RetrogeneDB ID: | retro_eeur_134 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | GeneScaffold_8443:420768..421049(+) | ||
| Located in intron of: | ENSEEUG00000004720 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DYNLRB2 | ||
| Ensembl ID: | ENSEEUG00000013344 | ||
| Aliases: | None | ||
| Description: | dynein, light chain, roadblock-type 2 [Source:HGNC Symbol;Acc:15467] |
Retrocopy-Parental alignment summary:
>retro_eeur_134
ATGGCAGAAGTAGAGGAGACACTGAAATGACTTCAGAGCCAAAAAGGAGTGCAGTGCATCATCTTGGTGAACACAGAAGG
CATTCCCATCAAAAGCACTATGGACAAACCCACCACCACACAATATGCCAACCTATGTACAACTTCATCCTGAAGACCTA
GAGCACCATGTGCAAAATTGACCCACAGAATGATCTCACCTTTCTTCGAATTCACTCCAAGAAAAATGAAGTTATAGTTG
CACTAGATAAAGACTATTTCCTGATTGTGATTCAGAATCCA
ORF - retro_eeur_134 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.11 % |
| Parental protein coverage: | 97.92 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MTEVEETLKRIQSHKGVIGTMVVNAEGIPIRTTLDNSTTVQYAGL-LHQLTMKARSTVRDIDPQNDLTFL |
| M.EVEETLK..QS.KGV.....VN.EGIPI..T.D..TT.QYA.L.......K..ST...IDPQNDLTFL | |
| Retrocopy | MAEVEETLK*LQSQKGVQCIILVNTEGIPIKSTMDKPTTTQYANL<MYNFILKT*STMCKIDPQNDLTFL |
| Parental | RIRSKKHEIMVAPDKEYLLIVIQNP |
| RI.SKK.E..VA.DK.Y.LIVIQNP | |
| Retrocopy | RIHSKKNEVIVALDKDYFLIVIQNP |
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 | 10 .47 RPM | 5 .96 RPM |
| SRP017611_kidney | 21 .19 RPM | 2 .81 RPM |
| SRP017611_liver | 7 .23 RPM | 0 .16 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_134 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 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000020024 | 1 retrocopy | |
| Erinaceus europaeus | ENSEEUG00000013344 | 2 retrocopies |
retro_eeur_134 , retro_eeur_552,
|
| Sarcophilus harrisii | ENSSHAG00000002755 | 1 retrocopy |