Smco4 (single-pass membrane protein with coiled-coil domains 4) - Rat Genome Database

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Gene: Smco4 (single-pass membrane protein with coiled-coil domains 4) Rattus norvegicus
Analyze
Symbol: Smco4
Name: single-pass membrane protein with coiled-coil domains 4
RGD ID: 1309410
Description: Predicted to be located in membrane. Orthologous to human SMCO4 (single-pass membrane protein with coiled-coil domains 4); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hypothetical protein LOC363020; LOC363020; RGD1309410; single-pass membrane and coiled-coil domain-containing protein 4; uncharacterized protein LOC363020
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
GRCr8820,594,633 - 20,646,916 (+)NCBIGRCr8
mRatBN7.2812,313,235 - 12,365,534 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl812,313,328 - 12,365,529 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx816,332,747 - 16,352,331 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0814,630,498 - 14,650,082 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0812,608,185 - 12,627,766 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0814,026,637 - 14,079,977 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl814,060,394 - 14,079,972 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0814,139,544 - 14,159,122 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4812,328,341 - 12,347,919 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1812,328,421 - 12,347,919 (+)NCBI
Celera813,812,588 - 13,832,166 (+)NCBICelera
Cytogenetic Map8q12NCBI
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
membrane  (IEA)

Molecular Function

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
Smco4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8820,594,633 - 20,646,916 (+)NCBIGRCr8
mRatBN7.2812,313,235 - 12,365,534 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl812,313,328 - 12,365,529 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx816,332,747 - 16,352,331 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0814,630,498 - 14,650,082 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0812,608,185 - 12,627,766 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0814,026,637 - 14,079,977 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl814,060,394 - 14,079,972 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0814,139,544 - 14,159,122 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4812,328,341 - 12,347,919 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1812,328,421 - 12,347,919 (+)NCBI
Celera813,812,588 - 13,832,166 (+)NCBICelera
Cytogenetic Map8q12NCBI
SMCO4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381193,478,472 - 93,553,979 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1193,478,472 - 93,543,391 (-)EnsemblGRCh38hg38GRCh38
GRCh371193,211,638 - 93,276,557 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361192,851,286 - 92,925,437 (-)NCBINCBI36Build 36hg18NCBI36
Celera1190,503,166 - 90,568,014 (-)NCBICelera
Cytogenetic Map11q21NCBI
HuRef1189,289,224 - 89,353,972 (-)NCBIHuRef
CHM1_11193,094,639 - 93,159,538 (-)NCBICHM1_1
T2T-CHM13v2.01193,394,933 - 93,470,364 (-)NCBIT2T-CHM13v2.0
Smco4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39915,379,736 - 15,456,556 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl915,404,728 - 15,456,556 (+)EnsemblGRCm39 Ensembl
GRCm38915,468,440 - 15,545,260 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl915,493,432 - 15,545,260 (+)EnsemblGRCm38mm10GRCm38
MGSCv37915,309,662 - 15,349,704 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36915,255,611 - 15,295,653 (+)NCBIMGSCv36mm8
Celera912,784,367 - 12,824,350 (+)NCBICelera
Cytogenetic Map9A2NCBI
cM Map94.95NCBI
Smco4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955414976,105 - 1,029,825 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955414976,105 - 1,029,825 (+)NCBIChiLan1.0ChiLan1.0
SMCO4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2994,102,049 - 94,402,660 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11195,431,294 - 95,496,498 (-)NCBINHGRI_mPanPan1
PanPan1.1 Ensembl1191,987,559 - 91,987,738 (-)Ensemblpanpan1.1panPan2
SMCO4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1217,168,999 - 7,228,974 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl217,228,279 - 7,228,458 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha217,180,971 - 7,243,697 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0217,346,220 - 7,408,971 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1217,132,399 - 7,195,142 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0217,196,729 - 7,259,448 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0217,245,950 - 7,308,694 (+)NCBIUU_Cfam_GSD_1.0
Smco4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494778,599,527 - 78,667,297 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366741,291,227 - 1,291,406 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SMCO4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11661,756,420 - 61,757,094 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607732,518,331 - 32,518,798 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smco4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473538,134,480 - 38,134,659 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473538,133,940 - 38,202,222 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Smco4
333 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:246
Count of miRNA genes:158
Interacting mature miRNAs:174
Transcripts:ENSRNOT00000014827
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
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat

Markers in Region
RH140198  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2812,365,264 - 12,365,481 (+)MAPPERmRatBN7.2
Rnor_6.0814,079,708 - 14,079,924NCBIRnor6.0
Rnor_5.0814,158,858 - 14,159,074UniSTSRnor5.0
RGSC_v3.4812,347,655 - 12,347,871UniSTSRGSC3.4
Celera813,831,902 - 13,832,118UniSTS
RH 3.4 Map8113.4UniSTS
Cytogenetic Map8q12UniSTS


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: ENSRNOT00000014827   ⟹   ENSRNOP00000014827
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl812,345,951 - 12,365,529 (+)Ensembl
Rnor_6.0 Ensembl814,060,394 - 14,079,972 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000111313   ⟹   ENSRNOP00000087984
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl812,313,328 - 12,365,529 (+)Ensembl
RefSeq Acc Id: NM_001134584   ⟹   NP_001128056
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8820,627,338 - 20,646,916 (+)NCBI
mRatBN7.2812,345,951 - 12,365,529 (+)NCBI
Rnor_6.0814,060,394 - 14,079,972 (+)NCBI
Rnor_5.0814,139,544 - 14,159,122 (+)NCBI
RGSC_v3.4812,328,341 - 12,347,919 (+)RGD
Celera813,812,588 - 13,832,166 (+)RGD
Sequence:
RefSeq Acc Id: XM_017595724   ⟹   XP_017451213
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8820,594,633 - 20,646,916 (+)NCBI
mRatBN7.2812,313,235 - 12,365,534 (+)NCBI
Rnor_6.0814,027,912 - 14,079,977 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039081704   ⟹   XP_038937632
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8820,640,968 - 20,646,916 (+)NCBI
mRatBN7.2812,359,100 - 12,365,534 (+)NCBI
RefSeq Acc Id: XM_039081705   ⟹   XP_038937633
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8820,595,123 - 20,646,916 (+)NCBI
mRatBN7.2812,313,746 - 12,365,534 (+)NCBI
RefSeq Acc Id: XM_039081707   ⟹   XP_038937635
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8820,638,702 - 20,646,916 (+)NCBI
mRatBN7.2812,357,313 - 12,365,534 (+)NCBI
RefSeq Acc Id: XM_039081708   ⟹   XP_038937636
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8820,601,012 - 20,646,916 (+)NCBI
mRatBN7.2812,319,849 - 12,365,534 (+)NCBI
RefSeq Acc Id: XM_063265724   ⟹   XP_063121794
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8820,594,687 - 20,646,916 (+)NCBI
RefSeq Acc Id: NP_001128056   ⟸   NM_001134584
- UniProtKB: D4A7S6 (UniProtKB/TrEMBL),   A6JND3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451213   ⟸   XM_017595724
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000014827   ⟸   ENSRNOT00000014827
RefSeq Acc Id: XP_038937633   ⟸   XM_039081705
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038937636   ⟸   XM_039081708
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038937635   ⟸   XM_039081707
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038937632   ⟸   XM_039081704
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000087984   ⟸   ENSRNOT00000111313
RefSeq Acc Id: XP_063121794   ⟸   XM_063265724
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A7S6-F1-model_v2 AlphaFold D4A7S6 1-143 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:1309410 AgrOrtholog
BioCyc Gene G2FUF-31630 BioCyc
Ensembl Genes ENSRNOG00000011162 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014827.6 UniProtKB/TrEMBL
  ENSRNOT00000111313.1 UniProtKB/TrEMBL
InterPro DUF4519 UniProtKB/TrEMBL
KEGG Report rno:363020 UniProtKB/TrEMBL
NCBI Gene 363020 ENTREZGENE
PANTHER PTHR34644 UniProtKB/TrEMBL
  SINGLE-PASS MEMBRANE AND COILED-COIL DOMAIN-CONTAINING PROTEIN 4 UniProtKB/TrEMBL
Pfam DUF4519 UniProtKB/TrEMBL
PhenoGen Smco4 PhenoGen
RatGTEx ENSRNOG00000011162 RatGTEx
UniProt A0A8I6GFP3_RAT UniProtKB/TrEMBL
  A6JND3 ENTREZGENE, UniProtKB/TrEMBL
  D4A7S6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-03-20 Smco4  single-pass membrane protein with coiled-coil domains 4  RGD1309410  LOC363020  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1309410  LOC363020   RGD1309410_predicted  LOC363020 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1309410_predicted  LOC363020 (predicted)  LOC363020_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC363020_predicted  LOC363020 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL