RetrogeneDB ID: | retro_cjac_3543 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01183761.1:3244..3529(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | LTBP4 | ||
| Ensembl ID: | ENSCJAG00000037941 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3543
CAGTCTTGCTCTGTCACTCAGGTTGGAGTGCAATGGCACAATCTTAGCTCATTGCAACCACTGCCTCCCAGCTTCAAGCG
ATTCTCCTGCCTCAGCCTCCTGAGTAGCAGGGATTACAGGCACCTGCCACCATGCCCAGCTAATTACATTTAAGTAGAGA
TGGGGTTTCAGCATGTTGTCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGACTCACCTGCCTCCACCTCCCAAACTGCT
GGGATGACAGGTGTGAGTCCCTGTGCCCAGCCACAGCTGCACCTT
CAGTCTTGCTCTGTCACTCAGGTTGGAGTGCAATGGCACAATCTTAGCTCATTGCAACCACTGCCTCCCAGCTTCAAGCG
ATTCTCCTGCCTCAGCCTCCTGAGTAGCAGGGATTACAGGCACCTGCCACCATGCCCAGCTAATTACATTTAAGTAGAGA
TGGGGTTTCAGCATGTTGTCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGACTCACCTGCCTCCACCTCCCAAACTGCT
GGGATGACAGGTGTGAGTCCCTGTGCCCAGCCACAGCTGCACCTT
ORF - retro_cjac_3543 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 60.42 % |
| Parental protein coverage: | 53.33 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ESCCVVQTGVQWHDLGSLQPPPPGFKRFSCLSLPSSWDYRRTPPCPANFLVLLPTGFCHVGKAGLKFLAS |
| .SC.V.Q.GVQWH.L.SLQP.PP.FKRFSCLSL.SS.DYR..PPCPAN.......GF.HV..AGLK.L.S | |
| Retrocopy | QSCSVTQVGVQWHNLSSLQPLPPSFKRFSCLSLLSSRDYRHLPPCPANY-I*VEMGFQHVVQAGLKLLTS |
| Parental | SDPPIFASQSAGITGVSHSAENRLNI |
| .D.P...SQ.AG.TGVS..A...L.. | |
| Retrocopy | GDSPASTSQTAGMTGVSPCAQPQLHL |
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 | 13 .16 RPM |
| SRP051959_heart | 0 .00 RPM | 81 .88 RPM |
| SRP051959_kidney | 0 .00 RPM | 6 .41 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .04 RPM |
| SRP051959_lung | 0 .00 RPM | 17 .91 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 4 .06 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 8 .63 RPM |
| SRP051959_spleen | 0 .00 RPM | 13 .36 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3543 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3543 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3543 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 38 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000017963 | 3 retrocopies | |
| Callithrix jacchus | ENSCJAG00000037941 | 35 retrocopies |
retro_cjac_3343, retro_cjac_3355, retro_cjac_3369, retro_cjac_3372, retro_cjac_3389, retro_cjac_3391, retro_cjac_3423, retro_cjac_3425, retro_cjac_3430, retro_cjac_3445, retro_cjac_3456, retro_cjac_3474, retro_cjac_3476, retro_cjac_3477, retro_cjac_3487, retro_cjac_3491, retro_cjac_3543 , retro_cjac_3545, retro_cjac_3547, retro_cjac_3549, retro_cjac_3566, retro_cjac_3583, retro_cjac_3598, retro_cjac_3609, retro_cjac_3616, retro_cjac_3622, retro_cjac_3633, retro_cjac_3641, retro_cjac_3656, retro_cjac_3672, retro_cjac_3674, retro_cjac_3677, retro_cjac_3682, retro_cjac_3733, retro_cjac_3736,
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