RetrogeneDB ID: | retro_dnov_125 | ||
Retrocopylocation | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | GeneScaffold_1911:28658..29133(+) | ||
| Located in intron of: | ENSDNOG00000008591 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | SAV1 | ||
| Ensembl ID: | ENSDNOG00000005318 | ||
| Aliases: | None | ||
| Description: | salvador homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:17795] |
Retrocopy-Parental alignment summary:
>retro_dnov_125
AACCATGGCTCTGAAGATTTACCCCTTTTTCCTGGCAGGTCTGTGGACAGGACAATGAGAGGAAGAAAGTATTACACGGA
TCGTGACACAATAAATACAACTCACTGGAGCCATCCTCTTGAGTGGGAAGGCCCTCCTCCAGGATGCGAGCAAGTTGAGT
CATCAGAATTTGGAACCTATTATGCAGATCCCATAAGTAAGGCGGCTCCCTGCAGGCTTCCCTGTTTACCTAGCATACCT
CGGTACGGTCACCCTCCTCCAGTCACACACCAGCCACAGCAAACTGAAAGAAATCAGTCTCCTTCTGGTACCCGCAAATC
CATATCCCACTGCAGAAATTCCTAACTGGTTTCAGGTTTACATGTGAACCCCTGTGAAACGTGACCACATTCTGAAACGG
GAACTCTTCCAGCTGCCTGATCTGGATACATACCAGAGAATGCTAAAATTGTTCTTCATGAAAGAACTGGAGCAG
AACCATGGCTCTGAAGATTTACCCCTTTTTCCTGGCAGGTCTGTGGACAGGACAATGAGAGGAAGAAAGTATTACACGGA
TCGTGACACAATAAATACAACTCACTGGAGCCATCCTCTTGAGTGGGAAGGCCCTCCTCCAGGATGCGAGCAAGTTGAGT
CATCAGAATTTGGAACCTATTATGCAGATCCCATAAGTAAGGCGGCTCCCTGCAGGCTTCCCTGTTTACCTAGCATACCT
CGGTACGGTCACCCTCCTCCAGTCACACACCAGCCACAGCAAACTGAAAGAAATCAGTCTCCTTCTGGTACCCGCAAATC
CATATCCCACTGCAGAAATTCCTAACTGGTTTCAGGTTTACATGTGAACCCCTGTGAAACGTGACCACATTCTGAAACGG
GAACTCTTCCAGCTGCCTGATCTGGATACATACCAGAGAATGCTAAAATTGTTCTTCATGAAAGAACTGGAGCAG
ORF - retro_dnov_125 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.99 % |
| Parental protein coverage: | 76.96 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | NHGSEDLPLPPGWSVDWTMRGRKYYIDHNT-NTTHWSHPLEREGLPPGWERVESSEFGTYYVDHINKKAQ |
| NHGSEDLPL.PG.SVD.TMRGRKYY.D..T.NTTHWSHPLE.EG.PPG.E.VESSEFGTYY.D.I.K.A. | |
| Retrocopy | NHGSEDLPLFPGRSVDRTMRGRKYYTDRDTINTTHWSHPLEWEGPPPGCEQVESSEFGTYYADPISKAAP |
| Parental | YRHPCAPSVPRYDQPPPVTYQPQQTERNQS-LLVPANPYHTAEIPDWLQVYARAPVKYDHILKWELFQLA |
| .R.PC.PS.PRY..PPPVT.QPQQTERNQS.LLVPANPY.TAEIP.W.QVY...PVK.DHILK.ELFQL. | |
| Retrocopy | CRLPCLPSIPRYGHPPPVTHQPQQTERNQS>LLVPANPYPTAEIPNWFQVYM*TPVKRDHILKRELFQLP |
| Parental | DLDTYQGMLKLLFMKELEQ |
| DLDTYQ.MLKL.FMKELEQ | |
| Retrocopy | DLDTYQRMLKLFFMKELEQ |
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 .19 RPM | 6 .81 RPM |
| SRP012922_cerebellum | 0 .41 RPM | 5 .22 RPM |
| SRP012922_heart | 0 .00 RPM | 4 .18 RPM |
| SRP012922_kidney | 0 .82 RPM | 2 .46 RPM |
| SRP012922_liver | 0 .00 RPM | 2 .17 RPM |
| SRP012922_lung | 0 .46 RPM | 18 .79 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 4 .50 RPM |
| SRP012922_spleen | 0 .11 RPM | 7 .33 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_125 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000006590 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000005318 | 1 retrocopy |
retro_dnov_125 ,
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