RetrogeneDB ID: | retro_dnov_863 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_11533:62370..62968(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSDNOG00000014426 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CALU | ||
| Ensembl ID: | ENSDNOG00000010477 | ||
| Aliases: | None | ||
| Description: | calumenin [Source:HGNC Symbol;Acc:1458] |
Retrocopy-Parental alignment summary:
>retro_dnov_863
CCATCGGTGCGCAAGGAACGAGAGGTGGCGCTCGACTCGTAGTTCCGGAATCGAACTCCCGAAGACAATCAGAGCTTCCA
GTAAGACCAAATAGTCTTTCCTGGGTAAAGAGGACTTCAAGACTATAGATCAGCTCATCCCAGATGAGAGCAAGGAGAGG
CTGGGGATGATTGTCAATCGAATCGACAGTGATGGAGGTGGCTTGGTCACCACCTAGGAACTGAGAACAGGGATCAATCG
GGTGCAGAAAAGATACATCTATGACAATGTCGCTGAAGTGTGGAAGGATTATGATCGGGACAAAGACGATACGATTTCCT
GGAAAGAATACAAACAAGTCACCTATGGATACTATCTAGGAAACCCCGAAGAGTTTCATGATACTTCAGATCATCAAACC
TTCAAAAAGATGCTTCCACGTGACGAGAGAAGGTTCAAGGCTGCAGAGCTCAAAGGTGACCAGACGGCCACTCGGGAGGA
GTTCACAGCCTTTCTGCACCCTGAGGAGTTCGAGCATATGAAGGAAATCGTGGTTTTGGAAACTCTGGAGGACATCGACA
AGAACGGGGAGGGCTTCGTGGATGAGGATGACTATATT
ORF - retro_dnov_863 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.0 % |
| Parental protein coverage: | 90.65 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PTEKKDR-VHHEPQLSDKVHDDAQSFDYDHD-AFLGAEEAKTFDQLTPEESKERLGKIVSKIDGDKDGFV |
| P...K.R.V............D.QSF..D....FLG.E..KT.DQL.P.ESKERLG.IV..ID.D..G.V | |
| Retrocopy | PSVRKEREVALDS*FRNRTPEDNQSFQ*DQI>SFLGKEDFKTIDQLIPDESKERLGMIVNRIDSDGGGLV |
| Parental | TVDELKDWIKFAQKRWIYEDVERQWKGHDLNEDGLVSWEEYKNATYGYVLDDPD----PDDGFNYKQMMV |
| T..EL...I...QKR.IY..V...WK..D...D...SW.EYK..TYGY.L..P.......D....K.M.. | |
| Retrocopy | TT*ELRTGINRVQKRYIYDNVAEVWKDYDRDKDDTISWKEYKQVTYGYYLGNPEEFHDTSDHQTFKKMLP |
| Parental | RDERRFKMADKDGDLIATKEEFTAFLHPEEYDYMKDIVVQETMEDIDKNADGFIDLEEYI |
| RDERRFK.A...GD..AT.EEFTAFLHPEE...MK.IVV.ET.EDIDKN..GF.D...YI | |
| Retrocopy | RDERRFKAAELKGDQTATREEFTAFLHPEEFEHMKEIVVLETLEDIDKNGEGFVDEDDYI |
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 | 10 .89 RPM | 26 .84 RPM |
| SRP012922_cerebellum | 19 .66 RPM | 7 .84 RPM |
| SRP012922_heart | 6 .96 RPM | 9 .28 RPM |
| SRP012922_kidney | 4 .11 RPM | 8 .21 RPM |
| SRP012922_liver | 7 .43 RPM | 16 .56 RPM |
| SRP012922_lung | 20 .62 RPM | 25 .96 RPM |
| SRP012922_quadricep_muscle | 3 .63 RPM | 11 .25 RPM |
| SRP012922_spleen | 23 .69 RPM | 30 .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_863 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 | ENSDNOG00000010477 | 1 retrocopy |
retro_dnov_863 ,
|
| Pongo abelii | ENSPPYG00000017982 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000019668 | 1 retrocopy |