SMNDC1 (survival motor neuron domain containing 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: SMNDC1 (survival motor neuron domain containing 1) Sus scrofa
Analyze
Symbol: SMNDC1
Name: survival motor neuron domain containing 1
RGD ID: 14174685
Description: ENCODES a protein that exhibits RNA binding (inferred); INVOLVED IN mRNA processing (inferred); regulation of alternative mRNA splicing, via spliceosome (inferred); RNA splicing (inferred); ASSOCIATED WITH Cornelia de Lange syndrome 3 (ortholog); genetic disease (ortholog); FOUND IN Cajal body (inferred); cytoplasm (inferred); membrane (inferred); INTERACTS WITH deoxynivalenol
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: survival of motor neuron-related-splicing factor 30
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:14681463   PMID:15679890   PMID:16484796   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3810110,290,730 - 110,304,920 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl10110,290,730 - 110,304,938 (-)EnsemblGRCh38hg38GRCh38
GRCh3710112,050,488 - 112,064,678 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3610112,042,788 - 112,054,687 (-)NCBINCBI36Build 36hg18NCBI36
Build 3410112,042,788 - 112,054,687NCBI
Celera10105,784,468 - 105,796,377 (-)NCBICelera
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 (-)NCBIT2T-CHM13v2.0
Smndc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391953,367,603 - 53,379,065 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1953,367,821 - 53,379,009 (-)EnsemblGRCm39 Ensembl
GRCm381953,379,214 - 53,390,701 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1953,379,390 - 53,390,578 (-)EnsemblGRCm38mm10GRCm38
MGSCv371953,453,704 - 53,465,063 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361953,432,526 - 53,443,885 (-)NCBIMGSCv36mm8
Celera1955,561,243 - 55,572,623 (-)NCBICelera
Cytogenetic Map19D2NCBI
cM Map1947.67NCBI
Smndc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81262,395,034 - 262,406,104 (-)NCBIGRCr8
mRatBN7.21252,389,675 - 252,400,749 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1252,389,673 - 252,401,616 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1260,578,802 - 260,589,853 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01267,284,868 - 267,295,919 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01259,940,504 - 259,951,557 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11259,807,858 - 259,817,787 (-)NCBI
Celera1248,112,016 - 248,123,086 (-)NCBICelera
Cytogenetic Map1q55NCBI
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
NHGRI_mPanPan1-v28122,171,810 - 122,183,793 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan110122,174,560 - 122,189,122 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v010106,881,965 - 106,896,496 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.110110,334,594 - 110,346,882 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10110,334,594 - 110,345,633 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02822,186,207 - 22,198,029 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2822,186,176 - 22,197,464 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12821,746,442 - 21,758,273 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02821,750,408 - 21,762,241 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02821,886,296 - 21,898,128 (-)NCBIUU_Cfam_GSD_1.0
Smndc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721324,369,802 - 24,381,204 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364861,180,069 - 1,190,117 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364861,180,069 - 1,192,227 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMNDC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.19103,217,216 - 103,229,422 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl9103,218,308 - 103,228,053 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604864,420,375 - 64,432,540 (-)NCBIVero_WHO_p1.0Vero_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_1.0HetGla 1.0hetGla2

Variants

.
Variants in SMNDC1
202 total Variants

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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 5 2 1 5 1 3 3 3
Low 5 2 2 1 20 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000028296   ⟹   ENSSSCP00000026180
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl14120,725,387 - 120,738,527 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000050809   ⟹   ENSSSCP00000034018
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl14120,728,265 - 120,739,622 (-)Ensembl
RefSeq Acc Id: NM_001166309   ⟹   NP_001159781
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.114120,728,377 - 120,739,673 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005671451   ⟹   XP_005671508
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.114120,726,077 - 120,739,661 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_005671508   ⟸   XM_005671451
- Peptide Label: isoform X1
- UniProtKB: A0A286ZR12 (UniProtKB/TrEMBL),   A0A4X1TH37 (UniProtKB/TrEMBL),   A0A8D1M0F1 (UniProtKB/TrEMBL),   A0A8D1I5C2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001159781   ⟸   NM_001166309
- UniProtKB: C9VZF4 (UniProtKB/TrEMBL),   A0A8D0N984 (UniProtKB/TrEMBL),   A0A8D0SWD1 (UniProtKB/TrEMBL),   F1S5M7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000034018   ⟸   ENSSSCT00000050809
RefSeq Acc Id: ENSSSCP00000026180   ⟸   ENSSSCT00000028296
Protein Domains
Tudor


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000030507 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00005012236 UniProtKB/TrEMBL
  ENSSSCG00015025477 UniProtKB/TrEMBL
  ENSSSCG00025062461 UniProtKB/TrEMBL
  ENSSSCG00030057474 UniProtKB/TrEMBL
  ENSSSCG00035000572 UniProtKB/TrEMBL
  ENSSSCG00040010533 UniProtKB/TrEMBL
  ENSSSCG00045023686 UniProtKB/TrEMBL
  ENSSSCG00050028533 UniProtKB/TrEMBL
  ENSSSCG00055009894 UniProtKB/TrEMBL
  ENSSSCG00060065163 UniProtKB/TrEMBL
  ENSSSCG00065018071 UniProtKB/TrEMBL
  ENSSSCG00070008823 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000028296 ENTREZGENE
  ENSSSCT00000028296.4 UniProtKB/TrEMBL
  ENSSSCT00000050809 ENTREZGENE
  ENSSSCT00000050809.2 UniProtKB/TrEMBL
  ENSSSCT00005019192.1 UniProtKB/TrEMBL
  ENSSSCT00015033840.1 UniProtKB/TrEMBL
  ENSSSCT00015033998.1 UniProtKB/TrEMBL
  ENSSSCT00025085558.1 UniProtKB/TrEMBL
  ENSSSCT00025085682.1 UniProtKB/TrEMBL
  ENSSSCT00030080145.1 UniProtKB/TrEMBL
  ENSSSCT00030080166.1 UniProtKB/TrEMBL
  ENSSSCT00035000631.1 UniProtKB/TrEMBL
  ENSSSCT00035000640.1 UniProtKB/TrEMBL
  ENSSSCT00040013730.1 UniProtKB/TrEMBL
  ENSSSCT00040013786.1 UniProtKB/TrEMBL
  ENSSSCT00045040487.1 UniProtKB/TrEMBL
  ENSSSCT00045040583.1 UniProtKB/TrEMBL
  ENSSSCT00050038373.1 UniProtKB/TrEMBL
  ENSSSCT00050038391.1 UniProtKB/TrEMBL
  ENSSSCT00055019372.1 UniProtKB/TrEMBL
  ENSSSCT00055019418.1 UniProtKB/TrEMBL
  ENSSSCT00060088964.1 UniProtKB/TrEMBL
  ENSSSCT00060088987.1 UniProtKB/TrEMBL
  ENSSSCT00065024003.1 UniProtKB/TrEMBL
  ENSSSCT00065024015.1 UniProtKB/TrEMBL
  ENSSSCT00070017109.1 UniProtKB/TrEMBL
  ENSSSCT00070017120.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.140 UniProtKB/TrEMBL
InterPro Survival_motor_neuron UniProtKB/TrEMBL
  Tudor UniProtKB/TrEMBL
KEGG Report ssc:100127466 UniProtKB/TrEMBL
NCBI Gene SMNDC1 ENTREZGENE
PANTHER SURVIVAL OF MOTOR NEURON-RELATED-SPLICING FACTOR 30 UniProtKB/TrEMBL
  SURVIVAL OF MOTOR NEURON-RELATED-SPLICING FACTOR 30-RELATED UniProtKB/TrEMBL
Pfam SMN UniProtKB/TrEMBL
PROSITE TUDOR UniProtKB/TrEMBL
SMART TUDOR UniProtKB/TrEMBL
Superfamily-SCOP Tudor/PWWP/MBT UniProtKB/TrEMBL
UniProt A0A286ZR12 ENTREZGENE
  A0A4X1TH37 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0IP74_PIG UniProtKB/TrEMBL
  A0A8D0N984 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0SWD1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1I5C2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1M0F1 ENTREZGENE, UniProtKB/TrEMBL
  C9VZF4 ENTREZGENE, UniProtKB/TrEMBL
  F1S5M7 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary A0A286ZR12 UniProtKB/TrEMBL
VGNC ID VGNC:93257 ENTREZGENE