RetrogeneDB ID: | retro_eeur_378 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_275419:3223..3495(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSEEUG00000008642 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ARFRP1 | ||
| Ensembl ID: | ENSEEUG00000005894 | ||
| Aliases: | None | ||
| Description: | ADP-ribosylation factor related protein 1 [Source:HGNC Symbol;Acc:662] |
Retrocopy-Parental alignment summary:
>retro_eeur_378
GAATCCTAGAGAGCATTTGAGAAGATGGTCACAAGTGAGGCTTTGGTAGGCATCCCCATCCTGGTGCTGGCCAACAAGCA
GGATGTGCAGATGTGCCTCTGTCTCCCCGACATCAAGACTGCCTTCAGTCACTGCACCTCTAAGATCAGTCAGGGGACTG
CCTCAGCCAGGCCTGCTCAGTCCTCAGGGGCCAGGGGGTGCAATGTGGCATAGAGTGGATGGTGAAGTGTGTCTTATTGA
ACATGCACCAGGCACTGCAGCAGAGGGACATC
ORF - retro_eeur_378 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.74 % |
| Parental protein coverage: | 53.53 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | ESKKAFEKMVTSEALDGVPILVLANKQDVQXXXSIPDIKTAFSDCTSKIGR-RDCLTQACSALTGQGVRE |
| ES..AFEKMVTSEAL.G.PILVLANKQDVQ.....PDIKTAFS.CTSKI....DCL.QACS.L.GQGV.. | |
| Retrocopy | ES*RAFEKMVTSEALVGIPILVLANKQDVQMCLCLPDIKTAFSHCTSKISQ<GDCLSQACSVLRGQGVQC |
| Parental | GIEWMVKCVVRNVHRPPRQRDI |
| GIEWMVKCV..N.H....QRDI | |
| Retrocopy | GIEWMVKCVLLNMHQALQQRDI |
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 | 11 .12 RPM |
| SRP017611_kidney | 0 .38 RPM | 19 .69 RPM |
| SRP017611_liver | 0 .16 RPM | 13 .51 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_378 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000014423 | 1 retrocopy | |
| Erinaceus europaeus | ENSEEUG00000005894 | 1 retrocopy |
retro_eeur_378 ,
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