Vwde (von Willebrand factor D and EGF domains) - Rat Genome Database

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Gene: Vwde (von Willebrand factor D and EGF domains) Rattus norvegicus
Analyze
Symbol: Vwde
Name: von Willebrand factor D and EGF domains
RGD ID: 1561223
Description: Predicted to enable signaling receptor binding activity. Predicted to be active in cell surface and extracellular region. Orthologous to human VWDE (von Willebrand factor D and EGF domains); INTERACTS WITH bisphenol A; indole-3-methanol; 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC502731; RGD1561223; similar to Neurogenic locus notch homolog protein 1 precursor (Notch 1) (Motch A) (mT14) (p300); similar to Neurogenic locus notch homolog protein 1 precursor (Notch1); von Willebrand factor D and EGF domain-containing protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8442,419,676 - 42,468,992 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl442,419,669 - 42,511,840 (-)EnsemblGRCr8
mRatBN7.2441,453,573 - 41,525,421 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl441,455,281 - 41,533,374 (-)EnsemblmRatBN7.2
Rnor_6.0439,632,555 - 39,711,430 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl439,665,015 - 39,711,271 (-)Ensemblrn6Rnor6.0
Rnor_5.0439,463,984 - 39,536,390 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4438,625,182 - 38,704,716 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera436,816,409 - 36,893,983 (-)NCBICelera
Cytogenetic Map4q21NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Vwde
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8442,419,676 - 42,468,992 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl442,419,669 - 42,511,840 (-)EnsemblGRCr8
mRatBN7.2441,453,573 - 41,525,421 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl441,455,281 - 41,533,374 (-)EnsemblmRatBN7.2
Rnor_6.0439,632,555 - 39,711,430 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl439,665,015 - 39,711,271 (-)Ensemblrn6Rnor6.0
Rnor_5.0439,463,984 - 39,536,390 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4438,625,182 - 38,704,716 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera436,816,409 - 36,893,983 (-)NCBICelera
Cytogenetic Map4q21NCBI
VWDE
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38712,330,885 - 12,403,865 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl712,330,201 - 12,403,941 (-)Ensemblhg38GRCh38
GRCh37712,370,511 - 12,443,491 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36712,337,034 - 12,410,377 (-)NCBIBuild 36Build 36hg18NCBI36
Celera712,348,231 - 12,421,579 (-)NCBICelera
Cytogenetic Map7p21.3NCBI
HuRef712,246,755 - 12,320,091 (-)NCBIHuRef
CHM1_1712,370,884 - 12,444,220 (-)NCBICHM1_1
T2T-CHM13v2.0712,461,770 - 12,534,760 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2712,423,482 - 12,496,820 (-)NCBI
Vwde
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39613,156,439 - 13,224,964 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl613,156,298 - 13,224,964 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38613,156,440 - 13,224,965 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl613,156,299 - 13,224,965 (-)Ensemblmm10GRCm38
MGSCv37613,135,610 - 13,174,965 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36613,135,610 - 13,174,965 (-)NCBIMGSCv36mm8
Celera613,287,643 - 13,327,039 (-)NCBICelera
Cytogenetic Map6A1NCBI
cM Map65.64NCBI
Vwde
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495543218,687,192 - 18,752,679 (-)NCBIChiLan1.0ChiLan1.0
VWDE
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2617,202,959 - 17,285,303 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1765,527,675 - 65,610,012 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0713,028,161 - 13,106,766 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1712,372,840 - 12,450,339 (-)NCBIPanPan1.1PanPan1.1panPan2
VWDE
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11427,183,263 - 27,280,746 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1427,175,631 - 27,280,776 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1426,695,181 - 26,792,631 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01427,009,378 - 27,106,967 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1427,032,666 - 27,107,030 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11427,179,733 - 27,277,119 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01426,910,333 - 27,007,784 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01427,162,167 - 27,259,627 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Vwde
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511840,625,050 - 40,697,730 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049367611,749,471 - 1,818,294 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VWDE
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl981,916,966 - 81,986,831 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1981,916,966 - 81,987,106 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2990,080,191 - 90,150,188 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VWDE
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12145,724,553 - 45,803,637 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2145,735,728 - 45,803,638 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604258,664,197 - 58,727,475 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vwde
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248276,897,485 - 6,955,783 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248276,896,018 - 6,957,732 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Vwde
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v16125,477,968 - 125,569,159 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Vwde
397 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:94
Count of miRNA genes:89
Interacting mature miRNAs:89
Transcripts:ENSRNOT00000029602
Prediction methods:Microtar, Miranda, Rnahybrid
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)41308014658080146Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41564430960644309Rat
5685012Bmd87Bone mineral density QTL 875.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)43511329080113290Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)439431983123203361Rat
61445Strs3Sensitivity to stroke QTL 33cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)44140057786400577Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41103870656038706Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)427730518170099664Rat
8655949Rf62Renal function QTL 6222blood urea nitrogen amount (VT:0005265)plasma urea nitrogen level (CMO:0000586)43539660045429897Rat
1331807Rf31Renal function QTL 312.988urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)44049044275726188Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41103870656038706Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)426234499134199155Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4589457557613242Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41103870656038706Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41170660492690519Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41890069763900697Rat
8655961Kidm43Kidney mass QTL 4318kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)43726957782269577Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4145429897Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)427862204126119996Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41103870656038706Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45889999148002343Rat
61475Aia2Adjuvant induced arthritis QTL 25.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)44047145375939996Rat
8694439Bw168Body weight QTL 1689.570.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)44140060386400603Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42228845363245191Rat
2290374Gluco32Glucose level QTL 326.27blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43814419445429897Rat
8552807Vie4Viral induced encephalitis QTL 47.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)41890069763900697Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41103870656038706Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)43044896182336920Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4588999950889999Rat
7387227Uae40Urinary albumin excretion QTL 402.90.0052urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)41891315163913151Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42786220462997402Rat
1558651Swd3Spike wave discharge measurement QTL 34.620.000024brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)44140057786400577Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42192515166925151Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)4163900697Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41103870656038706Rat
1300139Hrtrt6Heart rate QTL 62.85heart pumping trait (VT:2000009)heart rate (CMO:0000002)440490442117737312Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)433538597116185060Rat
11530004Niddm71Non-insulin dependent diabetes mellitus QTL 710.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43353881653719714Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)412212457182430611Rat
1354665Stl10Serum triglyceride level QTL 103.57blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42228845345429897Rat

Markers in Region
AU048071  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2441,373,614 - 41,373,766 (+)MAPPERmRatBN7.2
Rnor_6.0439,561,136 - 39,561,287NCBIRnor6.0
Rnor_5.0439,396,295 - 39,396,446UniSTSRnor5.0
RGSC_v3.4438,542,750 - 38,542,901UniSTSRGSC3.4
Celera436,745,399 - 36,745,550UniSTS
Cytogenetic Map4q21UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
4 1 4 51 23 23 17 2 17 6 74 10 1 48 43 77 6 5 5

Sequence


Ensembl Acc Id: ENSRNOT00000029602   ⟹   ENSRNOP00000029955
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl442,421,390 - 42,499,486 (-)Ensembl
mRatBN7.2 Ensembl441,455,281 - 41,533,374 (-)Ensembl
Rnor_6.0 Ensembl439,665,015 - 39,711,271 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000173353   ⟹   ENSRNOP00000104070
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl442,419,669 - 42,511,840 (-)Ensembl
RefSeq Acc Id: XM_063286914   ⟹   XP_063142984
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8442,419,676 - 42,468,992 (-)NCBI
Protein Sequences
Protein RefSeqs XP_063142984 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM15084 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000029955.6
  ENSRNOP00000104070
  ENSRNOP00000104070.1
Ensembl Acc Id: ENSRNOP00000029955   ⟸   ENSRNOT00000029602
RefSeq Acc Id: XP_063142984   ⟸   XM_063286914
Ensembl Acc Id: ENSRNOP00000104070   ⟸   ENSRNOT00000173353
Protein Domains
EGF-like   VWFD

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AEB5-F1-model_v2 AlphaFold D4AEB5 1-927 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:1561223 AgrOrtholog
BioCyc Gene G2FUF-45619 BioCyc
Ensembl Genes ENSRNOG00000024709 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029602.7 UniProtKB/TrEMBL
  ENSRNOT00000173353 ENTREZGENE
  ENSRNOT00000173353.1 UniProtKB/TrEMBL
Gene3D-CATH Laminin UniProtKB/TrEMBL
InterPro Dev_Signal_Modulators UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/TrEMBL
  EGF_Ca-bd_CS UniProtKB/TrEMBL
  Growth_fac_rcpt_cys_sf UniProtKB/TrEMBL
  VWF_type-D UniProtKB/TrEMBL
NCBI Gene 502731 ENTREZGENE
PANTHER EGF-LIKE-DOMAIN, MULTIPLE 7, 8 UniProtKB/TrEMBL
  VON WILLEBRAND FACTOR D AND EGF DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam D8C_UMOD UniProtKB/TrEMBL
  EGF_TEN UniProtKB/TrEMBL
  Ig_VWDE UniProtKB/TrEMBL
  VWD UniProtKB/TrEMBL
PhenoGen Vwde PhenoGen
PROSITE EGF_1 UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  VWFD UniProtKB/TrEMBL
RatGTEx ENSRNOG00000024709 RatGTEx
SMART EGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  VWD UniProtKB/TrEMBL
Superfamily-SCOP EGF/Laminin UniProtKB/TrEMBL
  SSF57184 UniProtKB/TrEMBL
UniProt A0ABK0LH07_RAT UniProtKB/TrEMBL
  D4AEB5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-09 Vwde  von Willebrand factor D and EGF domains  RGD1561223  similar to Neurogenic locus notch homolog protein 1 precursor (Notch1)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1561223  similar to Neurogenic locus notch homolog protein 1 precursor (Notch1)   RGD1561223_predicted  similar to Neurogenic locus notch homolog protein 1 precursor (Notch1) (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-10 RGD1561223_predicted  similar to Neurogenic locus notch homolog protein 1 precursor (Notch1) (predicted)    similar to Neurogenic locus notch homolog protein 1 precursor (Notch 1) (Motch A) (mT14) (p300) (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1561223_predicted  similar to Neurogenic locus notch homolog protein 1 precursor (Notch 1) (Motch A) (mT14) (p300) (predicted)  LOC502731  similar to Neurogenic locus notch homolog protein 1 precursor (Notch 1) (Motch A) (mT14) (p300)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC502731  similar to Neurogenic locus notch homolog protein 1 precursor (Notch 1) (Motch A) (mT14) (p300)      Symbol and Name status set to provisional 70820 PROVISIONAL