RetrogeneDB ID: | retro_pabe_3744 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | X:46052836..46053378(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PLLP | ||
| Ensembl ID: | ENSPPYG00000007385 | ||
| Aliases: | None | ||
| Description: | plasmolipin [Source:HGNC Symbol;Acc:18553] |
Retrocopy-Parental alignment summary:
>retro_pabe_3744
ATGGCCGAGTTCCCGTCAAAAGTGAGCACACGGACCAGCAGTCCCGCGCAGGACGCCGGAGCCTGGTGTAGGCGCTGCGC
ACCGACCTGGGCTTCGTGCGCTCCCGCCTCGGGGCGTTCATGCAGCTGCAGCTGGTGCTGGGGCTGCTGGTGTGGGCCCT
GATTGCGGACACCCCGTACCACCTGTACCCGGCCTATGGCTGGGTGATGTTCGTAGCTGTCTTCCTCTGGCTGGTGACAA
TCGTCTTCTTCAACCTCTACCTGTTTCAGCTGCACATGAAGTTGTACATGGTGCCCTGGCCACTAGTGTTAATGATGTTT
AACGTCAGTGCCACCGTTCTTTACGTCACCGCCTTCATCGCCTGCTCTGCGGCAGTTGATGAGACGTCCCTGAAGGGCAC
GCAGCCGTATAACCAGCGTGCGGCTACCTCGTTCTTTGCGTGTTTGGTGATTATCCTACGGAGCTAGCGCCTTCTTCAGC
TACCATGCCTGGCGAGGACTAGGCAGCAATGCGCCACCAGTCAGATGGCTGGCGTCTATGCC
ORF - retro_pabe_3744 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.24 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEFPSKVSTRTSSPAQGAGA-SVSALRPDLGFVRSRLGALMLLQLVLGLLVWALIADTPYHLYPAYGWV |
| MAEFPSKVSTRTSSPAQ.AGA..V.ALR.DLGFVRSRLGA.M.LQLVLGLLVWALIADTPYHLYPAYGWV | |
| Retrocopy | MAEFPSKVSTRTSSPAQDAGA<LV*ALRTDLGFVRSRLGAFMQLQLVLGLLVWALIADTPYHLYPAYGWV |
| Parental | MFVAVFLWLVTIVLFIFYLFQLHMKLYMVPWPLVLMIFNISATVLYITAFIACSAAVDLTSLRGTRPYNQ |
| MFVAVFLWLVTIV.F..YLFQLHMKLYMVPWPLVLM.FN.SATVLY.TAFIACSAAVD.TSL.GT.PYNQ | |
| Retrocopy | MFVAVFLWLVTIVFFNLYLFQLHMKLYMVPWPLVLMMFNVSATVLYVTAFIACSAAVDETSLKGTQPYNQ |
| Parental | RAAASFFACLVMI-AYGVSAFFSYQAWRGVGSNA-ATSQMAGGYA |
| RA.A..F.....I..YG.SAFFSY.AWRG.GSNA.ATSQMAG.YA | |
| Retrocopy | RA-ATSFFACLVI>SYGASAFFSYHAWRGLGSNA<ATSQMAGVYA |
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 .06 RPM | 2 .93 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 2 .55 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .36 RPM |
| SRP007412_kidney | 0 .00 RPM | 5 .54 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .03 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3744 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3744 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3744 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_4816 |
| Pan troglodytes | retro_ptro_3205 |
| Macaca mulatta | retro_mmul_2569 |
| Callithrix jacchus | retro_cjac_4155 |
Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000012103 | 1 retrocopy | |
| Homo sapiens | ENSG00000102934 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000008636 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000008924 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000002825 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000007353 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000007385 | 1 retrocopy |
retro_pabe_3744 ,
|
| Pan troglodytes | ENSPTRG00000008151 | 1 retrocopy |