RetrogeneDB ID: | retro_dnov_2405 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_72059:1553..1957(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TPK1 | ||
| Ensembl ID: | ENSDNOG00000018545 | ||
| Aliases: | None | ||
| Description: | thiamin pyrophosphokinase 1 [Source:HGNC Symbol;Acc:17358] |
Retrocopy-Parental alignment summary:
>retro_dnov_2405
TTTTTGCCTAAATACATCAAGGCAGATTTTGATTCCATTAGGCCTGAAGTCAATGGGTACTATACTTGTAAATGATGTGA
GCTGATTTCAACTCCTGATCAAAACTGCACTGACTTTACCAATTACCTTCTAGTACTCTAAAAGAAGATAGATGTAAAAC
ACCTACAGGTTAATATGAATGTCACACTCCCAGGACTTGCTGGACATTTTGAATGGAGTATGGCATCTGTGTGTACCCTA
TTTCAAGTGAATCATATAACTCTTTGCCAATTATAATAATTCAAGAGGAAACTCTCATCTACCTGCCCCAACCAGGAAAG
GAAAAGATTCATGTAAACACTGGAATAGAAGATGATTGTTGTGGCCTTATTCCTGTTGTATGATAACACAATCACATTGC
CACA
ORF - retro_dnov_2405 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.71 % |
| Parental protein coverage: | 55.0 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | FLPEFINGDFDSIRPEVKEYYTSKGCELISTPDQNYTDFTKCLLELQKKIEEKNLEIDMIVTLGGLAGHF |
| FLP..I..DFDSIRPEV..YYT.K.CELISTPDQN.TDFT..LL.L.KKI..K.L...M.VTL.GLAGHF | |
| Retrocopy | FLPKYIKADFDSIRPEVNGYYTCK*CELISTPDQNCTDFTNYLLVL*KKIDVKHLQVNMNVTLPGLAGHF |
| Parental | DQIMS---ILFQATHIT-PLPLIIIQEESLIYLPQPGKHKLHVNTGMEGDWCGLVPIGQHCNHVTT |
| ...M.....LFQ..HIT..LP.IIIQEE.LIYLPQPGK.K.HVNTG.E.D.CGL.P.....NH..T | |
| Retrocopy | EWSMASVCTLFQVNHIT<SLPIIIIQEETLIYLPQPGKEKIHVNTGIEDDCCGLIPVV**HNHIAT |
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 .39 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 0 .27 RPM |
| SRP012922_heart | 0 .00 RPM | 0 .23 RPM |
| SRP012922_kidney | 0 .00 RPM | 1 .37 RPM |
| SRP012922_liver | 0 .00 RPM | 1 .08 RPM |
| SRP012922_lung | 0 .00 RPM | 1 .37 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 0 .35 RPM |
| SRP012922_spleen | 0 .00 RPM | 0 .69 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_2405 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 7 parental genes, and 34 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000001227 | 23 retrocopies |
retro_chof_1004, retro_chof_1093, retro_chof_1416, retro_chof_1458, retro_chof_1537, retro_chof_1683, retro_chof_1732, retro_chof_191, retro_chof_1927, retro_chof_2202, retro_chof_2413, retro_chof_2507, retro_chof_2577, retro_chof_468, retro_chof_472, retro_chof_550, retro_chof_630, retro_chof_665, retro_chof_701, retro_chof_801, retro_chof_917, retro_chof_954, retro_chof_988,
|
| Dasypus novemcinctus | ENSDNOG00000018545 | 4 retrocopies | |
| Macropus eugenii | ENSMEUG00000010062 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000004213 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000025468 | 2 retrocopies | |
| Ornithorhynchus anatinus | ENSOANG00000020728 | 1 retrocopy | |
| Vicugna pacos | ENSVPAG00000010214 | 2 retrocopies |