RetrogeneDB ID: | retro_eeur_623 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_368772:68387..69023(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LIX1L | ||
| Ensembl ID: | ENSEEUG00000015291 | ||
| Aliases: | None | ||
| Description: | Lix1 homolog (mouse)-like [Source:HGNC Symbol;Acc:28715] |
Retrocopy-Parental alignment summary:
>retro_eeur_623
GATATAATAAATGAAGGCCTGGTGGTCTATGAGTCGCTACCATCCCCTGGACCTCCCTTTGTGAGTTATGTCACCCTCCC
AGGGGGAAGCTGTTTTGGCAACTTTCAGTGCTGCCTAAGTAGAGCAGAGGCCAGACGGGATGCAGCTAAAGTGGCTCTAA
TCAACTCCCTCTTCAACGAGCTGCCCTCTCGCAGGATCACCAAGGAATTCATTATGGAGAGTGTGCAGGAAGCCGTTGCT
TCCACCAGTGGTACCCTAGATGATGCTGATGACCCCAGTACCAGCATTGGAGCCTATCACTACATGCTGGAGTCAAACAT
GGGGAAGACCATGTTAGAGTTTCAGGAACTGATGACCATTTTCCAGCTCTTGCACTGGAATGGCAGCCTTAAAGCTCTTC
GTGAAACAAAGTGTTCCCGACAGGAAGTCATCTCCTATTATTCCCAGTATTCCCTAGATGAAAAAATGCGCAGTCACATG
GCCCTGGATTGGATTACAAAGGAGCGAGAATCACCAGGAATTCTCTCGCAAGAGCTATGAATGGCCCTGAGAGAGTTGGA
GGAAGCAAGGAAAGCAGGACAAGAACTGAGATTTTACAAAGAAAAGAAAGAAATCCTGAGTTTAGCCCTGACTCAG
ORF - retro_eeur_623 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.62 % |
| Parental protein coverage: | 63.47 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | DLKNGALVVYEMVPSNSPPYVCYVTLPGGSCFGSFQFCPTKAEARRSAAKIALMNSVFNEHPSRRITDEF |
| D..N..LVVYE..PS..PP.V.YVTLPGGSCFG.FQ.C...AEARR.AAK.AL.NS.FNE.PSRRIT.EF | |
| Retrocopy | DIINEGLVVYESLPSPGPPFVSYVTLPGGSCFGNFQCCLSRAEARRDAAKVALINSLFNELPSRRITKEF |
| Parental | IEKSVSEALASFNGNREEADNPNTGIGAFRFMLESNKGKSMLEFQELMTVFQLLHWNGSLKAMRERQCSR |
| I..SV.EA.AS..G....AD.P.T.IGA...MLESN.GK.MLEFQELMT.FQLLHWNGSLKA.RE..CSR | |
| Retrocopy | IMESVQEAVASTSGTLDDADDPSTSIGAYHYMLESNMGKTMLEFQELMTIFQLLHWNGSLKALRETKCSR |
| Parental | QEVLAHYSHRALDDDIRHQMALDWVSREQSVPGALSRELASTEQELDEARLAGKELRFHKEKKDILMLAA |
| QEV...YS...LD...R..MALDW...E...PG.LS.EL.....EL.EAR.AG.ELRF.KEKK.IL.LA. | |
| Retrocopy | QEVISYYSQYSLDEKMRSHMALDWITKERESPGILSQEL*MALRELEEARKAGQELRFYKEKKEILSLAL |
| Parental | GQ |
| .Q | |
| Retrocopy | TQ |
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 .97 RPM | 6 .45 RPM |
| SRP017611_kidney | 2 .06 RPM | 3 .75 RPM |
| SRP017611_liver | 0 .00 RPM | 2 .25 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_623 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Erinaceus europaeus | ENSEEUG00000015291 | 1 retrocopy |
retro_eeur_623 ,
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