RetrogeneDB ID: | retro_cjac_1018 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 12:24211747..24212173(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | CHCHD10 | ||
| Ensembl ID: | ENSCJAG00000010824 | ||
| Aliases: | None | ||
| Description: | coiled-coil-helix-coiled-coil-helix domain containing 10 [Source:HGNC Symbol;Acc:15559] |
Retrocopy-Parental alignment summary:
>retro_cjac_1018
ATGCCTCGGGGAAGCCGCAGTGCGGCCGCCCGGCCAGTCAGCCGCCCCGCTGCGCCCTCTGCCCACCCGCCCGCGCACCC
ACCGCCCTCTGCAGCAGCCCCGGCTCCCGCCCCTTCGGGCCAGCCGGGCCTCATGGCTCAGATGGCATCCAAGGCGGCAG
GGGTAGCCGTGGGCTCGGCTGTGGGACATGTCATGGGCAGCGCCCTGACCGGAGCCTTCAGCGGGGGGAGCTCGGAGCCG
GCCCAGCCTGCCGCCCAGCAGGCTCCCACCCATGCTGCCTCCCAGCCCCTGCAGATGGGGCCCTGAGCCTATGAGATCAG
GCAGTTCCTGGACTGTTCCACCACTCAGAGTGACCTGTCCCTGTGTGAGGGCTTCAGCGAGGTCCTGAAGCAGTGCAAGT
ACAACCACGGTCTGAGCTCCCTGCCC
ATGCCTCGGGGAAGCCGCAGTGCGGCCGCCCGGCCAGTCAGCCGCCCCGCTGCGCCCTCTGCCCACCCGCCCGCGCACCC
ACCGCCCTCTGCAGCAGCCCCGGCTCCCGCCCCTTCGGGCCAGCCGGGCCTCATGGCTCAGATGGCATCCAAGGCGGCAG
GGGTAGCCGTGGGCTCGGCTGTGGGACATGTCATGGGCAGCGCCCTGACCGGAGCCTTCAGCGGGGGGAGCTCGGAGCCG
GCCCAGCCTGCCGCCCAGCAGGCTCCCACCCATGCTGCCTCCCAGCCCCTGCAGATGGGGCCCTGAGCCTATGAGATCAG
GCAGTTCCTGGACTGTTCCACCACTCAGAGTGACCTGTCCCTGTGTGAGGGCTTCAGCGAGGTCCTGAAGCAGTGCAAGT
ACAACCACGGTCTGAGCTCCCTGCCC
ORF - retro_cjac_1018 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.59 % |
| Parental protein coverage: | 100. % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MPRGSRSAAARPVSRPAAPSAHPPAHPPPSAAAPAPAPSGQPGLMAQMASTAAGVAVGSAVGHVMGSALT |
| MPRGSRSAAARPVSRPAAPSAHPPAHPPPSAAAPAPAPSGQPGLMAQMAS.AAGVAVGSAVGHVMGSALT | |
| Retrocopy | MPRGSRSAAARPVSRPAAPSAHPPAHPPPSAAAPAPAPSGQPGLMAQMASKAAGVAVGSAVGHVMGSALT |
| Parental | GAFSGGSSEPAQPAAQQAPTHAASQPLQMGPCAYEIRQFLDCSTTQSDLSLCEGFSEVLKQCKYNHGLSS |
| GAFSGGSSEPAQPAAQQAPTHAASQPLQMGP.AYEIRQFLDCSTTQSDLSLCEGFSEVLKQCKYNHGLSS | |
| Retrocopy | GAFSGGSSEPAQPAAQQAPTHAASQPLQMGP*AYEIRQFLDCSTTQSDLSLCEGFSEVLKQCKYNHGLSS |
| Parental | LP |
| LP | |
| Retrocopy | LP |
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 | 4 .04 RPM |
| SRP051959_heart | 0 .05 RPM | 22 .40 RPM |
| SRP051959_kidney | 0 .07 RPM | 15 .49 RPM |
| SRP051959_liver | 0 .11 RPM | 27 .40 RPM |
| SRP051959_lung | 0 .00 RPM | 3 .07 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 1 .51 RPM |
| SRP051959_skeletal_muscle | 0 .13 RPM | 34 .94 RPM |
| SRP051959_spleen | 0 .00 RPM | 2 .90 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1018 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1018 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1018 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000010824 | 2 retrocopies |
retro_cjac_1018 , retro_cjac_1204,
|
| Callithrix jacchus | ENSCJAG00000021267 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000008241 | 1 retrocopy |