RetrogeneDB ID: | retro_dnov_1653 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_257228:154..607(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SOD2 | ||
| Ensembl ID: | ENSDNOG00000007907 | ||
| Aliases: | None | ||
| Description: | superoxide dismutase 2, mitochondrial [Source:HGNC Symbol;Acc:11180] |
Retrocopy-Parental alignment summary:
>retro_dnov_1653
CCCCACATCAATATGCAGATCATGCAGCTGCACCACAGCAAACATCACGCTGTGTATGTGAATAATTTGAATGCTACTGA
GGAGAAACATAAGGAGGCACTGGCAAAGGGTGATATTACAGTTCAGATAGCTCTATACTCTGCACTGAAGTTCAATGGTG
GAGGCTGTATCAATCACACCATTTTCTGGACAAACCTGAGCCATAATGGTGATGGAGAACCCAAAAGGGAGTTGCTGGAA
GCTATCAAACCTGATTTTGGTTCCTTTGATAAATTTAAGGAAAAACTCTTATCTGTTGGCATTCAAGGCTTAGGTTGGGG
CTGGCTTGGCTTCAATAAGGAACAGAGCTGCTTACAGATTGCTACTTGTTCTAATTAGGATCCACTGCAGGTAACAACAG
ATCTTATTCCATTGCTGGGACCTGATGTATGAAAGCATGCTTATTACTTTCAG
ORF - retro_dnov_1653 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.05 % |
| Parental protein coverage: | 84.07 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PHISAQIMQLHHSKHHAAYVNNLNATEDKYKEALAKGDVTTQVALQPALKFNGGGHINHTIFWTNLSPNG |
| PHI..QIMQLHHSKHHA.YVNNLNATE.K.KEALAKGD.T.Q.AL..ALKFNGGG.INHTIFWTNLS.NG | |
| Retrocopy | PHINMQIMQLHHSKHHAVYVNNLNATEEKHKEALAKGDITVQIALYSALKFNGGGCINHTIFWTNLSHNG |
| Parental | GGEPKGELLEAIKRDFGSFDKFKEKLTAVSVGVQGSGWGWLGFNKEQSRLQIAACSNQDPLQGTTGLIPL |
| .GEPK.ELLEAIK.DFGSFDKFKEKL...SVG.QG.GWGWLGFNKEQS.LQIA.CSN.DPLQ.TT.LIPL | |
| Retrocopy | DGEPKRELLEAIKPDFGSFDKFKEKL--LSVGIQGLGWGWLGFNKEQSCLQIATCSN*DPLQVTTDLIPL |
| Parental | LGIDVWEHAYYLQ |
| LG.DV..HAYY.Q | |
| Retrocopy | LGPDV*KHAYYFQ |
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 | 71 .37 RPM |
| SRP012922_cerebellum | 0 .27 RPM | 19 .93 RPM |
| SRP012922_heart | 0 .00 RPM | 132 .03 RPM |
| SRP012922_kidney | 0 .00 RPM | 105 .68 RPM |
| SRP012922_liver | 0 .00 RPM | 66 .26 RPM |
| SRP012922_lung | 0 .00 RPM | 41 .24 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 128 .95 RPM |
| SRP012922_spleen | 0 .00 RPM | 27 .13 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_1653 was not experimentally validated.