RetrogeneDB ID: | retro_cjac_2959 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:153697975..153698262(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | VPS25 | ||
| Ensembl ID: | ENSCJAG00000013276 | ||
| Aliases: | None | ||
| Description: | vacuolar protein sorting 25 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28122] |
Retrocopy-Parental alignment summary:
>retro_cjac_2959
TCCAGCATGATGATGACGGACGCTTAGGAGAGCCTGCTCTTCAGTACTGTCAAGCTGTGGAGGCTTCCTGTGATCCAGGC
TGTATTAGAGGAACTGAGGCACAAAGGGAACTTAGAGTGACTGGGTAAGAGCAAATCTAGTTTCCTAATCATGTGGCGGA
GGCCGGAAGAATGGGAAAACTCCTCTATCAGTGGGTCTCCAGGAGTGGCCGGAACAACGCCATATTTAGCCTGTCTGCTG
AGCTGACCAACGGGGAAGACATGGAGAAGGAGGTGTTCCGTGGACTG
ORF - retro_cjac_2959 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.29 % |
| Parental protein coverage: | 55.93 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SSMTVMEAQESPLFNNVKLQRRKLPVESIQIVLEELRKKGNLEWLDKSKSSFLIMWRRPEEW-GKLIYQW |
| SSM....A.ES.LF..VKL.R..LPV..IQ.VLEELR.KGNLE.L.KSKSSFLIMWRRPEEW.GKL.YQW | |
| Retrocopy | SSMMMTDA*ESLLFSTVKLWR--LPV--IQAVLEELRHKGNLE*LGKSKSSFLIMWRRPEEW<GKLLYQW |
| Parental | VSRSGQNNSVFTL-YELTNGEDTEDEEFHGL |
| VSRSG.NN..F.L..ELTNGED.E.E.F.GL | |
| Retrocopy | VSRSGRNNAIFSLSAELTNGEDMEKEVFRGL |
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 .02 RPM | 9 .83 RPM |
| SRP051959_heart | 0 .00 RPM | 6 .89 RPM |
| SRP051959_kidney | 0 .02 RPM | 14 .98 RPM |
| SRP051959_liver | 0 .00 RPM | 11 .57 RPM |
| SRP051959_lung | 0 .02 RPM | 6 .07 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 4 .09 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 8 .71 RPM |
| SRP051959_spleen | 0 .02 RPM | 5 .86 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2959 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2959 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2959 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 9 parental genes, and 11 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000013276 | 1 retrocopy |
retro_cjac_2959 ,
|
| Homo sapiens | ENSG00000131475 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000016041 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000011611 | 2 retrocopies | |
| Macaca mulatta | ENSMMUG00000002149 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000011797 | 1 retrocopy | |
| Ochotona princeps | ENSOPRG00000012574 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000008377 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000009220 | 2 retrocopies |