RetrogeneDB ID: | retro_cpor_1512 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_91:5993256..5993686(+) | ||
| Located in intron of: | ENSCPOG00000019606 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCPOG00000013134 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1512
ATGGCAGAATGCTGTTACAGTTTTTGCTCACAACCTGCAGCCCATCTGGTAGGCTTGTCTAGCCTGAATATACATTGACT
GCTTTAGCTGGAGGAGCCCCTTCAGTGGGAATTAAAGCTGCAAATGGTGTAGTGTCGGCAACTGAGAAGGAACAGAGACT
TACTTTGTATGATAAGCAAAGGGCACGCAAAGTAGAGCCAATTAGCAAGCACACAGATTTGGTGTGCAGTGGCATGGGCC
CCGATCACAGGGTGCCTGTGCTCAAAGCTGAGAAACTCGCTGGGCAGCACTACCTTGTTCAACAGGAGCCACCCCTTCAG
CCCAGCAAGAACAGAGAGCAGCTTCCGCGATGCAGGAGCACACCCAGTCAGGTGGTGTCCCTCCAAGTGTGATGGAATGA
GAGGTGAGGATATTTGTTTCAGGCAGACCC
ORF - retro_cpor_1512 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.01 % |
| Parental protein coverage: | 61.54 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MAERGYSFS-LTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDERSVHKVEPIT |
| MAE..YSF..LTT.SPSG.LV..EY.L.A.AGGAPSVGIKAANGVV.ATEK.Q...LYD.....KVEPI. | |
| Retrocopy | MAECCYSFC<LTTCSPSGRLV*PEYTLTALAGGAPSVGIKAANGVVSATEKEQRLTLYDKQRARKVEPIS |
| Parental | KHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEP-IPTAQLVQRVASVMQEYTQSGGVRPFGVSLLICG |
| KH..LV.SGMGPD.RV.V..A.KLA.Q.YLV.QEP..P.AQ..QR.AS.MQE.TQSGGV.P......... | |
| Retrocopy | KHTDLVCSGMGPDHRVPVLKAEKLAGQHYLVQQEP<TPSAQQEQRAASAMQEHTQSGGVPPSVME*EVRI |
| Parental | WNEGRP |
| ...GRP | |
| Retrocopy | FVSGRP |
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 | 27 .55 RPM |
| SRP017611_kidney | 0 .00 RPM | 61 .97 RPM |
| SRP017611_liver | 0 .00 RPM | 68 .03 RPM |
| SRP040447_lung | 0 .03 RPM | 57 .78 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 61 .98 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1512 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1512 was not experimentally validated.