RetrogeneDB ID: | retro_dnov_1728 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_27818:42577..42883(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LSM3 | ||
| Ensembl ID: | ENSDNOG00000018032 | ||
| Aliases: | None | ||
| Description: | LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17874] |
Retrocopy-Parental alignment summary:
>retro_dnov_1728
ATGCCAGACAATGTGGACCAGCAACAAGCAACCAAAACTATAGAGGAGTCCTTGGACCTTCTCGGGCTCAGCCTGGATGA
GCGAATTTACGTGAAAATGAGAAACGACCGAGAGCTCTGAGGCAGGTTGCATGCTGATGATCAGCCTCTAAATATGATAC
TGGGAGATGTGGAAGAAACTGTGACCATGATAGAAATTGATGAAGAAACATATGATGAGATATTTAAGTCAACAAAACAG
AATATTCTGATGCTTTTTGTTCAAGGCGATGGTGTTGTATTTGTTGCCCCTCCATTGAGTGTTGGC
ORF - retro_dnov_1728 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.37 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MADDVDQQQTTNTVEEPLDLIRLSLDERIYVKMRNDRELRGRLHAYDQHLNMILGDVEETVTTIEIDEET |
| M.D.VDQQQ.T.T.EE.LDL..LSLDERIYVKMRNDREL.GRLHA.DQ.LNMILGDVEETVT.IEIDEET | |
| Retrocopy | MPDNVDQQQATKTIEESLDLLGLSLDERIYVKMRNDREL*GRLHADDQPLNMILGDVEETVTMIEIDEET |
| Parental | YEEIYKSTKRNIPMLFVRGDGVVLVAPPLRVG |
| Y.EI.KSTK.NI.MLFV.GDGVV.VAPPL.VG | |
| Retrocopy | YDEIFKSTKQNILMLFVQGDGVVFVAPPLSVG |
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 | 25 .09 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 12 .10 RPM |
| SRP012922_heart | 0 .00 RPM | 14 .15 RPM |
| SRP012922_kidney | 0 .00 RPM | 30 .12 RPM |
| SRP012922_liver | 0 .00 RPM | 8 .98 RPM |
| SRP012922_lung | 0 .00 RPM | 20 .47 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 11 .77 RPM |
| SRP012922_spleen | 0 .00 RPM | 21 .18 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_1728 was not experimentally validated.