Smg5 (SMG5 nonsense mediated mRNA decay factor) - Rat Genome Database

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Gene: Smg5 (SMG5 nonsense mediated mRNA decay factor) Ictidomys tridecemlineatus
Analyze
Symbol: Smg5
Name: SMG5 nonsense mediated mRNA decay factor
RGD ID: 12569827
Description: ENCODES a protein that exhibits histone deacetylase binding (inferred); protein phosphatase 2A binding (inferred); telomerase RNA binding (inferred); INVOLVED IN nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (inferred); regulation of dephosphorylation (inferred); regulation of telomere maintenance (inferred); ASSOCIATED WITH Charcot-Marie-Tooth disease type 2 (ortholog); gastrointestinal stromal tumor (ortholog); genetic disease (ortholog); FOUND IN cytoplasm (inferred); nucleus (inferred); telomerase holoenzyme complex (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: SMG5, nonsense mediated mRNA decay factor
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_02440505826,457,140 - 26,486,078 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365805,487,533 - 5,516,521 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365805,487,522 - 5,516,448 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Smg5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505826,457,140 - 26,486,078 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365805,487,533 - 5,516,521 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365805,487,522 - 5,516,448 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMG5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381156,249,224 - 156,291,516 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1156,249,224 - 156,282,825 (-)EnsemblGRCh38hg38GRCh38
GRCh371156,219,015 - 156,261,307 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361154,485,639 - 154,519,244 (-)NCBINCBI36Build 36hg18NCBI36
Celera1129,291,997 - 129,325,601 (-)NCBICelera
Cytogenetic Map1q22NCBI
HuRef1127,580,113 - 127,613,290 (-)NCBIHuRef
CHM1_11157,614,993 - 157,648,597 (-)NCBICHM1_1
T2T-CHM13v2.01155,387,685 - 155,429,979 (-)NCBIT2T-CHM13v2.0
Smg5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39388,242,050 - 88,269,645 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl388,243,567 - 88,269,645 (+)EnsemblGRCm39 Ensembl
GRCm38388,336,259 - 88,362,338 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl388,336,260 - 88,362,338 (+)EnsemblGRCm38mm10GRCm38
MGSCv37388,140,182 - 88,166,259 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36388,422,076 - 88,448,265 (+)NCBIMGSCv36mm8
Celera388,375,893 - 88,401,966 (+)NCBICelera
Cytogenetic Map3F1NCBI
cM Map338.8NCBI
Smg5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82176,102,812 - 176,129,925 (+)NCBIGRCr8
mRatBN7.22173,804,987 - 173,832,102 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2173,805,019 - 173,832,102 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.02187,708,247 - 187,735,355 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2187,708,234 - 187,735,355 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02207,110,275 - 207,138,298 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42180,448,782 - 180,475,237 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2167,749,851 - 167,776,844 (+)NCBICelera
Cytogenetic Map2q34NCBI
Smg5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555452,386,877 - 2,418,418 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555452,386,877 - 2,418,418 (-)NCBIChiLan1.0ChiLan1.0
SMG5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2193,558,697 - 93,596,047 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1193,294,619 - 93,327,940 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01131,592,368 - 131,634,443 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11135,422,268 - 135,455,739 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1135,422,268 - 135,455,734 (-)Ensemblpanpan1.1panPan2
SMG5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1741,598,111 - 41,624,575 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl741,598,104 - 41,624,575 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha741,086,046 - 41,112,528 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0741,462,624 - 41,489,187 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl741,462,689 - 41,494,389 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1741,244,007 - 41,270,487 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0741,297,221 - 41,323,693 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0741,581,284 - 41,607,773 (+)NCBIUU_Cfam_GSD_1.0
SMG5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl493,770,378 - 93,800,650 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1493,770,329 - 93,801,808 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24102,470,396 - 102,501,868 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMG5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1207,579,716 - 7,618,060 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl207,579,726 - 7,618,999 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660386,875,413 - 6,910,581 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smg5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248851,532,101 - 1,560,307 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248851,532,101 - 1,565,811 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005331382 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAESOR010000117 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSSTOT00000001786   ⟹   ENSSTOP00000001593
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_0049365805,487,533 - 5,516,521 (-)Ensembl
RefSeq Acc Id: XM_005331382   ⟹   XP_005331439
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440505826,457,140 - 26,486,078 (-)NCBI
SpeTri2.0NW_0049365805,487,522 - 5,516,448 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_005331439 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000001593.2
GenBank Protein KAG3281783 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_005331439   ⟸   XM_005331382
- UniProtKB: I3LZ77 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSTOP00000001593   ⟸   ENSSTOT00000001786
Protein Domains
PIN


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000001780 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000001786.3 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_dom UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/TrEMBL
NCBI Gene Smg5 ENTREZGENE
PANTHER NONSENSE-MEDIATED MRNA DECAY FACTOR SMG5 UniProtKB/TrEMBL
  PTHR15696 UniProtKB/TrEMBL
Pfam EST1 UniProtKB/TrEMBL
  EST1_DNA_bind UniProtKB/TrEMBL
  PIN_4 UniProtKB/TrEMBL
SMART PINc UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt I3LZ77 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-01-29 Smg5  SMG5 nonsense mediated mRNA decay factor    SMG5, nonsense mediated mRNA decay factor  Symbol and/or name change 5135510 APPROVED