RetrogeneDB ID: | retro_dnov_2372 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_68320:45708..46325(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | HAT1 | ||
| Ensembl ID: | ENSDNOG00000011848 | ||
| Aliases: | None | ||
| Description: | histone acetyltransferase 1 [Source:HGNC Symbol;Acc:4821] |
Retrocopy-Parental alignment summary:
>retro_dnov_2372
ACGCTCTTTACAACCGTGGACTACACAACAGTCTATAATCACTACGTGTACCTAGACAAAACCTGGCCACGTGTAAGTCA
GATGCTGATACAGACTCATTTGAAGGTCAAGGCCATGGTGTTCAACTTCTGGAAACAGTGCATAGAAACAACATTGCATC
TCCTTCGGTTCTTGATAATACAGGGGAAGATCCATCCAAAAGCTTTGGGAAATTATGAGACTTTGTGCTTGTGAAGCTTT
GTCAAGATTTACCCTGTTTTTCCCAGGAAAAGTTAATGCAAGGATTCAATGACGATATGGCAACAGAGGCAAAATGCAAG
TTAAAAATAAATAAGGAACATGCTAGACGGGCTTATGAAATTCTTCAACTATTAGTAACTGACATGAGTGATGCTGAACA
GTACAGAAACTATAGATCGGATATTAAAAGAAGACTAATAAGTCCATATAAGAAAAAGCAGGGGGATCTTGCCAAGATGA
GAAAATGTCTCAGACCAGAAGAACTGACAAACCAGATGAACCAAATAGAAATAAGCATGCGGCATGAACAGCTGGAAGAA
AGCTTTCAGGAACTAATGGAAGACTACCAAAGTGTTATTGAACGACTTGCTCAAGAG
ORF - retro_dnov_2372 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.57 % |
| Parental protein coverage: | 52.02 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | TLFATVGYMTVYNYYVYPDKTRPRVSQMLILT-PFQGQGHGAQLLETVHRYYMASPSVLDITAEDPSKSY |
| TLF.TV.Y.TVYN.YVY.DKT.PRVSQMLI.T..F.GQGHG.QLLETVHR...ASPSVLD.T.EDPSKS. | |
| Retrocopy | TLFTTVDYTTVYNHYVYLDKTWPRVSQMLIQT<SFEGQGHGVQLLETVHRNNIASPSVLDNTGEDPSKSF |
| Parental | VKLRDFVLVKLCQDLPCFSREKLMQGFNDDMAIEAQHKFKINKQHARRVYEILRLLVTDMSDAEQYRSYR |
| .KL.DFVLVKLCQDLPCFS.EKLMQGFNDDMA.EA..K.KINK.HARR.YEIL.LLVTDMSDAEQYR.YR | |
| Retrocopy | GKL*DFVLVKLCQDLPCFSQEKLMQGFNDDMATEAKCKLKINKEHARRAYEILQLLVTDMSDAEQYRNYR |
| Parental | LDIKRRLISPYKKKQRDLAKMRKCLRPEELTNQMNQIEISMQHEQLEESFQELVEDYRRVIERLAQE |
| .DIKRRLISPYKKKQ.DLAKMRKCLRPEELTNQMNQIEISM.HEQLEESFQEL.EDY..VIERLAQE | |
| Retrocopy | SDIKRRLISPYKKKQGDLAKMRKCLRPEELTNQMNQIEISMRHEQLEESFQELMEDYQSVIERLAQE |
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 | 33 .45 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 28 .73 RPM |
| SRP012922_heart | 0 .00 RPM | 22 .97 RPM |
| SRP012922_kidney | 0 .00 RPM | 23 .82 RPM |
| SRP012922_liver | 0 .00 RPM | 9 .60 RPM |
| SRP012922_lung | 0 .00 RPM | 37 .88 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 27 .00 RPM |
| SRP012922_spleen | 0 .00 RPM | 49 .68 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_2372 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 | ENSDNOG00000011848 | 1 retrocopy |
retro_dnov_2372 ,
|
| Oryctolagus cuniculus | ENSOCUG00000005313 | 1 retrocopy | |
| Sorex araneus | ENSSARG00000005620 | 1 retrocopy |