RetrogeneDB ID: | retro_eeur_393 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_282445:5910..6500(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ASPA | ||
| Ensembl ID: | ENSEEUG00000000496 | ||
| Aliases: | None | ||
| Description: | aspartoacylase [Source:HGNC Symbol;Acc:756] |
Retrocopy-Parental alignment summary:
>retro_eeur_393
ATTTTTGGCCTTCATAATGCTACTTCTAACATGGGATGCACTCTTATTATTGAAGATTCCAGGAATGAATTTTAATTCAG
GTGTTTCATTACATTAAGACTTCCTTGGCTCCATCACCCTGCTATGTTTATCTTTTGGAGCATCCTTCCCTCAAATACGC
AACCCCACATTCTATAGCCAAGTATCCTGTTGGCATAGAAGCTGGTCCCCATCCTCAAGGGGTTCTGAGAGCTGATATTT
TTGATCAAGTGAGAACAAATAATAAGTATGTCCTTGATTTTATACATAACTTCAATACAGGAAAATAACTTCCTCCATGT
GCTACTGAAATCTATAAGATAATAGAGAAAGTTGATTATCCTGGGAATAAAAATGGATAAATTATTGCTGTTATCCATGC
TAATCTGCAGGATTAAGACAGGAAACTACTGTGCCCTGGGAATCTCATGCTTTGAACACTTGATGAAAAGACTATTCCAC
TGGGTGGTGACTGTATTGTGTACCCAGTGTTTGTAAACAAGGCTGCATATGATGAAAAGAAAGAAGCTTTGGCAAAAATA
ACTGAACACTCAGCACAAAAGAGTATTCAC
ORF - retro_eeur_393 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.87 % |
| Parental protein coverage: | 63.46 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | IFDLHNTTANMGCTLILEDSRNNF-LIQMFHYIKTSLAPLPCYVYLTEHPSLKYATTRSIAKYPVGIEVG |
| IF.LHN.T.NMGCTLI.EDSRN.F.LIQ.FHYIKTSLAP.PCYVYL.EHPSLKYAT..SIAKYPVGIE.G | |
| Retrocopy | IFGLHNATSNMGCTLIIEDSRNEF<LIQVFHYIKTSLAPSPCYVYLLEHPSLKYATPHSIAKYPVGIEAG |
| Parental | PQPQGVLRADILDQMRKIIKHALDFIQKFNTGKEFPPCAIEVYKIIEKVDYPRNENGEIIAVIHPNLQDQ |
| P.PQGVLRADI.DQ.R...K..LDFI..FNTGK..PPCA.E.YKIIEKVDYP.N.NG.IIAVIH.NLQD. | |
| Retrocopy | PHPQGVLRADIFDQVRTNNKYVLDFIHNFNTGK*LPPCATEIYKIIEKVDYPGNKNG*IIAVIHANLQD* |
| Parental | DWKPLRPGDPVFLTLDGKTIPLGGDCIVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIH |
| D.K.L.PG.....TLD.KTIPLGGDCIVYPVFVN.AAY.EKKEA.AK.T......KSIH | |
| Retrocopy | DRKLLCPGNLML*TLDEKTIPLGGDCIVYPVFVNKAAYDEKKEALAKITEHSAQ-KSIH |
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 | 3 .71 RPM |
| SRP017611_kidney | 0 .00 RPM | 109 .90 RPM |
| SRP017611_liver | 0 .00 RPM | 41 .00 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_393 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 | ENSEEUG00000000496 | 1 retrocopy |
retro_eeur_393 ,
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