RetrogeneDB ID: | retro_pabe_3425 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 9:76586529..76586897(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TEN1 | ||
| Ensembl ID: | ENSPPYG00000008646 | ||
| Aliases: | None | ||
| Description: | TEN1 CST complex subunit [Source:HGNC Symbol;Acc:37242] |
Retrocopy-Parental alignment summary:
>retro_pabe_3425
GTGATGCTGCCCAAACCTGGGACCTATTCCCTCCACTGGGAGGTCAGTACAAGCCAAGTTCCTGGTGGGGTCACACTGAG
AACATTTGGCAGGTTGTGCCTCTATGACGTGATCAGTCCGGAGTGACGCTGATGGCTCAGCATGGATCTGATCGGCACCA
GGTTCTTGTCTGTACCAAGCTGGTGAAGCCCTTCCAAGCCCAGGTGGGCTCCCTGTACCTTGTCCTCGGGGGGCTCCAGG
ACCAGCAGTAAGGAGGCTCCATGGTAAAGGCACTGGTGCTGAACTGTGTGGAGGGGATGGACCTGCCCTTGTAAGAACAA
GCCAAGCGGGAGCAGAGGCAGTACTAGCGTGTGAGGGACGGCGGCCAG
ORF - retro_pabe_3425 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.81 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MMLPKPGTYYLPWEVSAGQVPDGSTLRTFGRLCLYDMI-QSRVTLMAQHGSDQHQVLVCTKLVEPFHAQV |
| .MLPKPGTY.L.WEVS..QVP.G.TLRTFGRLCLYD.I.QS.VTLMAQHGSD.HQVLVCTKLV.PF.AQV | |
| Retrocopy | VMLPKPGTYSLHWEVSTSQVPGGVTLRTFGRLCLYDVI<QSGVTLMAQHGSDRHQVLVCTKLVKPFQAQV |
| Parental | GSLYVVLGELQHQQDRGSVVKARVLTCVEGMNLPLLEQAIREQRLYKQERGGSQ |
| GSLY.VLG.LQ.QQ..GS.VKA.VL.CVEGM.LPL.EQA.REQR.Y...R.G.Q | |
| Retrocopy | GSLYLVLGGLQDQQ*GGSMVKALVLNCVEGMDLPL*EQAKREQRQY*RVRDGGQ |
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 | 3 .10 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 4 .99 RPM |
| SRP007412_heart | 0 .00 RPM | 1 .57 RPM |
| SRP007412_kidney | 0 .00 RPM | 7 .06 RPM |
| SRP007412_liver | 0 .00 RPM | 3 .67 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3425 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3425 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3425 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Gorilla gorilla | retro_ggor_2810 |
| Macaca mulatta | retro_mmul_1164 |
| Callithrix jacchus | retro_cjac_582 |
Parental genes homology:
Parental genes homology involve 5 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000013878 | 5 retrocopies | |
| Gorilla gorilla | ENSGGOG00000013858 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000029820 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000001980 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000008646 | 1 retrocopy |
retro_pabe_3425 ,
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