,469,956 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21175,772,893 - 75,775,385 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TM9SF2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1378,143,850 - 78,217,461 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl378,144,078 - 78,216,828 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604634,638,569 - 34,713,435 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tm9sf2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479311,511,446 - 11,579,008 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462479311,515,047 - 11,644,073 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tm9sf2
284 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:214
Count of miRNA genes:149
Interacting mature miRNAs:167
Transcripts:ENSRNOT00000017211
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
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1567588667101769107Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1575788062101769107Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1568327165100062518Rat
1641889Colcr6Colorectal carcinoma resistance QTL 62.90.0126intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)157369051899794247Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1576306099101769107Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1575788062101769107Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1558156477101769107Rat

Markers in Region
RH142372  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21599,253,734 - 99,253,892 (+)MAPPERmRatBN7.2
Rnor_6.015108,578,949 - 108,579,106NCBIRnor6.0
Rnor_5.015111,966,887 - 111,967,044UniSTSRnor5.0
RGSC_v3.415107,280,977 - 107,281,134UniSTSRGSC3.4
Celera1598,026,943 - 98,027,100UniSTS
RH 3.4 Map15708.6UniSTS
Cytogenetic Map15q25UniSTS
BE120307  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21599,254,050 - 99,254,210 (+)MAPPERmRatBN7.2
Rnor_6.015108,579,265 - 108,579,424NCBIRnor6.0
Rnor_5.015111,967,203 - 111,967,362UniSTSRnor5.0
RGSC_v3.415107,281,293 - 107,281,452UniSTSRGSC3.4
Celera1598,027,259 - 98,027,418UniSTS
RH 3.4 Map15710.3UniSTS
Cytogenetic Map15q25UniSTS
RH124295  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21599,245,496 - 99,245,591 (+)MAPPERmRatBN7.2
Rnor_6.015108,570,368 - 108,570,462NCBIRnor6.0
Rnor_5.015111,958,306 - 111,958,400UniSTSRnor5.0
RGSC_v3.415107,272,740 - 107,272,834UniSTSRGSC3.4
Celera1598,018,706 - 98,018,800UniSTS
Cytogenetic Map15q25UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000017211   ⟹   ENSRNOP00000017211
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1599,201,496 - 99,254,049 (+)Ensembl
Rnor_6.0 Ensembl15108,526,014 - 108,579,256 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000113532   ⟹   ENSRNOP00000086158
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1599,201,489 - 99,254,049 (+)Ensembl
RefSeq Acc Id: NM_001005554   ⟹   NP_001005554
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815105,608,208 - 105,660,715 (+)NCBI
mRatBN7.21599,201,556 - 99,254,054 (+)NCBI
Rnor_6.015108,526,341 - 108,579,268 (+)NCBI
Rnor_5.015111,911,685 - 111,967,206 (+)NCBI
RGSC_v3.415107,228,796 - 107,281,296 (+)RGD
Celera1597,974,851 - 98,027,262 (+)RGD
Sequence:
RefSeq Acc Id: XM_063274359   ⟹   XP_063130429
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815105,606,082 - 105,660,714 (+)NCBI
RefSeq Acc Id: XM_063274360   ⟹   XP_063130430
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815105,606,104 - 105,660,714 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001005554 (Get FASTA)   NCBI Sequence Viewer  
  XP_063130429 (Get FASTA)   NCBI Sequence Viewer  
  XP_063130430 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH81873 (Get FASTA)   NCBI Sequence Viewer  
  EDM02575 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000017211.5
  ENSRNOP00000086158.1
  ENSRNOP00060011348
GenBank Protein Q66HG5 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001005554   ⟸   NM_001005554
- Peptide Label: precursor
- UniProtKB: Q66HG5 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000017211   ⟸   ENSRNOT00000017211
Ensembl Acc Id: ENSRNOP00000086158   ⟸   ENSRNOT00000113532
RefSeq Acc Id: XP_063130429   ⟸   XM_063274359
- Peptide Label: isoform X1
- UniProtKB: Q66HG5 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_063130430   ⟸   XM_063274360
- Peptide Label: isoform X1
- UniProtKB: Q66HG5 (UniProtKB/Swiss-Prot)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q66HG5-F1-model_v2 AlphaFold Q66HG5 1-663 view protein structure

Transcriptome

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

Promoters
RGD ID:13699882
Promoter ID:EPDNEW_R10406
Type:initiation region
Name:Tm9sf2_1
Description:transmembrane 9 superfamily member 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_6.015108,526,376 - 108,526,436EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359230 AgrOrtholog
BioCyc Gene G2FUF-12359 BioCyc
Ensembl Genes ENSRNOG00000012751 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00060008789 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000017211.7 UniProtKB/Swiss-Prot
  ENSRNOT00000113532.1 UniProtKB/TrEMBL
  ENSRNOT00060014695 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7107003 IMAGE-MGC_LOAD
InterPro EMP70 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:306197 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93724 IMAGE-MGC_LOAD
NCBI Gene 306197 ENTREZGENE
PANTHER PTHR10766 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSMEMBRANE 9 SUPERFAMILY MEMBER 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam EMP70 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB TM9SF2 RGD
PhenoGen Tm9sf2 PhenoGen
RatGTEx ENSRNOG00000012751 RatGTEx
  ENSRNOG00060008789 RatGTEx
UniProt A0A8I6A1N3_RAT UniProtKB/TrEMBL
  A6HUL2_RAT UniProtKB/TrEMBL
  Q66HG5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Tm9sf2  transmembrane 9 superfamily member 2      Symbol and Name status set to approved 1299863 APPROVED
2005-07-29 Tm9sf2  transmembrane 9 superfamily member 2      Symbol and Name status set to provisional 70820 PROVISIONAL