RetrogeneDB ID: | retro_cjac_2297 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:170592297..170592714(-) | ||
| Located in intron of: | ENSCJAG00000012812 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000010339 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2297
GAGGAAGGAAGGAAAGAAGGAAGGGAAAAAGGAAGGAAGGATGGATTGAGGGAGAGAGGAAAGGAGAAAAGGGAGAGAAG
GAGGGAGGGAAGGTAGGAAAGGAGGAAAGGAAGGGAGGGAGATAAGTTAGGCATAGGGAGGGAGGGAGGGAGGGAGGGAG
GGAGGGAGGGAGGGAAGGAGGAAGGATGGAAGAGGGGAAAGGAGAGAGGGAGGGAAAGAGGATGGCAGGGAGGAAGGGAA
GGGAGGAGGGAGGGAGGGGAGGGAGATAGGCACAGGGAGGGAGGGAAGGAAGAATAGAAGGGAGGAAGGGAGGAGGGAAG
GGAGATAAGTTAGACACAGGGAAGAAGGAAGGGAGGAAGGGAAGGGAGGGAGGGAGGAAGGAAAGAAGGGAGGACGGAGG
GAAGGAGGGCAGGGAGA
GAGGAAGGAAGGAAAGAAGGAAGGGAAAAAGGAAGGAAGGATGGATTGAGGGAGAGAGGAAAGGAGAAAAGGGAGAGAAG
GAGGGAGGGAAGGTAGGAAAGGAGGAAAGGAAGGGAGGGAGATAAGTTAGGCATAGGGAGGGAGGGAGGGAGGGAGGGAG
GGAGGGAGGGAGGGAAGGAGGAAGGATGGAAGAGGGGAAAGGAGAGAGGGAGGGAAAGAGGATGGCAGGGAGGAAGGGAA
GGGAGGAGGGAGGGAGGGGAGGGAGATAGGCACAGGGAGGGAGGGAAGGAAGAATAGAAGGGAGGAAGGGAGGAGGGAAG
GGAGATAAGTTAGACACAGGGAAGAAGGAAGGGAGGAAGGGAAGGGAGGGAGGGAGGAAGGAAAGAAGGGAGGACGGAGG
GAAGGAGGGCAGGGAGA
ORF - retro_cjac_2297 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.03 % |
| Parental protein coverage: | 85.45 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | EGGRNEGAREREGEEGKRE-GKGGREGGKEGRKGRERGRKEGGREREGEEGKREGRREGGKE-GRKKERK |
| E.GR.EG.RE.....G.RE.GK..RE...EGR..R..GR.EG.....G.EG.REG.REGGKE.G.K.... | |
| Retrocopy | EEGRKEG-REKGRKDGLRERGKEKRERRREGR*ERRKGR-EGDKLGIGREGGREGGREGGKEEGWKRGKE |
| Parental | REREREKERERERERE-REREERKERKRKKERKRKEGRKEGKRERERE-RKEGRKEGRFEEERKEGRKEG |
| R.RER.....RE..RE...RE....R...K.R.R.EGR.EG...R.RE.R..G..EGR.E..RKEGR.EG | |
| Retrocopy | RGRERGWQGGREGRRE>EGREIGTGREGRKNR-REEGRREGR*VRHRE<RRKGGREGR-EGGRKEGRTEG |
| Parental | RKEGR |
| R..GR | |
| Retrocopy | RRAGR |
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 | 0 .00 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .00 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .02 RPM | 0 .00 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .00 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2297 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2297 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2297 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000010339 | 9 retrocopies |
retro_cjac_1356, retro_cjac_2297 , retro_cjac_2882, retro_cjac_3255, retro_cjac_3637, retro_cjac_3700, retro_cjac_3728, retro_cjac_386, retro_cjac_420,
|