RetrogeneDB ID: | retro_dnov_1385 | ||
Retrocopylocation | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_19228:21193..21619(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | REEP1 | ||
| Ensembl ID: | ENSDNOG00000011015 | ||
| Aliases: | None | ||
| Description: | receptor accessory protein 1 [Source:HGNC Symbol;Acc:25786] |
Retrocopy-Parental alignment summary:
>retro_dnov_1385
TTAGTGTTTGGGATGTTTTATCAGCCTATGCAGCCTACAAGTCTGTGAAGACTAAGAGTATTTGTGGATATATCTGGTAT
TTATGTAAATAGATTTTCTTTGCACTCTTTATGTCAGGGGAAATCTTCACAGACTTTATATCCTGGTTTCCTTTCTACTA
TGAGATCAAGATAACCTTTGTGCTGTGGTATACCAAGGGAGCCAGCTTACTTTACCACAAGTTTGTCCATCTGTCTGTAT
CCTGCCATGAGAAGGAGATCGACACGTACATCCTACAGGCCAAGGAGCGCAGCTGTGAGACCATGCTCAGCTTCAGGAAG
TAGGGCCTCAATATCCACGTCTTGTCCACTCTACAGGCTGCCACCAAAAGTTAGGTGTGCTGGCTGGTAGGCTGCAGAGC
TTCTCCATGCAGATCTACATGCCATC
TTAGTGTTTGGGATGTTTTATCAGCCTATGCAGCCTACAAGTCTGTGAAGACTAAGAGTATTTGTGGATATATCTGGTAT
TTATGTAAATAGATTTTCTTTGCACTCTTTATGTCAGGGGAAATCTTCACAGACTTTATATCCTGGTTTCCTTTCTACTA
TGAGATCAAGATAACCTTTGTGCTGTGGTATACCAAGGGAGCCAGCTTACTTTACCACAAGTTTGTCCATCTGTCTGTAT
CCTGCCATGAGAAGGAGATCGACACGTACATCCTACAGGCCAAGGAGCGCAGCTGTGAGACCATGCTCAGCTTCAGGAAG
TAGGGCCTCAATATCCACGTCTTGTCCACTCTACAGGCTGCCACCAAAAGTTAGGTGTGCTGGCTGGTAGGCTGCAGAGC
TTCTCCATGCAGATCTACATGCCATC
ORF - retro_dnov_1385 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.32 % |
| Parental protein coverage: | 77.49 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | LIFGTLYP-AYYSYKAVKSKDIKEYVKWMMYWIIFALFTTAETFTDIFLCWFPFYYELKIAFVAWLLSPY |
| L.FG..Y..AY..YK.VK.K.I..Y.......I.FALF...E.FTD.F..WFPFYYE.KI.FV.W....Y | |
| Retrocopy | LVFGMFYQ<AYAAYKSVKTKSICGYIWYLCK*IFFALFMSGEIFTD-FISWFPFYYEIKITFVLW----Y |
| Parental | TKGSSLLYRKFVHPTLSSKEKEIDDCLVQAKDRSYDALVHFGKRGLNVAATAAVMAASKG-QGALSERLR |
| TKG.SLLY.KFVH...S..EKEID....QAK.RS......F.K.GLN........AA.K...G.L..RL. | |
| Retrocopy | TKGASLLYHKFVHLSVSCHEKEIDTYILQAKERSCETMLSFRK*GLNIHVLSTLQAATKS<LGVLAGRLQ |
| Parental | SFSMQ-DLTAI |
| SFSMQ.DL.AI | |
| Retrocopy | SFSMQ<DLHAI |
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 | 2 .72 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 8 .11 RPM |
| SRP012922_heart | 0 .00 RPM | 0 .70 RPM |
| SRP012922_kidney | 0 .00 RPM | 0 .27 RPM |
| SRP012922_liver | 0 .00 RPM | 0 .31 RPM |
| SRP012922_lung | 0 .15 RPM | 1 .53 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 2 .60 RPM |
| SRP012922_spleen | 0 .00 RPM | 1 .95 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_1385 was not experimentally validated.
Retrocopy orthology:
Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000011015 | 2 retrocopies |
retro_dnov_1180, retro_dnov_1385 ,
|