RetrogeneDB ID: | retro_dnov_1782 | ||
Retrocopylocation | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_30012:47207..47605(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | TM2D2 | ||
| Ensembl ID: | ENSDNOG00000009863 | ||
| Aliases: | None | ||
| Description: | TM2 domain containing 2 [Source:HGNC Symbol;Acc:24127] |
Retrocopy-Parental alignment summary:
>retro_dnov_1782
CCCGATGAATTTATAAAATATAAAGACCCAGTGAATCATGTTGAAAACGCGACTATAACCCAGGAGCTTGGTTATGGTTG
TCTCAAGTTTGGTGGCCAGGCCTATGGTGATGTGGAGCACACTTCAATCCAGTGCCAGACCCTGGACGGAATAGACTGTG
CCAGTCCTAGGATCTTCTTATGAGAAAATAAACCTTATATAAAGTATACCAGACACTACTTCATGACCACTTTACTCTAC
TCCTTCTTCCTGTGATTTTTGGAGTAGATTGTTTCTATCTGAGACACACTGGCACAGTAGTAGGAAAACTGTTGACAATT
GGTGGACTAAGAATTTGGTGTTTTTTTTACCTTATTTTGCTCATTACTGGTGGACTGATGCCAAGTAATGGCAGCAAC
CCCGATGAATTTATAAAATATAAAGACCCAGTGAATCATGTTGAAAACGCGACTATAACCCAGGAGCTTGGTTATGGTTG
TCTCAAGTTTGGTGGCCAGGCCTATGGTGATGTGGAGCACACTTCAATCCAGTGCCAGACCCTGGACGGAATAGACTGTG
CCAGTCCTAGGATCTTCTTATGAGAAAATAAACCTTATATAAAGTATACCAGACACTACTTCATGACCACTTTACTCTAC
TCCTTCTTCCTGTGATTTTTGGAGTAGATTGTTTCTATCTGAGACACACTGGCACAGTAGTAGGAAAACTGTTGACAATT
GGTGGACTAAGAATTTGGTGTTTTTTTTACCTTATTTTGCTCATTACTGGTGGACTGATGCCAAGTAATGGCAGCAAC
ORF - retro_dnov_1782 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.12 % |
| Parental protein coverage: | 62.15 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PDEFIECEDPVDHVGNATAFQELGYGCVKFGGQAYDDVERTSVQCRALDGIECASPRIFLRENKPCIKYT |
| PDEFI...DPV.HV.NAT..QELGYGC.KFGGQAY.DVE.TS.QC..LDGI.CASPRIFL.ENKP.IKYT | |
| Retrocopy | PDEFIKYKDPVNHVENATITQELGYGCLKFGGQAYGDVEHTSIQCQTLDGIDCASPRIFL*ENKPYIKYT |
| Parental | GHYFITTLLYSFFL-GCFGVDRFCLGHTGTAVGKLLTLGGLGIWWFVDLILLITGGLMPSDGSN |
| .HYF.TTLLYSFFL...FGVD.F.L.HTGT.VGKLLT.GGL.IW....LILLITGGLMPS.GSN | |
| Retrocopy | RHYFMTTLLYSFFL<VIFGVDCFYLRHTGTVVGKLLTIGGLRIWXXXXLILLITGGLMPSNGSN |
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 | 8 .56 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 22 .68 RPM |
| SRP012922_heart | 0 .00 RPM | 4 .41 RPM |
| SRP012922_kidney | 0 .00 RPM | 7 .94 RPM |
| SRP012922_liver | 0 .00 RPM | 10 .37 RPM |
| SRP012922_lung | 0 .00 RPM | 15 .12 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 13 .67 RPM |
| SRP012922_spleen | 0 .11 RPM | 20 .49 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_1782 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000009863 | 2 retrocopies |
retro_dnov_1384, retro_dnov_1782 ,
|