RetrogeneDB ID: | retro_cjac_2158 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:94485257..94485581(+) | ||
| 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_2158
AAAGAGAAGCAAAAGAAAACAAGAAAGTTTGTCGCCATGAAGTGAATCCTTAGTGTCAGAGATCAGAGGCATGAAGAAAA
GGATCGATTAAACCCAAAAAATAAAGAGAAGAAAGATCCCAGCATGCCACAGGAAAGAGAAGTTCCCCAACACCCATCCT
GCTTATTTTTCCAATAAAATACACAGCTGGGCCCACTTTATCATGTTGGTATTTTTGTCGATACCAACTTTATCAACTAT
TCCATTAAAGTCAAACTGGACTTAGTATAGTCAATGATGAGCTGTATGTATGCCAAGTATATCCCTTATATAACTGATTG
TGTA
ORF - retro_cjac_2158 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.93 % |
| Parental protein coverage: | 53.54 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | KGKQKKTRKYATMKRMLSLRDQRLKEKDRLKPKKKEKKDPSALKEREVPQHPSCLFFQYNTQLGPPYH-- |
| K.KQKKTRK...MK..LS.RDQR..EKDRL.PK.KEKKDPS...EREVPQHPSCLFFQ.NTQLGP.YH.. | |
| Retrocopy | KEKQKKTRKFVAMK*ILSVRDQRHEEKDRLNPKNKEKKDPSMPQEREVPQHPSCLFFQ*NTQLGPLYHVG |
| Parental | ILVDTNFINFSIKAKLDLVQSMMDCLYAKCIPCITDCV |
| I.VDTNFIN.SIK.KLDLV.SMM.C.YAK.IP.ITDCV | |
| Retrocopy | IFVDTNFINYSIKVKLDLV*SMMSCMYAKYIPYITDCV |
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 | 3 .31 RPM |
| SRP051959_heart | 0 .00 RPM | 3 .16 RPM |
| SRP051959_kidney | 0 .00 RPM | 4 .99 RPM |
| SRP051959_liver | 0 .02 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_2158 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2158 was not experimentally validated.