RetrogeneDB ID: | retro_dnov_1036 | ||
Retrocopylocation | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_139046:40434..40854(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | LAPTM4A | ||
| Ensembl ID: | ENSDNOG00000001419 | ||
| Aliases: | None | ||
| Description: | lysosomal protein transmembrane 4 alpha [Source:HGNC Symbol;Acc:6924] |
Retrocopy-Parental alignment summary:
>retro_dnov_1036
AATGCCTGCGTTCTTTTTGCCGTCTCTGTTCTTACGTTTATAATCAGTTCAATGATGGTATATGGAGCAATTTCTTATCA
AGTGGGTTGGCTGATTCCATTCTTTTGTTACCGCCTTTTTGATTTTGTTCTCAGTTGCCAGGTTACTATCAGTTCTCTCA
CTTACTTGCCAAGAATCAAGGAATATCTGGATCAATTACCTGATTTTCCCTACAAAGATGACCTCCTGGCATTGGACTCC
AGCTGCTTCCTCTTCATTTTTCTTGTGTTCTTTGCTTTATTCATCGTGTTTAAGGCTTATCTAATAAACTGCATTTGGAA
CTGCTATAAATATATTAACAACAGAAATGTGCCAGAGATTGCTGAGTATCCTGCCTTTGAAGCACCTCCACAGCCTCTAT
TGCCAACCTATGAAATGGCA
AATGCCTGCGTTCTTTTTGCCGTCTCTGTTCTTACGTTTATAATCAGTTCAATGATGGTATATGGAGCAATTTCTTATCA
AGTGGGTTGGCTGATTCCATTCTTTTGTTACCGCCTTTTTGATTTTGTTCTCAGTTGCCAGGTTACTATCAGTTCTCTCA
CTTACTTGCCAAGAATCAAGGAATATCTGGATCAATTACCTGATTTTCCCTACAAAGATGACCTCCTGGCATTGGACTCC
AGCTGCTTCCTCTTCATTTTTCTTGTGTTCTTTGCTTTATTCATCGTGTTTAAGGCTTATCTAATAAACTGCATTTGGAA
CTGCTATAAATATATTAACAACAGAAATGTGCCAGAGATTGCTGAGTATCCTGCCTTTGAAGCACCTCCACAGCCTCTAT
TGCCAACCTATGAAATGGCA
ORF - retro_dnov_1036 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.29 % |
| Parental protein coverage: | 63.72 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | NACVLFAVSVLMFIISSMLVYGAISYQVGWLIPFF-YRLFDLVLSCLVAISSLTYLPRIKEYLDQLPDFP |
| NACVLFAVSVL.FIISSM.VYGAISYQVGWLIPFF.YRLFD.VLSC.V.ISSLTYLPRIKEYLDQLPDFP | |
| Retrocopy | NACVLFAVSVLTFIISSMMVYGAISYQVGWLIPFFCYRLFDFVLSCQVTISSLTYLPRIKEYLDQLPDFP |
| Parental | YKDDLLALDSSCLLFIVLVFFALFIVFKAYLINCVWNCYKYINNRNVPEIAVYPAFEAPPQP--PPYKPA |
| YKDDLLALDSSC.LFI.LVFFALFIVFKAYLINC.WNCYKYINNRNVPEIA.YPAFEAPPQP..P.Y..A | |
| Retrocopy | YKDDLLALDSSCFLFIFLVFFALFIVFKAYLINCIWNCYKYINNRNVPEIAEYPAFEAPPQPLLPTYEMA |
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 | 10 .70 RPM | 30 .14 RPM |
| SRP012922_cerebellum | 4 .81 RPM | 17 .87 RPM |
| SRP012922_heart | 6 .96 RPM | 24 .83 RPM |
| SRP012922_kidney | 11 .50 RPM | 34 .50 RPM |
| SRP012922_liver | 10 .53 RPM | 26 .78 RPM |
| SRP012922_lung | 13 .29 RPM | 53 .00 RPM |
| SRP012922_quadricep_muscle | 5 .37 RPM | 15 .92 RPM |
| SRP012922_spleen | 16 .02 RPM | 51 .51 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_1036 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 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000001419 | 1 retrocopy |
retro_dnov_1036 ,
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