RetrogeneDB ID: | retro_dnov_1112 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_14923:42746..43324(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LIN28A | ||
| Ensembl ID: | ENSDNOG00000010710 | ||
| Aliases: | None | ||
| Description: | lin-28 homolog A (C. elegans) [Source:HGNC Symbol;Acc:15986] |
Retrocopy-Parental alignment summary:
>retro_dnov_1112
GGCTACACTAAGGCAGCAGAGGAAGCACTGCAGAACTCAACCCAGGAGGTGGAGTTGCTGTAGCTACTGCATGGTGCCAG
CACCTATAAGTGGTTCAATGTACATATGGGGTTCATCTTTCTGTCCATGACTGTCCACACTGGGATCATTATTGACCCCC
AGTGCCTATCTTTGTGCATCACAGTAAGCTGCATGTATGGAAGACTTCTGAAGCCTGAAGGAGGATGTGGCAGTGGAGTT
CAACTATAAGATATTTTCCAAGGGCCTGGAATCTATCTGTGTCACTAGACCCGATGGGGTGTTCTGTATAGGGAGCAAGA
GGTGGCCAAAGGGGAAGAACATGGAGAAATGCAGATCGAAAGCAGACAAGAGCTACAACTGTGCAGATTAGATCACCATG
CCAAGAAATCAAGCTGCCAGTCCAGCTAAGAAGTGCCACTCCTCCAGAGCATCAGCCATAATGTGGCCTCATGTCCACTG
AAAGCTCAGCACGGCCCCATATCACTGGAAATCTCTCCTACCTTTGGGAAGAATAAGAAGAGATACACAGCCCTGCCCTG
ACCCCAAAGGCCCAGAAT
ORF - retro_dnov_1112 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 61.5 % |
| Parental protein coverage: | 94.63 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | GCAKAAEEAPENAAREGEEPQLLHGAGICKWFNVRMGFGFLSMTARAGVALD-PPVDVFVHQSKLHMEGF |
| G..KAAEEA..N...E.E...LLHGA...KWFNV.MGF.FLSMT...G...D.P.......Q....ME.F | |
| Retrocopy | GYTKAAEEALQNSTQEVELL*LLHGASTYKWFNVHMGFIFLSMTVHTGIIID>PSAYLCASQ*AACMEDF |
| Parental | RSLKEGEAVEFTFKKSAKGLESIRVTGPGGVFCIGSERRPKGKNMQKRRSKGDRCYNCGG-LDHHAK-EC |
| .SLKE..AVEF..K...KGLESI.VT.P.GVFCIGS.R.PKGKNM.K.RSK.D..YNC...LDHHAK.E. | |
| Retrocopy | *SLKEDVAVEFNYKIFSKGLESICVTRPDGVFCIGSKRWPKGKNMEKCRSKADKSYNCAD<LDHHAK<EI |
| Parental | KLPPQ-PKKCH-FCQSISHMVASCPLKAQQAPSS-QGKPSYFREEEEEIHSPALLPEAQN |
| KLP.Q..KKCH...QSISH.VASCPLKAQ..P.S..G..SY..EE.EEIHSPAL.P.AQN | |
| Retrocopy | KLPVQ<AKKCH<LLQSISHNVASCPLKAQHGPIS<TGNLSYLWEE*EEIHSPALTPKAQN |
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 | 0 .00 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 0 .14 RPM |
| SRP012922_heart | 0 .00 RPM | 0 .00 RPM |
| SRP012922_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP012922_liver | 0 .00 RPM | 0 .00 RPM |
| SRP012922_lung | 0 .00 RPM | 0 .15 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP012922_spleen | 0 .00 RPM | 0 .11 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_1112 was not experimentally validated.