RetrogeneDB ID: | retro_eeur_653 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_375942:3780..4101(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CSDC2 | ||
| Ensembl ID: | ENSEEUG00000003639 | ||
| Aliases: | None | ||
| Description: | cold shock domain containing C2, RNA binding [Source:HGNC Symbol;Acc:30359] |
Retrocopy-Parental alignment summary:
>retro_eeur_653
AGTCCGCTGCCCACCTGCCGCACCAGGACCTTCTCTGCGACAGTGAGGGTGTCCCTGGGCACCGTGTACAAGGGCGTCTG
CAAGTGCTTCTGCTGTTCCAAGGGCCACGACTTCATCACGCTGGCCGATGGAGGCCCTGACATCTTCCTGCATATCTCTG
ACGTGGAAGGCGAGTACGTGTCTGTGGAAGGTGATGAGGTGACCTACAAGATGTGCTCGATCCCACCCAAGAACGAGAGG
CTGCAGGCCGTGGAAGTTGTCATCACCCACCTGGCGCCAGGCACCAAGCACGAGACCTGGTCGGGCCACGTGGTCAGCTC
C
ORF - retro_eeur_653 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.03 % |
| Parental protein coverage: | 69.93 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SPLPTKRTRTYSATARASAGPVFKGVCKQFSRSQGHGFITPENGSEDIFVHVSDIEGEYVPVEGDEVTYK |
| SPLPT.RTRT.SAT.R.S.G.V.KGVCK.F..S.GH.FIT...G..DIF.H.SD.EGEYV.VEGDEVTYK | |
| Retrocopy | SPLPTCRTRTFSATVRVSLGTVYKGVCKCFCCSKGHDFITLADGGPDIFLHISDVEGEYVSVEGDEVTYK |
| Parental | MCPIPPKNQKFQAVEVVLTQLAPHTPHETWSGQVVGS |
| MC.IPPKN...QAVEVV.T.LAP.T.HETWSG.VV.S | |
| Retrocopy | MCSIPPKNERLQAVEVVITHLAPGTKHETWSGHVVSS |
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 | 1 .29 RPM | 10 .64 RPM |
| SRP017611_kidney | 5 .63 RPM | 2 .06 RPM |
| SRP017611_liver | 2 .41 RPM | 0 .00 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_653 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 | ENSEEUG00000003639 | 1 retrocopy |
retro_eeur_653 ,
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