RetrogeneDB ID: | retro_dnov_1903 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_36098:4392..5547(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DDX17 | ||
| Ensembl ID: | ENSDNOG00000006499 | ||
| Aliases: | None | ||
| Description: | DEAD (Asp-Glu-Ala-Asp) box helicase 17 [Source:HGNC Symbol;Acc:2740] |
Retrocopy-Parental alignment summary:
>retro_dnov_1903
ACCGAACCCACTGCTATTCAAGCTCAGGGATGGCCAGTTGCTCTTAGTGGATTGGATATGGTGGAGTAGCACAGACTGGA
TCTGGGAAAACGTTATCTTATTTGCTGCCTGCCCATTGTCCATATCAGTCATCAGCCATTCCTAGAGAGAGGTGATGGGC
CTATTTGCTTGGTGCTGGCACCAACTCGGGAACTGGCCCAACAAGTGCAGCAAGTAGCTGCCGAGTACTGTAGAGCATGT
TGCTTAAAGTCTACTTGTATCTATGGTGGTGCTCCCAAGGGACCACAAATACGTGATTTGGAAAGAGGTGTGGAAATCTG
TATTGCAACACCTGGAAGACTGATTGACTTTTTAGAGTGCGGGAAAACCAATTTGAGAAGAACAACCTATCTTGTCCTTG
ATGAAGCAGATAGAATGCTTGATATGGGCTTCGAACCCCAAATAAGGAAGATTGTGGATCAAATAAGACCTGATAGGCAA
ACTCTAATGTGGAGTGTGACTTGGCCAAAAGAAGTAAGACAGCTTGCTGAAGATTTCCTGAAAGACTATATTCATATAAA
CATTGGTGCACTAGAACTGAGTGCAAACCACAATATTCTTCAGATTGTAGATGTGTGTCATGATGTAGAAAAAGATGAAA
AACTTATTCGTCTAATGGAAGAAATCATGAGTGAGAAGGACAATACAACCATCGTTTTTGTGGAAACCAAAAGAAGATGT
GGTGAGTTTATCAGAAAAATGGAGAGAAATGGGTGGCCTGCCATGGGTATCCATGGTGACAAAAGTCAACAGGAACGTGA
CTGGGTTCTAAATGAATTCAAACATGGAAAAGCTCCTATTCTGATTGCTACAGATGTGGCCTCCAGAGGGCTAGATGTGG
AAGATGTGAAATTTGTCATCAGTTATGACTACCCTAACTCCTCAGAGGATTATATTCATCGAATTGGAAGAACTGCTCGC
AGTACCAAAACAGGCACAGCATACACTTTCTTTACACCTAATAACATAAAGCAAGTGAGCGACCTTATCTCTGTGCTTCG
TGAAGCCAATCAAGCAATTAATCCCAAGTTGCTTCAGTTGGTTGAAGACAGAGGTTCAGGTCGTTCCAGGGGTAGAGGAG
GCATGAAGGATGACCGTCGAGACAGATACTCTGCA
ORF - retro_dnov_1903 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.88 % |
| Parental protein coverage: | 57.88 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | TEPTPIQCQGFSLALSGRDMV-GIAQTGSGKTLAYLLPA-IVHINHQPYLERGDGPICLVLAPTRELAQQ |
| TEPT.IQ.QG...ALSG.DMV.G.AQTGSGKTL.YLLPA.IVHI.HQP.LERGDGPICLVLAPTRELAQQ | |
| Retrocopy | TEPTAIQAQGWPVALSGLDMV<GVAQTGSGKTLSYLLPA>IVHISHQPFLERGDGPICLVLAPTRELAQQ |
| Parental | VQQVADDYGKCSRLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLESGKTNLRRCTYLVLDEADR |
| VQQVA..Y.....LKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLE.GKTNLRR.TYLVLDEADR | |
| Retrocopy | VQQVAAEYCRACCLKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADR |
| Parental | MLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLRDYTQINVGNLELSANHNILQIVDVCME |
| MLDMGFEPQIRKIVDQIRPDRQTLMWS.TWPKEVRQLAEDFL.DY..IN.G.LELSANHNILQIVDVC.. | |
| Retrocopy | MLDMGFEPQIRKIVDQIRPDRQTLMWSVTWPKEVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHD |
| Parental | SEKDHKLIQLMEEIMAEKENKTIIFVETKRRCDDLTRRMRRDGWPAMCIHGDKSQPERDWVLNEFRSGKA |
| .EKD.KLI.LMEEIM.EK.N.TI.FVETKRRC....R.M.R.GWPAM.IHGDKSQ.ERDWVLNEF..GKA | |
| Retrocopy | VEKDEKLIRLMEEIMSEKDNTTIVFVETKRRCGEFIRKMERNGWPAMGIHGDKSQQERDWVLNEFKHGKA |
| Parental | PILIATDVASRGLDVEDVKFVINYDYPNSSEDYVHRIGRTARSTNKGTAYTFFTPGNLKQARELIKVLEE |
| PILIATDVASRGLDVEDVKFVI.YDYPNSSEDY.HRIGRTARST..GTAYTFFTP.N.KQ...LI.VL.E | |
| Retrocopy | PILIATDVASRGLDVEDVKFVISYDYPNSSEDYIHRIGRTARSTKTGTAYTFFTPNNIKQVSDLISVLRE |
| Parental | ANQAINPKLMQLVDHRGGG---GGGGGRSRYRTTSSA |
| ANQAINPKL.QLV..RG.G...G.GG.....R...SA | |
| Retrocopy | ANQAINPKLLQLVEDRGSGRSRGRGGMKDDRRDRYSA |
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 | 219 .94 RPM | 198 .55 RPM |
| SRP012922_cerebellum | 260 .92 RPM | 211 .29 RPM |
| SRP012922_heart | 86 .55 RPM | 50 .12 RPM |
| SRP012922_kidney | 144 .02 RPM | 47 .64 RPM |
| SRP012922_liver | 140 .10 RPM | 81 .43 RPM |
| SRP012922_lung | 346 .99 RPM | 165 .25 RPM |
| SRP012922_quadricep_muscle | 42 .92 RPM | 51 .41 RPM |
| SRP012922_spleen | 314 .20 RPM | 229 .04 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_1903 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000006499 | 1 retrocopy |
retro_dnov_1903 ,
|
| Otolemur garnettii | ENSOGAG00000001539 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000013691 | 1 retrocopy |