RetrogeneDB ID:

retro_eeur_637

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_372563:3805..6136(+)
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_637
CTGATCCTGCTGTGCGCCTTCCTGGCCACAATGTGGGAGGTCGGAAGGGGACAGCTCCACTACTCGGTGCCTGAAGAGAG
TGACAAAGGGTCATTTGTAGGTAATATATCCAAGGACCTGGGACTAGAGTCACCAGAGCCAGTGAAGCACGGAGTCCGCA
TCGTTTCCCGAGGAAGGACGCAGCTTTTTGCTTTGAACGCCCGCGGTGGCAGTTTGGTCACAGCAGGCAGGATCGACCGC
GAAGAGCTCTGCGCTCAGAGCGCGCGGTGTCTTATAAATATCAACATCCTGGTTGAGGATAAAGGGAGACTTTTTGGAAT
AGAAATAGAAATTATTGATATCAATGACAATAACCCCAAGTTCCAAGTGGAACACCAGGAGGTGAAAATTAATGAGATCG
CTGCGCCCGGAACTCGTTATCCACTCCCAGAGGCTGTTGACCCGGATGTGGGCGTGAATTCCCTACAGAGCTACCAGCTC
AGCCCCAACGACCATTTCTCCCTGGATGTGCAAACTGGAGACGACGGAACTAGGAACCCAGAGCTGGTGCTGGAGCGCGC
CCTGGACCGGGAGGAAAGGGTTGTTCATCACTTGGTGCTCACCGCCTCGGATGGCGGTGACCCGCGTCGCTCCAGCACGA
TGCACATCCAAGTGACAGTGCTGGATACGAACGACAATGCCCCTGTTTTTGCGCAACAGATTTACCGCGTGAAAGTCCCA
GAAGACTTGCCCCCTGGCACCCTGCTGCTGACTGTCAGAGCCAGCGACCCAGATGAAGGAAGCAATGGAGAAGTGACATA
TAAATTCTGGAAAATCAGTGAAAAACAATCTCCGTTATTCCAGCTTAATGAAGACACTGGGGAAATAGCAATAGCAAAGA
GTCTAGATTATGAAGAATGTGCTTTTTATGAAATGGAAATACAAGCTGAAGATGTGGGGGCACTACTGGGGCGGACCAAA
GTGTTCATTTCAGTAGAAGATGTAAATGACAATAGGCCGGAAGTGATTATTACATCTCTGTTTAACCCAGTTTTGGAAAA
TACTCTGCCGGGCACAGTAATTGCCTTCTTGAATGTGCATGACCGAGACTCTGGGAAGAATGGTCAAATCATCTGTCACA
CACGTGAAAATATACCTTTTCAGTTAGAAAAATCAATTGATAATTATTATAGATTAGTAACATGGAAATATTTGGATAGA
GAAAAGACCTCTATGTACAATATTACAGTGATAGCCTCAGATCTAGGAATTCCACCTCTGTCTACTGAAACATATATTGC
TGTGCATGTGGCAGATACCAATGACAATCCACCCACTTTCACTCAGTCCTCCTACTCGGCTTATGTCCCTGAGAATAATC
TCAGAGGTGTTTCGATCTTCTCTATGACTGCCTATGACCCTGACAGTGGCAACAATGCAGTGGTCACTTACTCTGTAGTG
GAGAACACCATCATGGATGCACCACTCTCCTCTACTATCTCTATCAACTCTGACACTGGTGTGTTGTATGCTCTGTGCTC
ATTTGACTATGAACAGATTCAAGACGTGCAGTTATTGGTGATAGCTAGTGACAATGGGGACCCACCACTCAGTAGTAATG
TGTCCCTGAGGCTGTTCATTCTGGACCAGAATGACAACATACCAGAGATCCTCTACCCCATTCTTCCTACTGATGGTTCC
ACTGGGGTGGAGCTGGCACCCCGCTATGCAGAGCCCGGATACCTGGTGACCAAGGTGGTGGCAGTGGACAGAGACTCAGG
CCAGAATGCCTGGCTGTCCTACCGCCTGCTCAAGGCCAGTGAGCCAGGGCTCTTCTCAGTGGGGCTGCACACAGGTGAAG
TGCACACTGCCAGGGCCCTGCTGGACAGAGATGCTCTCAAGCAGAGCCTAGTGGTGGCAGTGCAGGACCATGGCCAGCCC
CCTCTCTCAGCCACTGTCACACTCACTGTGGCCATAGCTGACAGCATCCCAGATGTGCTGGCTGACCTGGGCAGCCTGGA
GTCTCCTGCCAGTCCTGAAGATTCTGACCTCACACTCTACCTGGTGGTGGCACTAGCCTCTGTGTCCTGCATCTTCCTTG
CCTTTGTCATCGTGCTGCTGGCTGTCAGGCTGAGGCGCTGGCACACATCCCACCTGCTCCAGGCTTCAGCAGGTGGACTG
GCTGGCCTTCCTGCCTCTCACTTTATGGGTGTGGATGGGGTGCAGGCTTTCCTGCAGACCTATTCCCATGAAGTGTCCCT
CACTGCAGACTCCAGGAAGAGTCACCTGATCTTCCCCCAGCCCAACTATGCTGACACCCTCATCAGCCAGGAGAGCTGTG
AGAAAAGTGAG

ORF - retro_eeur_637 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.59 %
Parental protein coverage: 94.76 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLVQLCLFVGLLLEVQAGKILYFVPEETVKGFFVGSIAKDLGLQAQELAGRGIRIVSRGRTQLFALNPRSG
L..LC.F.....EV..G...Y.VPEE..KG.FVG.I.KDLGL...E....G.RIVSRGRTQLFALN.R.G
RetrocopyLILLCAFLATMWEVGRGQLHYSVPEESDKGSFVGNISKDLGLESPEPVKHGVRIVSRGRTQLFALNARGG
ParentalSLVTAGRIDREELCAQSARCLVSFNILVEDKMKLFPIEVEILDINDNAPHFQIEELELKMNEITSPGTRI
SLVTAGRIDREELCAQSARCL...NILVEDK..LF.IE.EI.DINDN.P.FQ.E..E.K.NEI..PGTR.
RetrocopySLVTAGRIDREELCAQSARCLININILVEDKGRLFGIEIEIIDINDNNPKFQVEHQEVKINEIAAPGTRY
ParentalPLPFGQDFDVGVNSLQSYQLSSNPHFFLDVQQGADGLQHPEMVLQSPLDREQEAVHHLVLTASDGGDPVR
PLP...D.DVGVNSLQSYQLS.N.HF.LDVQ.G.DG...PE.VL...LDRE...VHHLVLTASDGGDP.R
RetrocopyPLPEAVDPDVGVNSLQSYQLSPNDHFSLDVQTGDDGTRNPELVLERALDREERVVHHLVLTASDGGDPRR
ParentalSGMLRIHVQVVDANVNPPTFTQAQYQVSVLENVPLGTQLLTVKATDPDEGANGEVTYAFHNIDHRVAQIF
S....I.V.V.D.N.N.P.F.Q..Y.V.V.E..P.GT.LLTV.A.DPDEG.NGEVTY.F..I.......F
RetrocopySSTMHIQVTVLDTNDNAPVFAQQIYRVKVPEDLPPGTLLLTVRASDPDEGSNGEVTYKFWKISEKQSPLF
ParentalQLDPHMGEITNKEPLDFEEYNLYPMEIQAQDGAGLMARAKVLVKVLDINDNAPEVTITSVTASVPENFPP
QL....GEI.....LD.EE...Y.MEIQA.D...L..R.KV...V.D.NDN.PEV.ITS....V.EN..P
RetrocopyQLNEDTGEIAIAKSLDYEECAFYEMEIQAEDVGALLGRTKVFISVEDVNDNRPEVIITSLFNPVLENTLP
ParentalGTIIALINVHDQDSGDNGHTTCSISRNLPFKLEKLVDNYYRLVTEKTLDRELTPTYNITVTATDQGTPAL
GT.IA..NVHD.DSG.NG...C....N.PF.LEK..DNYYRLVT.K.LDRE.T..YNITV.A.D.G.P.L
RetrocopyGTVIAFLNVHDRDSGKNGQIICHTRENIPFQLEKSIDNYYRLVTWKYLDREKTSMYNITVIASDLGIPPL
ParentalSTEAHISLHITDINDNSPVFSQDSYSAYIPENNPRGASIFSVTAHDADSNENAQVNYFLAEDDILGAPLS
STE..I..H..D.NDN.P.F.Q.SYSAY.PENN.RG.SIFS.TA.D.DS..NA.V.Y...E..I..APLS
RetrocopySTETYIAVHVADTNDNPPTFTQSSYSAYVPENNLRGVSIFSMTAYDPDSGNNAVVTYSVVENTIMDAPLS
ParentalSYVSINSDIGVLYALCSFDYEQFRELQLWVTALDSGKPPLSSNVSLRLFILDQNDNVPEILYPTLPTDGS
S..SINSD.GVLYALCSFDYEQ....QL.V.A.D.G.PPLSSNVSLRLFILDQNDN.PEILYP.LPTDGS
RetrocopySTISINSDTGVLYALCSFDYEQIQDVQLLVIASDNGDPPLSSNVSLRLFILDQNDNIPEILYPILPTDGS
ParentalTGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTARALLDRDALKQSL
TGVELAPR.AEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTARALLDRDALKQSL
RetrocopyTGVELAPRYAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTARALLDRDALKQSL
ParentalVVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASPGDSDLTLYLVVAVAVVSCVFLAFVIVLL
VVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASP.DSDLTLYLVVA.A.VSC.FLAFVIVLL
RetrocopyVVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASPEDSDLTLYLVVALASVSCIFLAFVIVLL
ParentalAVRLRRWHTSRLLQASAGELAGLPASHFVGVDGVQAFLQTYSHEVSLTADSRKSHLIFPQPNYADTLISQ
AVRLRRWHTS.LLQASAG.LAGLPASHF.GVDGVQAFLQTYSHEVSLTADSRKSHLIFPQPNYADTLISQ
RetrocopyAVRLRRWHTSHLLQASAGGLAGLPASHFMGVDGVQAFLQTYSHEVSLTADSRKSHLIFPQPNYADTLISQ
ParentalESCEKRE
ESCEK.E
RetrocopyESCEKSE

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 6 .61 RPM 6 .77 RPM
SRP017611_kidney 1 .13 RPM 0 .75 RPM
SRP017611_liver 0 .00 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_637 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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