RetrogeneDB ID:

retro_eeur_570

Retrocopy
location
Organism:Hedgehog (Erinaceus europaeus)
Coordinates:scaffold_346440:53525..55339(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GNPAT
Ensembl ID:ENSEEUG00000012167
Aliases:None
Description:glyceronephosphate O-acyltransferase [Source:HGNC Symbol;Acc:4416]


Retrocopy-Parental alignment summary:






>retro_eeur_570
TCGTTTCTCTGTCGGCTCGGCTCCACTAGTCCCGGCGCTGTCGTTCTCTACTCAAAGGAGCTCAAAAAGTGGGATGAATT
TGAAGATATTTTAGAAGAGAGGAGACATGTCAGTAACCTGAAATTTGCAATGAAATGTTACACACCTCTTCTCTACAAGG
GAATTACTCCTTGCAAGCCAAGTGATATTAAATATAGTGTACTTAATTCTGAAGAAGTTCATTATGTCATTAAGCGGCTT
TCCAAGGAATCCCTTCATTCTGTTGATGTCCTCAGAGAGGAAGTTTCTGATATCTTGGATGAAATGAGCCACAACCTATG
TCTAGGAGCCATCCGCTTTTTGGCTTTCACTCTAAGCAAAATATTTAAGCAAATTTTCTCTAAAGTGTGTGTGAATGAAG
AAGGCATTCAGAAACTACAACAAGCCATCCAGGAGCATCCAGTTGTCCTGCTGCCTAGTCACCGAAGTTACATTGACTTT
CTGATGCTATCTTTTCTTCTATACAACTATGATTTGCCTATACCAGTAATAGCAGCAGGAATGGACTTCCTAGGAATGAA
AATGGTTGGTGAACTGCTACGGATGTCGGGTGCCTTTTTCATGTGGTGCACCTGTGGTGGCAATAAATTGTACTGGGCTG
TATTCTCAGAATATGTAAAAACAATGTTATGGAATGGTTATACTCCTGTTGAGTTTTTCCTCGAAGGGACAAGAAGTCGC
TCTGTTAAAACATTGACCCCTAAATTTGGTCTTCTGAATATTGTGATGGAACCATTTTTTAAAAGAGAAGTTTTTGATAC
CTATCTTGTTCCTATTAGCATCAGTTATGACAAGATAATAGAAGAAGCCCTTTATGTATATGAGCTCCTAGGGGTTCCCA
AGCCTAAAGAAACTGCAACTCGGTTATTGCGAGCCAGGAAGATTCTCTCTGAAAATTTTGGAAGCATTCATGTATACTTT
GGAGACCCAGTATCACTTCGATCTCTGGCAGCTGGAAGAATGAGTCGCAGCCCATATAACCTGGTTCCAAGATATATTCC
TCAAAAACAATCAAAAGACATCCATACGTTTGTCACTGAAGTTGCATACAAAATGCAGCTTCTGCAAATTCAAAACCTGG
TTTTGAGTCCATGGACCCTAATAATTGCTGTTCTGCTTCAGAATCGACCATCCATGAACTTAGATGATCTGGTAGAAAAG
ACTTTATGGCTGAAAGGTTTAACTCATACCTTTGGAGGGTTTCTCACTTGGCCTGATAATGAATCTACTGAAGGAGTTAT
CCAGTCCAGCATCCTTCTGCATTCCAACATTGCCAGCCTTGTCAAAGACCAAGTGATTTTGAAAATGGACTCCGGAGACT
CAGAAGTAGTCAATGGACTTATTTTTCAGCAGATCACTCTTCTCATGTGTTCAGCATACAGGAACCAGTTGCTCATCATT
TTTGTCCGTCCTTCCTTAGTAGCTTTGGCATTACAAATGACTTCCAGGGCCAGAAAAGAGGATGTCTACAGTTGCTTTCA
CTTTCTATATGATGTTTTTTTCAGATGAGTTAATCTTCCTCCTAGGAAACACACTAAAGGACTTTGAAGAAGGCTGTTAC
CTGCTTTGCAAAAAGTGAAGCCATACAAATTACAAGGGACATCCTAGTTACAGAGAAAGGAAATACTGTGTTAGAATTCT
TAATAGGGCTCTTTCAACCTTTTGTAGAATGTTATCACATGATTTGCAAATACCTTTTGAAAGAAGATGACTACTTCACT
GAGAAACAGTACCTTGCTGGAGTTAGAATTTTCACAAATCAGCTTCTCGATCAA

ORF - retro_eeur_570 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.4 %
Parental protein coverage: 91.23 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalNFRFSVGSTSPGAVVLYSKELKKWDEFEDILEERRHVSDLKFAMKCYTPLVYKGITPCKPSDIKYSVLNS
.F....GSTSPGAVVLYSKELKKWDEFEDILEERRHVS.LKFAMKCYTPL.YKGITPCKPSDIKYSVLNS
RetrocopySFLCRLGSTSPGAVVLYSKELKKWDEFEDILEERRHVSNLKFAMKCYTPLLYKGITPCKPSDIKYSVLNS
ParentalEEVHYVIKQLSKESLHSVDVLREEVSDILDEMSHNLRLGAIRFLAFTLSKIFKQIFSKVCVNEEGIQKLQ
EEVHYVIK.LSKESLHSVDVLREEVSDILDEMSHNL.LGAIRFLAFTLSKIFKQIFSKVCVNEEGIQKLQ
RetrocopyEEVHYVIKRLSKESLHSVDVLREEVSDILDEMSHNLCLGAIRFLAFTLSKIFKQIFSKVCVNEEGIQKLQ
ParentalQAIQEHPVVLLPSHRSYIDFLMLSFLLYNYDLPIPVIAAGMDFLGMKMVGELLRMSGAFFMRRTFGGNKL
QAIQEHPVVLLPSHRSYIDFLMLSFLLYNYDLPIPVIAAGMDFLGMKMVGELLRMSGAFFM..T.GGNKL
RetrocopyQAIQEHPVVLLPSHRSYIDFLMLSFLLYNYDLPIPVIAAGMDFLGMKMVGELLRMSGAFFMWCTCGGNKL
ParentalYWAVFSEYVKTMLRNGYAPVEFFLEGTRSRSAKTLTPKFGLLNIVMEPFFKREVFDTYLVPISISYDKII
YWAVFSEYVKTML.NGY.PVEFFLEGTRSRS.KTLTPKFGLLNIVMEPFFKREVFDTYLVPISISYDKII
RetrocopyYWAVFSEYVKTMLWNGYTPVEFFLEGTRSRSVKTLTPKFGLLNIVMEPFFKREVFDTYLVPISISYDKII
ParentalEEALYVYELLGVPKPKETTTGLLRARKILSENFGSIHVYFGDPESLRSLAAGRMSRSPYT-VPRYIPQKQ
EEALYVYELLGVPKPKET.T.LLRARKILSENFGSIHVYFGDP.SLRSLAAGRMSRSPY..VPRYIPQKQ
RetrocopyEEALYVYELLGVPKPKETATRLLRARKILSENFGSIHVYFGDPVSLRSLAAGRMSRSPYNLVPRYIPQKQ
ParentalSEDMHTFVTEVAYRMQLLQIQNLVLSPWTLIIAVLLQNRPSMNLDALVEKTLWLKGLTHTFGGFLTWPDN
S.D.HTFVTEVAY.MQLLQIQNLVLSPWTLIIAVLLQNRPSMNLD.LVEKTLWLKGLTHTFGGFLTWPDN
RetrocopySKDIHTFVTEVAYKMQLLQIQNLVLSPWTLIIAVLLQNRPSMNLDDLVEKTLWLKGLTHTFGGFLTWPDN
ParentalESAEAVIQSNILLHSNIASLVKDQVILKMDSGDSEVVNGLIFQHITLLMCSAYRNQLLNIFVRPSLVALA
ES.E.VIQS.ILLHSNIASLVKDQVILKMDSGDSEVVNGLIFQ.ITLLMCSAYRNQLL.IFVRPSLVALA
RetrocopyESTEGVIQSSILLHSNIASLVKDQVILKMDSGDSEVVNGLIFQQITLLMCSAYRNQLLIIFVRPSLVALA
ParentalLQMTPRARKEDVYSCFRFLHDV-FSDEFIFLPGNTLKDFEEGCYPLC-RSEAIQITRDILVTEKGNTVLE
LQMT.RARKEDVYSCF.FL.DV.FSDE.IFL.GNTLKDFEEGCY.LC..SEAIQITRDILVTEKGNTVLE
RetrocopyLQMTSRARKEDVYSCFHFLYDV>FSDELIFLLGNTLKDFEEGCYLLC>KSEAIQITRDILVTEKGNTVLE
ParentalFLIGLFQPFVECYQIICKYLLKEDDYFTEKQYLAGVRIFTNQLLDQ
FLIGLFQPFVECY..ICKYLLKEDDYFTEKQYLAGVRIFTNQLLDQ
RetrocopyFLIGLFQPFVECYHMICKYLLKEDDYFTEKQYLAGVRIFTNQLLDQ

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 17 .24 RPM 53 .66 RPM
SRP017611_kidney 21 .19 RPM 71 .64 RPM
SRP017611_liver 11 .58 RPM 23 .96 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_570 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 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Erinaceus europaeus ENSEEUG00000012167 1 retrocopy
retro_eeur_570 ,
Xenopus tropicalis ENSXETG000000225351 retrocopy
retro_xtro_30,


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