RetrogeneDB ID: | retro_dnov_955 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_126520:4176..4485(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRAPPC3 | ||
| Ensembl ID: | ENSDNOG00000019015 | ||
| Aliases: | None | ||
| Description: | trafficking protein particle complex 3 [Source:HGNC Symbol;Acc:19942] |
Retrocopy-Parental alignment summary:
>retro_dnov_955
CTGACCTATGGAGCTCTGGTCACCCAGTTATGCAAGGACTATGAAAATAATGAAGATGTGAATAAACAACTGGACAAAAT
GGGGTATAACATTGGAGTCTGACTGATTGAAGATTTCTTGGCATGGTCAAACGTTGGAAGGTGCCATGACTTTTGGGAAA
CTGTGGATGTCATTGCCAAAGTGGCATTTAAGATGTACTTGGGCATCATGCCGAGCATCACCAATTGGAGCCCAGCTGGT
GACGAATTCTCCCTCATTTTGGAATATAAGCCCTTGGTGGACTTTGTGAAACTTCCTAATAACCACTCA
ORF - retro_dnov_955 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.32 % |
| Parental protein coverage: | 62.05 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LTYGALVTQLCKDYENDEDVNKQLDKMGYNIGVRLIEDFLARSNVGRCHDFRETADVIAKVAFKMYLGIT |
| LTYGALVTQLCKDYEN.EDVNKQLDKMGYNIGV.LIEDFLA.SNVGRCHDF.ET.DVIAKVAFKMYLGI. | |
| Retrocopy | LTYGALVTQLCKDYENNEDVNKQLDKMGYNIGV*LIEDFLAWSNVGRCHDFWETVDVIAKVAFKMYLGIM |
| Parental | PGITNWSPAGDEFSLILENNPLVDFVELPDNHS |
| P.ITNWSPAGDEFSLILE..PLVDFV.LP.NHS | |
| Retrocopy | PSITNWSPAGDEFSLILEYKPLVDFVKLPNNHS |
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 .81 RPM |
| SRP012922_cerebellum | 0 .14 RPM | 30 .24 RPM |
| SRP012922_heart | 0 .00 RPM | 10 .21 RPM |
| SRP012922_kidney | 0 .27 RPM | 26 .28 RPM |
| SRP012922_liver | 0 .15 RPM | 18 .89 RPM |
| SRP012922_lung | 0 .15 RPM | 30 .54 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 3 .46 RPM |
| SRP012922_spleen | 0 .11 RPM | 25 .64 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_955 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 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000019015 | 2 retrocopies |
retro_dnov_1727, retro_dnov_955 ,
|
| Macropus eugenii | ENSMEUG00000013169 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000002140 | 1 retrocopy |