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: VALIDATED
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
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8820,594,633 - 20,646,916 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl820,627,338 - 20,646,916 (+)EnsemblGRCr8
mRatBN7.2812,313,235 - 12,365,534 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl812,313,328 - 12,365,529 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx816,332,747 - 16,352,331 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0814,630,498 - 14,650,082 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0812,608,185 - 12,627,766 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0814,026,637 - 14,079,977 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl814,060,394 - 14,079,972 (+)Ensemblrn6Rnor6.0
Rnor_5.0814,139,544 - 14,159,122 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4812,328,341 - 12,347,919 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera813,812,588 - 13,832,166 (+)NCBICelera
RGSC_v3.1812,328,421 - 12,347,919 (+)NCBI
Cytogenetic Map8q12NCBI
JBrowse:




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 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl820,627,338 - 20,646,916 (+)EnsemblGRCr8
mRatBN7.2812,313,235 - 12,365,534 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl812,313,328 - 12,365,529 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx816,332,747 - 16,352,331 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0814,630,498 - 14,650,082 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0812,608,185 - 12,627,766 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0814,026,637 - 14,079,977 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl814,060,394 - 14,079,972 (+)Ensemblrn6Rnor6.0
Rnor_5.0814,139,544 - 14,159,122 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4812,328,341 - 12,347,919 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera813,812,588 - 13,832,166 (+)NCBICelera
RGSC_v3.1812,328,421 - 12,347,919 (+)NCBI
Cytogenetic Map8q12NCBI
SMCO4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381193,478,472 - 93,553,979 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1193,478,468 - 93,543,764 (-)Ensemblhg38GRCh38
GRCh371193,211,638 - 93,276,557 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361192,851,286 - 92,925,437 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm38915,468,440 - 15,545,260 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl915,493,432 - 15,545,260 (+)Ensemblmm10GRCm38
MGSCv37915,309,662 - 15,349,704 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (+)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha217,180,971 - 7,243,697 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0217,346,220 - 7,408,971 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (+)EnsemblSpeTri2.0 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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473538,133,940 - 38,202,222 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Smco4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1811,312,916 - 11,313,591 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Smco4
195 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
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)81799410550763951Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81699464261994642Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)81038254055382540Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)81296416557964165Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)81595227960952279Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)81296416557964165Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81799386262252873Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)81038254055382540Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8132882639Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)81038254055382540Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81699464261994642Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)81296416557964165Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)81038254055382540Rat

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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001134584 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001437145 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001437146 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001437147 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001437149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001437150 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001437151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595722 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595723 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081704 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081708 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063265724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC105648 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000014827   ⟹   ENSRNOP00000014827
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl820,627,338 - 20,646,916 (+)Ensembl
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
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
- 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, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014827.7 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 A6JND3_RAT UniProtKB/TrEMBL
  D4A7S6_RAT 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