Eda (ectodysplasin-A) - Rat Genome Database

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Gene: Eda (ectodysplasin-A) Rattus norvegicus
Analyze
Symbol: Eda
Name: ectodysplasin-A
RGD ID: 1563178
Description: Predicted to enable death receptor agonist activity and death receptor binding activity. Predicted to be involved in animal organ development; cytokine-mediated signaling pathway; and regulation of non-canonical NF-kappaB signal transduction. Predicted to act upstream of or within several processes, including hair follicle placode formation; positive regulation of signal transduction; and trachea gland development. Predicted to be located in several cellular components, including apical part of cell; endoplasmic reticulum membrane; and lipid droplet. Predicted to be active in extracellular space. Human ortholog(s) of this gene implicated in ectodermal dysplasia 1 and tooth agenesis. Orthologous to human EDA (ectodysplasin A); PARTICIPATES IN cytokine mediated signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC302424; RGD1563178; similar to ectodysplasin-A isoform Ta A; Tnlg7c; tumor necrosis factor ligand 7c
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
mRatBN7.2X65,078,454 - 65,480,172 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX65,078,673 - 65,480,172 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX66,562,137 - 66,963,601 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X70,062,528 - 70,463,991 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X67,623,411 - 68,024,880 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X69,730,123 - 70,222,693 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX69,730,242 - 70,220,329 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X70,602,479 - 71,095,806 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X87,982,303 - 88,390,680 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX65,441,737 - 65,840,991 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Role of ectodysplasin signalling in middle ear and nasal pathology in rat and mouse models of hypohidrotic ectodermal dysplasia. Del-Pozo J, etal., Dis Model Mech. 2019 Apr 25;12(4). pii: 12/4/dmm037804. doi: 10.1242/dmm.037804.
2. 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.
3. X-linked anhidrotic (hypohidrotic) ectodermal dysplasia is caused by mutation in a novel transmembrane protein. Kere J, etal., Nat Genet. 1996 Aug;13(4):409-16.
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:544312   PMID:4561716   PMID:5893447   PMID:10534613   PMID:10610025   PMID:11039935   PMID:12629675   PMID:15973734   PMID:17673451   PMID:18508042   PMID:18689798   PMID:19619491  
PMID:26646413   PMID:27144394   PMID:35964664  


Genomics

Comparative Map Data
Eda
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X65,078,454 - 65,480,172 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX65,078,673 - 65,480,172 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX66,562,137 - 66,963,601 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X70,062,528 - 70,463,991 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X67,623,411 - 68,024,880 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X69,730,123 - 70,222,693 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX69,730,242 - 70,220,329 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X70,602,479 - 71,095,806 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X87,982,303 - 88,390,680 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX65,441,737 - 65,840,991 (+)NCBICelera
Cytogenetic MapXq22NCBI
EDA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X69,616,113 - 70,039,472 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX69,616,067 - 70,039,472 (+)EnsemblGRCh38hg38GRCh38
GRCh37X68,835,957 - 69,259,322 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X68,752,636 - 69,176,047 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X68,618,931 - 69,042,340NCBI
CeleraX69,189,229 - 69,612,705 (+)NCBICelera
Cytogenetic MapXq13.1NCBI
HuRefX62,655,756 - 63,080,124 (+)NCBIHuRef
CHM1_1X68,729,282 - 69,152,930 (+)NCBICHM1_1
T2T-CHM13v2.0X68,049,526 - 68,472,825 (+)NCBIT2T-CHM13v2.0
Eda
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X99,019,212 - 99,444,366 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX99,019,212 - 99,444,368 (+)EnsemblGRCm39 Ensembl
GRCm38X99,975,606 - 100,400,760 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX99,975,606 - 100,400,762 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X97,170,945 - 97,596,099 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X82,816,290 - 83,239,228 (+)NCBIMGSCv36mm8
MGSCv36X96,178,325 - 96,603,479 (+)NCBIMGSCv36mm8
CeleraX86,912,424 - 87,326,326 (+)NCBICelera
Cytogenetic MapXC3NCBI
cM MapX43.59NCBI
Eda
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554759,178,234 - 9,588,440 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554759,177,911 - 9,592,150 (+)NCBIChiLan1.0ChiLan1.0
EDA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1X69,293,970 - 69,720,913 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X58,881,660 - 59,308,451 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X68,946,036 - 69,371,175 (+)NCBIpanpan1.1PanPan1.1panPan2
EDA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X54,078,694 - 54,515,535 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX54,078,966 - 54,515,535 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX44,906,268 - 45,341,896 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X55,046,702 - 55,482,183 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX55,046,981 - 55,482,183 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X53,014,333 - 53,451,228 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X54,343,122 - 54,782,021 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X54,267,090 - 54,709,181 (+)NCBIUU_Cfam_GSD_1.0
Eda
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X47,673,194 - 47,996,323 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367771,238,272 - 1,557,410 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049367771,545,293 - 1,561,109 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EDA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX55,771,041 - 56,103,265 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X55,770,958 - 56,103,296 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X62,968,935 - 63,300,549 (+)NCBISscrofa10.2Sscrofa10.2susScr3
EDA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X59,453,157 - 59,861,555 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660651,311,650 - 1,730,565 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Eda
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462489158,991 - 488,788 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462489155,310 - 489,072 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Eda
723 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:128
Count of miRNA genes:110
Interacting mature miRNAs:115
Transcripts:ENSRNOT00000004505
Prediction methods:Microtar, Miranda, Pita, 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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
70221Bp56Blood pressure QTL 564.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X5704214165612192Rat

Markers in Region
DXGot192  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X65,100,822 - 65,101,007 (+)MAPPERmRatBN7.2
Rnor_6.0X69,752,473 - 69,752,657NCBIRnor6.0
Rnor_5.0X70,624,818 - 70,625,002UniSTSRnor5.0
RGSC_v3.4X88,004,431 - 88,004,615UniSTSRGSC3.4
CeleraX65,463,606 - 65,463,790UniSTS
Cytogenetic MapXq31UniSTS
AU049644  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X65,395,966 - 65,396,248 (+)MAPPERmRatBN7.2
Rnor_6.0X70,140,273 - 70,140,554NCBIRnor6.0
Rnor_5.0X71,012,668 - 71,012,949UniSTSRnor5.0
RGSC_v3.4X88,309,323 - 88,309,604UniSTSRGSC3.4
CeleraX65,757,132 - 65,757,416UniSTS
Cytogenetic MapXq31UniSTS
PMC24264P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X65,386,875 - 65,386,987 (+)MAPPERmRatBN7.2
Rnor_6.0X70,131,313 - 70,131,424NCBIRnor6.0
Rnor_5.0X71,003,708 - 71,003,819UniSTSRnor5.0
RGSC_v3.4X88,299,881 - 88,299,992UniSTSRGSC3.4
CeleraX65,748,055 - 65,748,166UniSTS
Cytogenetic MapXq31UniSTS
PMC24264P4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X65,476,374 - 65,476,520 (+)MAPPERmRatBN7.2
Rnor_6.0X70,218,896 - 70,219,041NCBIRnor6.0
Rnor_5.0X71,092,009 - 71,092,154UniSTSRnor5.0
RGSC_v3.4X88,390,066 - 88,390,211UniSTSRGSC3.4
CeleraX65,837,194 - 65,837,339UniSTS
Cytogenetic MapXq31UniSTS


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
Low 43 16 4 9 4 8 10 74 29 38 11 8
Below cutoff 3 41 37 10 37 1 6 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000075980   ⟹   ENSRNOP00000067997
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX65,078,673 - 65,480,172 (+)Ensembl
Rnor_6.0 EnsemblX69,730,242 - 70,220,329 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076425   ⟹   ENSRNOP00000067898
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX65,078,673 - 65,480,172 (+)Ensembl
Rnor_6.0 EnsemblX69,730,370 - 70,219,513 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076977
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX69,730,242 - 70,132,510 (+)Ensembl
RefSeq Acc Id: NM_001305243   ⟹   NP_001292172
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X65,078,693 - 65,480,172 (+)NCBI
Rnor_6.0X69,730,242 - 70,222,693 (+)NCBI
CeleraX65,441,737 - 65,840,991 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257111   ⟹   XP_006257173
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X65,078,469 - 65,480,172 (+)NCBI
Rnor_6.0X69,730,123 - 70,222,693 (+)NCBI
Rnor_5.0X70,602,479 - 71,095,806 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257112   ⟹   XP_006257174
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X65,078,464 - 65,480,172 (+)NCBI
Rnor_6.0X69,730,123 - 70,222,693 (+)NCBI
Rnor_5.0X70,602,479 - 71,095,806 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773301   ⟹   XP_008771523
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X65,078,464 - 65,480,172 (+)NCBI
Rnor_6.0X69,730,123 - 70,222,693 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099598   ⟹   XP_038955526
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X65,078,454 - 65,476,344 (+)NCBI
RefSeq Acc Id: XM_228582   ⟹   XP_228582
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X65,078,464 - 65,480,172 (+)NCBI
Rnor_6.0X69,730,123 - 70,222,693 (+)NCBI
Rnor_5.0X70,602,479 - 71,095,806 (+)NCBI
RGSC_v3.4X87,982,303 - 88,390,680 (+)RGD
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_228582   ⟸   XM_228582
- Peptide Label: isoform X3
- UniProtKB: A0A096MJ56 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257174   ⟸   XM_006257112
- Peptide Label: isoform X2
- UniProtKB: A0A096MJ56 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257173   ⟸   XM_006257111
- Peptide Label: isoform X1
- UniProtKB: A0A0U5J6T2 (UniProtKB/TrEMBL),   A0A096MJ56 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771523   ⟸   XM_008773301
- Peptide Label: isoform X4
- UniProtKB: A0A096MJ56 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001292172   ⟸   NM_001305243
- UniProtKB: A0A096MIW0 (UniProtKB/TrEMBL),   A0A096MJ56 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000067997   ⟸   ENSRNOT00000075980
RefSeq Acc Id: ENSRNOP00000067898   ⟸   ENSRNOT00000076425
RefSeq Acc Id: XP_038955526   ⟸   XM_039099598
- Peptide Label: isoform X5
Protein Domains
TNF family profile

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A096MJ56-F1-model_v2 AlphaFold A0A096MJ56 1-378 view protein structure

Transcriptome

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

Promoters
RGD ID:13701866
Promoter ID:EPDNEW_R12386
Type:single initiation site
Name:Eda_1
Description:ectodysplasin-A
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_6.0X69,730,231 - 69,730,291EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563178 AgrOrtholog
BioCyc Gene G2FUF-2141 BioCyc
Ensembl Genes ENSRNOG00000032208 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000075980.3 UniProtKB/TrEMBL
  ENSRNOT00000076425 ENTREZGENE
  ENSRNOT00000076425.2 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.40 UniProtKB/TrEMBL
InterPro TNF_family UniProtKB/TrEMBL
  Tumour_necrosis_fac-like UniProtKB/TrEMBL
KEGG Report rno:302424 UniProtKB/TrEMBL
NCBI Gene 302424 ENTREZGENE
PANTHER ECTODYSPLASIN-A UniProtKB/TrEMBL
  PROTEIN EIGER UniProtKB/TrEMBL
Pfam TNF UniProtKB/TrEMBL
PhenoGen Eda PhenoGen
PROSITE TNF_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000032208 RatGTEx
Superfamily-SCOP TNF_like UniProtKB/TrEMBL
UniProt A0A096MIW0 ENTREZGENE, UniProtKB/TrEMBL
  A0A096MJ56 ENTREZGENE, UniProtKB/TrEMBL
  A0A0U5J6T2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Eda  ectodysplasin-A  RGD1563178_predicted  similar to ectodysplasin-A isoform Ta A (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1563178_predicted  similar to ectodysplasin-A isoform Ta A (predicted)  LOC302424  similar to ectodysplasin-A isoform Ta A  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302424  similar to ectodysplasin-A isoform Ta A      Symbol and Name status set to provisional 70820 PROVISIONAL