SDE2 (SDE2 telomere maintenance homolog) - 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 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
Advanced Search (OLGA)
Gene: SDE2 (SDE2 telomere maintenance homolog) Pan paniscus
Analyze
Symbol: SDE2
Name: SDE2 telomere maintenance homolog
RGD ID: 11701342
Description: ENCODES a protein that exhibits damaged DNA binding (inferred); DNA binding (inferred); RNA binding (inferred); INVOLVED IN cell division (inferred); cellular response to UV (inferred); DNA replication (inferred); ASSOCIATED WITH gastrointestinal stromal tumor (ortholog); parathyroid carcinoma (ortholog); FOUND IN mitochondrion (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: replication stress response regulator SDE2; splicing regulator SDE2
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly
Position:
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2123,538,033 - 23,554,768 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1123,486,635 - 23,503,370 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01201,443,945 - 201,460,668 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11206,441,517 - 206,457,679 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1206,441,517 - 206,457,679 (-)Ensemblpanpan1.1panPan2
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

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
SDE2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2123,538,033 - 23,554,768 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1123,486,635 - 23,503,370 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01201,443,945 - 201,460,668 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11206,441,517 - 206,457,679 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1206,441,517 - 206,457,679 (-)Ensemblpanpan1.1panPan2
SDE2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381225,982,702 - 225,999,343 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1225,982,702 - 225,999,343 (-)EnsemblGRCh38hg38GRCh38
GRCh371226,170,403 - 226,187,044 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361224,237,026 - 224,253,689 (-)NCBINCBI36Build 36hg18NCBI36
Celera1199,361,495 - 199,378,155 (-)NCBICelera
Cytogenetic Map1q42.12NCBI
HuRef1196,688,260 - 196,704,921 (-)NCBIHuRef
CHM1_11227,443,144 - 227,459,807 (-)NCBICHM1_1
T2T-CHM13v2.01225,170,616 - 225,187,257 (-)NCBIT2T-CHM13v2.0
Sde2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391180,678,716 - 180,695,678 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1180,678,692 - 180,695,678 (+)EnsemblGRCm39 Ensembl
GRCm381180,851,151 - 180,868,113 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1180,851,127 - 180,868,113 (+)EnsemblGRCm38mm10GRCm38
MGSCv371182,781,282 - 182,798,244 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361182,687,826 - 182,704,788 (+)NCBIMGSCv36mm8
Celera1187,914,171 - 187,931,333 (+)NCBICelera
Cytogenetic Map1H4NCBI
cM Map184.46NCBI
Sde2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81395,110,598 - 95,126,929 (+)NCBIGRCr8
mRatBN7.21392,578,843 - 92,595,142 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1392,578,874 - 92,595,140 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1395,084,206 - 95,100,471 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01396,484,131 - 96,500,394 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01393,658,827 - 93,675,094 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01399,136,921 - 99,153,187 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1399,136,871 - 99,153,181 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013104,135,522 - 104,151,788 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41396,585,245 - 96,601,482 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11396,757,755 - 96,788,687 (+)NCBI
Celera1392,124,002 - 92,140,248 (+)NCBICelera
Cytogenetic Map13q26NCBI
Sde2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955489180,414 - 210,900 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955489181,425 - 210,966 (-)NCBIChiLan1.0ChiLan1.0
SDE2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1738,857,220 - 38,871,584 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl738,857,234 - 38,870,157 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha738,337,558 - 38,351,932 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0738,689,246 - 38,703,633 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl738,689,287 - 38,703,628 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1738,529,069 - 38,543,423 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0738,537,375 - 38,551,733 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0738,806,874 - 38,821,298 (+)NCBIUU_Cfam_GSD_1.0
Sde2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934451,967,783 - 51,984,054 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365262,760,639 - 2,779,657 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365262,763,243 - 2,779,506 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDE2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1013,876,386 - 13,897,862 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11013,879,482 - 13,897,847 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21015,889,651 - 15,908,417 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SDE2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1253,779,561 - 3,793,496 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl253,779,560 - 3,795,893 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660553,784,535 - 3,798,569 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sde2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480797,383 - 127,785 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480797,646 - 127,844 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_003814918 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JARIFH020000001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSPPAT00000051973   ⟹   ENSPPAP00000029125
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
PanPan1.1 Ensembl1206,441,517 - 206,457,679 (-)Ensembl
RefSeq Acc Id: XM_003814918   ⟹   XP_003814966
Type: CODING
Position:
Bonobo AssemblyChrPosition (strand)Source
NHGRI_mPanPan1-v2123,538,033 - 23,554,768 (+)NCBI
NHGRI_mPanPan1123,486,635 - 23,503,370 (+)NCBI
Mhudiblu_PPA_v01201,443,945 - 201,460,668 (-)NCBI
PanPan1.11206,441,517 - 206,457,679 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_003814966 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSPPAP00000029125.1
RefSeq Acc Id: XP_003814966   ⟸   XM_003814918
- UniProtKB: A0A2R9BHI8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSPPAP00000029125   ⟸   ENSPPAT00000051973
Protein Domains
SDE2-like   SDE2/SF3A3 SAP   Splicing regulator SDE2 ubiquitin


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSPPAG00000037583 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSPPAT00000051973.1 UniProtKB/TrEMBL
InterPro RNA_Proc_DNA_Dmg_Regulator UniProtKB/TrEMBL
  SDE2-like_C_dom UniProtKB/TrEMBL
  SDE2-like_dom UniProtKB/TrEMBL
  Sde2_Ubi UniProtKB/TrEMBL
KEGG Report pps:100970067 UniProtKB/TrEMBL
NCBI Gene SDE2 ENTREZGENE
PANTHER REPLICATION STRESS RESPONSE REGULATOR SDE2 UniProtKB/TrEMBL
  SPLICING FACTOR SF3A-RELATED UniProtKB/TrEMBL
Pfam SDE2_2C UniProtKB/TrEMBL
  Sde2_C UniProtKB/TrEMBL
  Sde2_N_Ubi_vert UniProtKB/TrEMBL
UniProt A0A2R9BHI8 ENTREZGENE, UniProtKB/TrEMBL