RetrogeneDB ID: | retro_cpor_1474 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_9:38398655..38399161(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FBXO17 | ||
| Ensembl ID: | ENSCPOG00000000656 | ||
| Aliases: | None | ||
| Description: | F-box protein 17 [Source:HGNC Symbol;Acc:18754] |
Retrocopy-Parental alignment summary:
>retro_cpor_1474
CGGCCTCCAAGGGTGGGGCCGCCCGGGTTCCCACACCGCAGTCGCAGCCCTCAAAGGGGCTAGATCTGAGCCGGCTGCCG
CCGGAGCTCCTCCCGACTGTGCTGAGCCACGTGCCCCCGCGCGTGCGGCTCCGACGCTGCTGTCTCGTGTGCCGTAGCTG
GCGGGCCCTGGTGGATGGCCAGGCCCTGTGGCTGCTGATCTTGGCCCAGGACCACAGCGCCACCGGCCGCGCCCTGCTGT
CCCTCGTCCGCAGTTGCCTGCCCCCTGCCGGCGACACCAACCCCTGCCCTCTCGGCCGCTTCTGCGAGCGCAGACCCATT
GGAGGAAACCTCATCTGCAACCCCTGCGGACAGGAAGGCCTTCGGAAGTGGATGGTGTAGCATGGTGGAGATGGCTGGGT
GGTGGAGGAAAATATGACAACCGTGCCTGGGGCCTCTTCGCAGACCTGCTTTGTAGCCTCCTTCAGTTGGTGTCGGAAGA
AGCAGGTCTTGGATCTGGAGGAGGAG
ORF - retro_cpor_1474 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.45 % |
| Parental protein coverage: | 57.1 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RTPAVAMGGRPSR-QRQPVHPPATLDALPPELLVRVLSHVPPRALVTCCRPVCRAWRDVVDGPTVWLLQL |
| R.P.V...G.P.R.Q.QP......L..LPPELL..VLSHVPPR.....C..VCR.WR..VDG...WLL.L | |
| Retrocopy | RPPRVGPPGFPHR<QSQP-SKGLDLSRLPPELLPTVLSHVPPRVRLRRCCLVCRSWRALVDGQALWLLIL |
| Parental | ARDRSAEGRAIYALAQRCPPSSENEEELPLCALARFCVRAPLGRNLIFNSCGEQGFRGWEVEHGGNGWAV |
| A.D.SA.GRA...L...C.P..........C.L.RFC.R.P.G.NLI.N.CG..G.R.W.V.HGG.GW.V | |
| Retrocopy | AQDHSATGRALLSLVRSCLPPAGDTNP---CPLGRFCERRPIGGNLICNPCGQEGLRKWMV*HGGDGWVV |
| Parental | EKNITLVPGAPSQTCFVTSFEWCFKRQLVDLVME |
| E.N.T.VPGA.SQTCFV.SF.WC.K.Q..DL..E | |
| Retrocopy | EENMTTVPGASSQTCFVASFSWCRKKQVLDLEEE |
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 .86 RPM | 2 .47 RPM |
| SRP017611_kidney | 0 .84 RPM | 4 .50 RPM |
| SRP017611_liver | 0 .13 RPM | 0 .22 RPM |
| SRP040447_lung | 3 .28 RPM | 9 .56 RPM |
| SRP040447_skeletal_muscle | 0 .43 RPM | 3 .78 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1474 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1474 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 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000008717 | 1 retrocopy | |
| Cavia porcellus | ENSCPOG00000000656 | 1 retrocopy |
retro_cpor_1474 ,
|
| Cavia porcellus | ENSCPOG00000004611 | 1 retrocopy |