RetrogeneDB ID: | retro_pabe_2173 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 2b_random:1226806..1227312(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NOC2L | ||
| Ensembl ID: | ENSPPYG00000029645 | ||
| Aliases: | None | ||
| Description: | nucleolar complex associated 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24517] |
Retrocopy-Parental alignment summary:
>retro_pabe_2173
CTGGCGCTGCCTGTGGTCCTGCAGCTGAAGTCGTTCCTCCAGGAGTGCAAGGTGGCCAACTACTGCCGGCAGGTGCAGCA
GCTGCTTGGGAAGGTTCAGGAGAACTCAGAACACAACTGCAGCCGCTGCCAGAGGCTTTCCTTTGGTATCTCTGACCAGC
AGGCATGGAAGCCTGGGAGAAGCTGACCCGGCAAGAGGGGACCCCCCTGACCTTGTACTACAGCCACTGATGCAAGCTGC
GTGACCGGGAGATCCAGCTGGACATCAGTGGCAAAGAGCAGCTGGAAGACCTGAACTTCCCTGAGATCAAACGAAGGAAA
GTGGCTGACAGGAAGGATGAGGACAGGAAGCAATTTAAAGACCTCTTTGACCTGAACAGCTCTGAAGAGGAGGACACCGA
GGGATTCTCGGAGAGAGGGATACTGGGGCCCCTGAGCACTCAGCATGGGGTGGAAGAGGATGAAGAGGACGAGGAGGAGG
GCGAGGAGGACAGCAGCAACTCGGAG
ORF - retro_pabe_2173 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.65 % |
| Parental protein coverage: | 82.44 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VADPSLPQLKSFLRECKVANYCRQVQQLLGKVQENSAHICSRRQRVSFGVSDQQA-VEAWEKLTREEGTP |
| .A.P...QLKSFL.ECKVANYCRQVQQLLGKVQENS.H.CSR.QR.SFG.SDQQA..EAWEKLTR.EGTP | |
| Retrocopy | LALPVVLQLKSFLQECKVANYCRQVQQLLGKVQENSEHNCSRCQRLSFGISDQQA<MEAWEKLTRQEGTP |
| Parental | LTLYYSHWRKLRDREIQLEISGKERLEDLNFPEIKRRKVADRKDEDRKQFKDLFDLNSSEEDDTEGFSER |
| LTLYYSH..KLRDREIQL.ISGKE.LEDLNFPEIKRRKVADRKDEDRKQFKDLFDLNSSEE.DTEGFSER | |
| Retrocopy | LTLYYSH*CKLRDREIQLDISGKEQLEDLNFPEIKRRKVADRKDEDRKQFKDLFDLNSSEEEDTEGFSER |
| Parental | GILRPLSTWHGVEEDEEDEEEGEEDSSNSE |
| GIL.PLST.HGVEEDEEDEEEGEEDSSNSE | |
| Retrocopy | GILGPLSTQHGVEEDEEDEEEGEEDSSNSE |
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 | 1 .44 RPM | 15 .81 RPM |
| SRP007412_cerebellum | 0 .61 RPM | 12 .16 RPM |
| SRP007412_heart | 1 .51 RPM | 4 .40 RPM |
| SRP007412_kidney | 1 .66 RPM | 8 .82 RPM |
| SRP007412_liver | 0 .49 RPM | 4 .07 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2173 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2173 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2173 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000188976 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000029645 | 2 retrocopies |
retro_pabe_2173 , retro_pabe_3535,
|