RetrogeneDB ID: | retro_pabe_3287 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 8:115549948..115550357(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRMT10B | ||
| Ensembl ID: | ENSPPYG00000019056 | ||
| Aliases: | None | ||
| Description: | tRNA methyltransferase 10 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:26454] |
Retrocopy-Parental alignment summary:
>retro_pabe_3287
TGTGTGAAGAGCGAAGATGAATTTTCTAGCGACTTGCTAGACATAAAAGAAGACTTCTTTTAGTTTATTTCCTCTGGAAA
CCCTTGTGTTCCTGACTCCTGACTCAGAATACACTATTGAAGATGTTGATCTAAACAAAGTTTGTATCTTTGATGGACTT
GTGGATGAAAGCATTCAGAAGAAGGTGACATTTCAAAAGGCCCAGGAATACTCTTTCAGGACAGCCCACTTGTCTGTCAT
TCCAGGGATACATGATCAGACACCAGAGTACAAATAACTCTCATTTAGGGATGCTGGCCATCAATCAAGTATTTGATATT
CTGTCCACTTATTTTGAGACTCTTAACTGGCCTGAAGCATTGAAGACGGGAATTTCTTCCAGAAAAGTTATATTCTTCAG
AGCACAGTG
ORF - retro_pabe_3287 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.29 % |
| Parental protein coverage: | 57.14 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | CVRMNDGFSSYLLDITEED-CFSLFPLETLVYLTPDSEHALEDVDLNKVYILGGLVDESIQKKVT-FQKA |
| CV...D.FSS.LLDI..ED..FSLFPLETLV.LTPDSE...EDVDLNKV.I..GLVDESIQKKVT.F... | |
| Retrocopy | CVKSEDEFSSDLLDI-KED>SFSLFPLETLVFLTPDSEYTIEDVDLNKVCIFDGLVDESIQKKVT>FKRP |
| Parental | RE-YSVKTARLPIQEYMVRNQNGKNYHSEILAINQVFDILSTYLETHNWPEALKKGVSS-GKGYILRNSV |
| R...S.....L..Q.YM.R.Q...N.H...LAINQVFDILSTY.ET.NWPEALK.G.SS..K.YIL...V | |
| Retrocopy | RNTLSGQPTCLSFQGYMIRHQSTNNSHLGMLAINQVFDILSTYFETLNWPEALKTGISS<QKSYILQSTV |
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_prefrontal_cortex | 0 .00 RPM | 8 .02 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 17 .39 RPM |
| SRP007412_heart | 0 .00 RPM | 2 .53 RPM |
| SRP007412_kidney | 0 .00 RPM | 8 .42 RPM |
| SRP007412_liver | 0 .00 RPM | 5 .02 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3287 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3287 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3287 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Oryctolagus cuniculus | ENSOCUG00000010994 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000019056 | 1 retrocopy |
retro_pabe_3287 ,
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