RetrogeneDB ID: | retro_dnov_2540 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_83620:3573..3982(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GLT1D1 | ||
| Ensembl ID: | ENSDNOG00000017272 | ||
| Aliases: | None | ||
| Description: | glycosyltransferase 1 domain containing 1 [Source:HGNC Symbol;Acc:26483] |
Retrocopy-Parental alignment summary:
>retro_dnov_2540
GTTGATCCAGTGTTTGCAAGGGAAGTCAAAGACAAAGTAAGAAAGACAGCAGGTACGATTGATAGAAGAGACGTCTCCAA
AAGACCTCCACGCGGTTGTGAGAAATTACTTTGTGTTGGTGAATAGTTCCATTTCTGAAGGCAGGTCAGCAGCAATTCTG
GAGGCAATGGATTTAGAATTTCCAGTGTTGGCAAGGACTATTCTTGGAAATGCTGCTGTGGTGAGACATAAAGCTACAGG
GTTATTTACAGATCCTCAGGAGTTTGTTCAGCTAGCAAAGAGGCTGATCAGTGATCCTGCATTTGAGAAATGGATTATGG
CCAGCTAAAGAGTGTACGTGAGCATGCATCATTCCTGGCACTCAAACAGAGACACCTTTCAAAGCCTCATCCGGAGATTT
GAAGGGAGC
ORF - retro_dnov_2540 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.03 % |
| Parental protein coverage: | 56.79 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | VDPVFTREV-KAKVGRSAGVRLRAEMPRGDLHAAVKSCFAVVNSSVSEGMSAAILEAMDLEVPVLARNIP |
| VDPVF.REV.K.K..R...VRL..E....DLHA.V...F..VNSS.SEG.SAAILEAMDLE.PVLAR.I. | |
| Retrocopy | VDPVFAREV>KTK*ERQQ-VRLIEETSPKDLHAVVRNYFVLVNSSISEGRSAAILEAMDLEFPVLARTIL |
| Parental | GNAAVVRHGATGLLFSDPQEFVRLAKRLLRDPALERRIVAGGRAYVGAHHSWRSERDTYGRLVQSLAGS |
| GNAAVVRH.ATG.LF.DPQEFV.LAKRL..DPA.E..I.A..R.YV..HHSW.S.RDT...L.....GS | |
| Retrocopy | GNAAVVRHKATG-LFTDPQEFVQLAKRLISDPAFEKWIMAS*RVYVSMHHSWHSNRDTFQSLIRRFEGS |
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 | 13 .61 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 2 .20 RPM |
| SRP012922_heart | 0 .00 RPM | 0 .00 RPM |
| SRP012922_kidney | 0 .00 RPM | 2 .46 RPM |
| SRP012922_liver | 0 .00 RPM | 8 .20 RPM |
| SRP012922_lung | 0 .00 RPM | 2 .14 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP012922_spleen | 0 .00 RPM | 1 .49 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_2540 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 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Anolis carolinensis | ENSACAG00000025870 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000017272 | 2 retrocopies |
retro_dnov_1218, retro_dnov_2540 ,
|