Epyc (epiphycan) - Rat Genome Database

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Gene: Epyc (epiphycan) Rattus norvegicus
Analyze
Symbol: Epyc
Name: epiphycan
RGD ID: 1305904
Description: Predicted to be involved in articular cartilage development and bone development. Predicted to act upstream of or within sensory perception of sound. Predicted to be active in extracellular matrix. Orthologous to human EPYC (epiphycan); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; atrazine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: dermatan sulphate proteoglycan 3; Dspg3; LOC314772
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
GRCr8734,323,332 - 34,360,845 (+)NCBIGRCr8
mRatBN7.2732,436,620 - 32,474,326 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl732,436,620 - 32,474,135 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx734,410,533 - 34,448,089 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0736,592,032 - 36,629,589 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0736,333,092 - 36,370,648 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0738,897,278 - 38,934,989 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl738,897,278 - 38,934,985 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0738,938,395 - 38,984,932 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4735,160,934 - 35,198,459 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1735,184,757 - 35,218,169 (+)NCBI
Celera729,474,164 - 29,511,625 (+)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:19932218   PMID:28864419  


Genomics

Comparative Map Data
Epyc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8734,323,332 - 34,360,845 (+)NCBIGRCr8
mRatBN7.2732,436,620 - 32,474,326 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl732,436,620 - 32,474,135 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx734,410,533 - 34,448,089 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0736,592,032 - 36,629,589 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0736,333,092 - 36,370,648 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0738,897,278 - 38,934,989 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl738,897,278 - 38,934,985 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0738,938,395 - 38,984,932 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4735,160,934 - 35,198,459 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1735,184,757 - 35,218,169 (+)NCBI
Celera729,474,164 - 29,511,625 (+)NCBICelera
Cytogenetic Map7q13NCBI
EPYC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381290,963,682 - 91,004,972 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1290,963,682 - 91,005,026 (-)EnsemblGRCh38hg38GRCh38
GRCh371291,357,459 - 91,398,749 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361289,881,591 - 89,922,934 (-)NCBINCBI36Build 36hg18NCBI36
Build 341289,859,933 - 89,901,275NCBI
Celera1291,028,588 - 91,069,952 (-)NCBICelera
Cytogenetic Map12q21.33NCBI
HuRef1288,425,207 - 88,466,578 (-)NCBIHuRef
CHM1_11291,322,430 - 91,363,770 (-)NCBICHM1_1
T2T-CHM13v2.01290,941,190 - 90,982,485 (-)NCBIT2T-CHM13v2.0
Epyc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391097,479,930 - 97,517,770 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1097,479,930 - 97,518,316 (+)EnsemblGRCm39 Ensembl
GRCm381097,644,068 - 97,681,908 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1097,644,068 - 97,682,454 (+)EnsemblGRCm38mm10GRCm38
MGSCv371097,106,702 - 97,144,534 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361097,073,756 - 97,111,588 (+)NCBIMGSCv36mm8
Celera1099,615,059 - 99,652,892 (+)NCBICelera
Cytogenetic Map10C3NCBI
cM Map1050.35NCBI
Epyc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540528,182,829 - 28,212,870 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540528,182,890 - 28,212,864 (-)NCBIChiLan1.0ChiLan1.0
EPYC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21098,996,926 - 99,038,247 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11298,993,320 - 99,034,641 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01288,497,063 - 88,538,440 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11291,812,513 - 91,853,875 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1291,812,513 - 91,853,875 (-)Ensemblpanpan1.1panPan2
EPYC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11531,670,926 - 31,708,667 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1531,671,182 - 31,708,674 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1532,125,595 - 32,163,398 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01532,326,679 - 32,364,492 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1532,326,938 - 32,364,484 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11531,619,635 - 31,657,393 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01531,682,947 - 31,720,906 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01531,976,132 - 32,014,138 (-)NCBIUU_Cfam_GSD_1.0
Epyc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494528,473,084 - 28,509,259 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365077,726,646 - 7,759,989 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365077,726,539 - 7,759,989 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
EPYC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl591,832,291 - 91,877,982 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1591,837,672 - 91,877,779 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2596,316,644 - 96,356,417 (+)NCBISscrofa10.2Sscrofa10.2susScr3
EPYC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11186,373,807 - 86,423,670 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1186,374,285 - 86,419,226 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037158,763,843 - 158,811,341 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Epyc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475015,655,736 - 15,689,563 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475015,655,736 - 15,689,787 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Epyc
495 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:470
Count of miRNA genes:220
Interacting mature miRNAs:260
Transcripts:ENSRNOT00000006450, ENSRNOT00000072166
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
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)71903280735526300Rat
1300138Hrtrt9Heart rate QTL 94.72heart pumping trait (VT:2000009)heart rate (CMO:0000002)72940968353612950Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat


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
5 8 42 100 48 46 19 21 19 6 140 76 83 32 58 27

Sequence


Ensembl Acc Id: ENSRNOT00000006450   ⟹   ENSRNOP00000006450
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl732,436,620 - 32,474,135 (+)Ensembl
Rnor_6.0 Ensembl738,897,278 - 38,934,798 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000072166   ⟹   ENSRNOP00000067851
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl738,900,593 - 38,934,985 (+)Ensembl
RefSeq Acc Id: NM_001108088   ⟹   NP_001101558
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8734,323,332 - 34,360,845 (+)NCBI
mRatBN7.2732,436,620 - 32,474,135 (+)NCBI
Rnor_6.0738,897,278 - 38,934,798 (+)NCBI
Rnor_5.0738,938,395 - 38,984,932 (+)NCBI
RGSC_v3.4735,160,934 - 35,198,459 (+)RGD
Celera729,474,164 - 29,511,625 (+)RGD
Sequence:
RefSeq Acc Id: XM_006241286   ⟹   XP_006241348
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8734,326,541 - 34,360,727 (+)NCBI
mRatBN7.2732,439,824 - 32,474,326 (+)NCBI
Rnor_6.0738,900,440 - 38,934,989 (+)NCBI
Rnor_5.0738,938,395 - 38,984,932 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101558 (Get FASTA)   NCBI Sequence Viewer  
  XP_006241348 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI61903 (Get FASTA)   NCBI Sequence Viewer  
  EDM16829 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006450.5
RefSeq Acc Id: NP_001101558   ⟸   NM_001108088
- UniProtKB: G3V6L6 (UniProtKB/TrEMBL),   A6IG69 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006241348   ⟸   XM_006241286
- Peptide Label: isoform X1
- UniProtKB: B1WBV5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000006450   ⟸   ENSRNOT00000006450
Ensembl Acc Id: ENSRNOP00000067851   ⟸   ENSRNOT00000072166
Protein Domains
LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V6L6-F1-model_v2 AlphaFold G3V6L6 1-359 view protein structure

Transcriptome

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

Promoters
RGD ID:13695172
Promoter ID:EPDNEW_R5690
Type:initiation region
Name:Epyc_1
Description:epiphycan
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R5691  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0738,900,578 - 38,900,638EPDNEW
RGD ID:13695166
Promoter ID:EPDNEW_R5691
Type:initiation region
Name:Epyc_2
Description:epiphycan
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R5690  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0738,900,881 - 38,900,941EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305904 AgrOrtholog
BioCyc Gene G2FUF-34282 BioCyc
Ensembl Genes ENSRNOG00000004717 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006450.8 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8367209 IMAGE-MGC_LOAD
InterPro L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  LRR-contain_N UniProtKB/TrEMBL
  Mimecan/Epiphycan UniProtKB/TrEMBL
KEGG Report rno:314772 UniProtKB/TrEMBL
MGC_CLONE MGC:187623 IMAGE-MGC_LOAD
NCBI Gene 314772 ENTREZGENE
PANTHER PTHR46269 UniProtKB/TrEMBL
  PTHR46269:SF3 UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/TrEMBL
  LRRNT UniProtKB/TrEMBL
PhenoGen Epyc PhenoGen
PROSITE LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004717 RatGTEx
SMART LRR_TYP UniProtKB/TrEMBL
  LRRNT UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
UniProt A6IG69 ENTREZGENE, UniProtKB/TrEMBL
  B1WBV5 ENTREZGENE, UniProtKB/TrEMBL
  G3V6L6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-04 Epyc  epiphycan  Dspg3_predicted  dermatan sulphate proteoglycan 3 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Dspg3_predicted  dermatan sulphate proteoglycan 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED