RetrogeneDB ID: | retro_cjac_184 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 8:60686208..60687351(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000022875 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000012536 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_184
ATGAGTGAGACGGTCATCTGTTCCAGCCGGGCCACTGTGATGGTTTATGATGACGGCAACAAGCGATGGGTCCCTGCTCG
CATGGGTCCTCAGGCCTTCAGCCACGTCCAGATCTACCACAACCCCACAGCCAATTCCTTCTGCGTGGTGGGTCGGAAGA
TGCAGCCTGACCAGCAGGTGGTCATCAACTGTGCCATCGTCCAGGGCGTCAAGTATAATCAAGCCACCCCTAATTTCCAT
CAGTGGCGCGATGCCCGCCGGGTCTGGGGCCTCAACTTCAGCAGCAAGGAGGATGCCGCCCAGTTTGCTGCGGGCATGGC
CAGTGCCCTAGAGGCGTTGGAAGGAGGTGGGTCCCCTCCACCGCCAGCACCTCCTGCCTGGTCGGTCCTCAAGGGCCCCT
CCCCGGAGGAGGTGGAGCAGCAGAAAAGGCCCCAGCCCGGCCCGACAGAGCATGTAGAGCGCCGTGTCTCCAATGCAGGA
GGCCCACCTGCTCCCCCTGCTGGGGGTCCACACCCACCACCAGGACCTCCCCCTCCTCCAGGTCCTCCCCTACCCCCAGG
TTTGCCTCCCTCGGGGGTCCCAGCTGCAGCACACGGAGCTGGGGGAGGACCACCCCCTGCACCCCCTCTCCCAGCAGCAC
AGGGCCCCAGTGGTGGGGGGACTGGGGCCCCAGGCCTGGCTGCAGCTATTGCTGGAGCCAAACTCAGGAAAGTCAGCAAG
CAGGAGGAATCCTCAGCAGGGCCCGTAGCCCCCAAAGCTGAGAGCGGTCGAAGCGGAGGTGGGGGACTCATGGAAGAGAT
GAACGCCATGCTGGCCCGGAGAAGGAAAGCCACACAGGTTGGGGAGAAAACTCCCAAGGATGAATCTGCCAATCAGGAGG
AGCCAGAGGCCAGAGTCCTAGCCCAGAGTGAATCTGTGTGGAGACCCTGGGAGAAGAACAGCACAACCTTGCCAAGGATG
AAGTTGTCTTCTTCGGTCACCACTTCTGAGACCCACCCCTACACGCCCAGCTCCGGCGATGACTCGGACCTAGAGAGGGT
GAAACAGGAGCTTCTGGAAGAGGTGAAGAAGGAATTGCAGAAAGTGAAAGAGGAAATCATTGAAGCCTTTGTCCAGGAGC
TGAGGAAGCGGGGTTCTCCCTGA
ORF - retro_cjac_184 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.54 % |
| Parental protein coverage: | 55.65 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | GPPAPPAGGLPPSGVPAAAHGSGGGPPPAPPLPAAQGPSGGGTGAPGLAAAIAGAKLRKVSKQEESSAGP |
| GPP.PP..GLPPSGVPAAAHG.GGGPPPAPPLPAAQGPSGGGTGAPGLAAAIAGAKLRKVSKQEESSAGP | |
| Retrocopy | GPPLPP--GLPPSGVPAAAHGAGGGPPPAPPLPAAQGPSGGGTGAPGLAAAIAGAKLRKVSKQEESSAGP |
| Parental | VAPKAESGRSGGGGLMEEMNAMLARRRKATQVGEKTPKDESANQEEPEARVPAQSESVRRPWEKNSTTLP |
| VAPKAESGRSGGGGLMEEMNAMLARRRKATQVGEKTPKDESANQEEPEARV.AQSESV.RPWEKNSTTLP | |
| Retrocopy | VAPKAESGRSGGGGLMEEMNAMLARRRKATQVGEKTPKDESANQEEPEARVLAQSESVWRPWEKNSTTLP |
| Parental | RMKSSSSVTTSETHPCTPSSGDDSDLERVKQELLEAVKKELQKVKEEIIEAFVQELRKRGSP |
| RMK.SSSVTTSETHP.TPSSGDDSDLERVKQELLE.VKKELQKVKEEIIEAFVQELRKRGSP | |
| Retrocopy | RMKLSSSVTTSETHPYTPSSGDDSDLERVKQELLEEVKKELQKVKEEIIEAFVQELRKRGSP |
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 | 1 .80 RPM | 13 .98 RPM |
| SRP051959_heart | 1 .07 RPM | 5 .67 RPM |
| SRP051959_kidney | 1 .15 RPM | 4 .75 RPM |
| SRP051959_liver | 0 .65 RPM | 2 .90 RPM |
| SRP051959_lung | 1 .63 RPM | 11 .14 RPM |
| SRP051959_lymph_node | 2 .21 RPM | 15 .55 RPM |
| SRP051959_skeletal_muscle | 0 .59 RPM | 2 .42 RPM |
| SRP051959_spleen | 1 .79 RPM | 11 .81 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_184 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_184 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_184 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 | ENSCJAG00000012536 | 1 retrocopy |
retro_cjac_184 ,
|
| Ictidomys tridecemlineatus | ENSSTOG00000027705 | 1 retrocopy |