RetrogeneDB ID: | retro_cpor_294 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_12:10073204..10073545(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C14ORF1 | ||
| Ensembl ID: | ENSCPOG00000005620 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_294
GGGAACATGTTCCCCAGCTTCTGAGACCTGTCCTTTCTCAATGCAAAGGATCACACGGCAAGCCAAAGCTTGTGAATGGC
CTCTGCACTCTGACCCTTGGCATGTGGACCCTGCTCTTGCGAGTGATGCGCTGCCCCACATTATTGACATCTATAACACA
ACTGCACATGACGCTCTGGACCGTCCTTGCCCTGGGACACTTCCTCTTTGAGATGCCTGCACTGGGAACTGCGGCTCCCC
TGCCTGGTAACCTAGCACCTCTGCTGGTGGCACATTTCTCCATCCTCTGTTTGCTAGTTGTATTCTGTTAACTAGAGGTA
GAACCAGAATCCACATGGAAG
ORF - retro_cpor_294 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.93 % |
| Parental protein coverage: | 83.57 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GNTLQSFRDHSFLYEKLYT-GKPNLVNGLQARTFGIWTLLSSVIRCLCAIDIHNKTLYHITLWTFFLALG |
| GN...SF.D.SFL..K..T.GKP.LVNGL...T.G.WTLL..V.R..C.......T..H.TLWT..LALG | |
| Retrocopy | GNMFPSF*DLSFLNAKDHT<GKPKLVNGLCTLTLGMWTLLLRVMR--CPTLLTSITQLHMTLWTV-LALG |
| Parental | HFLSELLVFGTAAPTIGVLAPLMVASFSILGMLVGLRYLEVEPVSRQK |
| HFL.E....GTAAP..G.LAPL.VA.FSIL..LV....LEVEP.S..K | |
| Retrocopy | HFLFEMPALGTAAPLPGNLAPLLVAHFSILCLLVVFC*LEVEPESTWK |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 11 .33 RPM |
| SRP017611_kidney | 0 .00 RPM | 28 .16 RPM |
| SRP017611_liver | 0 .00 RPM | 17 .54 RPM |
| SRP040447_lung | 0 .05 RPM | 30 .74 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 2 .02 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_294 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_294 was not experimentally validated.
Retrocopy orthology:
Cavia porcellus 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 | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000005620 | 1 retrocopy |
retro_cpor_294 ,
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