RetrogeneDB ID: | retro_dnov_1860 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_33733:48574..48895(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | COMMD4 | ||
| Ensembl ID: | ENSDNOG00000013425 | ||
| Aliases: | None | ||
| Description: | COMM domain containing 4 [Source:HGNC Symbol;Acc:26027] |
Retrocopy-Parental alignment summary:
>retro_dnov_1860
GAGTTGCAGCAGCTGGGCCTGCCCAAAGAGCACGCAGCCAGCCTATGCCTCTGTTACTAGGAGAAGCAAAGCCCTCTGCA
GAAACACCTGCAGGCCTGCAGCCTGCACATGAACAGGCTGATGAGCATGGGCTGGCGCATAGACTACACACTGAGCTCCA
GCCTGCTGCAGACTGTGGAGGAGTCCATGGTACACCTGAGGCTGCATGTGGCAGCTGCAACAGGGGAAAAGGCCCAGCCC
ATCAACATGTTCCTCTCAGCAGACAAGTTCCAGGTCCTGCCGGCAGAACTGAGGCAGGCCCAGACCCTGATGAGCTCGCT
G
ORF - retro_dnov_1860 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.05 % |
| Parental protein coverage: | 53.77 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ELQQLGLPKEHAASLCRCYEEKQSPLQEHLRACSLRVNRLAGVGWRVDYTLSSSLLQTVEEPMVHLRLDV |
| ELQQLGLPKEHAASLC.CY.EKQSPLQ.HL.ACSL..NRL...GWR.DYTLSSSLLQTVEE.MVHLRL.V | |
| Retrocopy | ELQQLGLPKEHAASLCLCY*EKQSPLQKHLQACSLHMNRLMSMGWRIDYTLSSSLLQTVEESMVHLRLHV |
| Parental | AAALGEKAQPITMSLSADKFQVLLAELRQAQTLMSSL |
| AAA.GEKAQPI.M.LSADKFQVL.AELRQAQTLMSSL | |
| Retrocopy | AAATGEKAQPINMFLSADKFQVLPAELRQAQTLMSSL |
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 | 37 .14 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 38 .49 RPM |
| SRP012922_heart | 0 .00 RPM | 23 .90 RPM |
| SRP012922_kidney | 0 .00 RPM | 52 .84 RPM |
| SRP012922_liver | 0 .00 RPM | 12 .85 RPM |
| SRP012922_lung | 0 .00 RPM | 35 .74 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 17 .48 RPM |
| SRP012922_spleen | 0 .00 RPM | 43 .61 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_1860 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 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000010909 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000013425 | 1 retrocopy |
retro_dnov_1860 ,
|
| Loxodonta africana | ENSLAFG00000006259 | 1 retrocopy |