RetrogeneDB ID: | retro_mdom_462 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:675976783..675977147(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PRDX6 | ||
| Ensembl ID: | ENSMODG00000004032 | ||
| Aliases: | None | ||
| Description: | peroxiredoxin 6 [Source:HGNC Symbol;Acc:16753] |
Retrocopy-Parental alignment summary:
>retro_mdom_462
GTAAACGGATATAATAAAGATGATCCTATAGAGAAGTTTCCTTCCCATTTATTGGTGATCATTAATCAGATGTGCCATCA
TGTTGGGAATGTTAGACCCAGATGAGTGGACAGGGAGTGCATGTCCATGATTCTTTGTGTGGTATTTATTTTTGTCCACA
TAAAAAGTTGAAGCTCTCTATCCTCTACCCAGCCACTACTGGCAGGAACTTTGATGAGATCCTCAAAGTGGTTGATTCCC
TTCAGTTGACAATATACAAGAAGGTTGCTACTCTTATTGACTGGAGAGATGGACATAGCATCGTGATTATTCCAACTATC
TCTGAAGTGAAGGCCAAAAACCATTTTCTAAAGGTATCTTCAGT
ORF - retro_mdom_462 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.94 % |
| Parental protein coverage: | 54.91 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | INAYNGEPPVEKLP-FPIIDDHKRDL-AIKLGMLDPDERDGQGMP-VTARVVFIFG-PDKKLKLSVLYPA |
| .N.YN...P.EK.P.FP.I.DH..D..AI.LGMLDPDE..G...P.....VVFIF..P.KKLKLS.LYPA | |
| Retrocopy | VNGYNKDDPIEKFP<FPFIGDH*SDV<AIMLGMLDPDEWTGSACP<MILCVVFIFV<PHKKLKLSILYPA |
| Parental | TTGRNFDELLRVIDSLQLTAYKKVATPVDWKPGDSVMVVPTISEDEAK-ALFPKGVFT |
| TTGRNFDE.L.V.DSLQLT.YKKVAT..DW..G.S....PTISE..AK...F.KG.F. | |
| Retrocopy | TTGRNFDEILKVVDSLQLTIYKKVATLIDWRDGHSIVIIPTISEVKAK<KPFSKGIFS |
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 | 0 .00 RPM | 0 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_462 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_462 was not experimentally validated.