RetrogeneDB ID: | retro_dnov_1247 | ||
Retrocopylocation | Organism: | Armadillo (Dasypus novemcinctus) | |
| Coordinates: | scaffold_16886:44868..45377(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | PLSCR4 | ||
| Ensembl ID: | ENSDNOG00000002106 | ||
| Aliases: | None | ||
| Description: | phospholipid scramblase 4 [Source:HGNC Symbol;Acc:16497] |
Retrocopy-Parental alignment summary:
>retro_dnov_1247
TTGAGTCAGCCAACTGGTAGTGTTCTTCCTGTCCAGTATCAGCCTAGCGAATACCCTGTGCTAAATCAGTCTACTCCAAT
AATATGGATGCCAGGGCCAGCTCCTATGCTAAACTTCCTACCTGGTCTGAAATGCTTAGCTCAGTTGGACAACATACAAA
TTCCTCAGTGTTTTGAGCCTAAGGAAATGTCCACAGGCTTTGAAGCTAATAACAGATATGATGTTAAAAACAACTTAATC
CTGATGGTTTACATTGTAAATGATGATACAGATGATTTTATCAGAAATGCTTATAAGGCCTTAAGACTTTTTGTCCTCCA
TATTATTGACTGTACAGGCCAAGAAGTCATGACCACACAGAGGCCCTTCAGATGCACCTGCTGTTCCTTCTGTTGTCCCT
CAGCCAGGCAAGAGCTAGAGGTACAGTCTCTCCTGGCATAATCATTGACTTTGTGGGGGATCACTGGAACCTGCACAGGA
CAGTTTATAGCATCCAAAATGAGAAGAAA
TTGAGTCAGCCAACTGGTAGTGTTCTTCCTGTCCAGTATCAGCCTAGCGAATACCCTGTGCTAAATCAGTCTACTCCAAT
AATATGGATGCCAGGGCCAGCTCCTATGCTAAACTTCCTACCTGGTCTGAAATGCTTAGCTCAGTTGGACAACATACAAA
TTCCTCAGTGTTTTGAGCCTAAGGAAATGTCCACAGGCTTTGAAGCTAATAACAGATATGATGTTAAAAACAACTTAATC
CTGATGGTTTACATTGTAAATGATGATACAGATGATTTTATCAGAAATGCTTATAAGGCCTTAAGACTTTTTGTCCTCCA
TATTATTGACTGTACAGGCCAAGAAGTCATGACCACACAGAGGCCCTTCAGATGCACCTGCTGTTCCTTCTGTTGTCCCT
CAGCCAGGCAAGAGCTAGAGGTACAGTCTCTCCTGGCATAATCATTGACTTTGTGGGGGATCACTGGAACCTGCACAGGA
CAGTTTATAGCATCCAAAATGAGAAGAAA
ORF - retro_dnov_1247 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.59 % |
| Parental protein coverage: | 61.82 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LHQPASGVRPVQYQPGKYPMPNQPAPTMWMPGPAPMPNCPPGLECLTQLDNIHVLQHFEPLEMFTGFETN |
| L.QP...V.PVQYQP..YP..NQ..P..WMPGPAPM.N..PGL.CL.QLDNI...Q.FEP.EM.TGFE.N | |
| Retrocopy | LSQPTGSVLPVQYQPSEYPVLNQSTPIIWMPGPAPMLNFLPGLKCLAQLDNIQIPQCFEPKEMSTGFEAN |
| Parental | NRYDVKNNSNQMVYVVNEDTDDFTRNAYKTLRPFVLRVTDCLGREVITMQRPFRCTCCCFCCPSARQELE |
| NRYDVKNN...MVY.VN.DTDDF.RNAYK.LR.FVL...DC.G.EV.T.QRPFRCTCC.FCCPSARQELE | |
| Retrocopy | NRYDVKNNLILMVYIVNDDTDDFIRNAYKALRLFVLHIIDCTGQEVMTTQRPFRCTCCSFCCPSARQELE |
| Parental | VQ-CPPGVTIGFVAEHWNLCRAIYSIQNEKK |
| VQ...PG..I.FV..HWNL.R..YSIQNEKK | |
| Retrocopy | VQ<VSPGIIIDFVGDHWNLHRTVYSIQNEKK |
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 | 165 .49 RPM |
| SRP012922_cerebellum | 0 .00 RPM | 6 .32 RPM |
| SRP012922_heart | 0 .00 RPM | 10 .44 RPM |
| SRP012922_kidney | 0 .00 RPM | 10 .95 RPM |
| SRP012922_liver | 0 .00 RPM | 10 .99 RPM |
| SRP012922_lung | 0 .00 RPM | 67 .05 RPM |
| SRP012922_quadricep_muscle | 0 .00 RPM | 5 .88 RPM |
| SRP012922_spleen | 0 .00 RPM | 35 .48 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_1247 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 | ENSDNOG00000002106 | 1 retrocopy |
retro_dnov_1247 ,
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