RetrogeneDB ID: | retro_cjac_10 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 6:95771582..95772233(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000023039 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DEF6 | ||
| Ensembl ID: | ENSCJAG00000015575 | ||
| Aliases: | None | ||
| Description: | differentially expressed in FDCP 6 homolog (mouse) [Source:HGNC Symbol;Acc:2760] |
Retrocopy-Parental alignment summary:
>retro_cjac_10
AGCAGCAAAGTCTCTCGCGACACCCTGTACGAGGCGGTGCGGGAAGTCCTGCACGGGAACCAGCGCAAGCGCCGCAAGTT
CCTGGAGACGGTGGAGTTGCAGATCAGTTTGAAGAACTATGACCCCCAGAAGGACAAGCGTTTCTCGGGCACCGTCAGGC
TTAAGTCCACTCCTCGCCCCAAGTTCTCCGTGTGTGTCCTGGGGGACCAGCAGCACTGTGACGAGGCCAAGGCTGTGGAT
ATCCCCCACATGGACATCGAGGCGCTGAAAAAACTCAACAAGAATAAAAAACTGGTCAAGAAGCTGGCCAAGAAGTATGA
TGCATTTTTGGCCTCAGAGTCTCTGATCAAGCAGATTCCAGGAATCCTCGGCCCAGGCCTAAATAAGGCAGGAAAGTTCC
CCTCCCTGCTCACACACAATGAAAACATGGTGGCCAAAGTGGATGAGGTGAAGTCCACGATCAAGTTCCAAATGAAGAAG
GTGTTATGTCTGGCTGTGGCTGTTGGTCACATGAAGATGACAGATGATGAGCTTGTGTATAACATTCACCTGGCTGTCAA
TTTCTTGGTGTCATTGCTCAAGAAAAACTGGCAGAATGTCCGGGCCTTATATATCAAGAGCACCATGGGCAAGCCCCAGC
TCCTGTATTAA
ORF - retro_cjac_10 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.61 % |
| Parental protein coverage: | 99.54 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQ |
| SSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQ | |
| Retrocopy | SSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGDQ |
| Parental | QHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTHN |
| QHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIP.ILGPGLNKAGKFPSLLTHN | |
| Retrocopy | QHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPGILGPGLNKAGKFPSLLTHN |
| Parental | ENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMG |
| ENMVAKVDEVKSTIKFQMKKVLCLAVAVGH.KMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMG | |
| Retrocopy | ENMVAKVDEVKSTIKFQMKKVLCLAVAVGHMKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTMG |
| Parental | KPQRLY |
| KPQ.LY | |
| Retrocopy | KPQLLY |
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 .35 RPM | 85 .44 RPM |
| SRP051959_heart | 0 .26 RPM | 84 .86 RPM |
| SRP051959_kidney | 0 .29 RPM | 92 .56 RPM |
| SRP051959_liver | 0 .26 RPM | 115 .71 RPM |
| SRP051959_lung | 0 .26 RPM | 106 .37 RPM |
| SRP051959_lymph_node | 0 .53 RPM | 159 .31 RPM |
| SRP051959_skeletal_muscle | 0 .46 RPM | 149 .20 RPM |
| SRP051959_spleen | 0 .17 RPM | 135 .95 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_10 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_10 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_10 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000011252 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000015575 | 2 retrocopies |
retro_cjac_10 , retro_cjac_313,
|