Smchd1 (structural maintenance of chromosomes flexible hinge domain containing 1) - Rat Genome Database

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Pathways
Gene: Smchd1 (structural maintenance of chromosomes flexible hinge domain containing 1) Rattus norvegicus
Analyze
Symbol: Smchd1
Name: structural maintenance of chromosomes flexible hinge domain containing 1
RGD ID: 1307234
Description: Predicted to enable ATP hydrolysis activity and protein homodimerization activity. Predicted to be involved in dosage compensation by inactivation of X chromosome; nose development; and regulation of double-strand break repair. Predicted to act upstream of or within autosome genomic imprinting; inactivation of paternal X chromosome by genomic imprinting; and random inactivation of X chromosome. Predicted to be located in chromosome, telomeric region; nuclear body; and site of double-strand break. Predicted to be active in Barr body. Human ortholog(s) of this gene implicated in facioscapulohumeral muscular dystrophy 2. Orthologous to human SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC316732; RGD1307234; similar to RIKEN cDNA 4931400A14; structural maintenance of chromosomes flexible hinge domain-containing protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89118,690,050 - 118,837,281 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl9118,690,057 - 118,833,452 (-)EnsemblGRCr8
mRatBN7.29111,243,445 - 111,387,272 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9111,247,702 - 111,349,665 (-)EnsemblmRatBN7.2
Rnor_6.09119,675,750 - 119,818,620 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9119,676,628 - 119,818,310 (-)Ensemblrn6Rnor6.0
Rnor_5.09119,128,945 - 119,272,041 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.49110,535,987 - 110,680,034 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera9108,371,971 - 108,513,633 (-)NCBICelera
RGSC_v3.19110,753,793 - 110,888,830 (-)NCBI
Cytogenetic Map9q38NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene  (ISO)
1,2-dimethylhydrazine  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,4'-trichlorobiphenyl  (ISO)
2,4,6-tribromophenol  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
5-fluorouracil  (ISO)
acrolein  (ISO)
acrylamide  (EXP)
aflatoxin M1  (ISO)
alpha-pinene  (ISO)
aristolochic acid A  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Brodifacoum  (EXP)
butanal  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chloroprene  (EXP)
cisplatin  (ISO)
clorgyline  (ISO)
cypermethrin  (ISO)
decabromodiphenyl ether  (ISO)
deoxynivalenol  (ISO)
diarsenic trioxide  (ISO)
Dibutyl phosphate  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
elemental selenium  (ISO)
enzyme inhibitor  (ISO)
epoxiconazole  (ISO)
FR900359  (ISO)
geldanamycin  (ISO)
gentamycin  (EXP)
irinotecan  (ISO)
ivermectin  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
methylparaben  (ISO)
miconazole  (ISO)
nickel atom  (ISO)
nitrates  (ISO)
Nivalenol  (ISO)
okadaic acid  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
PCB138  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
thiram  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
tungsten  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:18425126   PMID:22082260   PMID:23542155   PMID:23754746   PMID:24270157   PMID:24790221   PMID:25294876   PMID:26391951   PMID:27059856   PMID:28067909   PMID:28067911  


Genomics

Comparative Map Data
Smchd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89118,690,050 - 118,837,281 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl9118,690,057 - 118,833,452 (-)EnsemblGRCr8
mRatBN7.29111,243,445 - 111,387,272 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9111,247,702 - 111,349,665 (-)EnsemblmRatBN7.2
Rnor_6.09119,675,750 - 119,818,620 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9119,676,628 - 119,818,310 (-)Ensemblrn6Rnor6.0
Rnor_5.09119,128,945 - 119,272,041 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.49110,535,987 - 110,680,034 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera9108,371,971 - 108,513,633 (-)NCBICelera
RGSC_v3.19110,753,793 - 110,888,830 (-)NCBI
Cytogenetic Map9q38NCBI
SMCHD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38182,655,726 - 2,805,017 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl182,655,726 - 2,805,017 (+)Ensemblhg38GRCh38
GRCh37182,655,725 - 2,805,015 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36182,645,886 - 2,795,015 (+)NCBIBuild 36Build 36hg18NCBI36
Celera182,531,141 - 2,680,454 (+)NCBICelera
Cytogenetic Map18p11.32NCBI
HuRef182,617,276 - 2,766,445 (+)NCBIHuRef
CHM1_1182,655,260 - 2,804,386 (+)NCBICHM1_1
T2T-CHM13v2.0182,811,308 - 2,960,649 (+)NCBIT2T-CHM13v2.0
Smchd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391771,651,484 - 71,782,361 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1771,651,484 - 71,782,338 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381771,344,489 - 71,475,366 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1771,344,489 - 71,475,343 (-)Ensemblmm10GRCm38
MGSCv371771,693,829 - 71,824,683 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361771,249,789 - 71,332,381 (-)NCBIMGSCv36mm8
Celera1775,615,403 - 75,745,635 (-)NCBICelera
Cytogenetic Map17E1.3NCBI
cM Map1741.87NCBI
Smchd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554027,544,265 - 7,649,067 (-)Ensembl
ChiLan1.0NW_0049554027,544,265 - 7,661,191 (-)NCBIChiLan1.0ChiLan1.0
SMCHD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21735,641,467 - 35,790,813 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11821,334,059 - 21,483,403 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01811,479,742 - 11,627,035 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11813,785,912 - 13,933,889 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1813,785,912 - 13,933,887 (-)EnsemblpanPan2panpan1.1
SMCHD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1769,359,286 - 69,505,067 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl769,358,447 - 69,621,067 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha768,814,232 - 68,960,329 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0769,420,889 - 69,567,321 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl769,420,904 - 69,565,345 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1769,103,483 - 69,249,691 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0769,123,627 - 69,269,690 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0769,420,839 - 69,567,137 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Smchd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494465,703,624 - 65,855,869 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366721,685,734 - 1,838,315 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366721,686,070 - 1,838,315 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMCHD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6103,808,066 - 103,965,335 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.16103,809,732 - 103,986,057 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2696,820,958 - 96,945,192 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMCHD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11861,921,477 - 62,069,187 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1861,921,124 - 62,070,878 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605036,779,796 - 36,928,892 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smchd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477013,000,316 - 13,124,031 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462477013,000,532 - 13,123,346 (+)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Smchd1
953 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:501
Count of miRNA genes:233
Interacting mature miRNAs:279
Transcripts:ENSRNOT00000019359
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
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat

Markers in Region
D9Rat165  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr89118,778,655 - 118,778,872 (+)Marker Load Pipeline
mRatBN7.29111,332,055 - 111,332,272 (+)MAPPERmRatBN7.2
Rnor_6.09119,763,728 - 119,763,944NCBIRnor6.0
Rnor_5.09119,217,142 - 119,217,358UniSTSRnor5.0
RGSC_v3.49110,623,520 - 110,623,737RGDRGSC3.4
RGSC_v3.49110,623,521 - 110,623,737UniSTSRGSC3.4
Celera9108,458,734 - 108,458,950UniSTS
RGSC_v3.19110,833,000 - 110,833,217RGD
RH 3.4 Map9867.0UniSTS
RH 3.4 Map9867.0RGD
RH 2.0 Map91042.8RGD
SHRSP x BN Map979.4799RGD
Cytogenetic Map9q38UniSTS
BF388560  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr89118,802,600 - 118,802,852 (+)Marker Load Pipeline
mRatBN7.29111,355,981 - 111,356,234 (+)MAPPERmRatBN7.2
Rnor_6.09119,787,653 - 119,787,904NCBIRnor6.0
Rnor_5.09119,241,067 - 119,241,318UniSTSRnor5.0
RGSC_v3.49110,647,470 - 110,647,721UniSTSRGSC3.4
Celera9108,482,685 - 108,482,936UniSTS
RH 3.4 Map9854.3UniSTS
Cytogenetic Map9q38UniSTS
RH142613  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29111,293,477 - 111,293,646 (+)MAPPERmRatBN7.2
Rnor_6.09119,725,759 - 119,725,927NCBIRnor6.0
Rnor_5.09119,179,173 - 119,179,341UniSTSRnor5.0
RGSC_v3.49110,586,029 - 110,586,197UniSTSRGSC3.4
Celera9108,421,923 - 108,422,091UniSTS
RH 3.4 Map9867.0UniSTS
Cytogenetic Map9q38UniSTS
RH138283  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29111,385,799 - 111,385,977 (+)MAPPERmRatBN7.2
Rnor_6.09119,817,471 - 119,817,648NCBIRnor6.0
Rnor_5.09119,270,885 - 119,271,062UniSTSRnor5.0
RGSC_v3.49110,678,880 - 110,679,057UniSTSRGSC3.4
Celera9108,512,484 - 108,512,661UniSTS
RH 3.4 Map9868.6UniSTS
Cytogenetic Map9q38UniSTS
RH139954  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29111,243,577 - 111,243,758 (+)MAPPERmRatBN7.2
Rnor_6.09119,675,883 - 119,676,063NCBIRnor6.0
Rnor_5.09119,129,078 - 119,129,258UniSTSRnor5.0
RGSC_v3.49110,536,120 - 110,536,300UniSTSRGSC3.4
Celera9108,372,104 - 108,372,284UniSTS
RH 3.4 Map9869.3UniSTS
Cytogenetic Map9q38UniSTS


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: ENSRNOT00000019359   ⟹   ENSRNOP00000019359
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl9118,695,036 - 118,833,452 (-)Ensembl
mRatBN7.2 Ensembl9111,247,702 - 111,349,665 (-)Ensembl
Rnor_6.0 Ensembl9119,676,628 - 119,818,310 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000102031   ⟹   ENSRNOP00000083499
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl9118,690,057 - 118,833,452 (-)Ensembl
mRatBN7.2 Ensembl9111,247,702 - 111,268,703 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000103751   ⟹   ENSRNOP00000095761
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl9118,690,057 - 118,833,452 (-)Ensembl
mRatBN7.2 Ensembl9111,247,702 - 111,336,124 (-)Ensembl
RefSeq Acc Id: XM_063267939   ⟹   XP_063124009
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr89118,690,050 - 118,837,281 (-)NCBI
Protein Sequences
Protein RefSeqs XP_063124009 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000019359.7
  ENSRNOP00000083499
  ENSRNOP00000083499.1
  ENSRNOP00000095761.1
Ensembl Acc Id: ENSRNOP00000019359   ⟸   ENSRNOT00000019359
Ensembl Acc Id: ENSRNOP00000095761   ⟸   ENSRNOT00000103751
Ensembl Acc Id: ENSRNOP00000083499   ⟸   ENSRNOT00000102031
RefSeq Acc Id: XP_063124009   ⟸   XM_063267939
Protein Domains
SMC hinge

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AAG8-F1-model_v2 AlphaFold D4AAG8 1-2006 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:1307234 AgrOrtholog
BioCyc Gene G2FUF-26327 BioCyc
Ensembl Genes ENSRNOG00000014319 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019359.8 UniProtKB/TrEMBL
  ENSRNOT00000102031 ENTREZGENE
  ENSRNOT00000102031.1 UniProtKB/TrEMBL
  ENSRNOT00000103751.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1060.20 UniProtKB/TrEMBL
  3.30.70.1620 UniProtKB/TrEMBL
InterPro SMC_hinge UniProtKB/TrEMBL
  SMC_hinge_sf UniProtKB/TrEMBL
  SMCHD1 UniProtKB/TrEMBL
  SMCHD1_S5 UniProtKB/TrEMBL
NCBI Gene 316732 ENTREZGENE
PANTHER PTHR22640 UniProtKB/TrEMBL
  STRUCTURAL MAINTENANCE OF CHROMOSOMES FLEXIBLE HINGE DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
Pfam SMC_hinge UniProtKB/TrEMBL
  SMCHD1_S5 UniProtKB/TrEMBL
PharmGKB SMCHD1 RGD
PhenoGen Smchd1 PhenoGen
RatGTEx ENSRNOG00000014319 RatGTEx
SMART SMC_hinge UniProtKB/TrEMBL
Superfamily-SCOP SMC_hinge UniProtKB/TrEMBL
UniProt A0A8I6AM37_RAT UniProtKB/TrEMBL
  A0A8I6GAU4_RAT UniProtKB/TrEMBL
  D4AAG8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-03-09 Smchd1  structural maintenance of chromosomes flexible hinge domain containing 1  RGD1307234  similar to RIKEN cDNA 4931400A14   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1307234  similar to RIKEN cDNA 4931400A14   RGD1307234_predicted  similar to RIKEN cDNA 4931400A14 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1307234_predicted  similar to RIKEN cDNA 4931400A14 (predicted)  LOC316732_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC316732_predicted  similar to RIKEN cDNA 4931400A14 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL