RetrogeneDB ID: | retro_eeur_690 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_75386:2..821(-) | ||
| Located in intron of: | None | ||
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_690
GATGCTTGTGAGAAAACATCATTCGTGTTTCTACGGAAAGAACTTCCCGTGCGCCTCGCCAGTACAGCGAGGGAAGTTGG
TCTTCTGCCAGATAAATTGCTACACCACCCTTCGGTAAACCTGGTGCGAAATGGGTACTTGCAGAGTTTCCTTGAGCTCT
TAGAATATGAGAACAAAAGCCCTGAGGATCCACAGGTCTTGGTCAACTTTCTTCAAGTTCTGATTAATATCAGAAATAGA
CACAATGATGTGGCACCTATGATAGCACAAGGAGTGATCGAATACAAAGAAAAGTTTGGCTTTGACCCGTTCACTAGTAG
TAACATCCAATATTTTCTGGATCGGTTTTATATCAACCGCATCTCTTTCCGCATGCTCATTAACCAACACACACTCCTGT
TTGGCGGTGACATCAATCCTGCTCATCCTAAACACATCGGAAGTATTGACCCCACCTGCAATGTGGCTGATGTTGTGAGA
GATGCTTATGAGAAGGCCAAGATGCTGTGTGAACAGTATTACCTCGTAGCTCCAGAACTGAAAATCGAAGAATTCAATGC
CCAAGCTCTAGACAAACCTATACAGGTAGTTTATGTGCCTTCACATCTGTTTCACATGTTATTTGAGTTGTTCAAGAACT
CAATGAGAGCAACAGTTGAACTGTATGAAGGTAGAAAGGAGGGTTGCCCAGCTATTAAGACCCTCGTTACTCTAGGTCAG
GAAGACTTGTCCATTAAGATAAGCGACCAAGGTGGTGGGGTCCCACTTCGAAAAATAGACCGTCTTTTTAACTACATGTA
TTCAACTGCTCCAGACCCA
ORF - retro_eeur_690 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.91 % |
| Parental protein coverage: | 73.78 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | NACEKTSYMFLRKELPVRLANTMREVNLLPDNLLNRPSVGLVQSWYMQSFLELLEYENKSPEDPQVLDNF |
| .ACEKTS..FLRKELPVRLA.T.REV.LLPD.LL..PSV.LV...Y.QSFLELLEYENKSPEDPQVL.NF | |
| Retrocopy | DACEKTSFVFLRKELPVRLASTAREVGLLPDKLLHHPSVNLVRNGYLQSFLELLEYENKSPEDPQVLVNF |
| Parental | LQVLINVRNRHNDVVPTMAQGVIEYKEKFGFDPFISSNIQYFLDRFYTNRISFRMLINQHTLLFGGDTNP |
| LQVLIN.RNRHNDV.P..AQGVIEYKEKFGFDPF.SSNIQYFLDRFY.NRISFRMLINQHTLLFGGD.NP | |
| Retrocopy | LQVLINIRNRHNDVAPMIAQGVIEYKEKFGFDPFTSSNIQYFLDRFYINRISFRMLINQHTLLFGGDINP |
| Parental | AHPKHIGSIDPTCNVADVVKDAYETAKMLCEQYYLVAPELEIEEFNAKAPDKPIQVVYVPSHLFHMLFEL |
| AHPKHIGSIDPTCNVADVV.DAYE.AKMLCEQYYLVAPEL.IEEFNA.A.DKPIQVVYVPSHLFHMLFEL | |
| Retrocopy | AHPKHIGSIDPTCNVADVVRDAYEKAKMLCEQYYLVAPELKIEEFNAQALDKPIQVVYVPSHLFHMLFEL |
| Parental | FKNSMRATVELYEDRKEAYPAVKTLVTLGKEDLSIKISDQGGGVPLRKIDRLFNYMYSTAPRP |
| FKNSMRATVELYE.RKE..PA.KTLVTLG.EDLSIKISDQGGGVPLRKIDRLFNYMYSTAP.P | |
| Retrocopy | FKNSMRATVELYEGRKEGCPAIKTLVTLGQEDLSIKISDQGGGVPLRKIDRLFNYMYSTAPDP |
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 .19 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_690 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 |