RetrogeneDB ID: | retro_cpor_1274 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_62:1191620..1192394(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ABI1 | ||
| Ensembl ID: | ENSCPOG00000014424 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1274
AAGCATGGAAATAACCAGCCTGCAAGAACTGGCACACTGTCGAGAACAAATCCTCCTACTCAGAAACCACCAAGTCAGAA
ACCACCTCCCATGTCAGGCCGGGGAGCATTGGGGCGAAATACTCCTTACAAAATCCTGGAGCCTGTTAAACTCCCAATAG
TCCCTAATGATTACATGACCAGTCCTGCAAGACTTGGAGGTCAGCATAGTCCAGGCAGGAGAGCTTCTTTAAATCAGAGA
CCAAGGACACACAGTGGAAGCAGTGGAGGAGAAGGAGCCGAGAGGACAGTGGGAGCAGTAGTATTGGCATTCCCACTGCT
GTACCTAAGCCTTCCCCATCCACTACTGATCAGCTGCCCCGGGCTCGGCTCCTGGTTCCCAGTACGGCACAATGACCAGG
CAGATTTCTCAATACAACTCTACCACTTCCTCGACATCTTCTGGAGGATACAGACAAACTCCCTCTGTGACTGCTCAGTT
TTCTGCTCAGCCTCATGTTAATGGAGGTCCACTTTACGCCCAAAATTCAATTTCTATTGCTCGCTCCTTCCCCCGATGCC
TCAATTGACTCCACAGATACCTCGCACAGGCTTCGTGGCCAGGGTGCAGAAAAATATTGCTGACAGCCCAACTCCACCGT
CACCACCTCCACCAGATGACATTCCCGTATTTGCTGACTCTCCACCTCCCCCGCCTCCTCCCCCAGTGGACTGTGAAGAT
GAGGGAGCTGCAGTAGTCCAGGATAATGACCCATATGCAGATGGGAATCCTGCC
ORF - retro_cpor_1274 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.26 % |
| Parental protein coverage: | 53.22 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | KHGNNQPARTGTLSRTNPPTQKPPS---PPMSGRGTLGRNTPYKTLEPVKPPTVPNDYMTSPARLGSQHS |
| KHGNNQPARTGTLSRTNPPTQKPPS...PPMSGRG.LGRNTPYK.LEPVK.P.VPNDYMTSPARLG.QHS | |
| Retrocopy | KHGNNQPARTGTLSRTNPPTQKPPSQKPPPMSGRGALGRNTPYKILEPVKLPIVPNDYMTSPARLGGQHS |
| Parental | PGRTASLNQRPRTHSGSSGGSG-SRENSGSSSIGIPIAVPTPSPPTIA-PAAPGSAPGSQYGTMTRQISR |
| PGR.ASLNQRPRTHSGSSGG.G.SRE.SGSSSIGIP.AVP.PSP.T....AAPGSAPGSQYGTMTRQIS. | |
| Retrocopy | PGRRASLNQRPRTHSGSSGGEG<SREDSGSSSIGIPTAVPKPSPSTTD<SAAPGSAPGSQYGTMTRQISQ |
| Parental | HNSTTSSTSSGGYRRTPSVTAQFSAQPHVNGGPLYSQNSISIAPPPP-PMPQLTPQIPLTGFVARVQENI |
| .NSTTSSTSSGGYR.TPSVTAQFSAQPHVNGGPLY.QNSISIA...P.PMPQLTPQIP.TGFVARVQ.NI | |
| Retrocopy | YNSTTSSTSSGGYRQTPSVTAQFSAQPHVNGGPLYAQNSISIARSFP<PMPQLTPQIPRTGFVARVQKNI |
| Parental | ADSPTPPPPPPPDDIPIFDDSPPPPPPPPVDYEDEEAAVVQYNDPYADGDPA |
| ADSPTPP.PPPPDDIP.F.DSPPPPPPPPVD.EDE.AAVVQ.NDPYADG.PA | |
| Retrocopy | ADSPTPPSPPPPDDIPVFADSPPPPPPPPVDCEDEGAAVVQDNDPYADGNPA |
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 .17 RPM | 35 .49 RPM |
| SRP017611_kidney | 0 .10 RPM | 30 .25 RPM |
| SRP017611_liver | 0 .00 RPM | 23 .85 RPM |
| SRP040447_lung | 0 .08 RPM | 47 .16 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 8 .59 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1274 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1274 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 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000014424 | 3 retrocopies |
retro_cpor_1274 , retro_cpor_1375, retro_cpor_1451,
|