RetrogeneDB ID: | retro_eeur_341 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_264464:4985..5338(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSEEUG00000002782 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CHCHD1 | ||
| Ensembl ID: | ENSEEUG00000015523 | ||
| Aliases: | None | ||
| Description: | coiled-coil-helix-coiled-coil-helix domain containing 1 [Source:HGNC Symbol;Acc:23518] |
Retrocopy-Parental alignment summary:
>retro_eeur_341
ATGGTGGTTCCCAGCCTGTGGGGCTGGCTAATGCAGCTTGGAAACTCACAGAAGCCTGTACTAAAACCCAGCAGACCCCT
CATTCTAACCAAGCAAGTGGGAGAACAGCATCAGGAGAGAGGTGAGGCAACGTGTGTCATGGAGATGCCATTGATGATGG
CTTGCTGGAAGCAGAATGAATTCCACGATGAAGAGTGTGGAAAAGAAATCAAGAACTTCTTCGATTGTGCTTCAGAGGCT
GAGCATCCCGAAAAATGAGATTAACACAGGATATCATGGGAGAGTTTGGGAGTTTACACCCCAAGAAGTTGAATAAATTA
TTACAGAGGTTTCCTAGTAAATCTTATATCCTC
ORF - retro_eeur_341 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.35 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAVPNLRGRLARLGNSQKPVLKPSRPLILANRVGERRRERGEATCVMEMSLMMACWKQNEFHDEACGKEI |
| M.VP.L.G.L..LGNSQKPVLKPSRPLIL...VGE...ERGEATCVMEM.LMMACWKQNEFHDE.CGKEI | |
| Retrocopy | MVVPSLWGWLMQLGNSQKPVLKPSRPLILTKQVGEQHQERGEATCVMEMPLMMACWKQNEFHDEECGKEI |
| Parental | KNFFDCASKAE-ASRKMKSTQEIMGELGSLHPKKLNKLLQRFPSKSYVL |
| KNFFDCAS.AE.ASRKM..TQ.IMGE.GSLHPKKLNKLLQRFPSKSY.L | |
| Retrocopy | KNFFDCASEAE<ASRKMRLTQDIMGEFGSLHPKKLNKLLQRFPSKSYIL |
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 | 11 .44 RPM |
| SRP017611_kidney | 0 .56 RPM | 11 .44 RPM |
| SRP017611_liver | 0 .16 RPM | 10 .13 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_341 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 | ENSEEUG00000015523 | 1 retrocopy |
retro_eeur_341 ,
|
| Echinops telfairi | ENSETEG00000018904 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000000361 | 1 retrocopy |