RetrogeneDB ID: | retro_cjac_1007 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 12:119319458..119320727(+) | ||
| Located in intron of: | ENSCJAG00000014418 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000013514 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_1007
AGGACCGGGCAGTTAAATGGCACCTGCACCAGCTCAGTGGACATGGAGCTCTTCCTCCATTACTCCCTCATCCCATCACT
CTTCATCATTTTGATCTTGTCCTTCCTCCAAAGACGAGAGCATCGTAGACAGAGAGATGATACCTCTTACCTTCTGGGGA
ACCGCTTTGGAATCATCATACCTCTGGACTTTGTGGGCACTTTCAGTAACCGATGGTCCTATGGAATCGCCTTTGGGGCC
ACAGCTAATAAGGTCATGTTTTTGTTCTCAGAAGGCTACCAGCCCCTGCAGATCCCGCAGTGGGCCCAAGCCTTTGAGCT
TATGATTGGAGGCCTTGAAGTTGGCCTGTCTCACTTCCCCTTCTTTGTGTGCCTCTCGTCAGAGTTCCAGCTGGTCAGCT
CCACCCTGGGCTTCTGCTACTCTCTTATCTGGTTTGCTGTCACCATTCTTCAAGTTTCACAGTGTCCCCATGGGCAGTTC
GTGGGGAAGTACGAGACCCTTGTGTTCTACTGGCCCTCACTGCTGTGCCTCGCCTTCCTGCTGGGCCGCTTCCTGTATAT
GTTTGTCAAGGCTCTGAGGGTACACCTTGGCTGGGAGCTCCAGGTGGAAGAAAAGCCTGTCCTGGAAGCGCACCAGGCAG
AGCACGTCAAGCAGCTCCTGAGGACACCCCACTCACAAGAAGAAAAAAAGTCTTGGTTCCAAACCAGGATATATGAGTGG
GATCCCTGCTTTCAATTCCCAAGCAGAATGATTGGAACCATTGTATTGGCTTTCATCTGCCTGTACCTTTTCATTGTCAT
CGAGTTCAGCATGTTTGTGTACGTGAGAGATGAGCTGGACATGTTTGAAAACAAGCTGGAGAGCTACATCAACTCCGTGA
ACCATTCAGGGATCCTGACCCCAGGTATCCTGCAGGTGAAAGAGCTGATCAGCGTTACCAAAGGAGTCTGGGTGGCGACC
ATTTTACCTGCCTCACTCACGTGTGTGAGCTATCTGTTCCACATTTTGGTCTGTTACAGAAAGCACATAAAGAGGCTCTG
GGCAGGAGATAAACACTTTCTGCCTTTGAGGTTTCATAACCCGGCCTCGTCGGAGAGCGTGGTGGCCATTGCAAGGTACT
CTGGCTGGCAAATAGCCTATATTCTATGGGGCTACCTCATCATTCACGTGGTGCAGAGCCTATGTGGCATGGCAATCATG
TACGGTCTGGTGCTGCCCATCATCCACAAACAGGGCCTAGAGATGCTGCGAGGGCTGGGCATCGGGATG
ORF - retro_cjac_1007 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.35 % |
| Parental protein coverage: | 68.23 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RTGQLNGTCTSSVDMELFLHYSLIPSLFIILILSFLQRREHRRQRDDTSYLLGNRFGIIMPLDFVGTFSN |
| RTGQLNGTCTSSVDMELFLHYSLIPSLFIILILSFLQRREHRRQRDDTSYLLGNRFGII.PLDFVGTFSN | |
| Retrocopy | RTGQLNGTCTSSVDMELFLHYSLIPSLFIILILSFLQRREHRRQRDDTSYLLGNRFGIIIPLDFVGTFSN |
| Parental | RWSYGIAFGATANKVMFLFSEGYQPLQIPQWAQAFELLIGGLEVGLSHFPFFACLSSEFQLVSSTLGFCY |
| RWSYGIAFGATANKVMFLFSEGYQPLQIPQWAQAFEL.IGGLEVGLSHFPFF.CLSSEFQLVSSTLGFCY | |
| Retrocopy | RWSYGIAFGATANKVMFLFSEGYQPLQIPQWAQAFELMIGGLEVGLSHFPFFVCLSSEFQLVSSTLGFCY |
| Parental | SLIWFAVTILQVSQCPHGQFVGKYETLVFYWPSLLCLAFLLGRFLYMFVKALRVHLGWELQVEEKPVLEA |
| SLIWFAVTILQVSQCPHGQFVGKYETLVFYWPSLLCLAFLLGRFLYMFVKALRVHLGWELQVEEKPVLEA | |
| Retrocopy | SLIWFAVTILQVSQCPHGQFVGKYETLVFYWPSLLCLAFLLGRFLYMFVKALRVHLGWELQVEEKPVLEA |
| Parental | HQAEHVKQLLRTPHSQEEKKSWFQTRIYEWDPCFQFPSRMIGTIVLAFICLYLFIVIEFCMFVYVRDELD |
| HQAEHVKQLLRTPHSQEEKKSWFQTRIYEWDPCFQFPSRMIGTIVLAFICLYLFIVIEF.MFVYVRDELD | |
| Retrocopy | HQAEHVKQLLRTPHSQEEKKSWFQTRIYEWDPCFQFPSRMIGTIVLAFICLYLFIVIEFSMFVYVRDELD |
| Parental | MFENKLESYITSVNHSGILTPGILQVKELISVTKGVWVATILPASLTCVSYLFHILVCYRKHIKRLWAGD |
| MFENKLESYI.SVNHSGILTPGILQVKELISVTKGVWVATILPASLTCVSYLFHILVCYRKHIKRLWAGD | |
| Retrocopy | MFENKLESYINSVNHSGILTPGILQVKELISVTKGVWVATILPASLTCVSYLFHILVCYRKHIKRLWAGD |
| Parental | KHFLPLRFHNPASSESVVAIARYSGWQIAYILWGYLIIHVVQSLCGMAIMYGLVLPIVHKQGLEMLRGLG |
| KHFLPLRFHNPASSESVVAIARYSGWQIAYILWGYLIIHVVQSLCGMAIMYGLVLPI.HKQGLEMLRGLG | |
| Retrocopy | KHFLPLRFHNPASSESVVAIARYSGWQIAYILWGYLIIHVVQSLCGMAIMYGLVLPIIHKQGLEMLRGLG |
| Parental | IGI |
| IG. | |
| Retrocopy | IGM |
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 | 1 .62 RPM |
| SRP051959_heart | 0 .00 RPM | 1 .05 RPM |
| SRP051959_kidney | 0 .95 RPM | 28 .93 RPM |
| SRP051959_liver | 3 .79 RPM | 87 .57 RPM |
| SRP051959_lung | 0 .26 RPM | 5 .17 RPM |
| SRP051959_lymph_node | 0 .07 RPM | 5 .16 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .13 RPM |
| SRP051959_spleen | 0 .04 RPM | 0 .29 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1007 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1007 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1007 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000013514 | 1 retrocopy |
retro_cjac_1007 ,
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