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

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Gene: Smg6 (SMG6 nonsense mediated mRNA decay factor) Rattus norvegicus
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Symbol: Smg6
Name: SMG6 nonsense mediated mRNA decay factor
RGD ID: 1595918
Description: Predicted to enable several functions, including DNA polymerase binding activity; RNA endonuclease activity; and nucleic acid binding activity. Predicted to be involved in negative regulation of telomere capping and nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Predicted to be located in cytosol and nucleolus. Predicted to be part of exon-exon junction complex and telomerase holoenzyme complex. Orthologous to human SMG6 (SMG6 nonsense mediated mRNA decay factor); PARTICIPATES IN mRNA decay pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC287522; LOC303309; LRRGT00040; RGD1309609; similar to KIAA0732 protein; similar to Telomerase-binding protein EST1A (Ever shorter telomeres 1A) (Telomerase subunit EST1A) (EST1-like protein A); Smg-6 homolog, nonsense mediated mRNA decay factor; Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans); telomerase-binding protein EST1A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
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
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

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12676087   PMID:12699629   PMID:14636577   PMID:15857955   PMID:17916692   PMID:17940095   PMID:18974281   PMID:19060897   PMID:20930030   PMID:22011238   PMID:25931508   PMID:38685156  


Genomics

Comparative Map Data
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
(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
(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
(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
(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

Variants

.
Variants in Smg6
683 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:103
Count of miRNA genes:87
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000004058, ENSRNOT00000072335
Prediction methods: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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
152025229Scl83Serum cholesterol level QTL 834.33blood cholesterol amount (VT:0000180)103571058068663659Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
152025227Bw195Body weight QTL 1955.73body mass (VT:0001259)104698969968663659Rat
631564Apr3Acute phase response QTL 33.9blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)101527595560275955Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)104944455181709989Rat
152025224Bw193Body weight QTL 1936.47body mass (VT:0001259)105166340575085664Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
1581497Esta1Estrogen-induced thymic atrophy QTL 1thymus mass (VT:0004954)thymus wet weight (CMO:0000855)102132980561345413Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
2306787Ean3Experimental allergic neuritis QTL 33.1nervous system integrity trait (VT:0010566)body weight loss (CMO:0001399)105379738566979128Rat
6893352Bw100Body weight QTL 1000.330.6body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
1354587Kidm21Kidney mass QTL 213.3kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)101502851360430477Rat
6893350Bw99Body weight QTL 990.870.16body mass (VT:0001259)body weight (CMO:0000012)11590666560906665Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
70224Eae3Experimental allergic encephalomyelitis QTL 34.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)102652195761345413Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
2298495Eae23Experimental allergic encephalomyelitis QTL 2316.93nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis duration (CMO:0001424)105527369660677262Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)104944455181709989Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104944455181709989Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)104287676679813922Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat

Markers in Region
RH137267  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21060,012,809 - 60,013,007 (+)MAPPERmRatBN7.2
Rnor_6.01062,005,440 - 62,005,637NCBIRnor6.0
Rnor_5.01061,719,830 - 61,720,027UniSTSRnor5.0
RGSC_v3.41062,469,026 - 62,469,223UniSTSRGSC3.4
Celera1059,042,757 - 59,042,954UniSTS
Cytogenetic Map10q24UniSTS
RH133616  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21060,005,411 - 60,005,619 (+)MAPPERmRatBN7.2
Rnor_6.01061,997,879 - 61,998,086NCBIRnor6.0
Rnor_5.01062,003,920 - 62,004,127UniSTSRnor5.0
Rnor_5.01061,712,269 - 61,712,476UniSTSRnor5.0
RGSC_v3.41062,460,683 - 62,460,890UniSTSRGSC3.4
Celera1059,035,255 - 59,035,462UniSTS
Cytogenetic Map10q24UniSTS
D11Bhm14  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21059,873,733 - 59,873,818 (+)MAPPERmRatBN7.2
Rnor_6.01061,860,316 - 61,860,400NCBIRnor6.0
Rnor_5.01061,580,977 - 61,581,061UniSTSRnor5.0
RGSC_v3.41062,322,202 - 62,322,286UniSTSRGSC3.4
Celera1058,903,903 - 58,903,987UniSTS
Cytogenetic Map10q24UniSTS
RH124699  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21060,014,518 - 60,014,663 (+)MAPPERmRatBN7.2
Rnor_6.01062,007,149 - 62,007,293NCBIRnor6.0
Rnor_5.01061,721,539 - 61,721,683UniSTSRnor5.0
RGSC_v3.41062,470,735 - 62,470,879UniSTSRGSC3.4
Celera1059,044,466 - 59,044,610UniSTS
Cytogenetic Map10q24UniSTS


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
nervous system
renal system
reproductive system
respiratory system
15 11 55 137 115 110 67 31 67 12 260 121 105 49 76 43

Sequence


Ensembl Acc Id: ENSRNOT00000004058   ⟹   ENSRNOP00000004058
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1059,786,258 - 60,014,395 (+)Ensembl
Rnor_6.0 Ensembl1061,772,449 - 62,007,030 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000052412
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1059,972,882 - 59,995,107 (+)Ensembl
Rnor_6.0 Ensembl1061,964,238 - 61,986,644 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092241   ⟹   ENSRNOP00000075895
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1061,776,996 - 62,006,032 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092746
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1061,527,462 - 61,540,774 (+)Ensembl
RefSeq Acc Id: NM_001105808   ⟹   NP_001099278
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81060,284,628 - 60,512,733 (+)NCBI
mRatBN7.21059,786,258 - 60,014,395 (+)NCBI
Rnor_6.01061,771,912 - 62,007,025 (+)NCBI
Rnor_5.01061,493,274 - 61,721,420 (+)NCBI
RGSC_v3.41062,234,450 - 62,470,611 (+)RGD
Celera1058,816,443 - 59,044,342 (+)RGD
Sequence:
RefSeq Acc Id: XM_039085509   ⟹   XP_038941437
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81060,286,996 - 60,512,738 (+)NCBI
mRatBN7.21059,788,033 - 60,012,902 (+)NCBI
RefSeq Acc Id: XM_039085511   ⟹   XP_038941439
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81060,285,047 - 60,512,738 (+)NCBI
mRatBN7.21059,786,677 - 60,012,902 (+)NCBI
RefSeq Acc Id: XM_063268674   ⟹   XP_063124744
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81060,285,047 - 60,393,798 (+)NCBI
RefSeq Acc Id: NP_001099278   ⟸   NM_001105808
- UniProtKB: D4A589 (UniProtKB/TrEMBL),   A6HGP2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000075895   ⟸   ENSRNOT00000092241
Ensembl Acc Id: ENSRNOP00000004058   ⟸   ENSRNOT00000004058
RefSeq Acc Id: XP_038941439   ⟸   XM_039085511
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038941437   ⟸   XM_039085509
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063124744   ⟸   XM_063268674
- Peptide Label: isoform X3
Protein Domains
PIN

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A589-F1-model_v2 AlphaFold D4A589 1-1418 view protein structure

Transcriptome

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

Promoters
RGD ID:13697418
Promoter ID:EPDNEW_R7943
Type:initiation region
Name:Smg6_1
Description:SMG6 nonsense mediated mRNA decay factor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01061,772,431 - 61,772,491EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1595918 AgrOrtholog
BioCyc Gene G2FUF-24236 BioCyc
Ensembl Genes ENSRNOG00000003041 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000062142 Ensembl
Ensembl Transcript ENSRNOT00000004058.9 UniProtKB/TrEMBL
  ENSRNOT00000052412.2 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
  PIN_domain-like UniProtKB/TrEMBL
  TPR-like_helical UniProtKB/TrEMBL
KEGG Report rno:287522 UniProtKB/TrEMBL
NCBI Gene 287522 ENTREZGENE
PANTHER PTHR15696 UniProtKB/TrEMBL
  TELOMERASE-BINDING PROTEIN EST1A UniProtKB/TrEMBL
Pfam EST1 UniProtKB/TrEMBL
  EST1_DNA_bind UniProtKB/TrEMBL
  PIN_4 UniProtKB/TrEMBL
PhenoGen Smg6 PhenoGen
RatGTEx ENSRNOG00000003041 RatGTEx
  ENSRNOG00000062142 RatGTEx
SMART PINc UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/TrEMBL
  SSF88723 UniProtKB/TrEMBL
UniProt A6HGP2 ENTREZGENE, UniProtKB/TrEMBL
  D4A589 ENTREZGENE, UniProtKB/TrEMBL
  Q6TXF9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-07-12 Smg6  SMG6 nonsense mediated mRNA decay factor  Smg6  Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-04 Smg6  Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)  RGD1309609  similar to KIAA0732 protein  Data merged from RGD:1309609 737654 APPROVED
2008-03-04 Smg6  Smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)  LOC287522  similar to Telomerase-binding protein EST1A (Ever shorter telomeres 1A) (Telomerase subunit EST1A) (EST1-like protein A)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC287522  similar to Telomerase-binding protein EST1A (Ever shorter telomeres 1A) (Telomerase subunit EST1A) (EST1-like protein A)      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-12-06 RGD1309609  similar to KIAA0732 protein  RGD1309609_predicted  similar to KIAA0732 protein (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1309609_predicted  similar to KIAA0732 protein (predicted)  LOC303309_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC303309_predicted  similar to KIAA0732 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL