RetrogeneDB ID: | retro_eeur_265 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_229037:2639..3023(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ABHD17A | ||
| Ensembl ID: | ENSEEUG00000001302 | ||
| Aliases: | None | ||
| Description: | abhydrolase domain containing 17A [Source:HGNC Symbol;Acc:28756] |
Retrocopy-Parental alignment summary:
>retro_eeur_265
CTGGGCCAGATGAGCCGCTTCTACGTGGGCCTGGGCTCCCACTGTGGCTGCAACATCCTCTCCTATGACTACTCGTCCGG
GCTATCGGGCCGGCCCTCTGAGAAGAACCTGTAGGCAGACATTGACGCTGCCGTCTGGCAGGTGCTGCGCACGAGGTACG
GGATCAGCCCCGACAGCGTGGTGCTATATGGCCAGAGCATCCGCACGGTGCCCACCGAGGGCTTGGCGGCCCGAACTGAG
TGAGCTGCGGTGGTGCTGCACTCGCCACTCACGTCGGGCATTCGGGTAGCCTTCCCCGACACCACGAAGACCTACTGCCT
CGACGCCTCCCCCAACATCTAGAAGGTGTCCCGCATCTCATCGCTGGTTTTGCTGATCCACGGC
ORF - retro_eeur_265 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.54 % |
| Parental protein coverage: | 65.15 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LGQMSSFYVGLGSRLGCNIFSYDYSGYGASSGRPSEKNLYADIDAA-WQALRTRYGISPDSVVLYGQSIG |
| LGQMS.FYVGLGS..GCNI.SYDYS.....SGRPSEKNL.ADIDAA.WQ.LRTRYGISPDSVVLYGQSI. | |
| Retrocopy | LGQMSRFYVGLGSHCGCNILSYDYSS--GLSGRPSEKNL*ADIDAAVWQVLRTRYGISPDSVVLYGQSIR |
| Parental | TVPTVDLAARYECAAVVLHSPLTSGMRVAFPDTKKTYCFDAFPNIEKVSRISSPVLVIHG |
| TVPT..LAAR.E.AAVVLHSPLTSG.RVAFPDT.KTYC.DA.PNI.KVSRISS.VL.IHG | |
| Retrocopy | TVPTEGLAARTE*AAVVLHSPLTSGIRVAFPDTTKTYCLDASPNI*KVSRISSLVLLIHG |
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 | 5 .16 RPM |
| SRP017611_kidney | 0 .00 RPM | 7 .88 RPM |
| SRP017611_liver | 0 .00 RPM | 8 .68 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_265 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000001302 | 1 retrocopy |
retro_eeur_265 ,
|
| Erinaceus europaeus | ENSEEUG00000013750 | 1 retrocopy | |
| Microcebus murinus | ENSMICG00000013508 | 1 retrocopy |