RetrogeneDB ID: | retro_xtro_40 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL174848.1:18234..18642(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | c7orf10 | ||
| Ensembl ID: | ENSXETG00000015599 | ||
| Aliases: | None | ||
| Description: | chromosome 7 open reading frame 10 [Source:Jamboree;Acc:XB-GENE-5750708] |
Retrocopy-Parental alignment summary:
>retro_xtro_40
CTGGCCGATCTGGGGGCCGAAGTCATCAAGGTGGAGCGGCCCGGCCTGGGCGACGAAACCCGGGGCTGGGGTCCGCCCTG
GATGCCGGCCGCTGCGGGCAGCCAACGGCACGATTCGGCCTATTTCGGCTCCGCCAACCGCGGCAAGAAATCGGTCACCA
TCGACTTCACCACCGCGCAGGGCCAGGCGCTACTCAGGGATCTGGTTCGGCAGTGCGACGTGCTGGTGGAGAACTACAAG
GCGGGCACCCTGGCACGCTACGGCCTGGGGTATGGTGACCTCAAGGCCATCCACCCCGGCCTCGTGTACTGCTCCGTCAC
CGGCTTCGGGCACACCGGCCCATACAGCCACAAGCCGGGCTACGACTTCGTGTTCCAGGCCATGAGCGGACTGATGAGCA
TCACCGGC
ORF - retro_xtro_40 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.94 % |
| Parental protein coverage: | 59.45 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LADLGAEVIKVERPGSGDDTRS----WGPPFVGSE---SAYFLSVNRNKKSIAVNMKNPNGSKIIQELAK |
| LADLGAEVIKVERPG.GD.TR.....W.P...GS....SAYF.S.NR.KKS.........G......L.. | |
| Retrocopy | LADLGAEVIKVERPGLGDETRGWGPPWMPAAAGSQRHDSAYFGSANRGKKSVTIDFTTAQGQALLRDLVR |
| Parental | ACDVFVENYIPGKLSKMGLGFEEIKEIAPHIIYCSITGYGQTGPLFQRAGYDAVACAMSGLMYITG |
| .CDV.VENY..G.L...GLG....K.I.P...YCS.TG.G.TGP.....GYD.V..AMSGLM.ITG | |
| Retrocopy | QCDVLVENYKAGTLARYGLGYGDLKAIHPGLVYCSVTGFGHTGPYSHKPGYDFVFQAMSGLMSITG |
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 |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 0 .07 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .57 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .57 RPM |
| SRP007412_liver | 0 .00 RPM | 1 .19 RPM |
| SRP007412_skeletal_muscle | 0 .00 RPM | 1 .29 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_40 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_40 was not experimentally validated.
Retrocopy orthology:
Xenopus tropicalis 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 | |
|---|---|---|---|
| Xenopus tropicalis | ENSXETG00000015599 | 1 retrocopy |
retro_xtro_40 ,
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