RetrogeneDB ID: | retro_cjac_4092 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:76875757..76876059(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FCF1 | ||
| Ensembl ID: | ENSCJAG00000020518 | ||
| Aliases: | None | ||
| Description: | FCF1 rRNA-processing protein [Source:HGNC Symbol;Acc:20220] |
Retrocopy-Parental alignment summary:
>retro_cjac_4092
CTGTATACCAAGTGTATTCCTAAATAAATAACTTTGTAATGGCTGAAATTGAGACTTTTAGGCAGAAATAGCTCGTGGCT
CTAAGGATCACCAAGTATTGAAGATTTGAATACTTAGCATGCACACACTGAATCACTTTTGAAGATGACTGCTTAGCACA
GAGAGTAATTCAGCACAAGTTTTACATTGTGGTCACAGTTGATCAGGACCTAAAATGAATCTGGAAGATCCCTGGAGCTC
ATATAATGTACATTTCTAACTATAGATACAACATTGAATGGATGCCAGATAATTATGGAGCC
ORF - retro_cjac_4092 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.96 % |
| Parental protein coverage: | 51.52 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LYAKCIPC-ITDCVMAEIEKLGQKYRVALRIAKDPRFERLPCTHKGTYADDCLVQRVTQHKCYIVATVDR |
| LY.KCIP..I...VMAEIE...QK..VALRI.K..RFE.L.CTH..T..DDCL.QRV.QHK.YIV.TVD. | |
| Retrocopy | LYTKCIPK<INNFVMAEIETFRQK*LVALRITKY*RFEYLACTH*ITFEDDCLAQRVIQHKFYIVVTVDQ |
| Parental | DLKRRIRKIPGVPIMYISNHRYNIERMPDDYGA |
| DLK..I.KIPG..IMYISN.RYNIE.MPD.YGA | |
| Retrocopy | DLK-*IWKIPGAHIMYISNYRYNIEWMPDNYGA |
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 .02 RPM | 3 .31 RPM |
| SRP051959_heart | 0 .12 RPM | 3 .16 RPM |
| SRP051959_kidney | 0 .00 RPM | 4 .99 RPM |
| SRP051959_liver | 0 .00 RPM | 4 .25 RPM |
| SRP051959_lung | 0 .00 RPM | 5 .45 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .89 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 3 .30 RPM |
| SRP051959_spleen | 0 .00 RPM | 6 .24 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4092 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4092 was not experimentally validated.