RetrogeneDB ID: | retro_cjac_3555 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01184347.1:5954..6233(+) | ||
| 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: | ENSCJAG00000001008 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3555
TTCATAAGAGTTCTTATCATAGCACTTAAACTGAGCTAAATCAAAGGCCAGTGTTCTGTTTTGCAGGTGTACATCCAAAG
ACTTATACAGTGTGCTCCTATGTACATTCGTCCAACCACCTGGAGGAGGATTATCCTCGGAGCCTTTCTTCTTGTCATCA
AGGTTGGGAGCAATGTGGCTGTGTGCAATGAGGATTTATGCATGCGCTTTGAGAAAACTACAGTTGACGATCTGTGAGTT
TGTATGGTTTTTGTGAACTTTCTAACCATTTTTGGATAC
ORF - retro_cjac_3555 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 58.06 % |
| Parental protein coverage: | 54.27 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | FIRTLFYVKKLK--VADAIITMVYIQRLIQYAHIYICSATWRRIILGAILVVIKVRSNVAVCNRDLCRRF |
| FIR.L....KL...........VYIQRLIQ.A..YI...TWRRIILGA.L.VIKV.SNVAVCN.DLC.RF | |
| Retrocopy | FIRVLIIALKLS*IKGQCSVLQVYIQRLIQCAPMYIRPTTWRRIILGAFLLVIKVGSNVAVCNEDLCMRF |
| Parental | EKTTVNDLNKLEMY--FLRLIGY |
| EKTTV.DL........FL...GY | |
| Retrocopy | EKTTVDDL*VCMVFVNFLTIFGY |
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 | 3 .13 RPM | 1 .29 RPM |
| SRP051959_heart | 1 .77 RPM | 1 .28 RPM |
| SRP051959_kidney | 3 .17 RPM | 2 .44 RPM |
| SRP051959_liver | 1 .10 RPM | 1 .62 RPM |
| SRP051959_lung | 3 .53 RPM | 1 .74 RPM |
| SRP051959_lymph_node | 3 .90 RPM | 2 .31 RPM |
| SRP051959_skeletal_muscle | 0 .94 RPM | 1 .03 RPM |
| SRP051959_spleen | 3 .09 RPM | 1 .66 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3555 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3555 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3555 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000001008 | 1 retrocopy |
retro_cjac_3555 ,
|
| Callithrix jacchus | ENSCJAG00000002901 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000011445 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000034702 | 1 retrocopy | |
| Homo sapiens | ENSG00000163249 | 3 retrocopies | |
| Mus musculus | ENSMUSG00000070871 | 1 retrocopy |