RetrogeneDB ID: | retro_cjac_1272 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 14:36800187..36800771(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000033350 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PTGES2 | ||
| Ensembl ID: | ENSCJAG00000019932 | ||
| Aliases: | None | ||
| Description: | prostaglandin E synthase 2 [Source:HGNC Symbol;Acc:17822] |
Retrocopy-Parental alignment summary:
>retro_cjac_1272
ATGGCCCCAGCTGCTCAGGTGGTGTGGGCGCTGTGGCCTGGCAGGTGCACCTTGGCCTGGAGGCTGGGCGGCCGCCCCCA
GCTGCTGCTCCCCACACAGAACCAGGCTGGCTTCACGGGGGTGGCGGGCGGCTCGGGTCCTGTGGCTGCCACCCATAAGG
GGAGCCCACGGCTGCTAGGGGCAGTGGCACTTGCCCTGGGGGGAACCCTGGGGCTGTACCACACAGCTCGGTGGCACCTG
CACACCCAGGACCTCCATGCAGAGCACTCAGCCACGCAGCTCTCCCTGTCCAGCCACCTGCAGCTGACCCTGTACCAATA
CAAGACGTGTCCCTTCTGCAGCAAGGTCCGAGCCTTCCTCGACTTCCATGCCCTGCCCTACCAGGTGGTGGAAGTCAATC
CTGTGCACAGGGCTGAGATCAAGTTCTCCTCCTACAGAAAGGTGCCCATCCTGGTGGCCCAGGTTGGAAAAAACAACAAC
TGAACAACTCCTCTGTCATCATCAGTGCCCTCAAGACGTACCTGGTTTCAGGGCAGCCCCTGGAAGAGATCATCACCTAC
TATCCAGCCATGAAGGCTGTGAAC
ORF - retro_cjac_1272 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.7 % |
| Parental protein coverage: | 51.99 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAPAARVARALWPGGCALAWRLSGRPQLLLPTQNRAGFAGSAGGPGPVAAALKGSPRLLGAAALALGGAL |
| MAPAA.V..ALWPG.C.LAWRL.GRPQLLLPTQN.AGF.G.AGG.GPVAA..KGSPRLLGA.ALALGG.L | |
| Retrocopy | MAPAAQVVWALWPGRCTLAWRLGGRPQLLLPTQNQAGFTGVAGGSGPVAATHKGSPRLLGAVALALGGTL |
| Parental | GLYHTARWHLRAQDLHAEHSAAQLSLSSHLQLTLYQYKTCPFCSKVRAFLDFHALPYQVVEVNPVRRAEI |
| GLYHTARWHL..QDLHAEH................QYKTCPFCSKVRAFLDFHALPYQVVEVNPV.RAEI | |
| Retrocopy | GLYHTARWHLHTQDLHAEHXXXXXXXXXXXXXXXXQYKTCPFCSKVRAFLDFHALPYQVVEVNPVHRAEI |
| Parental | KFSSYRKVPILVAQVGENS-QQLNDSSVIISALKTYLVSGQPLEEIITYYPAMKAVN |
| KFSSYRKVPILVAQVG.N..Q..N.S.VIISALKTYLVSGQPLEEIITYYPAMKAVN | |
| Retrocopy | KFSSYRKVPILVAQVGKNN<QLNNSS-VIISALKTYLVSGQPLEEIITYYPAMKAVN |
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 |
|---|---|---|
| SRP051959_colon | 0 .62 RPM | 14 .75 RPM |
| SRP051959_heart | 0 .23 RPM | 15 .35 RPM |
| SRP051959_kidney | 0 .42 RPM | 14 .64 RPM |
| SRP051959_liver | 0 .69 RPM | 11 .11 RPM |
| SRP051959_lung | 0 .81 RPM | 4 .52 RPM |
| SRP051959_lymph_node | 1 .51 RPM | 4 .82 RPM |
| SRP051959_skeletal_muscle | 0 .46 RPM | 31 .77 RPM |
| SRP051959_spleen | 0 .84 RPM | 5 .04 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1272 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1272 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1272 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000019932 | 1 retrocopy |
retro_cjac_1272 ,
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