RetrogeneDB ID: | retro_cjac_1265 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 14:17331832..17332379(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSCJAG00000031772 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | OCEL1 | ||
| Ensembl ID: | ENSCJAG00000009584 | ||
| Aliases: | None | ||
| Description: | occludin/ELL domain containing 1 [Source:HGNC Symbol;Acc:26221] |
Retrocopy-Parental alignment summary:
>retro_cjac_1265
CTGCAGGGACTGATGCCTCGAGACTTCAAAACCAGCACCCCCCGCCCTCCGTGCCAGCCCCAGCCGGGACCCCACAAGGC
AAGGCCGAAGACGATTGTGTTTGAGGATGAGCTGCTCTCCCAGGCCCTCCTGGGCACCAAGAAGCCTATTGGAGCCATCC
CTAAGGGGCATACGCCTAGACCCCACCCAGTGCCCGACTATGAGCTTTAAGTACCCACGGGTGAGCAGTGCGAGGGAACG
GAGCCGATATGCCGCAGTGTTCCAGGACCAGTACGGAGAGTACTTGGAGCTCCAGCGGGAGGTGGGGTGCGCACAGGCAA
AGCTCAGGCAGCTGGAGGCCCGGCTGAGCTCCCTGCCCCCACCCCAAAGCCAGAAGGAGGCCCAAGTTGCATTCCGAGTT
TGGAGGGAGTTTGAGAAGAAGCAAACGGATTCTGGCTTCCTGGACAAGCAGGCTCGCTGCCACTACCTGAAGCATAAACT
GAGGCATCTCAAGACCCAGATCCAGAAGTTGGATGACCGAGGAGACAGTGAGGGCTCTGTGTACTTC
CTGCAGGGACTGATGCCTCGAGACTTCAAAACCAGCACCCCCCGCCCTCCGTGCCAGCCCCAGCCGGGACCCCACAAGGC
AAGGCCGAAGACGATTGTGTTTGAGGATGAGCTGCTCTCCCAGGCCCTCCTGGGCACCAAGAAGCCTATTGGAGCCATCC
CTAAGGGGCATACGCCTAGACCCCACCCAGTGCCCGACTATGAGCTTTAAGTACCCACGGGTGAGCAGTGCGAGGGAACG
GAGCCGATATGCCGCAGTGTTCCAGGACCAGTACGGAGAGTACTTGGAGCTCCAGCGGGAGGTGGGGTGCGCACAGGCAA
AGCTCAGGCAGCTGGAGGCCCGGCTGAGCTCCCTGCCCCCACCCCAAAGCCAGAAGGAGGCCCAAGTTGCATTCCGAGTT
TGGAGGGAGTTTGAGAAGAAGCAAACGGATTCTGGCTTCCTGGACAAGCAGGCTCGCTGCCACTACCTGAAGCATAAACT
GAGGCATCTCAAGACCCAGATCCAGAAGTTGGATGACCGAGGAGACAGTGAGGGCTCTGTGTACTTC
ORF - retro_cjac_1265 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.35 % |
| Parental protein coverage: | 68.68 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LQGLTPRGLKTSAPRPPCQPQPGPHKARRKTIVFEDELLSQALLGAKKPIGAIPKGHTPRPHPVPDYEL- |
| LQGL.PR..KTS.PRPPCQPQPGPHKAR.KTIVFEDELLSQALLG.KKPIGAIPKGHTPRPHPVPDYEL. | |
| Retrocopy | LQGLMPRDFKTSTPRPPCQPQPGPHKARPKTIVFEDELLSQALLGTKKPIGAIPKGHTPRPHPVPDYEL> |
| Parental | KYPPVSSARERSRYAAVFQDLYGEYLELQREVGCAQAKLRQLEARLSSLPPPQSQKEAQVAVRVWREFEK |
| KYP.VSSARERSRYAAVFQD.YGEYLELQREVGCAQAKLRQLEARLSSLPPPQSQKEAQVA.RVWREFEK | |
| Retrocopy | KYPRVSSARERSRYAAVFQDQYGEYLELQREVGCAQAKLRQLEARLSSLPPPQSQKEAQVAFRVWREFEK |
| Parental | KQTDPGFLDKQARCHYLKGKLRHLKTQIQKFDDRRDSEGSVYF |
| KQTD.GFLDKQARCHYLK.KLRHLKTQIQK.DDR.DSEGSVYF | |
| Retrocopy | KQTDSGFLDKQARCHYLKHKLRHLKTQIQKLDDRGDSEGSVYF |
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 .07 RPM | 1 .46 RPM |
| SRP051959_heart | 0 .00 RPM | 1 .19 RPM |
| SRP051959_kidney | 0 .07 RPM | 3 .55 RPM |
| SRP051959_liver | 0 .06 RPM | 4 .27 RPM |
| SRP051959_lung | 0 .05 RPM | 1 .50 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 1 .16 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .85 RPM |
| SRP051959_spleen | 0 .00 RPM | 1 .28 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1265 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1265 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1265 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 | ENSCJAG00000009584 | 1 retrocopy |
retro_cjac_1265 ,
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