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

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Smchd1 (structural maintenance of chromosomes flexible hinge domain containing 1) Ictidomys tridecemlineatus
Analyze
Symbol: Smchd1
Name: structural maintenance of chromosomes flexible hinge domain containing 1
RGD ID: 12503582
Description: ENCODES a protein that exhibits ATP binding (inferred); ATP hydrolysis activity (inferred); protein homodimerization activity (inferred); INVOLVED IN inactivation of paternal X chromosome by genomic imprinting (ortholog); ASSOCIATED WITH Anosmia (ortholog); Arhinia, Choanal Atresia, and Microphthalmia (ortholog); chromosome 18p deletion syndrome (ortholog); FOUND IN Barr body (inferred); chromosome (inferred); chromosome, telomeric region (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: structural maintenance of chromosomes flexible hinge domain containing 1, transcript variant X1; structural maintenance of chromosomes flexible hinge domain containing 1, transcript variant X2; structural maintenance of chromosomes flexible hinge domain-containing protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
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 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366721,686,070 - 1,838,315 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366721,686,070 - 1,838,315 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
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 (+)EnsemblGRCh38hg38GRCh38
GRCh37182,655,725 - 2,805,015 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36182,645,886 - 2,795,015 (+)NCBINCBI36Build 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 Ensembl
GRCm381771,344,489 - 71,475,366 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1771,344,489 - 71,475,343 (-)EnsemblGRCm38mm10GRCm38
MGSCv371771,693,829 - 71,824,683 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361771,249,789 - 71,332,381 (-)NCBIMGSCv36mm8
Celera1775,615,403 - 75,745,635 (-)NCBICelera
Cytogenetic Map17E1.3NCBI
cM Map1741.87NCBI
Smchd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89118,690,050 - 118,837,281 (-)NCBIGRCr8
mRatBN7.29111,243,445 - 111,387,272 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9111,247,702 - 111,349,665 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.09119,675,750 - 119,818,620 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9119,676,628 - 119,818,310 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09119,128,945 - 119,272,041 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49110,535,987 - 110,680,034 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.19110,753,793 - 110,888,830 (-)NCBI
Celera9108,371,971 - 108,513,633 (-)NCBICelera
Cytogenetic Map9q38NCBI
Smchd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554027,544,265 - 7,649,067 (-)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha768,814,232 - 68,960,329 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0769,420,889 - 69,567,321 (+)NCBIROS_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_1.0
SMCHD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6103,808,066 - 103,965,335 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477013,000,532 - 13,123,346 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


RefSeq Acc Id: ENSSTOT00000028911   ⟹   ENSSTOP00000020707
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049366721,685,734 - 1,838,315 (-)Ensembl
RefSeq Acc Id: XM_005337120   ⟹   XP_005337177
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494465,703,624 - 65,855,869 (+)NCBI
SpeTri2.0NW_0049366721,686,070 - 1,838,315 (-)NCBI
Sequence:
RefSeq Acc Id: XR_005729148
Type: NON-CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494465,703,624 - 65,847,939 (+)NCBI
Protein Sequences
Protein RefSeqs XP_005337177 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000020707.2
GenBank Protein KAG3294137 (Get FASTA)   NCBI Sequence Viewer  
  KAG3294138 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_005337177   ⟸   XM_005337120
- UniProtKB: I3N8L1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSTOP00000020707   ⟸   ENSSTOT00000028911
Protein Domains
SMC hinge


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000022898 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000028911.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1060.20 UniProtKB/TrEMBL
  3.30.565.10 UniProtKB/TrEMBL
  3.30.70.1620 UniProtKB/TrEMBL
InterPro HATPase_C_sf UniProtKB/TrEMBL
  SMC_hinge UniProtKB/TrEMBL
  SMC_hinge_sf UniProtKB/TrEMBL
  SMCHD1 UniProtKB/TrEMBL
NCBI Gene Smchd1 ENTREZGENE
PANTHER PTHR22640 UniProtKB/TrEMBL
  STRUCTURAL MAINTENANCE OF CHROMOSOMES FLEXIBLE HINGE DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
Pfam HATPase_c_3 UniProtKB/TrEMBL
  SMC_hinge UniProtKB/TrEMBL
SMART SMC_hinge UniProtKB/TrEMBL
Superfamily-SCOP SSF55874 UniProtKB/TrEMBL
  SSF75553 UniProtKB/TrEMBL
UniProt I3N8L1 ENTREZGENE, UniProtKB/TrEMBL