RetrogeneDB ID: | retro_dnov_1272 | ||
Retrocopylocation | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_173531:3669..4085(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | TMED3 | ||
| Ensembl ID: | ENSDNOG00000002342 | ||
| Aliases: | None | ||
| Description: | transmembrane emp24 protein transport domain containing 3 [Source:HGNC Symbol;Acc:28889] |
Retrocopy-Parental alignment summary:
>retro_dnov_1272
CTGCTTGCACATCTGCTTCTCATCCTGGGACCTGGCTGCACCTCTGGGATCACCTTTGTGTCACCCAACAATGCCAAGTA
GTGCTTCTATGAGGACATCAGATGGGACAAAAACTGCACCCTTGAGTTTCAGATGATTGATGGCAGTCACTATGATGTAG
ATTGCCAATTAGAAAATCCTGATGGTAATGTGTTATGCAAAGAGGTGAAAAAACAGTATGATAGTTTCACCTTCACAGCC
TCCAAAAATGGGACACACAAATTTGCTTGAGCATTGAATTTTCTACTTTCAAACATAAAACCGTATATTTTGATTTTCAA
GTTGGAGAAGACCCACTTTTGTTTCCTAGTGTGAATGGAGTCAGTGCTTTTGTACAGATGGAGTCCGCCTGTATTTCAAT
TCAGGAAGTTCTGAAG
CTGCTTGCACATCTGCTTCTCATCCTGGGACCTGGCTGCACCTCTGGGATCACCTTTGTGTCACCCAACAATGCCAAGTA
GTGCTTCTATGAGGACATCAGATGGGACAAAAACTGCACCCTTGAGTTTCAGATGATTGATGGCAGTCACTATGATGTAG
ATTGCCAATTAGAAAATCCTGATGGTAATGTGTTATGCAAAGAGGTGAAAAAACAGTATGATAGTTTCACCTTCACAGCC
TCCAAAAATGGGACACACAAATTTGCTTGAGCATTGAATTTTCTACTTTCAAACATAAAACCGTATATTTTGATTTTCAA
GTTGGAGAAGACCCACTTTTGTTTCCTAGTGTGAATGGAGTCAGTGCTTTTGTACAGATGGAGTCCGCCTGTATTTCAAT
TCAGGAAGTTCTGAAG
ORF - retro_dnov_1272 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.75 % |
| Parental protein coverage: | 66.05 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LLLSLLLLLQAQRPRGAELTFELPDNAKQCFHEEVEQGVKFSLDYQVITGGHYDVDCYVEDPLGNTIYRE |
| LL..LLL.L......G...TF..P.NAK.CF.E.........L..Q.I.G.HYDVDC..E.P.GN....E | |
| Retrocopy | LLAHLLLILGPGCTSG--ITFVSPNNAK*CFYEDIRWDKNCTLEFQMIDGSHYDVDCQLENPDGNVLCKE |
| Parental | TKKQYDSFMHHAEVKGVYQF-CFSNEFSTFSHKTVYFDFQVGDEPPILPDMGNRVTALTQMESACVTIHE |
| .KKQYDSF...A...G...F.C.S.EFSTF.HKTVYFDFQVG..P...P...N.V.A..QMESAC..I.E | |
| Retrocopy | VKKQYDSFTFTASKNGTHKF<CLSIEFSTFKHKTVYFDFQVGEDPLLFPSV-NGVSAFVQMESACISIQE |
| Parental | ALK |
| .LK | |
| Retrocopy | VLK |
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 | 47 .84 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 21 .58 RPM |
| SRP012922_heart | 0 .00 RPM | 15 .55 RPM |
| SRP012922_kidney | 0 .00 RPM | 38 .61 RPM |
| SRP012922_liver | 0 .00 RPM | 42 .11 RPM |
| SRP012922_lung | 0 .00 RPM | 40 .78 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 10 .04 RPM |
| SRP012922_spleen | 0 .00 RPM | 57 .12 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_1272 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 | ENSDNOG00000002342 | 1 retrocopy |
retro_dnov_1272 ,
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