EDDM13 (epididymal protein 13) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: EDDM13 (epididymal protein 13) Homo sapiens
Analyze
Symbol: EDDM13
Name: epididymal protein 13
RGD ID: 12799211
HGNC Page HGNC:53168
Description: Predicted to be located in extracellular region and membrane.
Type: protein-coding
RefSeq Status: VALIDATED
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Squirrel
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381956,272,748 - 56,310,454 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1956,272,748 - 56,310,454 (+)EnsemblGRCh38hg38GRCh38
GRCh371956,784,117 - 56,821,823 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map19q13.43NCBI
HuRef1953,093,720 - 53,130,844 (+)NCBIHuRef
CHM1_11956,776,517 - 56,814,291 (+)NCBICHM1_1
T2T-CHM13v2.01959,371,075 - 59,408,175 (+)NCBIT2T-CHM13v2.0
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

References
Additional References at PubMed
PMID:7566098  


Genomics

Comparative Map Data
EDDM13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381956,272,748 - 56,310,454 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1956,272,748 - 56,310,454 (+)EnsemblGRCh38hg38GRCh38
GRCh371956,784,117 - 56,821,823 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map19q13.43NCBI
HuRef1953,093,720 - 53,130,844 (+)NCBIHuRef
CHM1_11956,776,517 - 56,814,291 (+)NCBICHM1_1
T2T-CHM13v2.01959,371,075 - 59,408,175 (+)NCBIT2T-CHM13v2.0
Eddm13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3976,255,636 - 6,284,860 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl76,255,709 - 6,285,065 (+)EnsemblGRCm39 Ensembl
GRCm3876,252,637 - 6,281,861 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl76,252,710 - 6,282,066 (+)EnsemblGRCm38mm10GRCm38
MGSCv3776,204,312 - 6,233,463 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3675,855,797 - 5,884,948 (+)NCBIMGSCv36mm8
Celera75,985,492 - 6,015,077 (+)NCBICelera
Cytogenetic Map7A1NCBI
cM Map73.62NCBI
Eddm13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2167,630,905 - 67,656,404 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl167,626,244 - 67,657,342 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0171,296,094 - 71,324,703 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Celera165,370,545 - 65,398,773 (-)NCBICelera
Cytogenetic Map1q12NCBI
EDDM13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22062,562,467 - 62,602,426 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11964,354,103 - 64,392,552 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01953,300,144 - 53,337,601 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11962,095,231 - 62,132,727 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1962,095,441 - 62,132,431 (+)Ensemblpanpan1.1panPan2
EDDM13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11101,672,412 - 101,702,976 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1101,670,790 - 101,702,951 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1101,855,460 - 101,887,864 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01102,315,507 - 102,343,360 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11101,954,114 - 101,981,928 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01101,671,632 - 101,699,648 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01102,428,508 - 102,456,340 (-)NCBIUU_Cfam_GSD_1.0
Eddm13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244093491,420,260 - 1,447,569 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493688233,145 - 60,264 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0

Variants

.
Variants in EDDM13
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 19q13.33-13.43(chr19:50191219-58535818)x3 copy number gain See cases [RCV000050883] Chr19:50191219..58535818 [GRCh38]
Chr19:50694476..59047185 [GRCh37]
Chr19:55386288..63738997 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:47908540-58539965)x3 copy number gain See cases [RCV000052914] Chr19:47908540..58539965 [GRCh38]
Chr19:48411797..59051332 [GRCh37]
Chr19:53103609..63743144 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:47929575-58572206)x3 copy number gain See cases [RCV000052915] Chr19:47929575..58572206 [GRCh38]
Chr19:48432832..59083573 [GRCh37]
Chr19:53124644..63775385 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:49907832-58557889)x3 copy number gain See cases [RCV000052925] Chr19:49907832..58557889 [GRCh38]
Chr19:50411089..59069256 [GRCh37]
Chr19:55102901..63761068 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:51141518-58539965)x3 copy number gain See cases [RCV000052926] Chr19:51141518..58539965 [GRCh38]
Chr19:51644775..59051332 [GRCh37]
Chr19:56336587..63743144 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:52955056-58581203)x3 copy number gain See cases [RCV000134139] Chr19:52955056..58581203 [GRCh38]
Chr19:53458309..59092570 [GRCh37]
Chr19:58150121..63784382 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:52612432-58581203)x3 copy number gain See cases [RCV000134174] Chr19:52612432..58581203 [GRCh38]
Chr19:53115685..59092570 [GRCh37]
Chr19:57807497..63784382 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.42-13.43(chr19:55550939-57031576)x1 copy number loss See cases [RCV000135287] Chr19:55550939..57031576 [GRCh38]
Chr19:56062305..57542944 [GRCh37]
Chr19:60754117..62234756 [NCBI36]
Chr19:19q13.42-13.43		 likely pathogenic
GRCh38/hg38 19q13.33-13.43(chr19:50152520-58581203)x3 copy number gain See cases [RCV000135843] Chr19:50152520..58581203 [GRCh38]
Chr19:50655777..59092570 [GRCh37]
Chr19:55347589..63784382 [NCBI36]
Chr19:19q13.33-13.43		 pathogenic
GRCh38/hg38 19q13.42-13.43(chr19:55048514-56972458)x3 copy number gain See cases [RCV000138139] Chr19:55048514..56972458 [GRCh38]
Chr19:55595687..57483826 [GRCh37]
Chr19:60251694..62175638 [NCBI36]
Chr19:19q13.42-13.43		 likely pathogenic
GRCh38/hg38 19q13.41-13.43(chr19:52143873-58445521)x3 copy number gain See cases [RCV000142008] Chr19:52143873..58445521 [GRCh38]
Chr19:52647126..58956888 [GRCh37]
Chr19:57338938..63648700 [NCBI36]
Chr19:19q13.41-13.43		 pathogenic
GRCh38/hg38 19q13.42-13.43(chr19:55037146-56982033)x3 copy number gain See cases [RCV000142245] Chr19:55037146..56982033 [GRCh38]
Chr19:55548514..57493401 [GRCh37]
Chr19:60240326..62185213 [NCBI36]
Chr19:19q13.42-13.43		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1823
Count of miRNA genes:796
Interacting mature miRNAs:963
Transcripts:ENST00000586573, ENST00000587247, ENST00000588026, ENST00000588154, ENST00000591188, ENST00000591810, ENST00000593116, ENST00000593151
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.


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 sensory system adipose tissue appendage entire extraembryonic component
High
Medium 1 1 1 217 3 9 41
Low 179 70 627 90 459 44 1269 58 685 137 818 842 53 152 709 1
Below cutoff 2171 2697 986 435 1225 320 2704 1999 2807 250 583 692 117 1044 1913 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000586573
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1956,284,134 - 56,286,680 (+)Ensembl
RefSeq Acc Id: ENST00000587247   ⟹   ENSP00000490008
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1956,301,990 - 56,310,450 (+)Ensembl
RefSeq Acc Id: ENST00000588154
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1956,295,828 - 56,297,869 (+)Ensembl
RefSeq Acc Id: ENST00000591188
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1956,284,181 - 56,310,450 (+)Ensembl
RefSeq Acc Id: ENST00000591810
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1956,298,091 - 56,302,077 (+)Ensembl
RefSeq Acc Id: ENST00000593116   ⟹   ENSP00000490076
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1956,272,769 - 56,302,043 (+)Ensembl
RefSeq Acc Id: ENST00000593151
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1956,301,936 - 56,310,446 (+)Ensembl
RefSeq Acc Id: ENST00000649256   ⟹   ENSP00000497858
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1956,272,748 - 56,310,454 (+)Ensembl
RefSeq Acc Id: NM_001354658   ⟹   NP_001341587
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381956,272,748 - 56,310,454 (+)NCBI
T2T-CHM13v2.01959,371,075 - 59,408,175 (+)NCBI
Sequence:
RefSeq Acc Id: XM_054319479   ⟹   XP_054175454
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01959,371,080 - 59,408,171 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001341587 (Get FASTA)   NCBI Sequence Viewer  
  XP_054175454 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A0A1B0GTR0 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000490008.1
  ENSP00000490076.1
  ENSP00000497858
  ENSP00000497858.1
Reference Protein Sequences
RefSeq Acc Id: NP_001341587   ⟸   NM_001354658
- Peptide Label: precursor
- UniProtKB: A0A1B0GTR0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000497858   ⟸   ENST00000649256
RefSeq Acc Id: ENSP00000490008   ⟸   ENST00000587247
RefSeq Acc Id: ENSP00000490076   ⟸   ENST00000593116
RefSeq Acc Id: XP_054175454   ⟸   XM_054319479
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A1B0GTR0-F1-model_v2 AlphaFold A0A1B0GTR0 1-161 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:53168 AgrOrtholog
COSMIC EDDM13 COSMIC
Ensembl Genes ENSG00000267710 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000587247.1 UniProtKB/TrEMBL
  ENST00000593116.5 UniProtKB/TrEMBL
  ENST00000649256 ENTREZGENE
  ENST00000649256.2 UniProtKB/Swiss-Prot
GTEx ENSG00000267710 GTEx
HGNC ID HGNC:53168 ENTREZGENE
Human Proteome Map EDDM13 Human Proteome Map
NCBI Gene EDDM13 ENTREZGENE
PharmGKB PA166180606 PharmGKB
UniProt A0A1B0GTR0 ENTREZGENE
  A0A1B0GU87_HUMAN UniProtKB/TrEMBL
  A0A1B0GUE6_HUMAN UniProtKB/TrEMBL
  EDD13_HUMAN UniProtKB/Swiss-Prot