RetrogeneDB ID: | retro_ogla_75 | ||
Retrocopy location | Organism: | African rice (Oryza glaberrima) | |
| Coordinates: | 9:9575217..9575930(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ORGLA05G0075600 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ogla_75
AGTTTGGTTGACATGTTTTCTACACAAGAGATTAGCAGCCACGTAAGCATCGTCCCAGCAGATAAAGCTCCTGGCCCAGA
TGGATTCAATGGCTATTTTCTGAATAAATGCTGGCACATTATAATCCAAGATTATTACGGACTAGCTGCACACTTCCATG
CTAGTTGTACTGATCTACAGATCCGTAATAGCTCTTACATAACTTTGGTCCCAAAGAAGAGTTCTCCAAAGACTGTCAAT
GATTTTAGACCTATTTCCCTCATGGGGCTCAGCCTAAAATTTCTTACCAAACTCATGGCAGATAGATTGCAAGGGGTAAT
TCTCAAGCTAGTCAGTGATAATTAGTATGGCTTTATCAAAGGAAGAACTATACAACACTGCCTTGCTTGGTCTTTTGAAT
ACATTCACCAGTGCCAACAGTCTAAGAGAGAGATCATACTCCTGAAATTGGACTTTGAAAAGGCTTTTGACACCATTGAG
CACTCTGCTATTCTCTCAGTCCTGAAGCATATGGGTTTTCCTGAAAAATGGATTCATTGGGTACAGATGGTCTTTTCCAT
ACCTCCTCTGTTGTTCTTCTTAATGGAGAGCCAGGGAATTCTTTCAAGTGTAAAAGAGGGGTGAGGCAAGGTGATCCTCT
GTCCCCTTTACTCTTTGTCTTAGGTGCTGAGCTTCTACAAAAAATAGTAAACAAAGCCTCTGATATGGGTTTG
ORF - retro_ogla_75 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.9 % |
| Parental protein coverage: | 66.67 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | NVISFYENPLLRSHLALAFVDKLEERRDLNLAEWNFRLFIKSKDFYNLCAQFCEGSLVLESINRSFITLV |
| ............SH......DK.......N....N....I...D.Y.L.A.F......L...N.S.ITLV | |
| Retrocopy | SLVDMFSTQEISSHVSIVPADKAPGPDGFNGYFLNKCWHIIIQDYYGLAAHFHASCTDLQIRNSSYITLV |
| Parental | PKKSSPEKVNDFRPISLQSVALKLLTKVLADRLQSVIIELIHQNQYGFIKARNIQDCLAWSFEYLHQCQH |
| PKKSSP..VNDFRPISL....LK.LTK..ADRLQ.VI..L...N.YGFIK.R.IQ.CLAWSFEY.HQCQ. | |
| Retrocopy | PKKSSPKTVNDFRPISLMGLSLKFLTKLMADRLQGVILKLVSDN*YGFIKGRTIQHCLAWSFEYIHQCQQ |
| Parental | SKREIVLLKLDFEKTFDTIEHSVILDIMRQKGFDSKWISWISQIFS-SASSSVILNGVLGKSFYCKRGVR |
| SKREI.LLKLDFEK.FDTIEHS.IL......GF..KWI.W....FS...SS.V.LNG..G.SF.CKRGVR | |
| Retrocopy | SKREIILLKLDFEKAFDTIEHSAILSVLKHMGFPEKWIHWVQMVFS<HTSSVVLLNGEPGNSFKCKRGVR |
| Parental | QGDPLSPLLFVLGADLLQSIVNKACSQGV |
| QGDPLSPLLFVLGA.LLQ.IVNKA...G. | |
| Retrocopy | QGDPLSPLLFVLGAELLQKIVNKASDMGL |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Oryza glaberrima was not studied using RNA-Seq expression data.
Oryza glaberrima was not studied using ChIP-Seq data.
Oryza glaberrima was not studied using EST data.
Oryza glaberrima was not studied using FANTOM5 data.
retro_ogla_75 was not experimentally validated.
Retrocopy orthology:
Oryza glaberrima 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 | |
|---|---|---|---|
| Oryza glaberrima | ORGLA05G0075600 | 1 retrocopy |
retro_ogla_75 ,
|