Smndc1 (survival motor neuron domain containing 1) - Rat Genome Database

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Gene: Smndc1 (survival motor neuron domain containing 1) Rattus norvegicus
Analyze
Symbol: Smndc1
Name: survival motor neuron domain containing 1
RGD ID: 1309151
Description: Predicted to enable RNA binding activity. Predicted to be involved in RNA splicing; apoptotic process; and mRNA processing. Predicted to be located in Cajal body; cytoplasm; and nuclear speck. Predicted to be part of spliceosomal complex. Predicted to be active in nucleus. Orthologous to human SMNDC1 (survival motor neuron domain containing 1); PARTICIPATES IN spliceosome pathway; INTERACTS WITH (+)-schisandrin B; 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC287768; MGC112663; survival motor neuron domain-containing protein 1; survival of motor neuron-related-splicing factor 30
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21252,389,675 - 252,400,749 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1252,389,673 - 252,401,616 (-)Ensembl
Rnor_6.01274,096,068 - 274,107,138 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1274,096,068 - 274,107,138 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01281,509,724 - 281,520,796 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41259,596,813 - 259,607,340 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11259,807,858 - 259,817,787 (-)NCBI
Celera1248,112,016 - 248,123,086 (-)NCBICelera
Cytogenetic Map1q55NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:22658674  


Genomics

Comparative Map Data
Smndc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21252,389,675 - 252,400,749 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1252,389,673 - 252,401,616 (-)Ensembl
Rnor_6.01274,096,068 - 274,107,138 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1274,096,068 - 274,107,138 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01281,509,724 - 281,520,796 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41259,596,813 - 259,607,340 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11259,807,858 - 259,817,787 (-)NCBI
Celera1248,112,016 - 248,123,086 (-)NCBICelera
Cytogenetic Map1q55NCBI
SMNDC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3810110,290,730 - 110,304,920 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl10110,290,730 - 110,304,938 (-)EnsemblGRCh38hg38GRCh38
GRCh3710112,050,488 - 112,064,678 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3610112,042,788 - 112,054,687 (-)NCBINCBI36hg18NCBI36
Build 3410112,042,788 - 112,054,687NCBI
Celera10105,784,468 - 105,796,377 (-)NCBI
Cytogenetic Map10q25.2NCBI
HuRef10105,683,016 - 105,694,926 (-)NCBIHuRef
CHM1_110112,334,567 - 112,346,476 (-)NCBICHM1_1
T2T-CHM13v2.010111,174,603 - 111,188,795 (-)NCBI
Smndc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391953,367,645 - 53,379,122 (-)NCBIGRCm39mm39
GRCm39 Ensembl1953,367,821 - 53,379,009 (-)Ensembl
GRCm381953,379,214 - 53,390,701 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1953,379,390 - 53,390,578 (-)EnsemblGRCm38mm10GRCm38
MGSCv371953,453,704 - 53,465,063 (-)NCBIGRCm37mm9NCBIm37
MGSCv361953,432,526 - 53,443,885 (-)NCBImm8
Celera1955,561,243 - 55,572,623 (-)NCBICelera
Cytogenetic Map19D2NCBI
Smndc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554851,070,236 - 1,081,979 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554851,070,596 - 1,081,979 (+)NCBIChiLan1.0ChiLan1.0
SMNDC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.110110,334,594 - 110,346,882 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10110,334,594 - 110,345,633 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v010106,881,965 - 106,896,496 (-)NCBIMhudiblu_PPA_v0panPan3
SMNDC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12821,660,501 - 21,672,279 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2821,661,881 - 21,671,781 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2821,813,977 - 21,825,801 (-)NCBI
ROS_Cfam_1.02822,186,207 - 22,198,029 (-)NCBI
ROS_Cfam_1.0 Ensembl2822,186,176 - 22,197,464 (-)Ensembl
UMICH_Zoey_3.12821,746,442 - 21,758,273 (-)NCBI
UNSW_CanFamBas_1.02821,750,408 - 21,762,241 (-)NCBI
UU_Cfam_GSD_1.02821,886,296 - 21,898,128 (-)NCBI
Smndc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721324,369,802 - 24,381,204 (+)NCBI
SpeTri2.0NW_0049364861,180,069 - 1,192,227 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMNDC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14120,725,387 - 120,739,622 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114120,726,077 - 120,739,673 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214131,613,337 - 131,627,220 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMNDC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.19103,217,216 - 103,229,422 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl9103,218,308 - 103,228,053 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604864,420,375 - 64,432,540 (-)NCBIVero_WHO_p1.0
Smndc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473735,938,946 - 35,956,540 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D1Swe7  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21252,398,190 - 252,398,396 (+)MAPPERmRatBN7.2
Rnor_6.01274,104,580 - 274,104,785NCBIRnor6.0
Rnor_5.01281,518,238 - 281,518,443UniSTSRnor5.0
RGSC_v3.41259,604,820 - 259,605,025UniSTSRGSC3.4
Celera1248,120,528 - 248,120,733UniSTS
Cytogenetic Map1q55UniSTS
BE101386  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21252,393,793 - 252,394,491 (+)MAPPERmRatBN7.2
mRatBN7.21091,870,853 - 91,871,018 (+)MAPPERmRatBN7.2
Rnor_6.01095,130,947 - 95,131,111NCBIRnor6.0
Rnor_6.01274,100,183 - 274,100,880NCBIRnor6.0
Rnor_5.01094,871,774 - 94,871,938UniSTSRnor5.0
Rnor_5.01281,513,841 - 281,514,538UniSTSRnor5.0
RGSC_v3.41259,600,423 - 259,601,120UniSTSRGSC3.4
RGSC_v3.41096,278,191 - 96,278,355UniSTSRGSC3.4
Celera1090,536,963 - 90,537,127UniSTS
Celera1248,116,131 - 248,116,828UniSTS
RH 3.4 Map10992.8UniSTS
Cytogenetic Map1q55UniSTS
RH128439  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21252,401,044 - 252,401,735 (+)MAPPERmRatBN7.2
Rnor_6.01274,107,434 - 274,108,124NCBIRnor6.0
Rnor_5.01281,521,092 - 281,521,782UniSTSRnor5.0
RGSC_v3.41259,607,674 - 259,608,364UniSTSRGSC3.4
Celera1248,123,382 - 248,124,072UniSTS
RH 3.4 Map11665.4UniSTS
Cytogenetic Map1q55UniSTS
RH129397  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21091,871,639 - 91,871,827 (+)MAPPERmRatBN7.2
mRatBN7.21252,390,321 - 252,390,509 (+)MAPPERmRatBN7.2
Rnor_6.01095,119,736 - 95,119,923NCBIRnor6.0
Rnor_6.01274,096,711 - 274,096,898NCBIRnor6.0
Rnor_5.01094,863,620 - 94,863,807UniSTSRnor5.0
Rnor_5.01281,510,369 - 281,510,556UniSTSRnor5.0
Celera1248,112,659 - 248,112,846UniSTS
Celera1090,537,749 - 90,537,936UniSTS
Cytogenetic Map10q32.1UniSTS
Cytogenetic Map1q55UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1151162512256448636Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1151162512256448636Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1153136852260522016Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1156677124256448636Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1176426412257976495Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1177227632256448636Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1177227632256448636Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1179567751260522016Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1195804352257091168Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1195804352257091168Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1199050459259647894Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1210702053260522016Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1213843987258843987Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1214647894259647894Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1214647894259647894Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1216255568260522016Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1216255568260522016Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1218748008257976495Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1218753816256448513Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221264111259647894Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1221414816260522016Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1222363780260522016Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1223201027260522016Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1224054293260122809Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1224054293260122809Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1224569538260122809Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1225126575260522016Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1228581588259647894Rat
1581544Rf52Renal function QTL 520.05total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1232156370259647894Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233190394258625266Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1233948574260522016Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1236125214260522016Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1237147813260522016Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1238699859259647894Rat
1598839Rf56Renal function QTL 56renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1245907761257976495Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:469
Count of miRNA genes:251
Interacting mature miRNAs:293
Transcripts:ENSRNOT00000020539
Prediction methods:Microtar, 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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 34 50 34 19 34 4 6 74 35 41 11 4
Low 9 7 7 7 4 5 4
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001025400 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001035234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_051995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006231608 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102802 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039102805 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005500333 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC115255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC097986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC098697 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB726049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473986 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CV106705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  EV778425 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220088 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ228387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000020539   ⟹   ENSRNOP00000020539
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1252,390,179 - 252,399,725 (-)Ensembl
Rnor_6.0 Ensembl1274,096,573 - 274,106,502 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000075874   ⟹   ENSRNOP00000068340
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1252,390,818 - 252,399,544 (-)Ensembl
Rnor_6.0 Ensembl1274,097,207 - 274,105,933 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076121   ⟹   ENSRNOP00000068081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1252,389,679 - 252,401,616 (-)Ensembl
Rnor_6.0 Ensembl1274,096,573 - 274,107,100 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076197   ⟹   ENSRNOP00000068456
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1274,097,004 - 274,107,100 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076330
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1274,100,597 - 274,107,069 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076623
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1274,100,156 - 274,105,989 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078670   ⟹   ENSRNOP00000071875
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1252,389,673 - 252,399,598 (-)Ensembl
Rnor_6.0 Ensembl1274,096,068 - 274,107,138 (-)Ensembl
RefSeq Acc Id: NM_001025400   ⟹   NP_001020571
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21252,389,679 - 252,400,113 (-)NCBI
Rnor_6.01274,096,068 - 274,106,502 (-)NCBI
Rnor_5.01281,509,724 - 281,520,796 (-)NCBI
RGSC_v3.41259,596,813 - 259,607,340 (-)RGD
Celera1248,112,016 - 248,122,450 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001035234   ⟹   NP_001030311
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21252,389,679 - 252,400,749 (-)NCBI
Rnor_6.01274,096,068 - 274,107,138 (-)NCBI
Rnor_5.01281,509,724 - 281,520,796 (-)NCBI
RGSC_v3.41259,596,813 - 259,607,340 (-)RGD
Celera1248,112,016 - 248,123,086 (-)NCBI
Sequence:
RefSeq Acc Id: NR_051995
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21252,389,679 - 252,400,749 (-)NCBI
Rnor_6.01274,096,068 - 274,107,138 (-)NCBI
Rnor_5.01281,509,724 - 281,520,796 (-)NCBI
Celera1248,112,016 - 248,123,086 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039102802   ⟹   XP_038958730
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21252,389,675 - 252,399,987 (-)NCBI
RefSeq Acc Id: XM_039102805   ⟹   XP_038958733
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21252,389,679 - 252,400,717 (-)NCBI
RefSeq Acc Id: XR_005500333
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21252,390,184 - 252,400,491 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001030311   ⟸   NM_001035234
- UniProtKB: Q4QQU6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001020571   ⟸   NM_001025400
- UniProtKB: Q4QQU6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000068340   ⟸   ENSRNOT00000075874
RefSeq Acc Id: ENSRNOP00000020539   ⟸   ENSRNOT00000020539
RefSeq Acc Id: ENSRNOP00000068456   ⟸   ENSRNOT00000076197
RefSeq Acc Id: ENSRNOP00000071875   ⟸   ENSRNOT00000078670
RefSeq Acc Id: ENSRNOP00000068081   ⟸   ENSRNOT00000076121
RefSeq Acc Id: XP_038958730   ⟸   XM_039102802
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038958733   ⟸   XM_039102805
- Peptide Label: isoform X2
Protein Domains
Tudor

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4QQU6-F1-model_v2 AlphaFold Q4QQU6 1-238 view protein structure

Transcriptome

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

Promoters
RGD ID:13690993
Promoter ID:EPDNEW_R1516
Type:initiation region
Name:Smndc1_1
Description:survival motor neuron domain containing 1
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_6.01274,107,123 - 274,107,183EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309151 AgrOrtholog
BioCyc Gene G2FUF-55396 BioCyc
Ensembl Genes ENSRNOG00000014833 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020539 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000068081 ENTREZGENE
  ENSRNOP00000068340.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020539 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000075874.2 UniProtKB/TrEMBL
  ENSRNOT00000076121 ENTREZGENE
  ENSRNOT00000078670 ENTREZGENE
IMAGE_CLONE IMAGE:7386640 IMAGE-MGC_LOAD
  IMAGE:7444662 IMAGE-MGC_LOAD
InterPro Survival_motor_neuron UniProtKB/Swiss-Prot
  Tudor UniProtKB/Swiss-Prot
KEGG Report rno:287768 UniProtKB/Swiss-Prot
MGC_CLONE MGC:112663 IMAGE-MGC_LOAD
  MGC:116124 IMAGE-MGC_LOAD
NCBI Gene 287768 ENTREZGENE
Pfam SMN UniProtKB/Swiss-Prot
PhenoGen Smndc1 PhenoGen
PROSITE TUDOR UniProtKB/Swiss-Prot
SMART TUDOR UniProtKB/Swiss-Prot
UniProt A0A096MK12_RAT UniProtKB/TrEMBL
  Q4QQU6 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q4KM88 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Smndc1  survival motor neuron domain containing 1  Smndc1_predicted  survival motor neuron domain containing 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Smndc1_predicted  survival motor neuron domain containing 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED