RetrogeneDB ID: | retro_slyc_76 | ||
Retrocopy location | Organism: | Tomato (Solanum lycopersicum) | |
| Coordinates: | 4:51877117..51877371(+) | ||
| Located in intron of: | Solyc04g054170.2 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | Solyc01g097870.2 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_slyc_76
ATGGCAGACAAGATAGTGACTATTAGAACTAGGAAGTTCATGACCAATAGATTATTTGCAAGGAAACAATTCATTATTGA
TGTCTTACATCCTGGAAGAGTCAATGTTTTTAACGCTGATTTGAAAGAAAATTGGCAAGGATGTATGAAGTGAAAGATTT
AAATGCCATCTATGTGAAGTTCAGAACCCACTTTCGAAGAGGCAAATCTTCTGGCTTTGATTTGATCTATGACTGTTGAG
AATGCAGAGAAAAA
ORF - retro_slyc_76 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.16 % |
| Parental protein coverage: | 64.66 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MADKAVTIRTRKFMTNRLLARKQFIIDVLHPGRANVSKAELKE-KLARMYEVKDANAIFVFKFRTHFGGG |
| MADK.VTIRTRKFMTNRL.ARKQFIIDVLHPGR.NV..A.LKE.KLARMYEVKD.NAI.V.KFRTHF..G | |
| Retrocopy | MADKIVTIRTRKFMTNRLFARKQFIIDVLHPGRVNVFNADLKE<KLARMYEVKDLNAIYV-KFRTHFRRG |
| Parental | KSTGFGLIYDSVENAKK |
| KS.GF.LIYD..E...K | |
| Retrocopy | KSSGFDLIYDC*ECREK |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Solanum lycopersicum was not studied using RNA-Seq expression data.
Solanum lycopersicum was not studied using ChIP-Seq data.
Solanum lycopersicum was not studied using EST data.
Solanum lycopersicum was not studied using FANTOM5 data.
retro_slyc_76 was not experimentally validated.
Retrocopy orthology:
Solanum lycopersicum 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 | |
|---|---|---|---|
| Solanum lycopersicum | Solyc01g097870.2 | 1 retrocopy |
retro_slyc_76 ,
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