RetrogeneDB ID: | retro_dnov_2218 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_56238:761..1238(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | STYX | ||
| Ensembl ID: | ENSDNOG00000016631 | ||
| Aliases: | None | ||
| Description: | serine/threonine/tyrosine interacting protein [Source:HGNC Symbol;Acc:11447] |
Retrocopy-Parental alignment summary:
>retro_dnov_2218
CTGGTTTTAGGCTCATATTCATCTGCTACGAAAAGCAAGCTACCTATACTACAGAAACATGGAATAACCCATATATTATG
CACAAGACAAATATTGAAGCAAGCTTTATTAAACCAAATTTTCAGCAGTTATTTAGATAATTAGTCTTGGATATTGCAGG
CAATCCAGTTGAAATATATAATATGTTTTTCCCCTATGACTAAAGAATTTATGGATGGGAGCTTACAAACTGGAGGAAAC
GTTCTTGTCCAGGGAAAGACAGGGATCTCCAGGACTACTGTCTTTGTTATTGAATACATTATGGAAACAGCTGGAATGAA
GTACAGAGAGGCATATGTCCAGGTTCAAGAAAGAAGGTCTTGTATTAGTCCTAACACTGGGTTCATCCACCAACTTTAGG
AATATGAAGCCATCTACCTAGAAGAATTAACAACACAGATGATGCCACAACAACAGATAGAAAGGTCCATTCTGGTA
ORF - retro_dnov_2218 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.53 % |
| Parental protein coverage: | 71.3 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LFLGPYSSAMKSKLPILQKHGITHIICIRQ-NIEANFIKPNFQQLFRYLVLDIADNPVE-NIIRFFPMTK |
| L.LG.YSSA.KSKLPILQKHGITHI.C.RQ.NIEA.FIKPNFQQLFR.LVLDIA.NPVE..II.F.PMTK | |
| Retrocopy | LVLGSYSSATKSKLPILQKHGITHILCTRQ<NIEASFIKPNFQQLFR*LVLDIAGNPVE>YIICFSPMTK |
| Parental | EFIDGSFQTGGKVLVHGNAGISRSAAFVIAYIMETFGMKYRDAFAYVQERRFCINPNAGFVHQLQEYEAI |
| EF.DGS.QTGG.VLV.G..GISR...FVI.YIMET.GMKYR.A...VQERR.CI.PN.GF.HQL.EYEAI | |
| Retrocopy | EFMDGSLQTGGNVLVQGKTGISRTTVFVIEYIMETAGMKYREAYVQVQERRSCISPNTGFIHQL*EYEAI |
| Parental | YLAKLTIQMMSPVQIERSLSV |
| YL..LT.QMM...QIERS..V | |
| Retrocopy | YLEELTTQMMPQQQIERSILV |
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 | 6 .03 RPM |
| SRP012922_cerebellum | 0 .27 RPM | 3 .44 RPM |
| SRP012922_heart | 0 .00 RPM | 4 .64 RPM |
| SRP012922_kidney | 0 .00 RPM | 4 .93 RPM |
| SRP012922_liver | 0 .00 RPM | 2 .63 RPM |
| SRP012922_lung | 0 .00 RPM | 4 .89 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 11 .77 RPM |
| SRP012922_spleen | 0 .00 RPM | 5 .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_2218 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 8 parental genes, and 16 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000016631 | 9 retrocopies |
retro_dnov_1713, retro_dnov_1720, retro_dnov_1914, retro_dnov_2138, retro_dnov_2186, retro_dnov_2218 , retro_dnov_2221, retro_dnov_461, retro_dnov_66,
|
| Echinops telfairi | ENSETEG00000000561 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000029372 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000053205 | 1 retrocopy | |
| Ochotona princeps | ENSOPRG00000016123 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000007956 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000014504 | 1 retrocopy | |
| Vicugna pacos | ENSVPAG00000012229 | 1 retrocopy |