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:
| Parental | NFRFSVGSTSPGAVVLYSKELKKWDEFEDILEERRHVSDLKFAMKCYTPLVYKGITPCKPSDIKYSVLNS |
| .F....GSTSPGAVVLYSKELKKWDEFEDILEERRHVS.LKFAMKCYTPL.YKGITPCKPSDIKYSVLNS | |
| Retrocopy | SFLCRLGSTSPGAVVLYSKELKKWDEFEDILEERRHVSNLKFAMKCYTPLLYKGITPCKPSDIKYSVLNS |
| Parental | EEVHYVIKQLSKESLHSVDVLREEVSDILDEMSHNLRLGAIRFLAFTLSKIFKQIFSKVCVNEEGIQKLQ |
| EEVHYVIK.LSKESLHSVDVLREEVSDILDEMSHNL.LGAIRFLAFTLSKIFKQIFSKVCVNEEGIQKLQ | |
| Retrocopy | EEVHYVIKRLSKESLHSVDVLREEVSDILDEMSHNLCLGAIRFLAFTLSKIFKQIFSKVCVNEEGIQKLQ |
| Parental | QAIQEHPVVLLPSHRSYIDFLMLSFLLYNYDLPIPVIAAGMDFLGMKMVGELLRMSGAFFMRRTFGGNKL |
| QAIQEHPVVLLPSHRSYIDFLMLSFLLYNYDLPIPVIAAGMDFLGMKMVGELLRMSGAFFM..T.GGNKL | |
| Retrocopy | QAIQEHPVVLLPSHRSYIDFLMLSFLLYNYDLPIPVIAAGMDFLGMKMVGELLRMSGAFFMWCTCGGNKL |
| Parental | YWAVFSEYVKTMLRNGYAPVEFFLEGTRSRSAKTLTPKFGLLNIVMEPFFKREVFDTYLVPISISYDKII |
| YWAVFSEYVKTML.NGY.PVEFFLEGTRSRS.KTLTPKFGLLNIVMEPFFKREVFDTYLVPISISYDKII | |
| Retrocopy | YWAVFSEYVKTMLWNGYTPVEFFLEGTRSRSVKTLTPKFGLLNIVMEPFFKREVFDTYLVPISISYDKII |
| Parental | EEALYVYELLGVPKPKETTTGLLRARKILSENFGSIHVYFGDPESLRSLAAGRMSRSPYT-VPRYIPQKQ |
| EEALYVYELLGVPKPKET.T.LLRARKILSENFGSIHVYFGDP.SLRSLAAGRMSRSPY..VPRYIPQKQ | |
| Retrocopy | EEALYVYELLGVPKPKETATRLLRARKILSENFGSIHVYFGDPVSLRSLAAGRMSRSPYNLVPRYIPQKQ |
| Parental | SEDMHTFVTEVAYRMQLLQIQNLVLSPWTLIIAVLLQNRPSMNLDALVEKTLWLKGLTHTFGGFLTWPDN |
| S.D.HTFVTEVAY.MQLLQIQNLVLSPWTLIIAVLLQNRPSMNLD.LVEKTLWLKGLTHTFGGFLTWPDN | |
| Retrocopy | SKDIHTFVTEVAYKMQLLQIQNLVLSPWTLIIAVLLQNRPSMNLDDLVEKTLWLKGLTHTFGGFLTWPDN |
| Parental | ESAEAVIQSNILLHSNIASLVKDQVILKMDSGDSEVVNGLIFQHITLLMCSAYRNQLLNIFVRPSLVALA |
| ES.E.VIQS.ILLHSNIASLVKDQVILKMDSGDSEVVNGLIFQ.ITLLMCSAYRNQLL.IFVRPSLVALA | |
| Retrocopy | ESTEGVIQSSILLHSNIASLVKDQVILKMDSGDSEVVNGLIFQQITLLMCSAYRNQLLIIFVRPSLVALA |
| Parental | LQMTPRARKEDVYSCFRFLHDV-FSDEFIFLPGNTLKDFEEGCYPLC-RSEAIQITRDILVTEKGNTVLE |
| LQMT.RARKEDVYSCF.FL.DV.FSDE.IFL.GNTLKDFEEGCY.LC..SEAIQITRDILVTEKGNTVLE | |
| Retrocopy | LQMTSRARKEDVYSCFHFLYDV>FSDELIFLLGNTLKDFEEGCYLLC>KSEAIQITRDILVTEKGNTVLE |
| Parental | FLIGLFQPFVECYQIICKYLLKEDDYFTEKQYLAGVRIFTNQLLDQ |
| FLIGLFQPFVECY..ICKYLLKEDDYFTEKQYLAGVRIFTNQLLDQ | |
| Retrocopy | FLIGLFQPFVECYHMICKYLLKEDDYFTEKQYLAGVRIFTNQLLDQ |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(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 |
Erinaceus europaeus was not studied using ChIP-Seq data.
Erinaceus europaeus was not studied using EST data.
Erinaceus europaeus was not studied using FANTOM5 data.
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 | ENSXETG00000022535 | 1 retrocopy |