Sdad1 (SDA1 domain containing 1) - Rat Genome Database

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Gene: Sdad1 (SDA1 domain containing 1) Rattus norvegicus
Analyze
Symbol: Sdad1
Name: SDA1 domain containing 1
RGD ID: 1359112
Description: Predicted to be involved in ribosomal large subunit biogenesis and ribosomal large subunit export from nucleus. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in nucleoplasm. Predicted to be active in nucleolus. Orthologous to human SDAD1 (SDA1 domain containing 1); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: MGC94390; protein SDA1 homolog; SDA1 domain-containing protein 1
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
GRCr81416,025,726 - 16,052,565 (+)NCBIGRCr8
mRatBN7.21415,741,489 - 15,768,271 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1415,741,434 - 15,771,066 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1415,749,738 - 15,777,109 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01417,068,591 - 17,095,962 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01415,764,032 - 15,791,402 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01417,247,381 - 17,274,228 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1417,247,362 - 17,274,623 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01417,163,867 - 17,190,705 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41417,302,948 - 17,329,725 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11417,302,947 - 17,329,725 (+)NCBI
Celera1415,135,901 - 15,162,678 (+)NCBICelera
Cytogenetic Map14p22NCBI
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
nucleolus  (IBA,IEA,ISO,ISS)
nucleoplasm  (IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Expression and localization studies of hSDA, the human ortholog of the yeast SDA1 gene. Babbio F, etal., Cell Cycle. 2004 Apr;3(4):486-90. Epub 2004 Apr 1.
2. Identification and characterization of RNA sequences to which human PUMILIO-2 (PUM2) and deleted in Azoospermia-like (DAZL) bind. Fox M, etal., Genomics. 2005 Jan;85(1):92-105.
3. 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.
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
7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:11790298   PMID:20439489   PMID:31026094   PMID:31904090  


Genomics

Comparative Map Data
Sdad1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81416,025,726 - 16,052,565 (+)NCBIGRCr8
mRatBN7.21415,741,489 - 15,768,271 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1415,741,434 - 15,771,066 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1415,749,738 - 15,777,109 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01417,068,591 - 17,095,962 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01415,764,032 - 15,791,402 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01417,247,381 - 17,274,228 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1417,247,362 - 17,274,623 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01417,163,867 - 17,190,705 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41417,302,948 - 17,329,725 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11417,302,947 - 17,329,725 (+)NCBI
Celera1415,135,901 - 15,162,678 (+)NCBICelera
Cytogenetic Map14p22NCBI
SDAD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38475,949,915 - 75,990,945 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl475,940,950 - 75,990,962 (-)EnsemblGRCh38hg38GRCh38
GRCh37476,871,068 - 76,912,098 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36477,090,092 - 77,131,137 (-)NCBINCBI36Build 36hg18NCBI36
Build 34477,228,247 - 77,260,314NCBI
Celera474,171,578 - 74,212,624 (-)NCBICelera
Cytogenetic Map4q21.1NCBI
HuRef472,623,470 - 72,664,485 (-)NCBIHuRef
CHM1_1476,847,707 - 76,888,663 (-)NCBICHM1_1
T2T-CHM13v2.0479,290,380 - 79,331,462 (-)NCBIT2T-CHM13v2.0
Sdad1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39592,431,869 - 92,457,883 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl592,431,869 - 92,458,338 (-)EnsemblGRCm39 Ensembl
GRCm38592,284,010 - 92,310,024 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl592,284,010 - 92,310,479 (-)EnsemblGRCm38mm10GRCm38
MGSCv37592,713,036 - 92,739,050 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36593,359,210 - 93,385,224 (-)NCBIMGSCv36mm8
Celera591,876,947 - 91,889,963 (+)NCBICelera
Cytogenetic Map5E2NCBI
cM Map546.42NCBI
Sdad1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955433689,577 - 717,737 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955433690,305 - 717,737 (-)NCBIChiLan1.0ChiLan1.0
SDAD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2354,082,068 - 54,123,098 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1454,271,832 - 54,312,910 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0448,214,836 - 48,255,872 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1454,052,727 - 54,093,549 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl454,052,727 - 54,093,544 (+)Ensemblpanpan1.1panPan2
SDAD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.132511,810 - 538,293 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl32514,697 - 538,140 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3241,345,354 - 41,371,936 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.032535,033 - 561,558 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.132534,950 - 561,299 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.032489,067 - 515,590 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03239,654,554 - 39,681,078 (+)NCBIUU_Cfam_GSD_1.0
Sdad1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528511,487,458 - 11,555,632 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366767,587 - 19,767 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDAD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl871,613,174 - 71,646,779 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1871,612,591 - 71,646,852 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2875,751,421 - 75,782,957 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SDAD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1724,458,854 - 24,496,946 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660372,801,286 - 2,839,273 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sdad1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475715,020,407 - 15,052,528 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475715,020,374 - 15,053,211 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sdad1
83 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:35
Count of miRNA genes:31
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000030222
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
2300159Bmd61Bone mineral density QTL 615.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
2300183Bmd60Bone mineral density QTL 605.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)14126541967Rat
619619Rf4Renal disease susceptibility QTL 44.10.002urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)14132754612Rat
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
70204Niddm20Non-insulin dependent diabetes mellitus QTL 205.10.000008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)14121760616960180Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)14381307418274691Rat
2293089Iddm31Insulin dependent diabetes mellitus QTL 314.7blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)14381307418274691Rat
1300114Srn2Serum renin concentration QTL 23.27blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)14381307421217635Rat
70195Mcs8Mammary carcinoma susceptibility QTL 84.28mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)14381307424531477Rat
1331740Bw26Body weight QTL 263.028body mass (VT:0001259)body weight (CMO:0000012)14381307430767156Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
731183Pia20Pristane induced arthritis QTL 203.55joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)14908897839057237Rat
2302277Gluco38Glucose level QTL 385.8blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062228035204Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
631212Bw5Body weight QTL55.43retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)141103081230320092Rat
1300140Srn3Serum renin concentration QTL 33.19blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)141487516830883947Rat


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 20 32 16 19 16 65 23 41 11
Low 23 25 25 25 8 11 9 12 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000030222   ⟹   ENSRNOP00000035588
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1415,741,434 - 15,764,832 (+)Ensembl
Rnor_6.0 Ensembl1417,247,362 - 17,274,623 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000119066   ⟹   ENSRNOP00000093210
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1415,741,434 - 15,771,066 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000120318   ⟹   ENSRNOP00000086108
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1415,741,434 - 15,765,093 (+)Ensembl
RefSeq Acc Id: NM_001006958   ⟹   NP_001006959
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81416,025,787 - 16,052,565 (+)NCBI
mRatBN7.21415,741,489 - 15,768,271 (+)NCBI
Rnor_6.01417,247,451 - 17,274,228 (+)NCBI
Rnor_5.01417,163,867 - 17,190,705 (+)NCBI
RGSC_v3.41417,302,948 - 17,329,725 (+)RGD
Celera1415,135,901 - 15,162,678 (+)RGD
Sequence:
RefSeq Acc Id: XR_010057348
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81416,025,726 - 16,048,804 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001006959   ⟸   NM_001006958
- UniProtKB: Q5XIQ5 (UniProtKB/Swiss-Prot),   A0A8I6A4P0 (UniProtKB/TrEMBL),   A0A8L2QIL2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000035588   ⟸   ENSRNOT00000030222
RefSeq Acc Id: ENSRNOP00000093210   ⟸   ENSRNOT00000119066
RefSeq Acc Id: ENSRNOP00000086108   ⟸   ENSRNOT00000120318
Protein Domains
SDA1 C-terminal   SDA1 middle   SDA1 N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XIQ5-F1-model_v2 AlphaFold Q5XIQ5 1-686 view protein structure

Transcriptome

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

Promoters
RGD ID:13699214
Promoter ID:EPDNEW_R9739
Type:multiple initiation site
Name:Sdad1_1
Description:SDA1 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_6.01417,247,414 - 17,247,474EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359112 AgrOrtholog
BioCyc Gene G2FUF-16258 BioCyc
Ensembl Genes ENSRNOG00000022229 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00055006325 UniProtKB/Swiss-Prot
  ENSRNOG00060018968 UniProtKB/Swiss-Prot
  ENSRNOG00065018020 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000030222 ENTREZGENE
  ENSRNOT00000030222.5 UniProtKB/TrEMBL
  ENSRNOT00000119066.1 UniProtKB/TrEMBL
  ENSRNOT00000120318.1 UniProtKB/TrEMBL
  ENSRNOT00055010284 UniProtKB/Swiss-Prot
  ENSRNOT00055010286 UniProtKB/Swiss-Prot
  ENSRNOT00060032912 UniProtKB/Swiss-Prot
  ENSRNOT00060032930 UniProtKB/Swiss-Prot
  ENSRNOT00065030256 UniProtKB/Swiss-Prot
  ENSRNOT00065030267 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7133993 IMAGE-MGC_LOAD
InterPro ARM-type_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sda1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SDA1_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SDA1_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Uncharacterised_NUC130/133_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:289504 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94390 IMAGE-MGC_LOAD
NCBI Gene 289504 ENTREZGENE
PANTHER PROTEIN SDA1 HOMOLOG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR12730 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam NUC130_3NT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SDA1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SDA1_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sdad1 PhenoGen
RatGTEx ENSRNOG00000022229 RatGTEx
  ENSRNOG00055006325 RatGTEx
  ENSRNOG00060018968 RatGTEx
  ENSRNOG00065018020 RatGTEx
Superfamily-SCOP SSF48371 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6A4P0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AI82_RAT UniProtKB/TrEMBL
  A0A8L2QIL2 ENTREZGENE, UniProtKB/TrEMBL
  Q5XIQ5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Sdad1  SDA1 domain containing 1      Symbol and Name status set to approved 1299863 APPROVED
2005-07-29 Sdad1  SDA1 domain containing 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_physical_interaction PUM2 and DAZL proteins, both of which are involved in germ cell development, bind a sequence in the 3' UTR of the human SDAD1 mRNA 1559285