Siah3 (siah E3 ubiquitin protein ligase family member 3) - Rat Genome Database

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Gene: Siah3 (siah E3 ubiquitin protein ligase family member 3) Rattus norvegicus
Analyze
Symbol: Siah3
Name: siah E3 ubiquitin protein ligase family member 3
RGD ID: 1592168
Description: Predicted to enable ubiquitin conjugating enzyme binding activity and ubiquitin protein ligase activity. Predicted to be involved in negative regulation of protein targeting to mitochondrion; proteasome-mediated ubiquitin-dependent protein catabolic process; and regulation of protein stability. Predicted to be located in mitochondrion and nucleoplasm. Predicted to be active in cytoplasm. Orthologous to human SIAH3 (siah E3 ubiquitin protein ligase family member 3); INTERACTS WITH bisphenol A; paracetamol; trichloroethene.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: LOC692004; seven in absentia homolog 3; seven in absentia homolog 3 (Drosophila); seven in absentia homolog 3-like; similar to Ubiquitin ligase Siah2 (Seven in absentia homolog 2-like) (Siah-2)
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
GRCr81557,180,245 - 57,247,608 (+)NCBIGRCr8
mRatBN7.21550,770,839 - 50,838,213 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1550,770,871 - 50,834,487 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1554,920,651 - 54,983,939 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01556,038,968 - 56,102,263 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01552,863,924 - 52,928,634 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01557,505,449 - 57,568,743 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1557,505,449 - 57,568,743 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01561,215,305 - 61,278,376 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41556,320,672 - 56,387,549 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1550,401,567 - 50,465,060 (+)NCBICelera
Cytogenetic Map15q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component
cytoplasm  (IBA)
mitochondrion  (IEA,ISO)
nucleoplasm  (IEA,ISO)

Molecular Function

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. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:24270810   PMID:36307912  


Genomics

Comparative Map Data
Siah3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81557,180,245 - 57,247,608 (+)NCBIGRCr8
mRatBN7.21550,770,839 - 50,838,213 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1550,770,871 - 50,834,487 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1554,920,651 - 54,983,939 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01556,038,968 - 56,102,263 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01552,863,924 - 52,928,634 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01557,505,449 - 57,568,743 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1557,505,449 - 57,568,743 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01561,215,305 - 61,278,376 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41556,320,672 - 56,387,549 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1550,401,567 - 50,465,060 (+)NCBICelera
Cytogenetic Map15q11NCBI
SIAH3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381345,777,242 - 45,851,753 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1345,777,242 - 45,851,753 (-)EnsemblGRCh38hg38GRCh38
GRCh371346,351,377 - 46,425,888 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361345,252,406 - 45,323,847 (-)NCBINCBI36Build 36hg18NCBI36
Celera1327,409,074 - 27,480,538 (-)NCBICelera
Cytogenetic Map13q14.13NCBI
HuRef1327,151,095 - 27,222,572 (-)NCBIHuRef
CHM1_11346,323,339 - 46,394,823 (-)NCBICHM1_1
T2T-CHM13v2.01344,998,546 - 45,073,093 (-)NCBIT2T-CHM13v2.0
Siah3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391475,693,372 - 75,767,148 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1475,693,422 - 75,767,148 (+)EnsemblGRCm39 Ensembl
GRCm381475,455,982 - 75,526,141 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1475,455,982 - 75,529,708 (+)EnsemblGRCm38mm10GRCm38
MGSCv371475,855,789 - 75,925,948 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361474,190,132 - 74,260,462 (+)NCBIMGSCv36mm8
Celera1472,957,859 - 73,027,877 (+)NCBICelera
Cytogenetic Map14D3NCBI
cM Map1440.08NCBI
Siah3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555183,472,425 - 3,539,115 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555183,473,120 - 3,539,086 (-)NCBIChiLan1.0ChiLan1.0
SIAH3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21445,539,882 - 45,612,512 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11336,593,953 - 36,666,560 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01327,180,382 - 27,255,005 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SIAH3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1225,320,083 - 5,390,389 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl225,320,249 - 5,386,508 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha225,309,191 - 5,379,473 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0225,438,371 - 5,508,337 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl225,438,394 - 5,510,519 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1225,219,846 - 5,290,132 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0225,283,539 - 5,353,477 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0225,288,339 - 5,358,617 (+)NCBIUU_Cfam_GSD_1.0
Siah3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945155,915,563 - 155,984,592 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936857339,615 - 406,806 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936857341,879 - 406,806 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIAH3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1121,501,492 - 21,562,077 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11121,500,605 - 21,562,301 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21122,075,723 - 22,078,885 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SIAH3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1323,840,947 - 23,909,954 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl323,841,195 - 23,908,631 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605720,108,328 - 20,176,080 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Siah3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247489,136,650 - 9,231,109 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247489,136,665 - 9,234,392 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Siah3
459 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:88
Count of miRNA genes:77
Interacting mature miRNAs:80
Transcripts:ENSRNOT00000064945
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)152788577486257085Rat
724545Niddm54Non-insulin dependent diabetes mellitus QTL 540.02blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)155079449473699215Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat

Markers in Region
D15Rat19  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21550,794,494 - 50,794,652 (+)MAPPERmRatBN7.2
Rnor_6.01557,528,970 - 57,529,125NCBIRnor6.0
Rnor_5.01561,238,603 - 61,238,758UniSTSRnor5.0
RGSC_v3.41556,346,569 - 56,346,725RGDRGSC3.4
RGSC_v3.41556,346,570 - 56,346,725UniSTSRGSC3.4
RGSC_v3.11556,362,349 - 56,362,505RGD
Celera1550,425,266 - 50,425,421UniSTS
SHRSP x BN Map1534.6299RGD
SHRSP x BN Map1534.6299UniSTS
FHH x ACI Map1547.47RGD
Cytogenetic Map15q11UniSTS
D15Rat122  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21550,782,130 - 50,782,301 (+)MAPPERmRatBN7.2
Rnor_6.01557,516,608 - 57,516,778NCBIRnor6.0
Rnor_5.01561,226,241 - 61,226,411UniSTSRnor5.0
RGSC_v3.41556,334,208 - 56,334,379RGDRGSC3.4
RGSC_v3.41556,334,209 - 56,334,379UniSTSRGSC3.4
RGSC_v3.11556,349,968 - 56,350,359RGD
Celera1550,412,906 - 50,413,076UniSTS
SHRSP x BN Map1534.6299RGD
SHRSP x BN Map1534.6299UniSTS
Cytogenetic Map15q11UniSTS
D15Rat146  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21550,819,755 - 50,819,957 (+)MAPPERmRatBN7.2
Rnor_6.01557,554,226 - 57,554,427NCBIRnor6.0
Rnor_5.01561,263,859 - 61,264,060UniSTSRnor5.0
RGSC_v3.41556,371,825 - 56,372,027RGDRGSC3.4
RGSC_v3.41556,371,826 - 56,372,027UniSTSRGSC3.4
RGSC_v3.11556,387,605 - 56,387,807RGD
Celera1550,450,526 - 50,450,727UniSTS
SHRSP x BN Map1534.6299RGD
SHRSP x BN Map1534.6299UniSTS
Cytogenetic Map15q11UniSTS
D15Got60  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21550,804,015 - 50,804,211 (+)MAPPERmRatBN7.2
Rnor_6.01557,538,489 - 57,538,682NCBIRnor6.0
Rnor_5.01561,248,122 - 61,248,315UniSTSRnor5.0
RGSC_v3.41556,356,088 - 56,356,282RGDRGSC3.4
RGSC_v3.41556,356,089 - 56,356,282UniSTSRGSC3.4
RGSC_v3.11556,371,868 - 56,372,062RGD
Celera1550,434,785 - 50,434,978UniSTS
RH 2.0 Map15370.8RGD
Cytogenetic Map15q11UniSTS


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
7 3 36 113 41 30 13 9 13 6 115 65 93 29 57 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001191118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide JAXUCZ010000015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000064945   ⟹   ENSRNOP00000059053
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1550,770,871 - 50,834,487 (+)Ensembl
Rnor_6.0 Ensembl1557,505,449 - 57,568,743 (+)Ensembl
RefSeq Acc Id: NM_001191118   ⟹   NP_001178047
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81557,180,245 - 57,247,608 (+)NCBI
mRatBN7.21550,770,839 - 50,838,213 (+)NCBI
Rnor_6.01557,505,449 - 57,568,743 (+)NCBI
Rnor_5.01561,215,305 - 61,278,376 (+)NCBI
Celera1550,401,567 - 50,465,060 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178047 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000059053.2
RefSeq Acc Id: NP_001178047   ⟸   NM_001191118
- UniProtKB: F1M4M8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000059053   ⟸   ENSRNOT00000064945
Protein Domains
Seven-in-absentia protein TRAF-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M4M8-F1-model_v2 AlphaFold F1M4M8 1-268 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1592168 AgrOrtholog
BioCyc Gene G2FUF-13126 BioCyc
Ensembl Genes ENSRNOG00000043061 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064945.3 UniProtKB/TrEMBL
Gene3D-CATH Classic Zinc Finger UniProtKB/TrEMBL
InterPro 7-in-absentia-prot UniProtKB/TrEMBL
  7-in-absentia-prot_TRAF-dom UniProtKB/TrEMBL
  TRAF-like UniProtKB/TrEMBL
KEGG Report rno:692004 UniProtKB/TrEMBL
NCBI Gene 692004 ENTREZGENE
PANTHER PTHR45877 UniProtKB/TrEMBL
  SEVEN IN ABSENTIA HOMOLOG 3 UniProtKB/TrEMBL
Pfam Sina UniProtKB/TrEMBL
PhenoGen Siah3 PhenoGen
RatGTEx ENSRNOG00000043061 RatGTEx
Superfamily-SCOP TRAF domain-like UniProtKB/TrEMBL
UniProt F1M4M8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Siah3  siah E3 ubiquitin protein ligase family member 3  LOC100366198  seven in absentia homolog 3-like  Data merged from RGD:2324160 1643240 APPROVED
2012-10-16 Siah3  siah E3 ubiquitin protein ligase family member 3  Siah3  seven in absentia homolog 3 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-06 LOC100366198  seven in absentia homolog 3-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-04-23 Siah3  seven in absentia homolog 3 (Drosophila)  LOC692004  similar to Ubiquitin ligase Siah2 (Seven in absentia homolog 2-like) (Siah-2)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC692004  similar to Ubiquitin ligase Siah2 (Seven in absentia homolog 2-like) (Siah-2)      Symbol and Name status set to provisional 70820 PROVISIONAL