RetrogeneDB ID: | retro_pabe_1456 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 17:43804034..43805403(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MAPK8IP1 | ||
| Ensembl ID: | ENSPPYG00000003328 | ||
| Aliases: | None | ||
| Description: | mitogen-activated protein kinase 8 interacting protein 1 [Source:HGNC Symbol;Acc:6882] |
Retrocopy-Parental alignment summary:
>retro_pabe_1456
TCTCAGGACACGCTGAATAATAATTCTTGCTGGGCAAAAAGCACAGTTGGCAGGATCGGGTGTCTCGATCACTTTCCTCA
CCTCTGAAGACCGGGGAGCAGACACCACCGCATGAACACATCTGCCTGAGCGATGAGCTGCCCCCCCAGAGCAGCCCCGC
CCCCACCACAGATCGAGGCACCTCCACCGACAGCCCTTGCCGCCGCAGCACAGCCACCCAGATGGCACCTCCGGGTGGTC
CCCCTGCTGCCCTGCCTGGGGGTCGGGGCCACTCGCATCGAGACCGAATCCACTACCAGGCCGATGTGCGACTGGAGGCC
ACTGAGGAGATCTACCTGACCCCAGTGCAGAGGCCCCCAAGACCCTGCAGAGCCCACCTCCGCCTTCCTGCCGCCCACAT
CGGAGCTGGATGTGGGTCAGCTCCGATCTAGACCCTGCCGCCTACCTCTCCACGGCAGGGCGGCCGCACCCCTCCATCAG
TGAAGAGGAGGAGGGCTTCGACTGCCTGTCGTCCCCAGAGCGGGCTGAGCCCCCAGGCGGAGGGTGGCGGGGGACCCTGG
GGGAGCCGCCGCCACCTCCACGGGCCTCTCTGAGCTCGGACACCAGCGCCCTGTCCTACAACTCTGCCAAGTACACGCTG
GTGGTAGACGAGCAGGCGCGGCTGGAGCTGGTGAGCCTGCGGCTGTGCTTCGGAGATTACAGTGACAAAAGTGACTCGGC
CACCGTCTACCACAACTGTGCTTACCGTCTCCTTGCCCTATGAGTCAGCCATCAGAGAGGAATATGAGGAAGCCCCCCTG
CCCCAGCCTCCTGCCTGCCTCTCCGAGGACTCCACGCTTGACGAACCCGAGGTCCATTTCTCCATGAAGTTCCTGAACGT
CTTCATGAGTGGCCGCTCCCGCTCCTCTAGTGCCTAGTCCTTCGGGCTGTTCTCCTGCATCATCCAACGGGGGAGGAGCA
GGAGCAGACCCATCCGGGCCATATTTCAGGTTTTGTGCCTCGACACGAAGACGAACCTTGAGCTGGAAGTGGATGACCCT
CTGCTAGTGGAGCTCCAGGCTGATGACTACTGCTACGAGGCCTACAACATGCGCACTGATGCCCAGGGCGTCTTTCCTGC
CTATTATGCCATCGAGGTCACCAAGGACCCTGAGCACATGGCAGCCCTGGCCAAAAACAGTGACTGGGTGGACCAGTTCC
GGGTGAAGTTCCTGGGCTCAGTCTGGGTTCTCTATCACAAGGGCCATCACGTCTTCTGGTGCCGCTATGCAAAAGATTGC
CACCACCCACCGGCTCACCGTGCACTTTAACCCCGCCCTCCAGCTGTGTCCTGGAGATCAGCGCGCAGGGTGTGAAGATA
GGTGTCAAA
ORF - retro_pabe_1456 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.12 % |
| Parental protein coverage: | 83.67 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 9 |
Retrocopy - Parental Gene Alignment:
| Parental | AQDTL-NNNS-LGKKHSWQDRVSRS-SSPLKTGEQTPPHEHICLSDELPPQSSPAPTTDRGTSTDSPCRR |
| .QDTL.NN...LGKKHSWQDRVSRS.SSPLKTGEQTPPHEHICLSDELPPQSSPAPTTDRGTSTDSPCRR | |
| Retrocopy | SQDTLNNNSC<LGKKHSWQDRVSRSLSSPLKTGEQTPPHEHICLSDELPPQSSPAPTTDRGTSTDSPCRR |
| Parental | STATQMAPPGGPPAAPPGGRGHSHRDRIHYQADVRLEATEEIYLTPVQRPP-DPAEPTSAFLPPTE-SRM |
| STATQMAPPGGPPAA.PGGRGHSHRDRIHYQADVRLEATEEIYLTPVQRPP.DPAEPTSAFLPPT..S.M | |
| Retrocopy | STATQMAPPGGPPAALPGGRGHSHRDRIHYQADVRLEATEEIYLTPVQRPP>DPAEPTSAFLPPTS>SWM |
| Parental | SVSSDPDPAAYPSTAGRPHPSISEEEEGFDCLSSPERAEPPGGGWRGSLGEPPPPPRASLSSDTSALSYD |
| .VSSD.DPAAY.STAGRPHPSISEEEEGFDCLSSPERAEPPGGGWRG.LGEPPPPPRASLSSDTSALSY. | |
| Retrocopy | WVSSDLDPAAYLSTAGRPHPSISEEEEGFDCLSSPERAEPPGGGWRGTLGEPPPPPRASLSSDTSALSYN |
| Parental | SVKYTLVVDEHAQLELVSLRPCFGDYSDESDSATVYDNCA-SVSSPYESAIGEEYEEAPRPQPPACLSED |
| S.KYTLVVDE.A.LELVSLR.CFGDYSD.SDSATVY.NCA..VS.PYESAI.EEYEEAP.PQPPACLSED | |
| Retrocopy | SAKYTLVVDEQARLELVSLRLCFGDYSDKSDSATVYHNCA>TVSLPYESAIREEYEEAPLPQPPACLSED |
| Parental | STPDEPDVHFSKKFLNVFMSGRSRSSSAESFGLFSCII-NG-EEQEQTHRA-IFRFVPRHEDE-LELEVD |
| ST.DEP.VHFS.KFLNVFMSGRSRSSSA.SFGLFSCII.NG.EEQEQTH...I..FVPRHEDE.LELEVD | |
| Retrocopy | STLDEPEVHFSMKFLNVFMSGRSRSSSA*SFGLFSCII>NG>EEQEQTHPGHISGFVPRHEDE>LELEVD |
| Parental | DPLLVELQAEDYWYEAYNMRTGARGVFPAYYAIEVTKEPEHMAALAKNSDWVDQFRVKFLGSVQVPYHKG |
| DPLLVELQA.DY.YEAYNMRT.A.GVFPAYYAIEVTK.PEHMAALAKNSDWVDQFRVKFLGSV.V.YHKG | |
| Retrocopy | DPLLVELQADDYCYEAYNMRTDAQGVFPAYYAIEVTKDPEHMAALAKNSDWVDQFRVKFLGSVWVLYHKG |
| Parental | NDVLC-AAMQKIATTRRLTVHFN-PPSSCVLEISVRGVKIGVK |
| ..V...AAMQKIATT.RLTVHFN.PPSSCVLEIS..GVKIGVK | |
| Retrocopy | HHVFW>AAMQKIATTHRLTVHFN>PPSSCVLEISAQGVKIGVK |
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 | 1 .38 RPM | 176 .93 RPM |
| SRP007412_cerebellum | 0 .24 RPM | 80 .74 RPM |
| SRP007412_heart | 0 .03 RPM | 4 .76 RPM |
| SRP007412_kidney | 0 .33 RPM | 31 .95 RPM |
| SRP007412_liver | 0 .03 RPM | 4 .96 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1456 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1456 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_1456 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Pongo abelii | ENSPPYG00000003328 | 1 retrocopy |
retro_pabe_1456 ,
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