RetrogeneDB ID: | retro_cjac_1851 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:145752659..145753218(+) | ||
| Located in intron of: | ENSCJAG00000015417 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SPDYC | ||
| Ensembl ID: | ENSCJAG00000002403 | ||
| Aliases: | None | ||
| Description: | speedy/RINGO cell cycle regulator family member C [Source:HGNC Symbol;Acc:32681] |
Retrocopy-Parental alignment summary:
>retro_cjac_1851
TTTAGCCATCGTATCATATGTATATGAAGATACATATACATGGAGGAGGAGGAGGACCTGGAGGGGCCCAAATGTGAGAC
TTTTCCATGGGCCCTGGGGAAAGATTGGTGTTTACAAGTGGGGAAGTTCCTGCAGCAGAGGGATAAGCTGTGGGCACGAT
GGGTTTCTGGGCTGTCGTGCGCCGCCCATGCTGTGAGGAGGTCATGGCAAAGGAGCCATTCCACTGGGCTTGGACTCGGA
ACTAGCGCTCCCACCACGGGGTTCAGAGGGTCTGTCCACAGGTCCCTGTCTGCCTTCCCTGGGGCCCTGGCCTCTCGCCG
CCCCACTGTTCCCTCTGCGGCTTGCCCCAGCACTGCAGCTGCCACCCACTTAAGCCTGTGGCATTCAAGTACTCTTCTCT
GACCTTGGAGTGTCATCGCCCTCCCTCCCAAAAATCTCTCTCAGGGTTCAAAAATGCCTGAGGTGGGGACTTTCTCATTG
TCTTGCCCCCTAGATGCAACTGGAACCTGACACCTACTGCCTCCGCATTTTCCCAAAGCCTCCACCACGCCCTGGGCAC
ORF - retro_cjac_1851 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.74 % |
| Parental protein coverage: | 64.16 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | YTHSSLFLALYLANDMEEDLEGPKCQIFPWALGRDWCLRVGKFLQQRDKLWAR-MGFRAVVSRQCCEEVM |
| ..H.......Y.....EEDLEGPKC..FPWALG.DWCL.VGKFLQQRDKLWAR.MGF.AVV.R.CCEEVM | |
| Retrocopy | FSHRIICI*RYIYMEEEEDLEGPKCETFPWALGKDWCLQVGKFLQQRDKLWAR<MGFWAVVRRPCCEEVM |
| Parental | AKEPFHWAWTRDRRPHHGGVQRVCPQVPFRLPRGPGLSPPHCSPCGLPQHPGCHPLKPVSLKCSSLTSEC |
| AKEPFHWAWTR..R.HH.GVQRVCPQVP..LP.GPGLSPPHCS.CGLPQH..CHPLKPV..K.SSLT.EC | |
| Retrocopy | AKEPFHWAWTRN*RSHH-GVQRVCPQVPVCLPWGPGLSPPHCSLCGLPQHCSCHPLKPVAFKYSSLTLEC |
| Parental | HRLPSQNSLSAFKNTWGGDFLLILPPQ-IQLEPDTYCLRIFPKLLPRPGH |
| HR.PSQ.SLS.FKN..GGDFL..LPP...QLEPDTYCLRIFPK..PRPGH | |
| Retrocopy | HRPPSQKSLSGFKNA*GGDFLIVLPPR<MQLEPDTYCLRIFPKPPPRPGH |
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 .38 RPM |
| SRP051959_heart | 0 .02 RPM | 0 .61 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .40 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .61 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .98 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .66 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .37 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .71 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1851 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1851 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1851 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000002403 | 2 retrocopies |
retro_cjac_1136, retro_cjac_1851 ,
|
| Monodelphis domestica | ENSMODG00000010068 | 3 retrocopies | |
| Otolemur garnettii | ENSOGAG00000015020 | 1 retrocopy |