RetrogeneDB ID: | retro_pabe_292 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 1:125414021..125414443(+) | ||
| Located in intron of: | ENSPPYG00000001103 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SOD2 | ||
| Ensembl ID: | ENSPPYG00000017143 | ||
| Aliases: | None | ||
| Description: | superoxide dismutase [Source:RefSeq peptide;Acc:NP_001127035] |
Retrocopy-Parental alignment summary:
>retro_pabe_292
GTAAAAGGTGATGTTAGAATCCAAATAACTCTTCAGCCTGCACTTAAGTTCAGTGGTGGAGACCATATTACTCTTACCAT
TTTATGGAGAAACCTAAGCCTCAGTGGTAGTGGAAGATTGAAAGGGGAGTTTCTGGGAGCCATCAAATATTACTTTTGTT
CCTTTGATTAACTTAAGGAGAAGCTGACAGATGTGTCTGTTAGTATTCAAAGTTCCAGTTGTGGTTGGCTTGGTTTCATT
AAGTAAAAGAGCTCTTATAGATCATTGCTTGTCCTAATCAGCATCCATTGCAAAGATCATCAGGTCTTATTCTACTTTTG
GGGATTGGTGTATGGAAGTTTTGTTAACTGTCTTCAGCATAAAAAATGTCAGACTTGATTATCCAAAAGCTTTTTTGGAG
TGTAATCAACTGAGAGAATGTA
ORF - retro_pabe_292 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.42 % |
| Parental protein coverage: | 88.61 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | VKGDVTAQIALQPALKFNGGGHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQ |
| VKGDV..QI.LQPALKF.GG.HI...I.W.NLS..G.G..KGE.L.AIK..F.SFD..KEKLT..SV..Q | |
| Retrocopy | VKGDVRIQITLQPALKFSGGDHITLTILWRNLSLSGSGRLKGEFLGAIKYYFCSFD*LKEKLTDVSVSIQ |
| Parental | GSGWGWLGFNKERGH-LQIAACPNQDPLQGTTGLIPLLGIDVWE-HAYYLQYK-NVRPDYLKA-IWNVIN |
| .S..GWLGF.K.....L.I.ACPNQ.PLQ...GLI.LLGI.VW......LQ.K.NVR.DY.KA..W.VIN | |
| Retrocopy | SSSCGWLGFIK*KSS<L*IIACPNQHPLQRSSGLILLLGIGVWK>FVNCLQHK>NVRLDYPKA>FWSVIN |
| Parental | WENV |
| .ENV | |
| Retrocopy | *ENV |
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 | 61 .26 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 42 .20 RPM |
| SRP007412_heart | 0 .00 RPM | 99 .22 RPM |
| SRP007412_kidney | 0 .00 RPM | 106 .60 RPM |
| SRP007412_liver | 0 .00 RPM | 289 .71 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_292 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_292 was not experimentally validated.