RetrogeneDB ID: | retro_dnov_752 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_104730:3743..4556(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AMD1 | ||
| Ensembl ID: | ENSDNOG00000006867 | ||
| Aliases: | None | ||
| Description: | adenosylmethionine decarboxylase 1 [Source:HGNC Symbol;Acc:457] |
Retrocopy-Parental alignment summary:
>retro_dnov_752
AAGCAGGGAGATTATGTGCTCAGAGAGAGTCACATGCTGTCTCCAAGAGACTTTTCATTTTGAAGATGTGGTCCCACCCT
CTTACTGAAAGCACTGGTTCCCCTGTTGAAGCTTGCTATGGAGTATGGTGGGTTCGACTCAGTTCAAAGCTTTTATTCTC
CTAAGAATTTCATGAAGCTTCTCACCAAGGGCACCCACACTGGAATTTCCAGGAAGAAATAAGGTTTCTTCATACAATTT
TCAAATGAGCTGCAGATTATATGGGACAGATGAATTTTGACTGTTAGCACTTATATATACTCTCGGTTTCCCAGAGAGCT
GTGTAATCAGTCAGCCAGATCAAACTCTGGAAACTCTGAAGAGTGCGCTTGCCCAGCAGTTATGGACCAGTTCTACGTGA
AAGTTGGTGTTACTGCAAAGGATGTCACTTGTGAGAGTGGATTCCTGACCTTATACCAGGTCTGTCGTTGATGCCACCCT
GTTCAATTTTTGTGGGTATTTGGTGAATGGAATGAATTTGGGTGGAACTTATTGGACTATTTGCATCACTCCAGAACCAG
AATTTTATGTTAACTCTGAAACAAACTTAAGTGAGTATTCCTTATGATGACCACATCAGGAAAGTTGTGGAAGTCTTCAA
GCCAGGAAAAGGTGGGACCACCTTGTTTGTAAACCAGAGTTGTAAATGTCACACAAGTGCTTTCTTCACTCCAGAAGACT
GAAGGTTTTAAACGTCTTGATTGCCAGAGTGCTATGTTCAATGATCACAATTTTATTACCAGCTTTGCTAAGAATCAGCA
ACAACAGCCAAGC
ORF - retro_dnov_752 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.83 % |
| Parental protein coverage: | 82.63 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 8 |
Retrocopy - Parental Gene Alignment:
| Parental | KQEAYVLSESSMFVSKRRFILKTCGTTLLLKALVPLLKLARDYSGFDSIQSFFYSRKNFMK-PSHQGYPH |
| KQ..YVL.ES.M..S.R.F....CG.TLLLKALVPLLKLA..Y.GFDS.QS.FYS.KNFMK..SHQG.PH | |
| Retrocopy | KQGDYVLRESHM-LSPRDFSF*RCGPTLLLKALVPLLKLAMEYGGFDSVQS-FYSPKNFMK<ASHQGHPH |
| Parental | RNFQEEIEFLNAIFPNGAAYCMGRMNSDCWYLYTLD-FP-ETRVISQPDQTLEILMSELD-PAVMDQFYM |
| .NFQEEI.FL..IF...A.Y.MG.MN.DC..LY.L..FP.E..VISQPDQTLE.L.S.L..PAVMDQFY. | |
| Retrocopy | WNFQEEIRFLHTIFK*AADY-MGQMNFDC*HLYILS>FP>ESCVISQPDQTLETLKSALA<PAVMDQFYV |
| Parental | KDGVTAKDVTRESG-IRDLIPG-SVIDATLFNPCGYSMNGXXXXXTYWTIHITPEPEFSYVSFETNLSLT |
| K.GVTAKDVT.ESG.I.DLIPG.SV.DATLFN.CGY..NG.....TYWTI.ITPEPEF.YV..ETNLS.. | |
| Retrocopy | KVGVTAKDVTCESG<IPDLIPG<SVVDATLFNFCGYLVNGMNLGGTYWTICITPEPEF-YVNSETNLSEY |
| Parental | S-YDDLIRKVVEVFKPGKFVTTLFVNQSSKCRT-VLSSPQKIEGFKRLDCQSAMFNDYNFVFTSFAKNQQ |
| S.YDD.IRKVVEVFKPGK..TTLFVNQS.KC.T.VLSS.QK.EGFKRLDCQSAMFND.NF..TSFAKNQQ | |
| Retrocopy | S>YDDHIRKVVEVFKPGKGGTTLFVNQSCKCHT>VLSSLQKTEGFKRLDCQSAMFNDHNFI-TSFAKNQQ |
| Parental | QQQS |
| QQ.S | |
| Retrocopy | QQPS |
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 | 31 .31 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 23 .23 RPM |
| SRP012922_heart | 0 .00 RPM | 14 .39 RPM |
| SRP012922_kidney | 0 .00 RPM | 12 .05 RPM |
| SRP012922_liver | 0 .00 RPM | 25 .39 RPM |
| SRP012922_lung | 0 .00 RPM | 18 .79 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 12 .46 RPM |
| SRP012922_spleen | 0 .00 RPM | 34 .80 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_752 was not experimentally validated.