RetrogeneDB ID: | retro_dnov_29 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | GeneScaffold_4168:6405..6981(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSDNOG00000002097 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RHOA | ||
| Ensembl ID: | ENSDNOG00000012825 | ||
| Aliases: | None | ||
| Description: | ras homolog family member A [Source:HGNC Symbol;Acc:667] |
Retrocopy-Parental alignment summary:
>retro_dnov_29
ATGCAGAGCATCAAGTGTGTGGCGGTGGGTGATGGGGCAGTGGGCAAGACGTGCCTGCTCATCTGCTACACAACTAACGC
TTTCCCCAAGGAGTACATCCCCACAGTGTTCGACAATTACAGTGCCCAGAGCGCAGTTGATGGGCGCACAGTGAACCTGA
ACCGGTGGGACACGGTGGGCCAGGAGGAGTACGACCGCCTCCTCACACTCTCCTACCCTCAGACCAACGTCTTTGTCATC
TGCTTCTCCATTGCCAGTCCGCCCTCCTACGAGAACGTGCGGCACAAGTGGCATCCAGAGGTGTGCCACCATTGCCCTGA
TGTGCCCATCCTCCTGGTGGGCACCAAGAAGGACCTGAGGGCGCAGCCTGACACCCTACGGCGCCTCAAGGAGCAGGGCC
AGGCGCCCATCATGCCGCAGCAGGGCCAGGCACTGGCCAAGCAGATCCACACTGTGCGCTACCTCGAGTGCTCGGCTCTG
CAGCAGGACGGCGTCAAGGAGGTGTTTGCTGAGGCTGTCCGGGCTGTGCTCAACCCCACGCCCATCAAGCGTGGGCGGTC
CTGTGTCCTCTTGTGA
ORF - retro_dnov_29 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.48 % |
| Parental protein coverage: | 96.89 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPD |
| K.V.VGDGA.GKTCLLI......FP..Y.PTVF.NY.A...VDG..V.L..WDT.GQE.YDRL..LSYP. | |
| Retrocopy | KCVAVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQSAVDGRTVNLNRWDTVGQEEYDRLLTLSYPQ |
| Parental | TDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRD |
| T.V...CFSI.SP.S.EN...KW.PEV.H.CP.VPI.LVG.KKDLR....T.R.L....Q.P..P..G.. | |
| Retrocopy | TNVFVICFSIASPPSYENVRHKWHPEVCHHCPDVPILLVGTKKDLRAQPDTLRRLKEQGQAPIMPQQGQA |
| Parental | MANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRGKKKSGCLVL |
| .A..I....Y.ECSA...DGV.EVF..A.RA.L.....K....C..L | |
| Retrocopy | LAKQIHTVRYLECSALQQDGVKEVFAEAVRAVLNPTPIKRGRSCVLL |
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 | 17 .70 RPM | 145 .85 RPM |
| SRP012922_cerebellum | 4 .95 RPM | 46 .46 RPM |
| SRP012922_heart | 2 .55 RPM | 27 .15 RPM |
| SRP012922_kidney | 11 .50 RPM | 92 .00 RPM |
| SRP012922_liver | 5 .88 RPM | 45 .98 RPM |
| SRP012922_lung | 21 .69 RPM | 108 .89 RPM |
| SRP012922_quadricep_muscle | 4 .33 RPM | 39 .98 RPM |
| SRP012922_spleen | 32 .05 RPM | 124 .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_29 was not experimentally validated.