RetrogeneDB ID: | retro_eeur_650 | ||
Retrocopy location | Organism: | Hedgehog (Erinaceus europaeus) | |
| Coordinates: | scaffold_375110:1309..1665(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LMO1 | ||
| Ensembl ID: | ENSEEUG00000002475 | ||
| Aliases: | None | ||
| Description: | LIM domain only 1 (rhombotin 1) [Source:HGNC Symbol;Acc:6641] |
Retrocopy-Parental alignment summary:
>retro_eeur_650
TGCAACCGCAAGATCAAGGACCGCTACCTGCTGTAGGCGCTTGCCAAGTACTGGCATGAGGACTGTCTCAAGTGTGCCTG
GGGCGACTGCCGCCTGGGGGAGGTGGGCTCCACCAAGGCCAAGCTCATCCTGTGCCAGCGCGATTACCACCTGAGGCTCT
TTGGCACCGCAGGGAACTGTGGCGCCTGTAGCAAGCTCATCCTGGCCTTCGAAATGGTGATGCGGGCCCGGAACAATGTG
TACCATTTCCACTGCTTTGCCTGTCAGCTGTGCAACCAGAGATTTTTGTGGGAAACAAATTCTTCCTGAAGAACAACAGG
ATCTTGTGTCAGATGGACTATGAGGAATCCCAGGTT
ORF - retro_eeur_650 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.11 % |
| Parental protein coverage: | 68.36 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | CNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY-LRLFGTTGNCAACSKLI |
| CNRKIKDRYLL.AL.KYWHEDCLKCA..DCRLGEVGS...TKA.LILC.RDY.LRLFGT.GNC.ACSKLI | |
| Retrocopy | CNRKIKDRYLL*ALAKYWHEDCLKCAWGDCRLGEVGS---TKAKLILCQRDYHLRLFGTAGNCGACSKLI |
| Parental | PAFEMVMRARDNVYHLDCFACQLCNQRFC-VGDKFFLKNNMILCQMDYEEGQL |
| .AFEMVMRAR.NVYH..CFACQLCNQRF..VG.KFFLKNN.ILCQMDYEE.Q. | |
| Retrocopy | LAFEMVMRARNNVYHFHCFACQLCNQRFL<VGNKFFLKNNRILCQMDYEESQV |
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 | 3 .22 RPM |
| SRP017611_kidney | 0 .00 RPM | 2 .06 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .16 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_650 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 | ENSEEUG00000002475 | 1 retrocopy |
retro_eeur_650 ,
|
| Otolemur garnettii | ENSOGAG00000013163 | 1 retrocopy |