RetrogeneDB ID: | retro_eeur_321 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_253473:4253..4968(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | COQ6 | ||
| Ensembl ID: | ENSEEUG00000000826 | ||
| Aliases: | None | ||
| Description: | coenzyme Q6 monooxygenase [Source:HGNC Symbol;Acc:20233] |
Retrocopy-Parental alignment summary:
>retro_eeur_321
GTCCAGATTGTTAGCTGGAACTATGACCAGTCTGCTGTTGTAACTACTCTGCGTTCATCAGAGGTCACAGAAAATAATGC
AGCTTGCCAGAGATTTCTTCCCTCTGGGCCCATTGCTCTGCTCCTGCTCTCAGACACCTCGAGTTCCTAGGTTTGGTCCA
TATCCTATGGACATGCAGCAAAGCTGATCAGCATGGATAAGGAAAAGTTTGTAAATGCCATTAACTCTGCCTTTGGGGGT
TATGTTAACCATGCAGACTTCATCGACTTCACTGGCACTATACTGCAATATGCTGTTGCCCTTCTGAAGCCTACTACTGT
TTCAGCTTGCCAGCTGCCCCCAAATGTGGTCAAGGTGGATGCCCAGAGCAGAGCACTGTTTCCTCTTGGGTTGGGACATG
CTGCTGAGTACGTGTGGCCTTGAGTGGCACTCAGTGAGGATGCATCCCACAGAGTCCATCCACTGGTGGGACAAGGTATC
AACATGGGCTTTGGGGATATTTCCAGTTTGGCTCATCATCTCAGTGCTGTAGCCTTCAATGGGAAAGACTTGGGTTCTAA
GAACCACCTCACAGGTTATGAGAAAGACAGACAGTGTCACACAACTGCTCTTCTGGTTGCTACAGATCTTCTAATAAAAA
TACTATTCCACCAATGCTAGTGTGCTTCTCAGGATGTAGGGATTGCAGACCACAAATGCATTATCTCCACTCAAA
ORF - retro_eeur_321 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.93 % |
| Parental protein coverage: | 51.17 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | IQNVSWNYDQSAVVATLHLSEATENNVAWQRFLPSGPIALLPLSDTFSSLVWSTSHEHAAELVSMDEEKF |
| .Q.VSWNYDQSAVV.TL..SE.TENN.A.QRFLPSGPIALL.LSDT.SS.VWS.S..HAA.L.SMD.EKF | |
| Retrocopy | VQIVSWNYDQSAVVTTLRSSEVTENNAACQRFLPSGPIALLLLSDTSSS*VWSISYGHAAKLISMDKEKF |
| Parental | VDAINSAFWSDVNHSDFIDSAGTILHYAVALLKPTKISARQLPPSVARVDAQSRALFPLGLGHAAEYVRP |
| V.AINSAF...VNH.DFID..GTIL.YAVALLKPT..SA.QLPP.V..VDAQSRALFPLGLGHAAEYV.P | |
| Retrocopy | VNAINSAFGGYVNHADFIDFTGTILQYAVALLKPTTVSACQLPPNVVKVDAQSRALFPLGLGHAAEYVWP |
| Parental | RVALIGDAAHRVHPLAGQGVNMGFGDISSLVHHLSAAAFNGKDLGSMSHLTGYETDRQRHNTALLVATDL |
| .VAL..DA.HRVHPL.GQG.NMGFGDISSL.HHLSA.AFNGKDLGS..HLTGYE.DRQ.H.TALLVATDL | |
| Retrocopy | *VALSEDASHRVHPLVGQGINMGFGDISSLAHHLSAVAFNGKDLGSKNHLTGYEKDRQCHTTALLVATDL |
| Parental | LKRL-YSTSVTPLVLLRTWGLQATNAVSPLK |
| L....YST.....VLLR..GLQ.TNA.SPLK | |
| Retrocopy | LIKI>YSTNAS--VLLRM*GLQTTNALSPLK |
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 | 29 .49 RPM |
| SRP017611_kidney | 0 .00 RPM | 44 .63 RPM |
| SRP017611_liver | 0 .00 RPM | 19 .45 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_321 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 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000000826 | 1 retrocopy |
retro_eeur_321 ,
|
| Tupaia belangeri | ENSTBEG00000008327 | 3 retrocopies |