RetrogeneDB ID: | retro_dnov_1016 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_135276:1154..1466(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GLO1 | ||
| Ensembl ID: | ENSDNOG00000019598 | ||
| Aliases: | None | ||
| Description: | glyoxalase I [Source:HGNC Symbol;Acc:4323] |
Retrocopy-Parental alignment summary:
>retro_dnov_1016
ATCGCAGATATGCAGCCCACAGCCAACGACCTTGCTGATCAGGCTGCCGTCAGTTGATCCTCCAATGTAGACCCCAGGAC
CAAGGATTTCCCGCTGCAGCAGACCATACTATGAAATTAAAGATTCTAAGAAGTCTTTAAATTTTTATGCTAGAATTCTT
GGAACGACACTAATTGAAAAATTGTATTTTCTCACTCTGAAATTTTCACTCCATTTCTTAGTTTATGAGGATAAAAATGG
CATCCCCAAAGATTAAAATTAAGGAGTAGCATGGGCACTCTCAGAAAAGCTACTTTAGAGGTGGCACACAAT
ORF - retro_dnov_1016 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.21 % |
| Parental protein coverage: | 56.04 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEPQPAPGGLTDEAAFSCCSDADPSTKDF-LLQTML-QIKHPKKSLDFYAR-LGMTLIEKLDFPTMKFS |
| .A..QP....L.D.AA.S..S..DP.TKDF.L.QT.L..IK..KKSL.FYAR.LG.TLIEKL.F.T.KFS | |
| Retrocopy | IADMQPTANDLADQAAVS*SSNVDPRTKDFPLQQTIL>EIKDSKKSLNFYARILGTTLIEKLYFLTLKFS |
| Parental | LYFLAYEDKNDIPKDKNEKVAWLFS-RKATLELTHN |
| L.FL.YEDKN.IPKD.N..VAW..S.RKATLE..HN | |
| Retrocopy | LHFLVYEDKNGIPKD*N*GVAWALS<RKATLEVAHN |
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 | 33 .25 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 46 .74 RPM |
| SRP012922_heart | 0 .00 RPM | 76 .80 RPM |
| SRP012922_kidney | 0 .00 RPM | 47 .09 RPM |
| SRP012922_liver | 0 .00 RPM | 71 .99 RPM |
| SRP012922_lung | 0 .00 RPM | 22 .60 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 98 .31 RPM |
| SRP012922_spleen | 0 .00 RPM | 40 .29 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_1016 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 12 parental genes, and 20 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000012703 | 2 retrocopies | |
| Cavia porcellus | ENSCPOG00000010050 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000019598 | 6 retrocopies |
retro_dnov_1016 , retro_dnov_1064, retro_dnov_1411, retro_dnov_1759, retro_dnov_2560, retro_dnov_735,
|
| Dipodomys ordii | ENSDORG00000006369 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000005978 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000024026 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000007945 | 2 retrocopies | |
| Rattus norvegicus | ENSRNOG00000000541 | 2 retrocopies | |
| Sus scrofa | ENSSSCG00000027778 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000005821 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000014386 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000004664 | 1 retrocopy |