RetrogeneDB ID: | retro_cpor_424 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_15:27624670..27625115(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CNBP | ||
| Ensembl ID: | ENSCPOG00000012816 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_424
GGTTCTGTAATGAGAAGCTGTGGTGAGGTGCTTTTACCTCACAGAGAGGCTTCCAGCTTGCTTCCTGCCTTTCAGATATC
TGTTAACACCCTGGGCACTCTGGTCATTTTGCCAAGGATTGTGATCTTCAGGACGATGACCACCATTGCTGCAGTAGAGG
TGGCCACATCACCAGGACAACAAGGAGCATGAAAGAGCTAGATCAGGGCTGCTACAACTGTGAGAGATCAGGCCACCTGG
AGGTGACTGTGATCATGTGTATGAGCCGAAGCATGGTTCTTGTAGGGACTTTGCACACATTAGAAAGAATGCACCAAAGT
GAAGTGCTCTTGTACTGGTGAGATTTGTCCATAGCCATCAACTTCAGCAGACAAATGAAGTCAACTGGTATTGCGGTGGC
AGATCAGGGCATCTTGCATGGGAATGCACAACTGAGGCCACAGCC
ORF - retro_cpor_424 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.05 % |
| Parental protein coverage: | 85.88 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 5 |
Retrocopy - Parental Gene Alignment:
| Parental | GRGMRSRGR-GGFTSDRGFQFVSSSLPDICYRCGESGHLAKDCDLQEDACYNCGRGGHIAKDCKEPKRER |
| G..MRS.G..G.FTS.RGFQ...S.L.DIC...G.SGH.AKDCDLQ.D....C.RGGHI.......K.E. | |
| Retrocopy | GSVMRSCGE<GAFTSQRGFQ-LASCLSDIC*HPGHSGHFAKDCDLQDDDHHCCSRGGHITRTTRSMK-EL |
| Parental | EQCCYNCGKPGHL-ARDCDHADEQKCYSCGEFGHIQ-KDCTKVKCYRCGETG-HVAINCSK-TSEVNCYR |
| .Q.CYNC...GHL...DCDH..E.K..SC..F.HI..K.CTKVKC...GE.....AIN.S..T.EVN.Y. | |
| Retrocopy | DQGCYNCERSGHL<GGDCDHVYEPKHGSCRDFAHIR<KECTKVKCSCTGEIC<SIAINFSR<TNEVNWYC |
| Parental | CGESGHLARECTIEATA |
| .G.SGHLA.ECT.EATA | |
| Retrocopy | GGRSGHLAWECTTEATA |
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 | 56 .71 RPM |
| SRP017611_kidney | 0 .00 RPM | 135 .05 RPM |
| SRP017611_liver | 0 .00 RPM | 93 .32 RPM |
| SRP040447_lung | 0 .00 RPM | 137 .73 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 234 .44 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_424 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_424 was not experimentally validated.