RetrogeneDB ID: | retro_pabe_1571 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 18:72714268..72715702(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NFE2L3 | ||
| Ensembl ID: | ENSPPYG00000017716 | ||
| Aliases: | None | ||
| Description: | nuclear factor (erythroid-derived 2)-like 3 [Source:HGNC Symbol;Acc:7783] |
Retrocopy-Parental alignment summary:
>retro_pabe_1571
TCCGTGCTCCGGGAAGAGCTGCTGTTCCTGGGCGGCCCGGCCAACTCCGCCTGCGCGCTGAGCCCCTTCTCGGCCTCGGG
AGGGTGGGGGCGCACGGGCCAGTTGCACCCCAAGGGCCGGGAGCTGGACCCTGCCGCGCCGCCCCAGGGCCAGCTGCTCC
GGGAGGTGCGCGCGCTAGGGGTCCCCTTCATCCCTTGCACCCAGGTGGATGCGTGGCTGGTGCACAGCGTGGCTGCCGGG
AGCGCGTACGAGGCCCACGGGCTGCTCGGCGCCGCCGCCGCCTCGTCCACCGGAGGAGCCGGCGCCAGCGTGGACGGCGG
CAGCCAGGCTGTGTAGGGGGGCGACGGGGACCCCCGAGCGGCTCGGAGTGGTCCCTTGGACGCCAGGGAAGAGGAGAAGG
CACCCGCGGAACCGACGGCTCGAGTGCCCGACGCTGGCGGGTGTGCGAGCGAGGAGAACAAGGTACTAACAGAAAAGCAC
GAAGCTGTGGATCATAGTTCCCAGGGTGAGGAAAATGAAGAAAGGGTGTCAGCCTAGAAGGAGAACTCACTTCAGCAGAA
TAATGATGATGAAAACAAAATAGCAGAGAAACCTGATTGGGAGGCAGAAGAGATCACTGAATCTAGAAATGAGAGACATC
TGAATGGGACAGATACTTCTTTCTCTCTGGAAGACTTATTCCAGTTGCTTTCATCACAGCCTGAGAATTCACTGGAGGGC
ATCTCATTGGGAGATATTCCTCTTCCAGGCAGTATCAGTGATGGCATGAATTCTTCAGCACATTCTCATGTAAACTTCAG
CCAGGCTATAAGTCAGGATGTGAATCTTCATGAGGCCATCTTGCTTTGTCCCAACAATACATTTAGAAGAGATCCAATAG
CAAGGACTTCACAGTCACAAGAACCATTTCTGCAGTTAAATTCTCATACCACCAATCCTGAGCAAACCCTTCCTGGAACT
AATTTGACAGGATTTCTTTCACTGGTTGACAATCATATGAGGAATCTAACAAGTCAAGACCTACTGTATGACCTTGACGT
AAATATATTTGATGAGATAAGCTTAATGTCATTGGCCGCAGAAGACGACTTTGATCCAATCGATGTTTCTCAGCTTTTTG
ATGAACCAGATTCTGATTCTGGCCTTTCTTTAGATTCAAGTCACAATAGTACCTCTGTCATCAAGTCTAATTCCTCTCAC
TCTGTGTGTGATGAAGGTGCTATAGGTTATTGTACTGACCATGAATCTAGTTCCCATCATGACTTAGAAGGTGCTGTAGG
CGGCTACTACCCAGAACCCAGTAAGCTTTGTCACTTGAATCAGAGTGATTCTGGTTTCCATGGGGATCTTACATTTCAAC
ACATATTTCATAACCACACTTACCACTTACAGCCAAGTGCACCAGAATCTACTTCTGAACCTTTTTCGTGGCCT
ORF - retro_pabe_1571 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.21 % |
| Parental protein coverage: | 68.88 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | TLLQDELLFLGGPASSAYALSPFSASGGWGRTGHLHPKGRELDPAAPPEGQLLREVRALGVPFVPRTRVD |
| ..L..ELLFLGGPA.SA.ALSPFSASGGWGRTG.LHPKGRELDPAAPP.GQLLREVRALGVPF.P.T.VD | |
| Retrocopy | SVLREELLFLGGPANSACALSPFSASGGWGRTGQLHPKGRELDPAAPPQGQLLREVRALGVPFIPCTQVD |
| Parental | AWLVHSVAAGSADEAHGPLGAATASSTGGAGASVDGGSQAVQGGGGDPRAARSGPLDAGEEEKAPAEPTA |
| AWLVHSVAAGSA.EAHG.LGAA.ASSTGGAGASVDGGSQAV.GG.GDPRAARSGPLDA.EEEKAPAEPTA | |
| Retrocopy | AWLVHSVAAGSAYEAHGLLGAAAASSTGGAGASVDGGSQAV*GGDGDPRAARSGPLDAREEEKAPAEPTA |
| Parental | QVPDPGGCASEENEVLREKHEGVDHSSQHEENEERVSAQKENSFPQNNDDGNKIAEKPDWEAEKTTESRN |
| .VPD.GGCASEEN.VL.EKHE.VDHSSQ.EENEERVSA.KENS..QNNDD.NKIAEKPDWEAE..TESRN | |
| Retrocopy | RVPDAGGCASEENKVLTEKHEAVDHSSQGEENEERVSA*KENSLQQNNDDENKIAEKPDWEAEEITESRN |
| Parental | ERHLNGTDTSFSLEDLFQLLSSQPENSLEGISLGDIPLPGSISDGMNSSAHYHVNFSQAISQDVNLHEAI |
| ERHLNGTDTSFSLEDLFQLLSSQPENSLEGISLGDIPLPGSISDGMNSSAH.HVNFSQAISQDVNLHEAI | |
| Retrocopy | ERHLNGTDTSFSLEDLFQLLSSQPENSLEGISLGDIPLPGSISDGMNSSAHSHVNFSQAISQDVNLHEAI |
| Parental | LLCPNNTFRRDPIARTSQSQEPFLQLNSHTTNPEQTLPGTNLTGFLSPVDNHTRNLTSQDLLYDLDINIF |
| LLCPNNTFRRDPIARTSQSQEPFLQLNSHTTNPEQTLPGTNLTGFLS.VDNH.RNLTSQDLLYDLD.NIF | |
| Retrocopy | LLCPNNTFRRDPIARTSQSQEPFLQLNSHTTNPEQTLPGTNLTGFLSLVDNHMRNLTSQDLLYDLDVNIF |
| Parental | DEINLMSLATEDNFDPIDVSQLFDEPDTDSGLSLDSSHNSTSVIKSNSSHSVCDEGAIGYCTDHESSSHH |
| DEI.LMSLA.ED.FDPIDVSQLFDEPD.DSGLSLDSSHNSTSVIKSNSSHSVCDEGAIGYCTDHESSSHH | |
| Retrocopy | DEISLMSLAAEDDFDPIDVSQLFDEPDSDSGLSLDSSHNSTSVIKSNSSHSVCDEGAIGYCTDHESSSHH |
| Parental | DLEGAVGGYYPEPSKLCHLDQSDSGYHGDLTFQHIFHNHTYHLQPSVPESTSEPYLWP |
| DLEGAVGGYYPEPSKLCHL.QSDSG.HGDLTFQHIFHNHTYHLQPS.PESTSEP..WP | |
| Retrocopy | DLEGAVGGYYPEPSKLCHLNQSDSGFHGDLTFQHIFHNHTYHLQPSAPESTSEPFSWP |
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 |
|---|---|---|
| SRP007412_brain_prefrontal_cortex | 0 .00 RPM | 1 .05 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 7 .42 RPM |
| SRP007412_heart | 0 .00 RPM | 1 .26 RPM |
| SRP007412_kidney | 0 .00 RPM | 4 .87 RPM |
| SRP007412_liver | 0 .00 RPM | 1 .10 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1571 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1571 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_1571 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000050344 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000017716 | 1 retrocopy |
retro_pabe_1571 ,
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