RetrogeneDB ID: | retro_eeur_100 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | GeneScaffold_6264:47152..47782(-) | ||
| Located in intron of: | ENSEEUG00000000100 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PDK3 | ||
| Ensembl ID: | ENSEEUG00000014090 | ||
| Aliases: | None | ||
| Description: | pyruvate dehydrogenase kinase, isozyme 3 [Source:HGNC Symbol;Acc:8811] |
Retrocopy-Parental alignment summary:
>retro_eeur_100
GCTGATGTTGTGAGAGATGCTTATGAGAAGGCCAAGATGCTGTGTGTACAGTATTACCTCGTAGCTCCAGAACTGAAAAT
CGAAGAATTCAATGCCCAAGCTCTAGACAAACCTATACAGGTAGTTTATGTGCCTTCACATCTGTTTCACATGTTATTTG
AGTTGTTCAAGAACTCAATGAGAGCAACAGTTGAACTGTATGAAGGTAGAAAGGAGGGTTGCCCAGCTATTAAGACCCTC
GTTACTCTAGGTCAGGAAGACTTGTCCATTAAGATAAGCGACCAAGGTGGTGGGGTCCCACTTCGAAAAATAGACCGTCT
TTTTAACTACATGTATTCAACTGCTCCCAGACCCAGCCTCGAGTCCAGAAGAGCGGCCCCCCTGGCTGGATTTGGTTATG
GTTTGCCGATTTGTCGCCTGTATGCTAGATATTTTCAAGGAGACTTAAAACTCTATTCCATGGAAGGAATGGGTACTGAT
ACCATCATTTACTTGAAGGCTCTTTCAAGTGAATCATTTGAGAGACTGCCAGTCTTTAACAAGTCTGCATGCCGCCATTA
CAAAACCGCTTCTGAAGCTGATGACTGGAGCAACCCGAGCAGCGAAGCCCGAGATGCTTCAAAATACAAA
ORF - retro_eeur_100 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.0 % |
| Parental protein coverage: | 56.76 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ADVVKDAYETAKMLCEQYYLVAPELEIEEFNAKAPDKPIQVVYVPSHLFHMLFELFKNSMRATVELYEDR |
| ADVV.DAYE.AKMLC.QYYLVAPEL.IEEFNA.A.DKPIQVVYVPSHLFHMLFELFKNSMRATVELYE.R | |
| Retrocopy | ADVVRDAYEKAKMLCVQYYLVAPELKIEEFNAQALDKPIQVVYVPSHLFHMLFELFKNSMRATVELYEGR |
| Parental | KEAYPAVKTLVTLGKEDLSIKISDQGGGVPLRKIDRLFNYMYSTAPRPSLEPTRAAPLAGFGYGLPISRL |
| KE..PA.KTLVTLG.EDLSIKISDQGGGVPLRKIDRLFNYMYSTAPRPSLE..RAAPLAGFGYGLPI.RL | |
| Retrocopy | KEGCPAIKTLVTLGQEDLSIKISDQGGGVPLRKIDRLFNYMYSTAPRPSLESRRAAPLAGFGYGLPICRL |
| Parental | YARYFQGDLKLYSMEGVGTDAVIYLKALSSESFERLPVFNKSAWRHYKTTPEADDWSNPSSEPRDASKYK |
| YARYFQGDLKLYSMEG.GTD..IYLKALSSESFERLPVFNKSA.RHYKT..EADDWSNPSSE.RDASKYK | |
| Retrocopy | YARYFQGDLKLYSMEGMGTDTIIYLKALSSESFERLPVFNKSACRHYKTASEADDWSNPSSEARDASKYK |
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 | 0 .00 RPM | 20 .95 RPM |
| SRP017611_kidney | 0 .94 RPM | 96 .02 RPM |
| SRP017611_liver | 0 .00 RPM | 1 .45 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_100 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 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000017832 | 1 retrocopy | |
| Erinaceus europaeus | ENSEEUG00000014090 | 2 retrocopies |
retro_eeur_100 , retro_eeur_690,
|
| Otolemur garnettii | ENSOGAG00000005598 | 2 retrocopies |