RetrogeneDB ID:

retro_eeur_527

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_338727:393..2068(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PCDHGA1
Ensembl ID:ENSEEUG00000002556
Aliases:None
Description:protocadherin gamma subfamily A, 1 [Source:HGNC Symbol;Acc:8696]


Retrocopy-Parental alignment summary:






>retro_eeur_527
AAAATAATCGATATTTAATGACAACTTCCCACGCTTCCGAGATGAAGTAGTAGAGGTGAAAATTAATGAGATTGCCACTA
CAGGAACGCGGCTAGCGCTGCCCTTTGCTCGAGATGCGGATGTGGGAGTCAACTCCCTTCAGAGTTACCAGCTCAGCTCC
AATAAGCACTTCTCTCTAGATGAGAAAAGCGGGAGTGATGGGCAAAAATACCCAGAGCTAATCTTGGAGTGGCCCCTGGA
CCGAGAGAAAGTGGCTGTTCACGACCTCCTCCTCACAGCTCTAGATGGTGGTCACCCCGTGCTCTCAGGGACCACGCACA
TCCGCGTGATGGTCCTGGACGCAAATGATAATGCGCCCCTGTTCACGCGACCAGAGTACACAGTGAATGTGCCAGAGAAC
CTACCTGTAGGCACCCGGCTGCTCACACTAACCGCCACGGATCCAGATGAGGGAATAAATGGGGAGTTGACCTACTATTT
CCGCAATGAAGAAGACAAGATTTCAGAGACTTTCCGACTTGATTCAAACCTGGGTGAAGTCACTACTGTGCAATCGCTGG
ATTATGAAGAATCCACTTCCTACCTGATGGAAGTCGTGGCTCAGGATGGAGGTGCTCTTCTTGCTAGCGCTAATGTGGTA
GTCACAGTACAGGATGTGAATGACAATGTCCCTGAAGTGATCCTCACGTCTCTGGTCAGTTCTGTCTCTGAAGACTGTCT
CCCAGGAACCATCATTGCGCTGTTTAGTGTACATGACAGTGATTCTGGTGAGAATGGTGAGGTTACATGTTCTATCCCTA
ACAGCTTGCCCTTTAAGCTGGAAAAATCAGTTGATAATTACTATCACTTATTGACAACCGGAGCCCTAGATAGGGAAGAA
ATCTCAGATTATAACATCACAGTAACTGTCACTGATCATGGTAACCCACCCTTGTCTACAGAAAATCACATCTCCCTGAA
GGTGGTAGACATCAATGACAACTCTCCCTTCTTCCTTCACACTTCATACTCTGCAAATATCCCAGAAAACAACCCCAGAG
GCATATCAATCTTCTCTGTAACTGCTCATGACCCAGACAGTGACAACAATGCCCTTGTTACTTACTCTTTAGCTGAGGAT
ATGTTTGAGGGAGCACCTCTGTCTTCTTTTGTCTCCATCAACTCTGACACAGGAGTCCTCTATGCACTTCGTTCTTTTGA
CTATGAACAGGTTAGATACCTGCAGCTATGGGTGAAGGCCACAGACAGTGGGGACCCTCCACTCAGCAGCAATGTGTCCC
TGAGGCTGTTCGTGCTGGACCAGAATGACAACACACCAGAGATCCTCTATCCCACTCTTCCTACTGATGGTTCCACTGGG
GTGGAGCTGGCACCCCGCTCTGCAGAGCCCGGATACCTGGTGACCAAGGTGGTGGCAGTGGACAGAGACTCAGGCCAGAA
TGCCTGGCTGTCCTACCGCCTGCTCAAGGCCAGTGAGCCAGGGCTCTTCTCAGTGGGACTGCACACAGGTGAGGTGCACA
CTGCCAGGGCCCTGCTGGACAGAGATGCTCTCAAGCAGAGCCTGGTGGTGGCAGTGCAGGACCATGGCCAGCCCCCTCTC
TCAGCCACTGTCACACTCACTGTGGCCATAGCTGACAGCATCCCAGATGTGCTGGCTGGACTGGGCAGCCTGGAG

ORF - retro_eeur_527 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.56 %
Parental protein coverage: 68.05 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalEILDI-NDNAPHFQIEELELKMNEITSPGTRIPLPFGQDFDVGVNSLQSYQLSSNPHFFLDVQQGADGLQ
.I.DI.NDN.P.F..E..E.K.NEI...GTR..LPF..D.DVGVNSLQSYQLSSN.HF.LD...G.DG..
RetrocopyKIIDI>NDNFPRFRDEVVEVKINEIATTGTRLALPFARDADVGVNSLQSYQLSSNKHFSLDEKSGSDGQK
ParentalHPEMVLQSPLDREQEAVHHLVLTASDGGDPVRSGMLRIHVQVVDANVNPPTFTQAQYQVSVLENVPLGTQ
.PE..L..PLDRE..AVH.L.LTA.DGG.PV.SG...I.V.V.DAN.N.P.FT...Y.V.V.EN.P.GT.
RetrocopyYPELILEWPLDREKVAVHDLLLTALDGGHPVLSGTTHIRVMVLDANDNAPLFTRPEYTVNVPENLPVGTR
ParentalLLTVKATDPDEGANGEVTYAFHNIDHRVAQIFQLDPHMGEITNKEPLDFEEYNLYPMEIQAQDGAGLMAR
LLT..ATDPDEG.NGE.TY.F.N........F.LD...GE.T....LD.EE...Y.ME..AQDG..L.A.
RetrocopyLLTLTATDPDEGINGELTYYFRNEEDKISETFRLDSNLGEVTTVQSLDYEESTSYLMEVVAQDGGALLAS
ParentalAKVLVKVLDINDNAPEVTITSVTASVPENFPPGTIIALINVHDQDSGDNGHTTCSISRNLPFKLEKLVDN
A.V.V.V.D.NDN.PEV..TS...SV.E...PGTIIAL..VHD.DSG.NG..TCSI...LPFKLEK.VDN
RetrocopyANVVVTVQDVNDNVPEVILTSLVSSVSEDCLPGTIIALFSVHDSDSGENGEVTCSIPNSLPFKLEKSVDN
ParentalYYRLVTEKTLDRELTPTYNITVTATDQGTPALSTEAHISLHITDINDNSPVFSQDSYSAYIPENNPRGAS
YY.L.T...LDRE....YNITVT.TD.G.P.LSTE.HISL...DINDNSP.F...SYSA.IPENNPRG.S
RetrocopyYYHLLTTGALDREEISDYNITVTVTDHGNPPLSTENHISLKVVDINDNSPFFLHTSYSANIPENNPRGIS
ParentalIFSVTAHDADSNENAQVNYFLAEDDILGAPLSSYVSINSDIGVLYALCSFDYEQFRELQLWVTALDSGKP
IFSVTAHD.DS..NA.V.Y.LAED...GAPLSS.VSINSD.GVLYAL.SFDYEQ.R.LQLWV.A.DSG.P
RetrocopyIFSVTAHDPDSDNNALVTYSLAEDMFEGAPLSSFVSINSDTGVLYALRSFDYEQVRYLQLWVKATDSGDP
ParentalPLSSNVSLRLFILDQNDNVPEILYPTLPTDGSTGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLK
PLSSNVSLRLF.LDQNDN.PEILYPTLPTDGSTGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLK
RetrocopyPLSSNVSLRLFVLDQNDNTPEILYPTLPTDGSTGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLK
ParentalASEPGLFSVGLHTGEVHTARALLDRDALKQSLVVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLE
ASEPGLFSVGLHTGEVHTARALLDRDALKQSLVVAVQDHGQPPLSATVTLTVAIADSIPDVLA.LGSLE
RetrocopyASEPGLFSVGLHTGEVHTARALLDRDALKQSLVVAVQDHGQPPLSATVTLTVAIADSIPDVLAGLGSLE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 7 .41 RPM 6 .77 RPM
SRP017611_kidney 0 .94 RPM 0 .75 RPM
SRP017611_liver 0 .16 RPM 0 .16 RPM

ChIP-Seq - click to see more details

Erinaceus europaeus was not studied using ChIP-Seq data.

EST - click to see more details

Erinaceus europaeus was not studied using EST data.

TSS - click to see more details

Erinaceus europaeus was not studied using FANTOM5 data.

Lab - click to see more details

retro_eeur_527 was not experimentally validated.

Retrocopy orthology:
Erinaceus europaeus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 3 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Erinaceus europaeus ENSEEUG00000002556 6 retrocopies
retro_eeur_140, retro_eeur_291, retro_eeur_527 , retro_eeur_630, retro_eeur_631, retro_eeur_637,
Ficedula albicollis ENSFALG000000084761 retrocopy
retro_falb_10,
Pelodiscus sinensis ENSPSIG000000048272 retrocopies
retro_psin_14, retro_psin_43,


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