RetrogeneDB ID: | retro_eeur_392 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_282386:182..1018(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PCGF2 | ||
| Ensembl ID: | ENSEEUG00000011789 | ||
| Aliases: | None | ||
| Description: | polycomb group ring finger 2 [Source:HGNC Symbol;Acc:12929] |
Retrocopy-Parental alignment summary:
>retro_eeur_392
ATGCATCGAACCACACGGATCAAAATCACGGAGCTGAACCCCAGCTCATGTGTGTCCTCTGTGGGGGTTACTTCATCGAC
TGCACGACCACAGCGGAGTGCCTGCATTCCTTCTGCAAAACCTGCATCGTGCTCTACCTGGAGACCAGCAAGTACTGCCC
CGTGTGTGATGCGCAGGTCCACAAAACCCGGCCGCTGCTGAGCATCAGATCCGACAAAACCCTCCAAGACATTGTTTACA
AATTGGTCCCTGGGCTTTTTAAAGATGAGATGAAACGGAGGCGGGATTTCTATGCAGCTTATCCCCTAACAGAAGTCCCC
AATGGCTCCAGTGAAGACCAAGGTGAGGTCCTGGAGCAGGAGAAGCGGGCTCCGAAGGACGAGATTGTCAGCCTCAGCAT
CGAGTTCTATGCAGGCATCAGAGGTAGAGAAGAGAAGACGTGCCCCCCGGAGAATGAAGATGGGGACAAGGAGAAGCAGA
CTGGGGGTGCGCTTCCCGCGATGCCCAGCAGCCATGACTTTCATAGCACCTCCCTAAATTTCTCCGCAACAAGATGGATG
TGCCCAGCAAATACAAGGTGCAGGTTGTATATGAGGACGAGCCTTTGAAGGAGTACTACACCCTCGTGGACATTGCCTAC
ATCTACCCCTGGCGGCGGAATGGCCCTCTCCCCCTCAAGTTCCGTGTCCAGCCAGCCTGCAAGCGGCTCACCTTGCCCAC
AGTACCCACCCCATCCGAGGGCACCAACACCAGCAGGGCGTCCGGGCAGCAACAAGGCTCCCAGCTCTGCCACGCTGCCT
GCCACCTCTTCTTCCCTGCCCAGCCCAGCCCAGCCA
ORF - retro_eeur_392 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.96 % |
| Parental protein coverage: | 81.98 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | MHRTTRIKITELNP-HLMCALCGGYFIDATTIVECLHSFCKTCIVRYLETNKYCPMCDVQVHKTRPLLSI |
| MHRTTRIKITELNP..LMC.LCGGYFID.TT..ECLHSFCKTCIV.YLET.KYCP.CD.QVHKTRPLLSI | |
| Retrocopy | MHRTTRIKITELNP<QLMCVLCGGYFIDCTTTAECLHSFCKTCIVLYLETSKYCPVCDAQVHKTRPLLSI |
| Parental | XXXXXXXXXXXXXXXXXXXXEMKRRRDFYAAYPLTEVPNGSNEDRGEVLEQEKGALSDDEIVSLSIEFYE |
| ....................EMKRRRDFYAAYPLTEVPNGS.ED.GEVLEQEK.A...DEIVSLSIEFY. | |
| Retrocopy | RSDKTLQDIVYKLVPGLFKDEMKRRRDFYAAYPLTEVPNGSSEDQGEVLEQEKRA-PKDEIVSLSIEFYA |
| Parental | GIRDREEKKGPLENGDGDKEK-TG-VRFLRCPAAMTVM-HLAKFLRNKMDVPSKYKVEVLYEDEPLKEYY |
| GIR.REEK..P.EN.DGDKEK.TG.VRF.RCPAAMT...HL.KFLRNKMDVPSKYKV.V.YEDEPLKEYY | |
| Retrocopy | GIRGREEKTCPPENEDGDKEKQTG>VRFPRCPAAMTFI>HLPKFLRNKMDVPSKYKVQVVYEDEPLKEYY |
| Parental | TLMDIAYIYPWRRNGPLPLKYRVQPACKRLTLPTVPTPSEGTNTSGASECESVS-DKAPSPATLPATSSS |
| TL.DIAYIYPWRRNGPLPLK.RVQPACKRLTLPTVPTPSEGTNTS.AS.....S...A..PAT....SSS | |
| Retrocopy | TLVDIAYIYPWRRNGPLPLKFRVQPACKRLTLPTVPTPSEGTNTSRASGQQQGS>SSATLPAT----SSS |
| Parental | LPSPATP |
| LPSPA.P | |
| Retrocopy | LPSPAQP |
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 .48 RPM | 12 .09 RPM |
| SRP017611_kidney | 0 .94 RPM | 16 .50 RPM |
| SRP017611_liver | 0 .80 RPM | 9 .81 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_392 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 | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000011789 | 1 retrocopy |
retro_eeur_392 ,
|
| Pan troglodytes | ENSPTRG00000009074 | 1 retrocopy |