RetrogeneDB ID: | retro_pabe_906 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 12:16546696..16547114(-) | ||
| Located in intron of: | ENSPPYG00000004335 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | EGLN3 | ||
| Ensembl ID: | ENSPPYG00000005732 | ||
| Aliases: | None | ||
| Description: | egl nine homolog 3 (C. elegans) [Source:HGNC Symbol;Acc:14661] |
Retrocopy-Parental alignment summary:
>retro_pabe_906
GGGAGAAACAAGAGGGGCTGCGAGGCCATTAGCTTCCTCCTGTCCCTCACTGACAGGCTGGTCCTCTAGTGCAGGAGCCG
GTGGGAAAATACTATGTCAAGGAGAGGTCCAAGGCAATGGTGGCTTGCTAATTTAAAAATGGAATAGGTTACATTCATTA
TGTGGACAACCCCAACGATGGCTGCTGCATCACCTGCATCTACTATTTGAACAAGAATAGGGATACAAGGCTACACAGTG
GGATCCTATGGCTATTTTCAGAGGAGAAATCGTTCATGGCAGATGTGGAGGCCATTTGTGAAAAATTGCTCTTCTGGTCA
GATTGCAGGAACCCACACGAGGTGCTGTCTTCCTATGAGACCAGATGTGCTATACCGTTTGGTATTTTGATAATGAAGAA
AGGACAGAAGCCAAAGAA
ORF - retro_pabe_906 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.53 % |
| Parental protein coverage: | 59.41 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | GGNEEGCEAISFLLSLIDRLVLYCGSR-LGKYYVKERSKAMVACYPGNGTGYVRHVDNPNGDGRCITCIY |
| G.N..GCEAISFLLSL.DRLVL.C.SR..GKYYVKERSKAMVAC...NG.GY...VDNPN.DG.CITCIY | |
| Retrocopy | GRNKRGCEAISFLLSLTDRLVL*CRSR<VGKYYVKERSKAMVAC*FKNGIGYIHYVDNPN-DGCCITCIY |
| Parental | YLNKNWDAKLHGGILRIFPEGKSFIADVEPIFDRLLFFWSDRRNPHEVQPSYATRYAM-TVWYFDAEERA |
| YLNKN.D..LH.GIL..F.E.KSF.ADVE.I...LL.FWSD.RNPHEV..SY.TR.A..TVWYFD.EER. | |
| Retrocopy | YLNKNRDTRLHSGILWLFSEEKSFMADVEAICEKLL-FWSDCRNPHEVLSSYETRCAI<TVWYFDNEERT |
| Parental | EAKK |
| EAK. | |
| Retrocopy | EAKE |
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 | 9 .07 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 10 .58 RPM |
| SRP007412_heart | 0 .00 RPM | 77 .06 RPM |
| SRP007412_kidney | 0 .00 RPM | 10 .61 RPM |
| SRP007412_liver | 0 .00 RPM | 5 .75 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_906 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_906 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_906 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_1088 |
| Pan troglodytes | retro_ptro_740 |
| Macaca mulatta | retro_mmul_845 |
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000129521 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000000040 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000008560 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000005732 | 1 retrocopy |
retro_pabe_906 ,
|
| Pan troglodytes | ENSPTRG00000006250 | 1 retrocopy |