RetrogeneDB ID: | retro_dnov_2130 | ||
Retrocopylocation | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_49968:10932..11319(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | NUBP1 | ||
| Ensembl ID: | ENSDNOG00000010609 | ||
| Aliases: | None | ||
| Description: | nucleotide binding protein 1 [Source:HGNC Symbol;Acc:8041] |
Retrocopy-Parental alignment summary:
>retro_dnov_2130
GTTCACCTGAAAGGCTCATGATGGTCTCCAGGGCATGTGGGAGACAATCTCAAGGTGATGTCAGTGGGTTTTTTGCTCAA
CAGTCCTAATGATGCCATTATCTGCAGAGAGACCAAAGAAAAATGGTCTGATTAAGCAATTCCTTCCTGACCTGGCCTGG
AGAGAAGTTGACTCCCTCCTTGTGGACACCCTACCTGGGACCGCCAACGAACGCGTCTCTCTCTGGTACCTCTCTATACA
CACATCGATGGGACTGTGATCGTCATCATTTCTCAGGAAGTATCTCTCCAGGATGTCCAGAAAGAAAGCAACTTCTGCCA
CAAGGCAAAGCTGCCCATCACTGGGGTGGTGGAGAACATGAGCAGCTTCATCTGCCCTAAATGTAAA
GTTCACCTGAAAGGCTCATGATGGTCTCCAGGGCATGTGGGAGACAATCTCAAGGTGATGTCAGTGGGTTTTTTGCTCAA
CAGTCCTAATGATGCCATTATCTGCAGAGAGACCAAAGAAAAATGGTCTGATTAAGCAATTCCTTCCTGACCTGGCCTGG
AGAGAAGTTGACTCCCTCCTTGTGGACACCCTACCTGGGACCGCCAACGAACGCGTCTCTCTCTGGTACCTCTCTATACA
CACATCGATGGGACTGTGATCGTCATCATTTCTCAGGAAGTATCTCTCCAGGATGTCCAGAAAGAAAGCAACTTCTGCCA
CAAGGCAAAGCTGCCCATCACTGGGGTGGTGGAGAACATGAGCAGCTTCATCTGCCCTAAATGTAAA
ORF - retro_dnov_2130 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.18 % |
| Parental protein coverage: | 61.61 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VHQSGSGWSPVYVEDNLGVMSVGFLLSSPDDAVIWRG-PKKNGLIKQFLRDVDWGEVDYLIVDTPPGTSD |
| VH..GS.WSP..V.DNL.VMSVGFLL.SP.DA.I.R..PKKNGLIKQFL.D..W.EVD.L.VDT.PGT.. | |
| Retrocopy | VHLKGS*WSPGHVGDNLKVMSVGFLLNSPNDAIICRE>PKKNGLIKQFLPDLAWREVDSLLVDTLPGTAN |
| Parental | EHLSVVQYLSA-ARIDGAVIITTPQEVSLQDVRKEINFCHKVKLPIIGVVENMSGFVCPKCK |
| E..S...YLS....IDG.VI....QEVSLQDV.KE.NFCHK.KLPI.GVVENMS.F.CPKCK | |
| Retrocopy | ERVSL-WYLSI<THIDGTVIVIISQEVSLQDVQKESNFCHKAKLPITGVVENMSSFICPKCK |
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 | 30 .34 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 18 .56 RPM |
| SRP012922_heart | 0 .00 RPM | 27 .38 RPM |
| SRP012922_kidney | 0 .00 RPM | 23 .27 RPM |
| SRP012922_liver | 0 .00 RPM | 11 .46 RPM |
| SRP012922_lung | 0 .00 RPM | 23 .67 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 14 .02 RPM |
| SRP012922_spleen | 0 .00 RPM | 30 .68 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_2130 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 | ENSDNOG00000010609 | 1 retrocopy |
retro_dnov_2130 ,
|