Smco1 (single-pass membrane protein with coiled-coil domains 1) - Rat Genome Database

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Gene: Smco1 (single-pass membrane protein with coiled-coil domains 1) Rattus norvegicus
Analyze
Symbol: Smco1
Name: single-pass membrane protein with coiled-coil domains 1
RGD ID: 1562500
Description: Orthologous to human SMCO1 (single-pass membrane protein with coiled-coil domains 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; alpha-Zearalanol; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC498096; LOC100911042; LOC498096; RGD1562500; similar to RIKEN cDNA 2310010M20; single-pass membrane and coiled-coil domain-containing protein 1; uncharacterized LOC100911042; uncharacterized protein LOC498096
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
GRCr81182,017,142 - 82,020,025 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1182,014,179 - 82,020,030 (-)EnsemblGRCr8
mRatBN7.21168,512,113 - 68,514,999 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1168,509,150 - 68,515,003 (-)EnsemblmRatBN7.2
Rnor_6.01171,747,457 - 71,750,147 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1171,754,902 - 71,757,801 (-)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl1171,747,565 - 71,750,014 (-)Ensemblrn6Rnor6.0
Rnor_5.01174,831,591 - 74,834,240 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41170,328,102 - 70,334,603 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1167,944,347 - 67,947,037 (-)NCBICelera
Cytogenetic Map11q22NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:28932249  


Genomics

Comparative Map Data
Smco1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81182,017,142 - 82,020,025 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1182,014,179 - 82,020,030 (-)EnsemblGRCr8
mRatBN7.21168,512,113 - 68,514,999 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1168,509,150 - 68,515,003 (-)EnsemblmRatBN7.2
Rnor_6.01171,747,457 - 71,750,147 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1171,754,902 - 71,757,801 (-)Ensemblrn6Rnor6.0
Rnor_6.0 Ensembl1171,747,565 - 71,750,014 (-)Ensemblrn6Rnor6.0
Rnor_5.01174,831,591 - 74,834,240 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41170,328,102 - 70,334,603 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1167,944,347 - 67,947,037 (-)NCBICelera
Cytogenetic Map11q22NCBI
SMCO1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383196,506,879 - 196,520,955 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3196,506,878 - 196,515,347 (-)Ensemblhg38GRCh38
GRCh373196,233,750 - 196,242,217 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363197,718,147 - 197,726,634 (-)NCBIBuild 36Build 36hg18NCBI36
Celera3194,816,034 - 194,824,582 (-)NCBICelera
Cytogenetic Map3q29NCBI
HuRef3193,530,708 - 193,539,748 (-)NCBIHuRef
CHM1_13196,205,174 - 196,213,588 (-)NCBICHM1_1
T2T-CHM13v2.03199,226,058 - 199,240,237 (-)NCBIT2T-CHM13v2.0
Smco1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391632,090,298 - 32,093,599 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1632,090,286 - 32,093,599 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381632,271,480 - 32,274,781 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1632,271,468 - 32,274,781 (+)Ensemblmm10GRCm38
MGSCv371632,271,695 - 32,274,865 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361632,191,215 - 32,194,526 (+)NCBIMGSCv36mm8
Celera1632,756,590 - 32,759,764 (+)NCBICelera
Cytogenetic Map16B2NCBI
cM Map1622.5NCBI
Smco1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542012,678,932 - 12,685,025 (-)Ensembl
ChiLan1.0NW_00495542012,680,494 - 12,685,018 (-)NCBIChiLan1.0ChiLan1.0
SMCO1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22194,377,612 - 194,391,599 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13194,382,330 - 194,396,318 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03193,851,672 - 193,882,810 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13203,794,369 - 203,804,106 (-)NCBIPanPan1.1PanPan1.1panPan2
SMCO1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13329,579,230 - 29,584,715 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3329,579,696 - 29,584,639 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3329,603,420 - 29,608,888 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03329,821,919 - 29,827,598 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3329,822,291 - 29,827,559 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13329,600,572 - 29,606,248 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03329,655,479 - 29,660,950 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03330,277,818 - 30,283,293 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Smco1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602124,782,057 - 124,784,728 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367841,100,495 - 1,105,058 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049367841,100,262 - 1,105,078 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMCO1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13133,615,398 - 133,621,074 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.113133,615,397 - 133,621,081 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SMCO1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11590,691,449 - 90,698,287 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1590,691,897 - 90,698,317 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604164,490,921 - 64,497,354 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smco1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473061,632,737 - 61,635,812 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473061,632,664 - 61,636,014 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Smco1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1417,090,752 - 17,093,358 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Smco1
15 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)112252474682951192Rat
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)117330848796070872Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)114644316891443168Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)115892833699753367Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)113294306789836615Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)117961851999753367Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)117385089499753367Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)115893182292356038Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)115441539196071021Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)115775483796071021Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112019354996351019Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)116796218499753367Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)117330831599753367Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)116859932196497754Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)116985594399753367Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)115107102196071021Rat


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
11 11 67 77 67 63 22 32 22 12 196 140 9 39 15 42 41 1 1

Sequence


Ensembl Acc Id: ENSRNOT00000029572   ⟹   ENSRNOP00000029459
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1182,014,179 - 82,020,030 (-)Ensembl
mRatBN7.2 Ensembl1168,509,150 - 68,515,003 (-)Ensembl
Rnor_6.0 Ensembl1171,754,902 - 71,757,801 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000072227   ⟹   ENSRNOP00000064951
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1171,747,565 - 71,750,014 (-)Ensembl
RefSeq Acc Id: XM_006248472   ⟹   XP_006248534
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81182,017,142 - 82,020,025 (-)NCBI
mRatBN7.21168,512,113 - 68,514,999 (-)NCBI
Rnor_6.01171,747,457 - 71,750,147 (-)NCBI
Rnor_5.01174,831,591 - 74,834,240 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001417732 (Get FASTA)   NCBI Sequence Viewer  
  NP_001417733 (Get FASTA)   NCBI Sequence Viewer  
  NP_001417734 (Get FASTA)   NCBI Sequence Viewer  
  XP_006248534 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM11429 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000029459
  ENSRNOP00000029459.5
RefSeq Acc Id: XP_006248534   ⟸   XM_006248472
- Sequence:
Ensembl Acc Id: ENSRNOP00000064951   ⟸   ENSRNOT00000072227
Ensembl Acc Id: ENSRNOP00000029459   ⟸   ENSRNOT00000029572

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LVE5-F1-model_v2 AlphaFold F1LVE5 1-214 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562500 AgrOrtholog
BioCyc Gene G2FUF-21089 BioCyc
Ensembl Genes ENSRNOG00000024960 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000048188 Ensembl
Ensembl Transcript ENSRNOT00000029572 ENTREZGENE
  ENSRNOT00000029572.8 UniProtKB/TrEMBL
InterPro DUF4547 UniProtKB/TrEMBL
KEGG Report rno:498096 UniProtKB/TrEMBL
NCBI Gene 498096 ENTREZGENE
PANTHER PTHR35979 UniProtKB/TrEMBL
  SINGLE-PASS MEMBRANE AND COILED-COIL DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
Pfam DUF4547 UniProtKB/TrEMBL
PhenoGen Smco1 PhenoGen
RatGTEx ENSRNOG00000024960 RatGTEx
  ENSRNOG00000048188 RatGTEx
UniProt A6IRS6 ENTREZGENE, UniProtKB/TrEMBL
  F1LVE5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Smco1  single-pass membrane protein with coiled-coil domains 1  LOC100911042  uncharacterized LOC100911042  Data merged from RGD:6495363 737654 PROVISIONAL
2013-04-01 Smco1  single-pass membrane protein with coiled-coil domains 1  RGD1562500  similar to RIKEN cDNA 2310010M20  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100911042  uncharacterized LOC100911042      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 RGD1562500  similar to RIKEN cDNA 2310010M20   RGD1562500_predicted  similar to RIKEN cDNA 2310010M20 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1562500_predicted  similar to RIKEN cDNA 2310010M20 (predicted)  LOC498096  similar to RIKEN cDNA 2310010M20  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC498096  similar to RIKEN cDNA 2310010M20      Symbol and Name status set to provisional 70820 PROVISIONAL