RetrogeneDB ID: | retro_dnov_2609 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_89837:7553..8193(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | IDO1 | ||
| Ensembl ID: | ENSDNOG00000002167 | ||
| Aliases: | None | ||
| Description: | indoleamine 2,3-dioxygenase 1 [Source:HGNC Symbol;Acc:6059] |
Retrocopy-Parental alignment summary:
>retro_dnov_2609
ATGGCCCATGAGCAGGCATCTCCCATGGAAAGTTCTTGGAGAATCCATGAGGAAGTCCACATAAAGGAAGATGTGGGCTT
TGCTCTGCTAGGTCCACTGGAGGGGTTGCCTAATAAGTATGCCGCCTGGACAGTCATTGTTCAAAACGTGCCTGACCTGA
TTAAGACCAGCCAGTCATGCACAGAAGTTGAAAAGTTGCCAGAACTCAGCATTGATGAGCTTGAAGGACACAAGTTGCAG
CACCTTGCCCACCTGATCTTGGGGTACATCACCATGGCCTACGTGTGGCATCAAGGTGCCCAAGATGTCTGTAAGGTCCT
GCCAAGAAATATTGCCATTTCTCACTGCAAAATCTTGGAGAAGCTGAGACTGCCTCTTAACCTGGTGTATGCAGGTTGTG
TCTTGCAAACTGGAAGAAAAAGGACCCCAGTGGGCCCATGACTTATGAAAACATGGACATCCTCTTCTCCTTCCCTGGTG
GAGACTGCAGAAAAGGTTGCTTCCTGGTGTCACTATTGTGGAAATAGCAGCTGCTTCTGCTATCAAAGAAATTCCTGTTA
TACTCAATGCTAAACAACGTCAGGACCAGGGAACTGTGAGAACAGAACTGGAAAAAATAACTGACTGCCTGAAGAAGGCC
ORF - retro_dnov_2609 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.15 % |
| Parental protein coverage: | 53.15 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MACDQASPMESPWRIREEFHINEDVGFALPDPLEELPKKYDDWMFIAQNLPDLIKTGKLREEVEKLPELS |
| MA..QASPMES.WRI.EE.HI.EDVGFAL..PLE.LP.KY..W..I.QN.PDLIKT.....EVEKLPELS | |
| Retrocopy | MAHEQASPMESSWRIHEEVHIKEDVGFALLGPLEGLPNKYAAWTVIVQNVPDLIKTSQSCTEVEKLPELS |
| Parental | IDDLEGHKLQRLAHLVLGYITMAYVWDRGDQDVRKVLPRNIAIPYCRISEMLKLPPILSYADCV-LANWK |
| ID.LEGHKLQ.LAHL.LGYITMAYVW..G.QDV.KVLPRNIAI..C.I.E.L.LP..L.YA.CV.LANWK | |
| Retrocopy | IDELEGHKLQHLAHLILGYITMAYVWHQGAQDVCKVLPRNIAISHCKILEKLRLPLNLVYAGCV<LANWK |
| Parental | KKDPSG---VKNMEILFSFPGGDCGKGFFLVSLL-VEIAAASVIKEIPILINAIQHQDQATVKTELEKIT |
| KKDPSG.....NM.ILFSFPGGDC.KG.FLVSLL.VEIAAAS.IKEIP...NA.Q.QDQ.TV.TELEKIT | |
| Retrocopy | KKDPSGPMTYENMDILFSFPGGDCRKGCFLVSLL<VEIAAASAIKEIPVILNAKQRQDQGTVRTELEKIT |
| Parental | GCLKEA |
| .CLK.A | |
| Retrocopy | DCLKKA |
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 | 3 .50 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 0 .14 RPM |
| SRP012922_heart | 0 .00 RPM | 10 .44 RPM |
| SRP012922_kidney | 0 .00 RPM | 1 .10 RPM |
| SRP012922_liver | 0 .00 RPM | 1 .08 RPM |
| SRP012922_lung | 0 .00 RPM | 411 .75 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 15 .58 RPM |
| SRP012922_spleen | 0 .00 RPM | 29 .42 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_2609 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 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000002167 | 3 retrocopies |
retro_dnov_1689, retro_dnov_2547, retro_dnov_2609 ,
|