RetrogeneDB ID: | retro_eeur_397 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_283344:2016..2526(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM221A | ||
| Ensembl ID: | ENSEEUG00000001634 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 221, member A [Source:HGNC Symbol;Acc:27977] |
Retrocopy-Parental alignment summary:
>retro_eeur_397
GGGAAACATTTTACTCCTGAGGAATATGAAAATTACAAAAGAAAACTTTTACAGAACAGATTATTTGTGAACTGGCGATC
ACCAACTGGAATGGACTGTAAACTTGTGGGTCCAGAGACACTGTGTTTTCGTACGCACAGGTATAAGCAACATGATACTG
ACTTTGAAATGATTCCACAACAGCGCCCCATTAGCTTGCTTTGCTGAGTGCCTGGCTGCCAGTGCAGGGCTTACCTTTAC
ATCTCTACGAATGGCACGCAGCCCATTCGCTGCAGGTGCAAGCACTTTGTTGATCAGCACAGTGCTGCACCTGGATCCAA
ATGCAATGCCTGCCCCGAGTGTTCAGGATTCCACAGCTCCTTCACTTGTGGTTTTGGCTATCCCTCATATGCCCATGACA
CAGTTGTAGAAACTAAGCAAGAAAGACTGGCTCAAGGAAGACCAGTGGGAGAAGACATTCTTTATGCAGCTATGCGAGGA
TTAACTGGCTTCAGCTCACTGGCAGACGGC
ORF - retro_eeur_397 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.18 % |
| Parental protein coverage: | 62.82 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | GKLFTPEEYEDYKRKVLPMRLQNRLFVSWRSPTGIDCKLVGPETLCFCTHRYKQHKTDFETIPQQRPISL |
| GK.FTPEEYE.YKRK.....LQNRLFV.WRSPTG.DCKLVGPETLCF.THRYKQH.TDFE.IPQQRPISL | |
| Retrocopy | GKHFTPEEYENYKRKL----LQNRLFVNWRSPTGMDCKLVGPETLCFRTHRYKQHDTDFEMIPQQRPISL |
| Parental | PCRVTGCQCRAYLYVPMNGTQPIRCRCKHFADQHSAAPGSKCNACSKCSGFHSCFTCGCGQPAYAHDTVV |
| .C.V.GCQCRAYLY...NGTQPIRCRCKHF.DQHSAAPGSKCNAC..CSGFHS.FTCG.G.P.YAHDTVV | |
| Retrocopy | LC*VPGCQCRAYLYISTNGTQPIRCRCKHFVDQHSAAPGSKCNACPECSGFHSSFTCGFGYPSYAHDTVV |
| Parental | ETKQERLALGKPVGQDIPYAAMGGLTGFSSLAEG |
| ETKQERLA.G.PVG.DI.YAAM.GLTGFSSLA.G | |
| Retrocopy | ETKQERLAQGRPVGEDILYAAMRGLTGFSSLADG |
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 | 2 .26 RPM |
| SRP017611_kidney | 0 .00 RPM | 5 .81 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .02 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_397 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 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000002784 | 1 retrocopy | |
| Erinaceus europaeus | ENSEEUG00000001634 | 2 retrocopies |
retro_eeur_349, retro_eeur_397 ,
|