RetrogeneDB ID: | retro_sscr_86 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | JH118515.1:66149..66662(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSSCG00000028206 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSSSCG00000022362 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_sscr_86
ATGGGAAATGAGCCCAGTAACCCAATGGAGATGTGCTCCCAGTTTGACCAAAACGAAATTAAACAGCTGAGCAAGCGGTT
TAAGAAGGTGGACTTGGACAGTTCGGGCACTCTGACTATGAAGGAGCTCATGTCCCTGCCGGGGCTGCAGGTGAACCCGT
TGGTGCAGCGAGTGTTCGACATTTTCGACACAGACGGCAACGGAGAAGTGGACTTCAAGGAATTCCTCGTGGGGACCTCC
CAGTTCAGTGTCAAGGGCGACAAGGAGCAGAAGCTGAGGTTTGCTTTCAGCATCTATGACATGGACAAAGACGGCTACAT
TTCCAACGGGGAGCTCTTCCAGGTGCTAAACATGATGGTGGGAGACAACCTGAAAGACTGGCAGTTACAGCAGCTGGTGG
ACAAAACCATCATCGCCCTGGACAAGGATGGAGATGGGAAAATATCCTTCCACGAATTCTGCGCTGTGGCCAGAAACCTG
AAGGTCCACGAGAAATTGGGGGTAATTGTGTGA
ORF - retro_sscr_86 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.5 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVDFKEFIEGVS |
| MCS.FD..EIK.L.KRFKK.DLD.SG.L...E.MSLP.LQ.NPLVQRV.DIFDTDGNGEVDFKEF..G.S | |
| Retrocopy | MCSQFDQNEIKQLSKRFKKVDLDSSGTLTMKELMSLPGLQVNPLVQRVFDIFDTDGNGEVDFKEFLVGTS |
| Parental | QFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISF |
| QFSVKGDKEQKLRFAF.IYDMDKDGYISNGELFQVL.MMVG.NLKD.QLQQ.VDKTII..DKDGDG.ISF | |
| Retrocopy | QFSVKGDKEQKLRFAFSIYDMDKDGYISNGELFQVLNMMVGDNLKDWQLQQLVDKTIIALDKDGDGKISF |
| Parental | EEFCAVVGGLDIHKKMVVDV |
| .EFCAV...L..H.K..V.V | |
| Retrocopy | HEFCAVARNLKVHEKLGVIV |
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 |
|---|---|---|
| SRP014902_placenta | 0 .00 RPM | 2 .12 RPM |
| SRP014902_testis | 0 .00 RPM | 7 .36 RPM |
| SRP018288_heart | 0 .00 RPM | 11 .81 RPM |
| SRP018288_kidney | 0 .00 RPM | 12 .02 RPM |
| SRP018288_liver | 0 .00 RPM | 12 .31 RPM |
| SRP018288_lung | 0 .00 RPM | 16 .70 RPM |
| SRP018856_adipose | 0 .00 RPM | 6 .11 RPM |
| SRP035408_brain | 0 .00 RPM | 54 .63 RPM |
| SRP035408_liver | 0 .00 RPM | 14 .33 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_86 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_86 was not experimentally validated.