RetrogeneDB ID: | retro_eeur_199 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_207085:3833..4172(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | UCK2 | ||
| Ensembl ID: | ENSEEUG00000013484 | ||
| Aliases: | None | ||
| Description: | uridine-cytidine kinase 2 [Source:HGNC Symbol;Acc:12562] |
Retrocopy-Parental alignment summary:
>retro_eeur_199
TACCGTGTCCTCACCTCTGAGCAGAAGGCCAAAGCCCTCAAGGGCCAGTTCAACTTTGATCACCCAGATGCCTTTGACAA
TGAACTCATCTTCAAGATGCTCAAAGAAATTATGGACGGGAAGACAGTGCAGATCCCAGTGTATGACTCTGTCTCTAATT
GCGGAAGGAGGAGACTTTCACCGTGTTATCCTGCCGACGTGGTGCCCTTTGAGAGGATCCTGGCCTTCTACTCCCAGGAA
GTGCAAAACCTGATCCAGATGAAGCTTTTTGTGGACAGAGATGCTGATACCCTGCTGTCCCGCAGAGTATTGGCGGACAT
CAGTGAACCAGGGAGGGAC
ORF - retro_eeur_199 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.87 % |
| Parental protein coverage: | 73.2 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | YRVLTSEQK-KALKGQFNFDHPDAFDNELIFMTLKEIMEGKTVQIPVYDFVSHS-RKEETVTV-YPADVV |
| YRVLTSEQK.KALKGQFNFDHPDAFDNELIF..LKEIM.GKTVQIPVYD.VS...RKEET.TV.YPADVV | |
| Retrocopy | YRVLTSEQKAKALKGQFNFDHPDAFDNELIFKMLKEIMDGKTVQIPVYDSVSNC<RKEETFTV>YPADVV |
| Parental | LFEGILAFYSQEVRDLFQMKLFVDTDADTRLSRRELRDISCKGPD |
| .FE.ILAFYSQEV..L.QMKLFVD.DADT.LSRR.L.DIS..G.D | |
| Retrocopy | PFERILAFYSQEVQNLIQMKLFVDRDADTLLSRRVLADISEPGRD |
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 .32 RPM | 4 .67 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .94 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .96 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_199 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 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000013484 | 1 retrocopy |
retro_eeur_199 ,
|
| Myotis lucifugus | ENSMLUG00000016012 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000008446 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000007694 | 1 retrocopy |