Smg5l1 (Smg5 nonsense mediated mRNA decay factor like 1) - Rat Genome Database

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Gene: Smg5l1 (Smg5 nonsense mediated mRNA decay factor like 1) Rattus norvegicus
Analyze
Symbol: Smg5l1 (Ensembl: RGD1309489)
Name: Smg5 nonsense mediated mRNA decay factor like 1 (Ensembl:similar to Est1p-like protein B)
RGD ID: 1309489
Description: Predicted to be involved in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Predicted to be located in nucleus; PARTICIPATES IN mRNA decay pathway; INTERACTS WITH bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC314915; RGD1309489; similar to Est1p-like protein B
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2775,917,527 - 76,051,832 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl775,917,392 - 76,052,413 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx777,763,496 - 77,904,123 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0779,965,988 - 80,106,626 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0779,837,764 - 79,972,019 (+)NCBIRnor_WKY
Rnor_6.0783,691,630 - 83,804,882 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0783,686,744 - 83,820,605 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4780,777,088 - 80,780,009 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera772,909,028 - 73,023,685 (+)NCBICelera
Cytogenetic Map7q31NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
bisphenol A  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IEA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD

Genomics

Variants

.
Variants in Smg5l1
668 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73429328279293282Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)74278731487787314Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74322875088228750Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)743747099102228765Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74486753389867533Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74659007091590070Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)74765143992651439Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)74765143992651439Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)74765143992651439Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)74765143992651439Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)74765143992651439Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)74765143992651439Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)74765143992651439Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)753612714103945643Rat
2317035Aia16Adjuvant induced arthritis QTL 162.71joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)759238038104238038Rat
1298528Bp169Blood pressure QTL 1690.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)761074194106074194Rat
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)762004452101773158Rat
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)762004452101773158Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)768938720113886318Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)768938720113886318Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)768938720113886318Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)769736226117455174Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)769736356112729554Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)773829340130221005Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)775918751120918751Rat

Markers in Region
D7Got214  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2776,029,175 - 76,029,461 (+)MAPPERmRatBN7.2
Rnor_6.0783,782,027 - 83,782,310NCBIRnor6.0
Rnor_5.0783,798,110 - 83,798,393UniSTSRnor5.0
RGSC_v3.4780,757,807 - 80,758,090UniSTSRGSC3.4
Celera772,999,791 - 73,000,074UniSTS
Cytogenetic Map7q31UniSTS
D7Got224  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2776,034,400 - 76,034,565 (+)MAPPERmRatBN7.2
Rnor_6.0783,787,452 - 83,787,616NCBIRnor6.0
Rnor_5.0783,803,535 - 83,803,699UniSTSRnor5.0
RGSC_v3.4780,763,030 - 80,763,194UniSTSRGSC3.4
Celera773,005,008 - 73,005,172UniSTS
Cytogenetic Map7q31UniSTS
RH143980  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2776,051,545 - 76,051,651 (+)MAPPERmRatBN7.2
Rnor_6.0117,588,937 - 7,589,047NCBIRnor6.0
Rnor_6.0783,804,596 - 83,804,701NCBIRnor6.0
Rnor_5.0783,820,679 - 83,820,784UniSTSRnor5.0
RGSC_v3.4780,780,175 - 80,780,280UniSTSRGSC3.4
Celera773,023,399 - 73,023,504UniSTS
RH 3.4 Map7523.6UniSTS
Cytogenetic Map7q31UniSTS
BE113572  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2775,915,780 - 75,915,955 (+)MAPPERmRatBN7.2
Rnor_6.0783,668,400 - 83,668,574NCBIRnor6.0
Rnor_5.0783,684,188 - 83,684,362UniSTSRnor5.0
RGSC_v3.4780,634,756 - 80,634,930UniSTSRGSC3.4
Celera772,885,763 - 72,885,937UniSTS
RH 3.4 Map7525.5UniSTS
Cytogenetic Map7q31UniSTS


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001346302 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001346303 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079148 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079149 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079150 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079152 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079153 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079154 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079155 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079156 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079157 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079158 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079159 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079160 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001839067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001844225 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473950 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000185 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000037006   ⟹   ENSRNOP00000091020
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl776,044,075 - 76,051,829 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095375   ⟹   ENSRNOP00000082139
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl775,917,392 - 76,052,413 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101664   ⟹   ENSRNOP00000095623
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl775,917,438 - 76,052,413 (+)Ensembl
RefSeq Acc Id: NM_001346302   ⟹   NP_001333231
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,917,562 - 76,051,832 (+)NCBI
RefSeq Acc Id: NM_001346303   ⟹   NP_001333232
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,917,562 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079148   ⟹   XP_038935076
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,917,532 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079149   ⟹   XP_038935077
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,918,446 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079150   ⟹   XP_038935078
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,917,527 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079151   ⟹   XP_038935079
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,917,532 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079152   ⟹   XP_038935080
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,917,532 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079153   ⟹   XP_038935081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,948,700 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079154   ⟹   XP_038935082
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,948,705 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079155   ⟹   XP_038935083
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,917,532 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079156   ⟹   XP_038935084
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,949,015 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079157   ⟹   XP_038935085
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,949,015 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079158   ⟹   XP_038935086
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,918,446 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079159   ⟹   XP_038935087
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,948,751 - 76,051,832 (+)NCBI
RefSeq Acc Id: XM_039079160   ⟹   XP_038935088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2775,948,702 - 76,051,832 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_038935078   ⟸   XM_039079150
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935079   ⟸   XM_039079151
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZUK4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038935076   ⟸   XM_039079148
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935080   ⟸   XM_039079152
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZUK4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038935083   ⟸   XM_039079155
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZUK4 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001333232   ⟸   NM_001346303
- Peptide Label: isoform 2
- UniProtKB: A0A8I5ZUK4 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001333231   ⟸   NM_001346302
- Peptide Label: isoform 1
RefSeq Acc Id: XP_038935077   ⟸   XM_039079149
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038935086   ⟸   XM_039079158
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZUK4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038935081   ⟸   XM_039079153
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZUK4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038935088   ⟸   XM_039079160
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZUK4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038935082   ⟸   XM_039079154
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZUK4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038935087   ⟸   XM_039079159
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZUK4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038935085   ⟸   XM_039079157
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZUK4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038935084   ⟸   XM_039079156
- Peptide Label: isoform X2
- UniProtKB: A0A8I5ZUK4 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000091020   ⟸   ENSRNOT00000037006
RefSeq Acc Id: ENSRNOP00000095623   ⟸   ENSRNOT00000101664
RefSeq Acc Id: ENSRNOP00000082139   ⟸   ENSRNOT00000095375
Protein Domains
DNA/RNA-binding   Telomerase activating protein Est1-like N-terminal

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-33476 BioCyc
Ensembl Genes ENSRNOG00000024507 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000082139 ENTREZGENE
  ENSRNOP00000082139.1 UniProtKB/TrEMBL
  ENSRNOP00000091020.1 UniProtKB/TrEMBL
  ENSRNOP00000095623 ENTREZGENE
  ENSRNOP00000095623.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037006.6 UniProtKB/TrEMBL
  ENSRNOT00000095375 ENTREZGENE
  ENSRNOT00000095375.1 UniProtKB/TrEMBL
  ENSRNOT00000101664 ENTREZGENE
  ENSRNOT00000101664.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/TrEMBL
  5'-nuclease UniProtKB/TrEMBL
InterPro DNA/RNA-bd_Est1-type UniProtKB/TrEMBL
  Est1/Ebs1-like UniProtKB/TrEMBL
  Est1_N UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/TrEMBL
NCBI Gene 314915 ENTREZGENE
PANTHER PROTEIN SMG5 UniProtKB/TrEMBL
  PTHR15696 UniProtKB/TrEMBL
Pfam EST1 UniProtKB/TrEMBL
  EST1_DNA_bind UniProtKB/TrEMBL
PhenoGen Smg5l1 PhenoGen
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
UniProt A0A8I5ZUK4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6ADQ4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-27 Smg5l1  Smg5 nonsense mediated mRNA decay factor like 1  RGD1309489  similar to Est1p-like protein B  Name and Symbol changed 629549 APPROVED
2008-04-30 RGD1309489  similar to Est1p-like protein B   RGD1309489_predicted  similar to Est1p-like protein B (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1309489_predicted  similar to Est1p-like protein B (predicted)  LOC314915_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC314915_predicted  similar to Est1p-like protein B (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL