RetrogeneDB ID: | retro_cjac_259 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 17:38384566..38384929(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000023360 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000034456 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_259
ATGGCGGAGCCCTCGTGCGCCCGACGCCCGGTGCCTCTCATCGAGTCGGAGCTATACTGCCTTATCGCCCGGTACCTATC
CGCGGGCCCGTGTCGGACAGCGGCCCAGGTGCTGGTGCAGGAGCTGGAGCAGTACCAATTGTTGCCAAAGAGGTCGGACT
GGGAGGGCAATGAGCACAACAGGAGCTACGAGGAATTGGTCTTGTCCAATAAGCATGTGGCTCCTGATCATCTGTTGCAA
ATCTGCCAACGCATGGGTCCTATGTTGGTTAAAGAAATTCCACCCAGTATTTCAAGAGTCACTTCTTTACTTGGTGCAGG
AAGGCAATCTTTGCTACATACAGCAAAAGATACCTTCATTTGA
ORF - retro_cjac_259 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.26 % |
| Parental protein coverage: | 67.95 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PPSSPELYYLIARFLQSGPCNKSAQVLVQELEEHQLIPRRLDWEGKEHRRSFEDLVAANAHIPPDYLLKI |
| P....ELY.LIAR.L..GPC...AQVLVQELE..QL.P.R.DWEG.EH.RS.E.LV..N.H..PD.LL.I | |
| Retrocopy | PLIESELYCLIARYLSAGPCRTAAQVLVQELEQYQLLPKRSDWEGNEHNRSYEELVLSNKHVAPDHLLQI |
| Parental | CERIGPLLDKEIPQSVPGVQTLLGVGRQSLLRDAKD |
| C.R.GP.L.KEIP.S...V..LLG.GRQSLL..AKD | |
| Retrocopy | CQRMGPMLVKEIPPSISRVTSLLGAGRQSLLHTAKD |
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 .18 RPM | 2 .57 RPM |
| SRP051959_heart | 0 .14 RPM | 1 .05 RPM |
| SRP051959_kidney | 0 .09 RPM | 1 .64 RPM |
| SRP051959_liver | 0 .13 RPM | 1 .06 RPM |
| SRP051959_lung | 0 .11 RPM | 2 .29 RPM |
| SRP051959_lymph_node | 0 .18 RPM | 2 .51 RPM |
| SRP051959_skeletal_muscle | 0 .09 RPM | 0 .52 RPM |
| SRP051959_spleen | 0 .15 RPM | 1 .95 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_259 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_259 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_259 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000034456 | 1 retrocopy |
retro_cjac_259 ,
|
| Nomascus leucogenys | ENSNLEG00000002210 | 1 retrocopy |