Smg6 (SMG6 nonsense mediated mRNA decay factor) - Rat Genome Database

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Gene: Smg6 (SMG6 nonsense mediated mRNA decay factor) Ictidomys tridecemlineatus
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Symbol: Smg6
Name: SMG6 nonsense mediated mRNA decay factor
RGD ID: 12693014
Description: ENCODES a protein that exhibits DNA polymerase binding (inferred); endonuclease activity (inferred); manganese ion binding (inferred); INVOLVED IN negative regulation of telomere capping (inferred); nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (inferred); regulation of telomere maintenance (inferred); ASSOCIATED WITH genetic disease (ortholog); Neurodevelopmental Disorders (ortholog); FOUND IN exon-exon junction complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: SMG6, nonsense mediated mRNA decay factor; SMG6, nonsense mediated mRNA decay factor, transcript variant X1; SMG6, nonsense mediated mRNA decay factor, transcript variant X2; SMG6, nonsense mediated mRNA decay factor, transcript variant X3; telomerase-binding protein EST1A
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_02440560245,248,360 - 45,483,960 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365388,126,291 - 8,361,920 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365388,126,307 - 8,361,920 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
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

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Smg6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560245,248,360 - 45,483,960 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365388,126,291 - 8,361,920 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365388,126,307 - 8,361,920 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMG6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38172,059,839 - 2,303,785 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl172,059,839 - 2,303,785 (-)EnsemblGRCh38hg38GRCh38
GRCh37171,963,133 - 2,207,079 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36171,909,883 - 2,153,819 (-)NCBINCBI36Build 36hg18NCBI36
Build 34171,909,887 - 2,153,769NCBI
Celera171,979,148 - 2,222,926 (-)NCBICelera
Cytogenetic Map17p13.3NCBI
HuRef171,858,147 - 2,101,841 (-)NCBIHuRef
CHM1_1171,971,903 - 2,215,708 (-)NCBICHM1_1
T2T-CHM13v2.0171,947,114 - 2,190,866 (-)NCBIT2T-CHM13v2.0
Smg6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391174,816,665 - 75,055,274 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1174,816,649 - 75,055,274 (+)EnsemblGRCm39 Ensembl
GRCm381174,925,854 - 75,164,448 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1174,925,823 - 75,164,448 (+)EnsemblGRCm38mm10GRCm38
MGSCv371174,739,374 - 74,977,950 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361174,742,067 - 74,980,643 (+)NCBIMGSCv36mm8
Celera1182,431,995 - 82,671,219 (+)NCBICelera
Cytogenetic Map11B5NCBI
cM Map1145.76NCBI
Smg6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81060,284,628 - 60,512,738 (+)NCBIGRCr8
mRatBN7.21059,786,258 - 60,014,395 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1059,786,258 - 60,014,395 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1064,432,825 - 64,661,021 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01063,938,408 - 64,166,602 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01059,400,792 - 59,628,982 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01061,526,024 - 61,542,583 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.01061,771,912 - 62,007,030 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1061,772,449 - 62,007,030 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl1061,527,462 - 61,540,774 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01061,248,898 - 61,263,673 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01061,493,274 - 61,721,420 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41062,234,450 - 62,470,611 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11062,437,519 - 62,461,510 (+)NCBI
Celera1058,816,443 - 59,044,342 (+)NCBICelera
Cytogenetic Map10q24NCBI
Smg6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955481940,041 - 1,177,998 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955481940,041 - 1,177,998 (+)NCBIChiLan1.0ChiLan1.0
SMG6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2199,640,209 - 9,884,321 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11711,607,598 - 11,851,656 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0172,050,825 - 2,294,892 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1171,937,630 - 2,179,535 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl171,937,630 - 2,179,535 (-)Ensemblpanpan1.1panPan2
SMG6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1946,162,991 - 46,405,856 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl946,164,492 - 46,405,748 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha945,313,087 - 45,555,769 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0946,993,865 - 47,236,967 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl946,993,875 - 47,236,917 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1945,760,897 - 46,003,941 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0946,055,223 - 46,298,431 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0946,110,273 - 46,353,691 (-)NCBIUU_Cfam_GSD_1.0
SMG6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1248,172,707 - 48,386,884 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11248,172,705 - 48,386,996 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21250,025,724 - 50,195,666 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMG6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1161,698,039 - 1,940,753 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl161,695,647 - 1,940,739 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605920,022,584 - 20,267,522 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smg6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247864,726,676 - 4,969,646 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247864,729,857 - 4,969,708 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSSTOT00000020820   ⟹   ENSSTOP00000023967
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049365388,126,291 - 8,361,920 (-)Ensembl
RefSeq Acc Id: ENSSTOT00000034842   ⟹   ENSSTOP00000032052
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049365388,148,753 - 8,293,389 (-)Ensembl
RefSeq Acc Id: XM_005327910   ⟹   XP_005327967
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440560245,250,012 - 45,483,960 (-)NCBI
SpeTri2.0NW_0049365388,126,307 - 8,361,920 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021728163   ⟹   XP_021583838
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440560245,250,012 - 45,483,753 (-)NCBI
SpeTri2.0NW_0049365388,126,307 - 8,361,607 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021728164   ⟹   XP_021583839
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440560245,250,014 - 45,483,907 (-)NCBI
SpeTri2.0NW_0049365388,126,307 - 8,361,908 (-)NCBI
Sequence:
RefSeq Acc Id: XM_040269285   ⟹   XP_040125219
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440560245,248,360 - 45,481,805 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_005327967   ⟸   XM_005327910
- Peptide Label: isoform X3
- UniProtKB: I3NHX0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_021583839   ⟸   XM_021728164
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_021583838   ⟸   XM_021728163
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_040125219   ⟸   XM_040269285
- Peptide Label: isoform X1
RefSeq Acc Id: ENSSTOP00000023967   ⟸   ENSSTOT00000020820
RefSeq Acc Id: ENSSTOP00000032052   ⟸   ENSSTOT00000034842
Protein Domains
DNA/RNA-binding   PIN


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000028127 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000020820.2 UniProtKB/TrEMBL
  ENSSTOT00000034842.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
  5'-nuclease UniProtKB/TrEMBL
InterPro DNA/RNA-bd_Est1-type UniProtKB/TrEMBL
  EST1 UniProtKB/TrEMBL
  Est1/Ebs1-like UniProtKB/TrEMBL
  PIN-like_dom_sf UniProtKB/TrEMBL
  PIN_dom UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/TrEMBL
NCBI Gene Smg6 ENTREZGENE
PANTHER PTHR15696 UniProtKB/TrEMBL
  TELOMERASE-BINDING PROTEIN EST1A UniProtKB/TrEMBL
Pfam EST1 UniProtKB/TrEMBL
  EST1_DNA_bind UniProtKB/TrEMBL
  PIN_4 UniProtKB/TrEMBL
SMART PINc UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
  SSF88723 UniProtKB/TrEMBL
UniProt A0A287DET1_ICTTR UniProtKB/TrEMBL
  I3NHX0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-01-29 Smg6  SMG6 nonsense mediated mRNA decay factor    SMG6, nonsense mediated mRNA decay factor  Symbol and/or name change 5135510 APPROVED