RetrogeneDB ID: | retro_eeur_363 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_269964:4563..5040(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PSEN1 | ||
| Ensembl ID: | ENSEEUG00000007027 | ||
| Aliases: | None | ||
| Description: | presenilin 1 [Source:HGNC Symbol;Acc:9508] |
Retrocopy-Parental alignment summary:
>retro_eeur_363
AAGGTACCCAAAACCCCCGGGTACAGTTCACAAGGTACAGACAATTAGAGTGATTCACACGACCCTGTGACAGAGTGATG
ATGGTGGCTTCAGTGAAGAGTGGGAAGCCCAGAGGGATAGCCACCTGGGGCCTCAGCGTTCCACCTTGGAGTCACAAGCT
GCTGTCCAGGAACTTTCCAGCAGCATCCTTGCCAATAAGGACCAGAGGAAAGGGAAGTAAAACCTGGATTAGGATATTTC
ATTTTCTACAGTGTTCTGGTTGGTAAAGCTTCTGCAATGGCCAGTGGTGACTGGAACACAACCATTGCCTGTTTTGTAGC
CATATTAATTGGTTTGTGCCTTACATTATCACTCCTCACCACTTTCAAGAAAGCATAGCCGGCTCTTCCAATCCCTATCG
CCTTTGGGCTTAATTTCTACTTTGCCACAGATTATCTTGTACAGCCCTTTATGGACCTATTAGAATTCCATCAATAT
ORF - retro_eeur_363 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.1 % |
| Parental protein coverage: | 51.47 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | KASKTPRYSSQGTDN--DSRDPVTE-SDDGGFSEEWEAQRDSRLGPQRSTSESRAAVQELSSSILASED- |
| K..KTP.YSSQGTDN..DS.DPVTE..D.G.FSEEWEAQRDS.LGPQRST.ES.AAVQELSSSILA..D. | |
| Retrocopy | KVPKTPGYSSQGTDN*SDSHDPVTE>DDGG-FSEEWEAQRDSHLGPQRSTLESQAAVQELSSSILANKD< |
| Parental | PEERGVKLGLGDFIFYSVLVGKASAMASGDWNTTIACFVAILIGLCLTLLLLAIFKKALPALPISITFGL |
| PEER.VK.GLG.FIFYSVLVGKASAMASGDWNTTIACFVAILIGLCLTL.LL..FKKA.PALPI.I.FGL | |
| Retrocopy | PEEREVKPGLGYFIFYSVLVGKASAMASGDWNTTIACFVAILIGLCLTLSLLTTFKKA*PALPIPIAFGL |
| Parental | IFYFATDYLVQPFMDQLAFHQF |
| .FYFATDYLVQPFMD.L.FHQ. | |
| Retrocopy | NFYFATDYLVQPFMDLLEFHQY |
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 .30 RPM |
| SRP017611_kidney | 0 .00 RPM | 46 .51 RPM |
| SRP017611_liver | 0 .16 RPM | 20 .58 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_363 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000007027 | 1 retrocopy |
retro_eeur_363 ,
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