RetrogeneDB ID:

retro_eeur_630

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_371214:3799..6196(+)
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_630
ATGGCGACCCGTCCTTCTCACCCAGGCTGCAGCCTACTAGCTGGGATCTGCGTTCTCCTGGGGACCCTGTGGGAAATCCG
GGCAGATCAGATCCGCTATGCAGTGCCTGAGGAGCTGGACAAAGGCGCTTTTGTTGGTAACATCGCCAAGGACCTGGGTT
TGGAGCCCCAGGAGCTGGTGGAGCACGGAGTCCGCATCGTCTCCCAAGGTAAGACACAGCTCTTTGCTCTGAACCGGCAC
AGCGGCAGCTTGGTCACCGCGGGCAGAATCGACCGCGAGGAGCTCTGTGACAGATCTCCAAAGTGTGTTGTAAGCCTGGA
GATTCTCCTGGAGGATAAAGTCAAGATTTTGGAAGTAGAAGTAGAAATAATGGATGTTAATGATAACGCGCCCAATTTTG
GGACAGAACAAAGGGAAATAAAAGTCGCTGAAAATGAAAACCCCGGGACTAGATTCCCTCTTCCTGAAGCTTTTGATTCA
GATATAGGGGTAAATTCTCTGCAGGGCTACCAACTCAGCTCCAGTGTTCACTTTTCCCTGGATGTGCAAAGTGGAGCCGA
TGGAATTAAGTATCCTGAGCTGGTTCTGGAGCGCACACTGGACAGGGAGGAAGAGGCTGTTCACTACCTGGTTCTCACAG
CCTTTGATGGAGGAGACCCAGTTCACTCTGGCACTGCCAAGATTCATGTTACACTTGTGGATACCAACGACAATGTCCCC
ATATTCACTCAGCCTGAGTATCGTGTGAGTGTTCAGGAGAATGTGCCAGTGGGCTCTCAGCTACTCACCCTAAGAGCCAC
TGATGCAGATGAAGGAGCCAATGGAGAAGTCACATATTCTTTCCGGAAAGTAAGAGATAAAATAGCCCAGCTATTCCAGT
TAAATTCTCAGAGTGGGGAGATAACAGTGATGGGAGATCTAGATTATGAGGACTCTGGATTCTATGACATAGATGTAGAG
GCTCATGATGGACCTGGTCTTCGAGCCAGAAGTAAGGTTCTTGTGACAGTTCTGGATATAAATGACAATGCCCCAGAAGT
CAAGATTACATCTCTCACCAGTTCCATCCAGGAAGCTTCCTCCCCAGGTACAGTAATCGCACTTTTTAGTGTGCATGACA
GTGATTCAGGAGAGAATGGTCTCGTCACCTGTTCTATTCCAGATAATCTTCCATTCACGCTGGAAAAGACCTATGGAAAT
TACTATCGGTTGTTAACCCAAAGGACTCTAGATAGGGAAGAAGTCTCAGAATATAATCTCACAGTAACTGCCACAGACCA
TGGAAGTCCACCACTATCTACAGAAACCCACATCACCCTACATGTAGCAGACATCAATGACAACCCACCTGTTTTTCCCC
AAGCTTCCTACTTTGCCTACATTCCTGAAAACAACCCCAGAGGAGCCTCCATTTTATCTGTGACAGCCAGGGACCCTGAC
AGTGTGGAGAATGCCAGAGTCAGTTACTCCCTCACTGAGGACTCACTGCAGGAGGTCCCCCTCTCCACCTACATCTCCAT
CAATTCTGAAACCGGTGTCTTGTATGCACTGCACTCCTTTGACTATGAACAGGTTAGAGACCTGCAACTGCAGGTGACAG
CCAGTGACAGTGGGGACCCTCCACTCAGTAGCAATGTATCTCTCACTCTATTCATTCTGGACCAGAATGACAACTCACCT
GAAATCCTGTACCCCACCTTCCCCACTGATGGTTCCACAGGAGTGGAGCTGGCACCCCGCTCTGCAGAGCCCGGATACCT
GGTGACCAAGGTGGTGGCAGTGGACAGAGACTCAGGCCAGAATGCCTGGCTGTCCTACCGCCTGCTCAAGGCCAGTGAGC
CAGGGCTCTTCTCAGTGGGGCTGCACACAGGTGAGGTGCACACTGCTAGGGCCCTGCTGGACAGAGATGCTCTCAAGCAG
AGCCTGGTGGTGGCAGTGCAGGACCATGGCCAGCCCCCTCTCTCAGCCACTGTCACACTCACTGTGGCCATAGCTGACAG
CATCCCAGATGTGCTGGCTGACCTGGGCAGCCTGGAGTCTCCTGCCAGTCCTGAAGATTCTGACCTCACACTCTACCTGG
TGGTGGCAGTGGCCGTGGTCTCCTGTGTCTTCCTTGCCTTTGTCATCGTGCTGCTGGCTGTCAGGCTGAGGCGCTGGCAC
ACATCCCGCCTGCTCCAGGCTTCAACAGGTGAACTGGCTGGCCTTCCTGCCTCTCACTTTGTGGGTGTGGATGGGGTGCA
GGCTTTCCTGCAGACCTATTCCCATGAGGTGTCCCTCACTTCAGACTCCAGGAAGAGTCACCTGATCTTCCCCCAGCCCA
ACTATGCTGACACCCTCATCAGCCAGGAGGAAAGTGAAAAAAGTGAGCCTCTTCTGATACCTCAGGATTTACTTGAA

ORF - retro_eeur_630 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.72 %
Parental protein coverage: 97.44 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAIRAELPRCWRLVQLCLFVGLLLEVQAGKILYFVPEETVKGFFVGSIAKDLGLQAQELAGRGIRIVSRG
MA.R...P.C..L...C...G.L.E..A..I.Y.VPEE..KG.FVG.IAKDLGL..QEL...G.RIVS.G
RetrocopyMATRPSHPGCSLLAGICVLLGTLWEIRADQIRYAVPEELDKGAFVGNIAKDLGLEPQELVEHGVRIVSQG
ParentalRTQLFALNPRSGSLVTAGRIDREELCAQSARCLVSFNILVEDKMKLFPIEVEILDINDNAPHFQIEELEL
.TQLFALN..SGSLVTAGRIDREELC..S..C.VS..IL.EDK.K....EVEI.D.NDNAP.F..E..E.
RetrocopyKTQLFALNRHSGSLVTAGRIDREELCDRSPKCVVSLEILLEDKVKILEVEVEIMDVNDNAPNFGTEQREI
ParentalKMNEITSPGTRIPLPFGQDFDVGVNSLQSYQLSSNPHFFLDVQQGADGLQHPEMVLQSPLDREQEAVHHL
K..E...PGTR.PLP...D.D.GVNSLQ.YQLSS..HF.LDVQ.GADG...PE.VL...LDRE.EAVH.L
RetrocopyKVAENENPGTRFPLPEAFDSDIGVNSLQGYQLSSSVHFSLDVQSGADGIKYPELVLERTLDREEEAVHYL
ParentalVLTASDGGDPVRSGMLRIHVQVVDANVNPPTFTQAQYQVSVLENVPLGTQLLTVKATDPDEGANGEVTYA
VLTA.DGGDPV.SG...IHV..VD.N.N.P.FTQ..Y.VSV.ENVP.G.QLLT..ATD.DEGANGEVTY.
RetrocopyVLTAFDGGDPVHSGTAKIHVTLVDTNDNVPIFTQPEYRVSVQENVPVGSQLLTLRATDADEGANGEVTYS
ParentalFHNIDHRVAQIFQLDPHMGEITNKEPLDFEEYNLYPMEIQAQDGAGLMARAKVLVKVLDINDNAPEVTIT
F.......AQ.FQL....GEIT....LD.E....Y.....A.DG.GL.AR.KVLV.VLDINDNAPEV.IT
RetrocopyFRKVRDKIAQLFQLNSQSGEITVMGDLDYEDSGFYDIDVEAHDGPGLRARSKVLVTVLDINDNAPEVKIT
ParentalSVTASVPENFPPGTIIALINVHDQDSGDNGHTTCSISRNLPFKLEKLVDNYYRLVTEKTLDRELTPTYNI
S.T.S..E...PGT.IAL..VHD.DSG.NG..TCSI..NLPF.LEK...NYYRL.T..TLDRE....YN.
RetrocopySLTSSIQEASSPGTVIALFSVHDSDSGENGLVTCSIPDNLPFTLEKTYGNYYRLLTQRTLDREEVSEYNL
ParentalTVTATDQGTPALSTEAHISLHITDINDNSPVFSQDSYSAYIPENNPRGASIFSVTAHDADSNENAQVNYF
TVTATD.G.P.LSTE.HI.LH..DINDN.PVF.Q.SY.AYIPENNPRGASI.SVTA.D.DS.ENA.V.Y.
RetrocopyTVTATDHGSPPLSTETHITLHVADINDNPPVFPQASYFAYIPENNPRGASILSVTARDPDSVENARVSYS
ParentalLAEDDILGAPLSSYVSINSDIGVLYALCSFDYEQFRELQLWVTALDSGKPPLSSNVSLRLFILDQNDNVP
L.ED.....PLS.Y.SINS..GVLYAL.SFDYEQ.R.LQL.VTA.DSG.PPLSSNVSL.LFILDQNDN.P
RetrocopyLTEDSLQEVPLSTYISINSETGVLYALHSFDYEQVRDLQLQVTASDSGDPPLSSNVSLTLFILDQNDNSP
ParentalEILYPTLPTDGSTGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTAR
EILYPT.PTDGSTGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTAR
RetrocopyEILYPTFPTDGSTGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTAR
ParentalALLDRDALKQSLVVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASPGDSDLTLYLVVAVAVV
ALLDRDALKQSLVVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASP.DSDLTLYLVVAVAVV
RetrocopyALLDRDALKQSLVVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASPEDSDLTLYLVVAVAVV
ParentalSCVFLAFVIVLLAVRLRRWHTSRLLQASAGELAGLPASHFVGVDGVQAFLQTYSHEVSLTADSRKSHLIF
SCVFLAFVIVLLAVRLRRWHTSRLLQAS.GELAGLPASHFVGVDGVQAFLQTYSHEVSLT.DSRKSHLIF
RetrocopySCVFLAFVIVLLAVRLRRWHTSRLLQASTGELAGLPASHFVGVDGVQAFLQTYSHEVSLTSDSRKSHLIF
ParentalPQPNYADTLISQESCEKREFLSAPQSSLE
PQPNYADTLISQE..EK.E.L..PQ..LE
RetrocopyPQPNYADTLISQEESEKSEPLLIPQDLLE

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 30 .62 RPM 6 .77 RPM
SRP017611_kidney 2 .81 RPM 0 .75 RPM
SRP017611_liver 0 .48 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_630 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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