RetrogeneDB ID: | retro_dnov_1730 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_278768:9..330(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GOLT1B | ||
| Ensembl ID: | ENSDNOG00000013576 | ||
| Aliases: | None | ||
| Description: | golgi transport 1B [Source:HGNC Symbol;Acc:20175] |
Retrocopy-Parental alignment summary:
>retro_dnov_1730
TTTTTTGACAAAGCACTACTGGCTACTGAAATGTTTATCGTGACCGACTGCTTTGTATTGGTTAAGAAAGAACATTCAGA
TTCTTTGCCAAAAACATAAAGTGAAAGCTCCAGGATTTTTCCTGGGTGAAGTATTTGTCGTTCTTATGGGTTGGCCTTGA
TAGGCATGGTCTCTGAAATGTGTGGGTTCTTTCTCTTGCTCAGGGGCTTCTGTGCTGTGGTAGTTGGCATTATTAGAAGA
GTGCCAGTGCTTGGCTCCCTCTTGAATTTACCTGGAATTAGATCAATTGTAGGTAAAGTTGAAGAAAGCAGCAATATGGT
A
ORF - retro_dnov_1730 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.57 % |
| Parental protein coverage: | 79.71 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | FFDKALLAIGNVLFVAGLAFV-IGLERTFRFFF-QKHKMKATGFFLGGVFVVLIGWP-LIGMIFEIYGFF |
| FFDKALLA.....F.....FV.IG.ERTFRFF..QKHK.KA.GFFLG.VFVVL.GWP.LIGM..E..GFF | |
| Retrocopy | FFDKALLA--TEMFIVTDCFV<IG*ERTFRFFA<QKHKVKAPGFFLGEVFVVLMGWP<LIGMVSEMCGFF |
| Parental | LLFRGFFPVVVGFIRRVPVLGSLLNLPGIRSFVDKVGESNNMV |
| LL.RGF..VVVG.IRRVPVLGSLLNLPGIRS.V.KV.ES.NMV | |
| Retrocopy | LLLRGFCAVVVGIIRRVPVLGSLLNLPGIRSIVGKVEESSNMV |
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 | 5 .06 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 3 .85 RPM |
| SRP012922_heart | 0 .00 RPM | 3 .71 RPM |
| SRP012922_kidney | 0 .00 RPM | 0 .82 RPM |
| SRP012922_liver | 0 .00 RPM | 2 .48 RPM |
| SRP012922_lung | 0 .00 RPM | 7 .33 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 2 .60 RPM |
| SRP012922_spleen | 0 .00 RPM | 4 .35 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_1730 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 9 parental genes, and 10 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000016231 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000012256 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000013576 | 2 retrocopies |
retro_dnov_158, retro_dnov_1730 ,
|
| Felis catus | ENSFCAG00000028655 | 1 retrocopy | |
| Loxodonta africana | ENSLAFG00000000965 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000008797 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000004756 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000006352 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000009234 | 1 retrocopy |