RetrogeneDB ID: | retro_cjac_752 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 10:1747498..1747967(-) | ||
| Located in intron of: | ENSCJAG00000002002 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | SYS1 | ||
| Ensembl ID: | ENSCJAG00000017516 | ||
| Aliases: | None | ||
| Description: | SYS1 Golgi-localized integral membrane protein homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16162] |
Retrocopy-Parental alignment summary:
>retro_cjac_752
ATGGTGGGCCAGTTCCGCAGCTACGTGTGGGACCCGCTGCTGATCCTGTGGCAGATCGTCCTCATGCAGATTGTGTATTA
CGGCTCACTGGGCCTGTGGCTGGCGCTGGTGGACTGGCTAGTGCGAAGCACCCCCTCGTTGGACCAGATGTTCGACGCGG
AGATCCTGGGCTTTTCCACCCCTCCAGACCGGCTCTCCATGATGTCCTTCATCCTCAGCGCCCTCACCTGTGCCCTGGGC
TTGCTGTACTTCATCCGCCGAGGGAAGCAGTGTCTGTATTTCACTGTCACTGTCCATTTCTTTCACCTCCTGGGCTGCTG
GTTCTACAGCTCCCGTTTCCCCTGGGCACTGACCTGGTGGCTGGTCCAAGCAGTGTTCATTGCACTCACGGCTGTCATCG
GGGAGTACCTGTGCATGCGGACGGAGCTCAAGGAGATCCCCCCTCAACTCAGCCCCTAAATCCAATGTC
ATGGTGGGCCAGTTCCGCAGCTACGTGTGGGACCCGCTGCTGATCCTGTGGCAGATCGTCCTCATGCAGATTGTGTATTA
CGGCTCACTGGGCCTGTGGCTGGCGCTGGTGGACTGGCTAGTGCGAAGCACCCCCTCGTTGGACCAGATGTTCGACGCGG
AGATCCTGGGCTTTTCCACCCCTCCAGACCGGCTCTCCATGATGTCCTTCATCCTCAGCGCCCTCACCTGTGCCCTGGGC
TTGCTGTACTTCATCCGCCGAGGGAAGCAGTGTCTGTATTTCACTGTCACTGTCCATTTCTTTCACCTCCTGGGCTGCTG
GTTCTACAGCTCCCGTTTCCCCTGGGCACTGACCTGGTGGCTGGTCCAAGCAGTGTTCATTGCACTCACGGCTGTCATCG
GGGAGTACCTGTGCATGCGGACGGAGCTCAAGGAGATCCCCCCTCAACTCAGCCCCTAAATCCAATGTC
ORF - retro_cjac_752 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.99 % |
| Parental protein coverage: | 100. % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGQFRSYVWDPLLILSQIVLMQTVYYGSLGLWLALVDGLVRSTPSLDQMFDAEILGFSTPPGRLSMMSF |
| M.GQFRSYVWDPLLIL.QIVLMQ.VYYGSLGLWLALVD.LVRSTPSLDQMFDAEILGFSTPP.RLSMMSF | |
| Retrocopy | MVGQFRSYVWDPLLILWQIVLMQIVYYGSLGLWLALVDWLVRSTPSLDQMFDAEILGFSTPPDRLSMMSF |
| Parental | ILNALTCALGLLYFIRRGKQCLDFTVTVHFFHLLGCWFYSSRFPSALTWWLVQAVCIALMAVIGEYLCMR |
| IL.ALTCALGLLYFIRRGKQCL.FTVTVHFFHLLGCWFYSSRFP.ALTWWLVQAV.IAL.AVIGEYLCMR | |
| Retrocopy | ILSALTCALGLLYFIRRGKQCLYFTVTVHFFHLLGCWFYSSRFPWALTWWLVQAVFIALTAVIGEYLCMR |
| Parental | TELKEI-PLNSAPKSNV |
| TELKEI.PLNSAPKSNV | |
| Retrocopy | TELKEI>PLNSAPKSNV |
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 .00 RPM | 3 .68 RPM |
| SRP051959_heart | 0 .02 RPM | 3 .82 RPM |
| SRP051959_kidney | 0 .00 RPM | 4 .46 RPM |
| SRP051959_liver | 0 .00 RPM | 4 .07 RPM |
| SRP051959_lung | 0 .00 RPM | 4 .46 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 4 .22 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 4 .08 RPM |
| SRP051959_spleen | 0 .00 RPM | 3 .74 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_752 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_752 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_752 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 | ENSCJAG00000017516 | 1 retrocopy |
retro_cjac_752 ,
|
| Myotis lucifugus | ENSMLUG00000005907 | 1 retrocopy |