RetrogeneDB ID: | retro_cjac_4074 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:65290089..65290406(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000012116 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_4074
AAACTCACGTACACACCAGTTTTTAATGAATACCTTTCTTTGGTAGAAAAATATATTGAAGAACAGCTGCTGGAGCATGA
GTCCCAAATTCAACATGGTGGCCTTCACAATGATATTGAAGCACCATAAAGAAGGAGTAGCTTGTGACATATTCAACATG
CTGCTCACATTGATGGACTTTCTGGCATTTAAAGGGATGTTTCTAGACTACAGTGCAGAAAAAAGAACGCTGTGGATGAG
ATTTAAGCAGTGGTTTAGTGGTGACTTTGTTGTGTAAAACATCTTCCATGCCAGCTATCCAGAAAAATCTGCGGCAC
ORF - retro_cjac_4074 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.96 % |
| Parental protein coverage: | 64.81 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | KLTYTPIFNEYISLVEKYVEEQLLER-IPGFNMAAFTVTLQHHRDEVAGDIFDMLLTFTDFLAFKEMFLD |
| KLTYTP.FNEY.SLVEKY.EEQLLE...P.FNM.AFT..L.HH...VA.DIF.MLLT..DFLAFK.MFLD | |
| Retrocopy | KLTYTPVFNEYLSLVEKYIEEQLLEH>SPKFNMVAFTMILKHHKEGVACDIFNMLLTLMDFLAFKGMFLD |
| Parental | YRAE-KEGRGLDLSSGLVVTSLCKSSSVPASPNNLRH |
| Y.AE.KE..G.DLSSGLVVT.LCK.SS.PA...NLRH | |
| Retrocopy | YSAE>KERCG*DLSSGLVVTLLCKTSSMPAIQKNLRH |
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 |
|---|---|---|
| SRP051959_colon | 0 .00 RPM | 5 .59 RPM |
| SRP051959_heart | 0 .00 RPM | 8 .37 RPM |
| SRP051959_kidney | 0 .00 RPM | 8 .39 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .86 RPM |
| SRP051959_lung | 0 .00 RPM | 11 .22 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 6 .89 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 4 .45 RPM |
| SRP051959_spleen | 0 .00 RPM | 5 .86 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4074 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4074 was not experimentally validated.