Smco2 (single-pass membrane protein with coiled-coil domains 2) - Rat Genome Database

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Gene: Smco2 (single-pass membrane protein with coiled-coil domains 2) Rattus norvegicus
Analyze
Symbol: Smco2
Name: single-pass membrane protein with coiled-coil domains 2
RGD ID: 2320294
Description: Predicted to be located in membrane. Orthologous to human SMCO2 (single-pass membrane protein with coiled-coil domains 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; paracetamol; trichloroethene.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: hypothetical LOC100361371; LOC100361371; single-pass membrane and coiled-coil domain-containing protein 2
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84181,491,290 - 181,521,746 (+)NCBIGRCr8
mRatBN7.24179,760,831 - 179,791,087 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4179,765,442 - 179,791,066 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.04181,240,710 - 181,268,691 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4181,243,338 - 181,268,634 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04245,393,044 - 245,418,899 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44184,438,784 - 184,472,620 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4168,259,406 - 168,284,515 (+)NCBICelera
Cytogenetic Map4q44NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Cellular Component
membrane  (IEA)

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Smco2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84181,491,290 - 181,521,746 (+)NCBIGRCr8
mRatBN7.24179,760,831 - 179,791,087 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4179,765,442 - 179,791,066 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.04181,240,710 - 181,268,691 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4181,243,338 - 181,268,634 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04245,393,044 - 245,418,899 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44184,438,784 - 184,472,620 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera4168,259,406 - 168,284,515 (+)NCBICelera
Cytogenetic Map4q44NCBI
SMCO2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381227,423,316 - 27,502,185 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1227,446,736 - 27,502,185 (+)EnsemblGRCh38hg38GRCh38
GRCh371227,599,669 - 27,655,118 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361227,514,689 - 27,546,385 (+)NCBINCBI36Build 36hg18NCBI36
Celera1232,765,333 - 32,800,716 (+)NCBICelera
Cytogenetic Map12p11.23NCBI
HuRef1227,388,846 - 27,423,993 (+)NCBIHuRef
CHM1_11227,584,772 - 27,620,150 (+)NCBICHM1_1
T2T-CHM13v2.01227,294,986 - 27,373,856 (+)NCBIT2T-CHM13v2.0
Smco2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396146,751,608 - 146,772,902 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6146,751,602 - 146,772,904 (+)EnsemblGRCm39 Ensembl
GRCm386146,850,110 - 146,871,404 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6146,850,104 - 146,871,406 (+)EnsemblGRCm38mm10GRCm38
MGSCv376146,798,632 - 146,819,926 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366146,807,280 - 146,828,571 (+)NCBIMGSCv36mm8
Celera6149,882,749 - 149,905,941 (+)NCBICelera
Cytogenetic Map6G3NCBI
cM Map677.7NCBI
SMCO2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21069,307,640 - 69,342,560 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11269,303,221 - 69,338,957 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01258,807,809 - 58,884,450 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11261,428,038 - 61,503,108 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1261,428,066 - 61,458,520 (-)Ensemblpanpan1.1panPan2
SMCO2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12720,204,272 - 20,248,509 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2720,221,608 - 20,248,482 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2726,152,066 - 26,196,042 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02720,398,159 - 20,442,365 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2720,412,477 - 20,442,338 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12720,221,901 - 20,248,692 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02720,232,225 - 20,276,326 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02726,308,970 - 26,353,236 (+)NCBIUU_Cfam_GSD_1.0
Smco2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494582,193,418 - 82,219,025 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004936548116,304 - 135,127 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMCO2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl546,244,212 - 46,279,120 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1546,244,220 - 46,274,049 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2549,802,521 - 49,837,433 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMCO2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11127,188,126 - 27,221,945 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1127,188,550 - 27,222,085 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660697,830,241 - 7,919,042 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Smco2
218 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:80
Count of miRNA genes:71
Interacting mature miRNAs:75
Transcripts:ENSRNOT00000034051
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
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (CMO:0000132)4135204660180204660Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)4135699135180699135Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4137755016181392681Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4144639524182687754Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4144639524182687754Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4144639524182687754Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4145568712182687754Rat
10053718Scort25Serum corticosterone level QTL 252.150.0097blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)4155561574182687754Rat
1300109Rf13Renal function QTL 133.91renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)4157710145182687754Rat


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

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 7
Low 17 1 1 7
Below cutoff 2 9 5 5 5 8 10 9 2 9 9 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000034051   ⟹   ENSRNOP00000031109
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4179,765,442 - 179,791,066 (+)Ensembl
Rnor_6.0 Ensembl4181,243,338 - 181,268,634 (+)Ensembl
RefSeq Acc Id: XM_039108891   ⟹   XP_038964819
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84181,496,911 - 181,521,746 (+)NCBI
mRatBN7.24179,766,262 - 179,791,085 (+)NCBI
RefSeq Acc Id: XM_039108893   ⟹   XP_038964821
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84181,491,290 - 181,521,746 (+)NCBI
mRatBN7.24179,760,831 - 179,791,086 (+)NCBI
RefSeq Acc Id: XM_039108894   ⟹   XP_038964822
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84181,496,911 - 181,520,299 (+)NCBI
mRatBN7.24179,766,262 - 179,787,016 (+)NCBI
RefSeq Acc Id: XM_039108895   ⟹   XP_038964823
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84181,499,506 - 181,521,746 (+)NCBI
mRatBN7.24179,768,832 - 179,791,087 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038964819 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964821 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964822 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964823 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000031109
  ENSRNOP00000031109.5
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000031109   ⟸   ENSRNOT00000034051
RefSeq Acc Id: XP_038964821   ⟸   XM_039108893
- Peptide Label: isoform X1
- UniProtKB: D3ZFT3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038964819   ⟸   XM_039108891
- Peptide Label: isoform X1
- UniProtKB: D3ZFT3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038964822   ⟸   XM_039108894
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038964823   ⟸   XM_039108895
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZFT3-F1-model_v2 AlphaFold D3ZFT3 1-350 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:2320294 AgrOrtholog
BioCyc Gene G2FUF-42423 BioCyc
Ensembl Genes ENSRNOG00000026883 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034051.5 UniProtKB/TrEMBL
InterPro SMCO2/5 UniProtKB/TrEMBL
NCBI Gene 100361371 ENTREZGENE
PANTHER PTHR22422 UniProtKB/TrEMBL
  SINGLE-PASS MEMBRANE AND COILED-COIL DOMAIN-CONTAINING PROTEIN 2 UniProtKB/TrEMBL
Pfam TMCO5 UniProtKB/TrEMBL
PhenoGen Smco2 PhenoGen
RatGTEx ENSRNOG00000026883 RatGTEx
UniProt D3ZFT3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-07-23 Smco2  single-pass membrane protein with coiled-coil domains 2  LOC100361371  hypothetical LOC100361371  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100361371  hypothetical LOC100361371      Symbol and Name status set to provisional 70820 PROVISIONAL