RetrogeneDB ID: | retro_pabe_2569 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 4:156092209..156092789(-) | ||
| Located in intron of: | ENSPPYG00000015116 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NEIL2 | ||
| Ensembl ID: | ENSPPYG00000018348 | ||
| Aliases: | None | ||
| Description: | endonuclease 8-like 2 [Source:RefSeq peptide;Acc:NP_001125714] |
Retrocopy-Parental alignment summary:
>retro_pabe_2569
ATGCCAGAAGGGCTGTTGGTGAGGACATTTCACCATTTGGTCTCTCCTTTTGTGGGCAAGCAGGTGGTAAAGACAGGGAG
CAACAGTAAGAAGCTATAGCCCACCAGCCTCCAGTCTCTGTGGCTCCAGGACACCCAGGTCCATGGAAAGAAATTATTCC
TTAGATTTGATCCAGATGAAGAAATGGGGCCCGCTGGCAACAGCCCACCGCCAGAGCCTCCACAAAAAGAAGCGCAGAAG
GAAGGGACTGCGAACTCAAAGCAGGCCCGGGAGCCCAGTGGGCAGAAGACCCTTGACACCTCCTCACGGTCCACAGAGCT
CGTCCCCCAGGGAGAGGATGATTAGGAATGTTTGAAGGGAGACACCCCTACAGGAGATGCTGGGAGGTGGCTGCGTGTCA
GCTCTTGTTTGTTTGGCAGCGTTTGGGTGAACGACTTCTCCAGAGCCAAGAAAGCCAAAAAGGGGGGACTGGAGGGACCC
TGCCCTGAGGTTGGTCCTGTACTTTGGTGGTGGTGGTTTCCTGGCATTTTATAATTGTCAGATGTCTTGGAGCTCTTCCC
CAGAGGTCACACCCACCTGT
ORF - retro_pabe_2569 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.03 % |
| Parental protein coverage: | 58.43 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MPEGPLVRKFHHLVSPFVGQQVVKTGGSSKKLQPASLQCLWLQDTQVNGKKLFLRFDPDEEMGPPGSSPP |
| MPEG.LVR.FHHLVSPFVG.QVVKTG..SKKL.P.SLQ.LWLQDTQV.GKKLFLRFDPDEEMGP.G.SPP | |
| Retrocopy | MPEGLLVRTFHHLVSPFVGKQVVKTGSNSKKL*PTSLQSLWLQDTQVHGKKLFLRFDPDEEMGPAGNSPP |
| Parental | PEPPQKEAQKEGAADPKQVGEPSGQKTPDGSSQSAELVPQGEDDSEYLERDAPAGDAGRWLRVSFGLFGS |
| PEPPQKEAQKEG.A..KQ..EPSGQKT.D.SS.S.ELVPQGEDD.E.L..D.P.GDAGRWLRVS..LFGS | |
| Retrocopy | PEPPQKEAQKEGTANSKQAREPSGQKTLDTSSRSTELVPQGEDD*ECLKGDTPTGDAGRWLRVSSCLFGS |
| Parental | VWVNEFSRAKQANKRG-DWRDPSPRLVLHFGGGGFLAFYNCQMSWSSSPVVTPTC |
| VWVN.FSRAK.A.K.G.DWRDP..RLVL.FGGGGFLAFYNCQMSWSSSP.VTPTC | |
| Retrocopy | VWVNDFSRAKKA-KKG>DWRDPALRLVLYFGGGGFLAFYNCQMSWSSSPEVTPTC |
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 | 47 .77 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 100 .93 RPM |
| SRP007412_heart | 0 .09 RPM | 39 .80 RPM |
| SRP007412_kidney | 0 .00 RPM | 53 .10 RPM |
| SRP007412_liver | 0 .00 RPM | 28 .52 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2569 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2569 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2569 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3111 |
| Pan troglodytes | retro_ptro_2103 |
| Macaca mulatta | retro_mmul_1982 |
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000154328 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000019209 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000015054 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000018348 | 1 retrocopy |
retro_pabe_2569 ,
|
| Pan troglodytes | ENSPTRG00000019995 | 1 retrocopy |