RetrogeneDB ID: | retro_eeur_325 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_254725:3349..3619(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LLPH | ||
| Ensembl ID: | ENSEEUG00000012195 | ||
| Aliases: | None | ||
| Description: | LLP homolog, long-term synaptic facilitation (Aplysia) [Source:HGNC Symbol;Acc:28229] |
Retrocopy-Parental alignment summary:
>retro_eeur_325
TTAAAAAGCATTCTTAAAGTAGATACTGATGTTTTAATGAAAGATGTGCAAGAAACAGCAACTGTGGTGGCACCCAAACA
TTGTCAAGAGAAAAATCCAGTGTGTCATAGGAGATAAAAAGGTGACATGAAAATGGAGACTGAAATGAAGAGAAACACAA
AGAGCCTTCTAGACCGGCATGGACAATACCCCATATGGATGAACCAGAGACAAAGAAAAAGGCTGAAGGCAAAACAAGGG
AAATGGAAAGGCAAAAGTCAAAGCAAAAGC
ORF - retro_eeur_325 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.43 % |
| Parental protein coverage: | 71.43 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LKSILKVDTDVLMKDVQEIATVVAPKNCQEK-IQCEVEDEK-GDMKMETEIKRNKKSLLDQHGQYPIWMN |
| LKSILKVDTDVLMKDVQE.ATVVAPK.CQEK.IQC...D.K.GDMKMETE.KRN.KSLLD.HGQYPIWMN | |
| Retrocopy | LKSILKVDTDVLMKDVQETATVVAPKHCQEK>IQCVIGDKK<GDMKMETEMKRNTKSLLDRHGQYPIWMN |
| Parental | QRQRKRLKAKREKRKGKSKANA |
| QRQRKRLKAK..K.KGKS.... | |
| Retrocopy | QRQRKRLKAKQGKWKGKSQSKS |
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 | 4 .67 RPM |
| SRP017611_kidney | 0 .00 RPM | 8 .81 RPM |
| SRP017611_liver | 0 .00 RPM | 4 .50 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_325 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 | ENSEEUG00000012195 | 1 retrocopy |
retro_eeur_325 ,
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