RetrogeneDB ID: | retro_dnov_1158 | ||
Retrocopy location | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_156351:4188..4702(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PDZK1 | ||
| Ensembl ID: | ENSDNOG00000000375 | ||
| Aliases: | None | ||
| Description: | PDZ domain containing 1 [Source:HGNC Symbol;Acc:8821] |
Retrocopy-Parental alignment summary:
>retro_dnov_1158
GAAAAGCCCTTAAAAAAACAGGTTGACTTGAAGGAGTTGGGTCAGAGTCAGAAGGTGCCAGGGTTTGAGTGATGAGGAAT
TGCTCCCAGTGATGACCGGTGGAGTGGACACTTGGCCCCAGCCTCAGCTGTGCTCCTGGTGAAGGAGGCGAATAGCAAGG
GCTTCTCTGGAAACTGTCCATGGTGAGAAAGGGAGTGCACACGGCTGGTAGAATGCCTCACGGTGGGCTCCGAAAGCTGG
TCTCCTGGCTGATGATCACTTGACTGGTGTGAATGGAGAGAACGTAGAAAATGCCAGCCATGAGGAAGTGATTGAAAAGG
CAAAGAAGTCAGGAAGCCACGCCACATTTCTGCTGGTGGATAAGGAAACAGATAAGTGCCACAGTGAGCAGAAGATAAAA
TTCAGGAGGGAAACAGCCAGTTTGAAGCTGCTACCCTCAAAGCCCCAGGTTGTAGAGCTTAAGAAGGGAAGCAATGGCTG
TGGGTTCTACCTGAGGGCAGCCCCAGACCAGAAA
ORF - retro_dnov_1158 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.86 % |
| Parental protein coverage: | 65.4 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | EKAIKNQVDLKELGQSQKVP-GLSDEELPPVMNGGVETWTQPRLC-YLVKEGNSYGFS-LKTVHGKKGVY |
| EK..K.QVDLKELGQSQKVP.GLSDEEL.PVM.GGV.TW.QP.LC..LVKE.NS.GFS..K.....KGV. | |
| Retrocopy | EKPLKKQVDLKELGQSQKVP>GLSDEELLPVMTGGVDTWPQPQLC<LLVKEANSKGFS<WKLSMVRKGVH |
| Parental | MTDILPQG-VAMKAGILADDHLIEVNGENVEDASHEEVVEKVKKSGSHVMFLLVDKETDKHHSEQKIKFK |
| .....P.G..A.KAG.LADDHL..VNGENVE.ASHEEV.EK.KKSGSH..FLLVDKETDK.HSEQKIKF. | |
| Retrocopy | TAGRMPHG<WAPKAGLLADDHLTGVNGENVENASHEEVIEKAKKSGSHATFLLVDKETDKCHSEQKIKFR |
| Parental | RETASLKLLPHKPRVVEIQKGSNGYGFYLRAGPDQK |
| RETASLKLLP.KP.VVE..KGSNG.GFYLRA.PDQK | |
| Retrocopy | RETASLKLLPSKPQVVELKKGSNGCGFYLRAAPDQK |
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 .19 RPM | 8 .36 RPM |
| SRP012922_cerebellum | 0 .14 RPM | 1 .65 RPM |
| SRP012922_heart | 0 .00 RPM | 0 .23 RPM |
| SRP012922_kidney | 0 .00 RPM | 282 .01 RPM |
| SRP012922_liver | 0 .00 RPM | 25 .85 RPM |
| SRP012922_lung | 0 .00 RPM | 1 .22 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 0 .17 RPM |
| SRP012922_spleen | 0 .00 RPM | 0 .80 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_1158 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 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000011153 | 1 retrocopy | |
| Dasypus novemcinctus | ENSDNOG00000000375 | 2 retrocopies |
retro_dnov_1158 , retro_dnov_1857,
|
| Myotis lucifugus | ENSMLUG00000028785 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000024935 | 1 retrocopy |