Hectd1 (HECT domain E3 ubiquitin protein ligase 1) - Rat Genome Database
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Gene: Hectd1 (HECT domain E3 ubiquitin protein ligase 1) Rattus norvegicus
Analyze
Symbol: Hectd1
Name: HECT domain E3 ubiquitin protein ligase 1
RGD ID: 1561653
Description: Predicted to have ubiquitin protein ligase activity. Predicted to be involved in several processes, including animal organ development; neural tube closure; and protein ubiquitination. Orthologous to human HECTD1 (HECT domain E3 ubiquitin protein ligase 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2-nitrofluorene; 4,4'-diaminodiphenylmethane.
Type: protein-coding
RefSeq Status: MODEL
Also known as: E3 ubiquitin-protein ligase HECTD1; HECT domain containing 1; HECT domain containing E3 ubiquitin protein ligase 1; LOC362736; RGD1561653; similar to HECT domain containing 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2669,181,429 - 69,267,803 (-)NCBI
Rnor_6.0 Ensembl672,510,255 - 72,596,446 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0672,509,658 - 72,596,285 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0682,073,583 - 82,157,571 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4671,842,842 - 71,930,042 (-)NCBIRGSC3.4rn4RGSC3.4
Celera668,057,228 - 68,144,745 (-)NCBICelera
Cytogenetic Map6q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

Additional References at PubMed
PMID:9636176   PMID:15755804   PMID:17442300   PMID:22431752   PMID:24855001   PMID:25807483   PMID:31505169  


Genomics

Comparative Map Data
Hectd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2669,181,429 - 69,267,803 (-)NCBI
Rnor_6.0 Ensembl672,510,255 - 72,596,446 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0672,509,658 - 72,596,285 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0682,073,583 - 82,157,571 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4671,842,842 - 71,930,042 (-)NCBIRGSC3.4rn4RGSC3.4
Celera668,057,228 - 68,144,745 (-)NCBICelera
Cytogenetic Map6q23NCBI
HECTD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1431,100,112 - 31,207,804 (-)EnsemblGRCh38hg38GRCh38
GRCh381431,100,117 - 31,207,793 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371431,569,323 - 31,676,999 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361430,639,075 - 30,746,440 (-)NCBINCBI36hg18NCBI36
Build 341430,639,074 - 30,746,274NCBI
Celera1411,434,814 - 11,542,175 (-)NCBI
Cytogenetic Map14q12NCBI
HuRef1411,686,880 - 11,794,092 (-)NCBIHuRef
CHM1_11431,568,487 - 31,675,874 (-)NCBICHM1_1
Hectd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391251,790,504 - 51,876,540 (-)NCBIGRCm39mm39
GRCm39 Ensembl1251,790,505 - 51,876,319 (-)Ensembl
GRCm381251,743,721 - 51,829,757 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1251,743,722 - 51,829,536 (-)EnsemblGRCm38mm10GRCm38
MGSCv371252,844,709 - 52,930,523 (-)NCBIGRCm37mm9NCBIm37
MGSCv361252,665,339 - 52,750,973 (-)NCBImm8
Celera1253,048,069 - 53,133,676 (-)NCBICelera
Cytogenetic Map12B3NCBI
cM Map1222.11NCBI
Hectd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540929,373,572 - 29,470,623 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540929,373,572 - 29,470,623 (+)NCBIChiLan1.0ChiLan1.0
HECTD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11430,070,567 - 30,176,915 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1430,070,567 - 30,176,915 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01411,871,973 - 11,979,548 (-)NCBIMhudiblu_PPA_v0panPan3
HECTD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl810,400,604 - 10,491,247 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1810,399,183 - 10,493,074 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hectd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364945,761,801 - 5,853,673 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HECTD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl768,318,417 - 68,422,396 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1768,318,167 - 68,422,403 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2773,199,984 - 73,303,548 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Hectd1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248201,097,323 - 1,196,556 (+)NCBI

Position Markers
RH142634  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0672,556,153 - 72,556,259NCBIRnor6.0
Rnor_5.0682,119,002 - 82,119,108UniSTSRnor5.0
RGSC_v3.4671,889,508 - 71,889,614UniSTSRGSC3.4
Celera668,104,576 - 68,104,682UniSTS
RH 3.4 Map6507.1UniSTS
Cytogenetic Map6q22UniSTS
AI844876  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0672,563,467 - 72,563,605NCBIRnor6.0
Rnor_5.0682,126,316 - 82,126,454UniSTSRnor5.0
RGSC_v3.4671,896,825 - 71,896,963UniSTSRGSC3.4
Celera668,111,891 - 68,112,029UniSTS
Cytogenetic Map6q22UniSTS
RH139635  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0672,511,435 - 72,511,637NCBIRnor6.0
Rnor_5.0682,075,360 - 82,075,562UniSTSRnor5.0
RGSC_v3.4671,844,358 - 71,844,560UniSTSRGSC3.4
Celera668,059,005 - 68,059,207UniSTS
RH 3.4 Map6509.6UniSTS
Cytogenetic Map6q22UniSTS
BI275482  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0672,509,777 - 72,509,973NCBIRnor6.0
Rnor_5.0682,073,702 - 82,073,898UniSTSRnor5.0
RGSC_v3.4671,842,700 - 71,842,896UniSTSRGSC3.4
Celera668,057,347 - 68,057,543UniSTS
RH 3.4 Map6511.9UniSTS
Cytogenetic Map6q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62204285484763421Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63436743680490628Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63499565675623393Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63626028884763275Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63760898075023446Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63810630883106308Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)64167904686679046Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)64167904686679046Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat
4889848Pur25Proteinuria QTL 25140.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)65980306594001333Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)660606431108154445Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)660606431108154445Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)662263348107263348Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)666129520111129520Rat
2293088Iddm28Insulin dependent diabetes mellitus QTL 285.21blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)66622261275023308Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)671206251116206251Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:89
Count of miRNA genes:78
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000008459
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.


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 43 57 41 19 41 8 11 74 35 40 11 8
Low 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008459   ⟹   ENSRNOP00000008459
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl672,510,255 - 72,596,446 (-)Ensembl
RefSeq Acc Id: XM_006240086   ⟹   XP_006240148
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2669,181,429 - 69,267,803 (-)NCBI
Rnor_6.0672,509,658 - 72,596,285 (-)NCBI
Rnor_5.0682,073,583 - 82,157,571 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240087   ⟹   XP_006240149
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2669,181,446 - 69,267,803 (-)NCBI
Rnor_6.0672,509,675 - 72,596,285 (-)NCBI
Rnor_5.0682,073,583 - 82,157,571 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006240088   ⟹   XP_006240150
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2669,181,579 - 69,267,803 (-)NCBI
Rnor_6.0672,510,019 - 72,596,285 (-)NCBI
Rnor_5.0682,073,583 - 82,157,571 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594442   ⟹   XP_017449931
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2669,181,579 - 69,267,803 (-)NCBI
Rnor_6.0672,510,019 - 72,596,285 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017603165   ⟹   XP_017458654
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera668,057,228 - 68,144,745 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039113180   ⟹   XP_038969108
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2669,181,579 - 69,267,803 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_006240150   ⟸   XM_006240088
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006240149   ⟸   XM_006240087
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006240148   ⟸   XM_006240086
- Peptide Label: isoform X1
- UniProtKB: D3ZLS5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017458654   ⟸   XM_017603165
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017449931   ⟸   XM_017594442
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: ENSRNOP00000008459   ⟸   ENSRNOT00000008459
RefSeq Acc Id: XP_038969108   ⟸   XM_039113180
- Peptide Label: isoform X2
Protein Domains
ANK_REP_REGION   HECT   MIB/HERC2

Transcriptome

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

Promoters
RGD ID:13694589
Promoter ID:EPDNEW_R5112
Type:initiation region
Name:Hectd1_2
Description:HECT domain E3 ubiquitin protein ligase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R5113  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0672,596,310 - 72,596,370EPDNEW
RGD ID:13694590
Promoter ID:EPDNEW_R5113
Type:initiation region
Name:Hectd1_1
Description:HECT domain E3 ubiquitin protein ligase 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R5112  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0672,596,539 - 72,596,599EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 82122034 82122035 G A snv LE/Stm (SOLiD) (KNAW), LE/Stm (Illumina) (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
6 72520172 72520173 G A snv F344/NRrrc (MCW)
6 72559185 72559186 G A snv LE/Stm (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561653 AgrOrtholog
Ensembl Genes ENSRNOG00000006905 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008459 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008459 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
  1.25.40.20 UniProtKB/TrEMBL
  2.30.30.920 UniProtKB/TrEMBL
  2.60.120.260 UniProtKB/TrEMBL
InterPro Ankyrin_rpt UniProtKB/TrEMBL
  Ankyrin_rpt-contain_dom UniProtKB/TrEMBL
  Ankyrin_rpt-contain_sf UniProtKB/TrEMBL
  ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  FKBP3_BTHB UniProtKB/TrEMBL
  Galactose-bd-like UniProtKB/TrEMBL
  HECT UniProtKB/TrEMBL
  Hect_E3_ubiquitin_ligase UniProtKB/TrEMBL
  Mib_Herc2 UniProtKB/TrEMBL
  Mib_Herc2_sf UniProtKB/TrEMBL
  Sad1_UNC_C UniProtKB/TrEMBL
KEGG Report rno:362736 UniProtKB/TrEMBL
NCBI Gene 362736 ENTREZGENE
Pfam Ank_2 UniProtKB/TrEMBL
  BTHB UniProtKB/TrEMBL
  HECT UniProtKB/TrEMBL
  MIB_HERC2 UniProtKB/TrEMBL
  Sad1_UNC UniProtKB/TrEMBL
PhenoGen Hectd1 PhenoGen
PROSITE ANK_REP_REGION UniProtKB/TrEMBL
  ANK_REPEAT UniProtKB/TrEMBL
  HECT UniProtKB/TrEMBL
  MIB_HERC2 UniProtKB/TrEMBL
SMART ANK UniProtKB/TrEMBL
  HECTc UniProtKB/TrEMBL
Superfamily-SCOP ANK UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  Gal_bind_like UniProtKB/TrEMBL
  HECT UniProtKB/TrEMBL
  SSF159034 UniProtKB/TrEMBL
UniProt D3ZLS5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-15 Hectd1  HECT domain E3 ubiquitin protein ligase 1  Hectd1  HECT domain containing E3 ubiquitin protein ligase 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-17 Hectd1  HECT domain containing E3 ubiquitin protein ligase 1  Hectd1  HECT domain containing 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Hectd1  HECT domain containing 1  RGD1561653_predicted  similar to HECT domain containing 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561653_predicted  similar to HECT domain containing 1 (predicted)  LOC362736  similar to HECT domain containing 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC362736  similar to HECT domain containing 1      Symbol and Name status set to provisional 70820 PROVISIONAL