Tm9sf1 (transmembrane 9 superfamily member 1) - Rat Genome Database

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Pathways
Gene: Tm9sf1 (transmembrane 9 superfamily member 1) Rattus norvegicus
Analyze
Symbol: Tm9sf1
Name: transmembrane 9 superfamily member 1
RGD ID: 1307085
Description: Predicted to be involved in protein localization to membrane. Predicted to be located in autophagosome membrane; cytoplasmic vesicle; and lysosomal membrane. Predicted to be active in membrane. Orthologous to human TM9SF1 (transmembrane 9 superfamily member 1); INTERACTS WITH 6-propyl-2-thiouracil; amitrole; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC361043
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
GRCr81533,097,541 - 33,108,106 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1533,097,552 - 33,105,290 (-)EnsemblGRCr8
mRatBN7.21529,127,585 - 29,135,334 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1529,127,584 - 29,135,349 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1530,973,298 - 30,981,027 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01532,120,498 - 32,128,248 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01530,362,840 - 30,370,591 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01534,314,645 - 34,322,172 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,314,656 - 34,322,115 (-)Ensemblrn6Rnor6.0
Rnor_5.01538,204,840 - 38,212,581 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41533,771,498 - 33,778,965 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1528,703,708 - 28,711,175 (-)NCBICelera
RGSC_v3.11533,787,200 - 33,794,665 (-)NCBI
Cytogenetic Map15p13NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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 GOA human gene data--August 2006 GOA data from the GO Consortium
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
Additional References at PubMed
PMID:12477932   PMID:15489334  


Genomics

Comparative Map Data
Tm9sf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81533,097,541 - 33,108,106 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1533,097,552 - 33,105,290 (-)EnsemblGRCr8
mRatBN7.21529,127,585 - 29,135,334 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1529,127,584 - 29,135,349 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1530,973,298 - 30,981,027 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01532,120,498 - 32,128,248 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01530,362,840 - 30,370,591 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01534,314,645 - 34,322,172 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1534,314,656 - 34,322,115 (-)Ensemblrn6Rnor6.0
Rnor_5.01538,204,840 - 38,212,581 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41533,771,498 - 33,778,965 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1528,703,708 - 28,711,175 (-)NCBICelera
RGSC_v3.11533,787,200 - 33,794,665 (-)NCBI
Cytogenetic Map15p13NCBI
TM9SF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381424,189,149 - 24,195,441 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1424,189,140 - 24,196,287 (-)Ensemblhg38GRCh38
GRCh371424,658,355 - 24,664,647 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361423,728,193 - 23,734,722 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341423,728,255 - 23,734,702NCBI
Celera144,522,825 - 4,529,352 (-)NCBICelera
Cytogenetic Map14q12NCBI
HuRef144,773,359 - 4,779,887 (-)NCBIHuRef
CHM1_11424,657,005 - 24,663,534 (-)NCBICHM1_1
T2T-CHM13v2.01418,387,459 - 18,393,751 (-)NCBIT2T-CHM13v2.0
Tm9sf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391455,873,422 - 55,881,263 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1455,873,422 - 55,881,263 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381455,635,965 - 55,643,806 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1455,635,965 - 55,643,806 (-)Ensemblmm10GRCm38
MGSCv371456,254,803 - 56,262,643 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361454,590,037 - 54,597,877 (-)NCBIMGSCv36mm8
Celera1453,441,039 - 53,448,879 (-)NCBICelera
Cytogenetic Map14C3NCBI
cM Map1428.19NCBI
Tm9sf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540936,208,797 - 36,214,830 (+)Ensembl
ChiLan1.0NW_00495540936,208,797 - 36,214,830 (+)NCBIChiLan1.0ChiLan1.0
TM9SF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21525,543,430 - 25,559,382 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11424,759,920 - 24,767,526 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0144,965,352 - 4,972,476 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11423,088,794 - 23,096,319 (-)NCBIPanPan1.1PanPan1.1panPan2
TM9SF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.184,180,496 - 4,186,249 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha84,102,184 - 4,108,022 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.084,291,288 - 4,297,130 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl84,292,350 - 4,310,761 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.183,981,679 - 3,987,520 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.084,043,510 - 4,049,351 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.084,305,816 - 4,311,657 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tm9sf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864036,029,087 - 36,035,171 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936722353,710 - 359,905 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936722352,918 - 359,905 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
IPO4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl775,100,273 - 75,110,446 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1775,103,971 - 75,110,027 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2780,375,458 - 80,381,325 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TM9SF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1241,174,808 - 1,181,558 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl241,174,551 - 1,180,864 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603612,857,515 - 12,864,489 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tm9sf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248208,343,776 - 8,352,095 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248208,345,959 - 8,352,280 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Tm9sf1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11269,363,244 - 69,370,756 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tm9sf1
19 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:241
Count of miRNA genes:149
Interacting mature miRNAs:166
Transcripts:ENSRNOT00000026734
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15231575947315759Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15139411584Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15144836456Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15231575953331089Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)153185580392671517Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152272835342072050Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152852773273527732Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1525285835104695021Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152233635152597086Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1525285835104695021Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151915576287086765Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15278592347785923Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151492659471614418Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152233635167336351Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1525285835104695021Rat

Markers in Region
RH129403  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21529,127,699 - 29,127,866 (+)MAPPERmRatBN7.2
Rnor_6.01534,314,760 - 34,314,926NCBIRnor6.0
Rnor_5.01538,204,955 - 38,205,121UniSTSRnor5.0
RGSC_v3.41533,771,610 - 33,771,776UniSTSRGSC3.4
Celera1528,703,820 - 28,703,986UniSTS
Cytogenetic Map15p13UniSTS


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 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000026734   ⟹   ENSRNOP00000026734
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1533,097,552 - 33,105,067 (-)Ensembl
mRatBN7.2 Ensembl1529,127,596 - 29,135,055 (-)Ensembl
Rnor_6.0 Ensembl1534,314,656 - 34,322,115 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000100213   ⟹   ENSRNOP00000080843
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1533,097,552 - 33,105,290 (-)Ensembl
mRatBN7.2 Ensembl1529,127,584 - 29,135,349 (-)Ensembl
RefSeq Acc Id: NM_001012155   ⟹   NP_001012155
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81533,097,541 - 33,105,067 (-)NCBI
mRatBN7.21529,127,585 - 29,135,111 (-)NCBI
Rnor_6.01534,314,648 - 34,322,115 (-)NCBI
Rnor_5.01538,204,840 - 38,212,581 (-)NCBI
RGSC_v3.41533,771,498 - 33,778,965 (-)RGD
Celera1528,703,708 - 28,711,175 (-)RGD
Sequence:
RefSeq Acc Id: NM_001399704   ⟹   NP_001386633
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81533,097,541 - 33,105,290 (-)NCBI
mRatBN7.21529,127,585 - 29,135,334 (-)NCBI
RefSeq Acc Id: NM_001399705   ⟹   NP_001386634
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81533,097,541 - 33,105,067 (-)NCBI
mRatBN7.21529,127,585 - 29,135,111 (-)NCBI
RefSeq Acc Id: NM_001399706   ⟹   NP_001386635
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81533,097,541 - 33,105,067 (-)NCBI
mRatBN7.21529,127,585 - 29,135,111 (-)NCBI
RefSeq Acc Id: XM_063274408   ⟹   XP_063130478
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81533,097,541 - 33,108,106 (-)NCBI
RefSeq Acc Id: XM_063274409   ⟹   XP_063130479
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81533,099,354 - 33,105,042 (-)NCBI
RefSeq Acc Id: NP_001012155   ⟸   NM_001012155
- Peptide Label: isoform 2 precursor
- UniProtKB: Q66HF2 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000026734   ⟸   ENSRNOT00000026734
Ensembl Acc Id: ENSRNOP00000080843   ⟸   ENSRNOT00000100213
RefSeq Acc Id: NP_001386633   ⟸   NM_001399704
- Peptide Label: isoform 1 precursor
- UniProtKB: A0A8I5ZRM6 (UniProtKB/TrEMBL),   A6KH26 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001386634   ⟸   NM_001399705
- Peptide Label: isoform 1 precursor
- UniProtKB: A0A8I5ZRM6 (UniProtKB/TrEMBL),   A6KH26 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001386635   ⟸   NM_001399706
- Peptide Label: isoform 1 precursor
- UniProtKB: A0A8I5ZRM6 (UniProtKB/TrEMBL),   A6KH26 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063130478   ⟸   XM_063274408
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZRM6 (UniProtKB/TrEMBL),   A6KH26 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063130479   ⟸   XM_063274409
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q66HF2-F1-model_v2 AlphaFold Q66HF2 1-589 view protein structure

Transcriptome

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

Promoters
RGD ID:13699678
Promoter ID:EPDNEW_R10201
Type:initiation region
Name:Tm9sf1_1
Description:transmembrane 9 superfamily member 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_6.01534,322,137 - 34,322,197EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307085 AgrOrtholog
BioCyc Gene G2FUF-13702 BioCyc
Ensembl Genes ENSRNOG00000019710 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000026734 ENTREZGENE
  ENSRNOT00000026734.7 UniProtKB/Swiss-Prot
  ENSRNOT00000100213 ENTREZGENE
IMAGE_CLONE IMAGE:7109579 IMAGE-MGC_LOAD
InterPro EMP70 UniProtKB/Swiss-Prot
KEGG Report rno:361043 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93788 IMAGE-MGC_LOAD
NCBI Gene 361043 ENTREZGENE
PANTHER PTHR10766 UniProtKB/Swiss-Prot
  TRANSMEMBRANE 9 SUPERFAMILY MEMBER 1 UniProtKB/Swiss-Prot
Pfam EMP70 UniProtKB/Swiss-Prot
PhenoGen Tm9sf1 PhenoGen
RatGTEx ENSRNOG00000019710 RatGTEx
UniProt A0A8I5ZRM6 ENTREZGENE, UniProtKB/TrEMBL
  A6KH26 ENTREZGENE, UniProtKB/TrEMBL
  Q66HF2 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Tm9sf1  transmembrane 9 superfamily member 1  Tm9sf1_predicted  transmembrane 9 superfamily member 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tm9sf1_predicted  transmembrane 9 superfamily member 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED