RetrogeneDB ID: | retro_dnov_745 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_104007:3295..3875(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PRDX3 | ||
| Ensembl ID: | ENSDNOG00000001359 | ||
| Aliases: | None | ||
| Description: | peroxiredoxin 3 [Source:HGNC Symbol;Acc:9354] |
Retrocopy-Parental alignment summary:
>retro_dnov_745
TCCTCATACTATGTTCCTGCAGTCCCCCAGGACATGCATACTTTCAGGGTACAGCTGTTGTCAACAGGAGGTAAATAACT
CAGTCTTGATGACTTGGGGACATATTTGGTGCTTTTCTTCTATCCTTTAGATTTTACCTTTGGGTGTCCTACAGAAAGTG
TTGCTTTTAGTGACAAAACCAATGAATTTCATGTGAACTGTGAAGTTGTTGCTGTTTCAATGGTTTCCTGCTTTATCCAC
TTTGCCTGGATAAATACATCAAGGAAGAACAGTGATTTGGGCCACATGAACATCACATCCTTGTAAGATTTAACAAAACA
AATCTCTAATACTGTGGTGTGCTATTAGACCTTGTTGGTCTTGTACTACATGGTCTCTCATTATTGACCCCAATGGAATC
ATCCAGCATTTGAGTGTCAGTGATCCCCCAATGGAAAGTGTGGAAGGGATCCTCTGCTTTGTGAAGTCATTCCAGTTGTG
GAGGCCATGGAGGAGTCTGTCCCACAAACTGACACCAAATTCTCCTAAGATCAAGCCAAACTTAACTGCTTCCAAAGAAA
ACTTTGAAATGATGAATCAG
ORF - retro_dnov_745 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.69 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | SSYCAPAVTQHAPYFKGTAVVNGEFKELSLDDFKGKYLVLFFYPLDF-FVC-TEIVAFSDKHD---VNCE |
| SSY..PAV.Q....F.......G..K.LSLDD..G.YLVLFFYPLDF.F.C.TE.VAFSDK.....VNCE | |
| Retrocopy | SSYYVPAVPQDMHTFRVQLLSTGG-K*LSLDDL-GTYLVLFFYPLDFTFGCPTESVAFSDKTNEFHVNCE |
| Parental | VXXXXXXXXXXXXXXXXXXXXNGGLGHMNIALLSDLTKQISRDY-GVLLEGAGLALRGL-FIIDPNGVIK |
| V....................N..LGHMNI..L.DLTKQIS....GVLL...GL.L.GL..IIDPNG.I. | |
| Retrocopy | VVAVSMVSCFIHFAWINTSRKNSDLGHMNITSL*DLTKQISNTV<GVLLDLVGLVLHGL<LIIDPNGIIQ |
| Parental | HLSVNDLSVGRSVEETLRLVKAFQF-VETHGE-VCPANWTQIL-STIKPNPTASKEYFEKVNQ |
| HLSV.D.....SVE..L..VK.FQ..VE...E.VCP.N..QIL...IKPN.TASKE.FE..NQ | |
| Retrocopy | HLSVSDPPM-ESVEGILCFVKSFQL<VEAMEE<VCPTN*HQIL<PKIKPNLTASKENFEMMNQ |
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 |
|---|---|---|
| SRP012922_ascending_colon | 0 .00 RPM | 56 .01 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 33 .68 RPM |
| SRP012922_heart | 0 .00 RPM | 44 .78 RPM |
| SRP012922_kidney | 0 .00 RPM | 82 .69 RPM |
| SRP012922_liver | 0 .00 RPM | 53 .41 RPM |
| SRP012922_lung | 0 .00 RPM | 19 .40 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 88 .10 RPM |
| SRP012922_spleen | 0 .00 RPM | 38 .57 RPM |
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_745 was not experimentally validated.