RetrogeneDB ID: | retro_cjac_106 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:105729642..105730158(+) | ||
| Located in intron of: | ENSCJAG00000006306 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000022857 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000016338 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_106
ATGGCCTCCAACTTTAAGAAGGCAAACATGGCATCAAGTGCCCAGCAAAACAGAATGAGTCCTAAGCCTGAGCTTACAGA
AGAGCAGAAGCAGGAGATCAGGGAAGCGTTTGATCTTTTTGATGCAGATGGAACTGGCAGCATAGATGTTAAGGAACTTA
AGGTGGCAACGAGGTCCCTGGGCTTTGAACCCAAGAAAGAAGAAATTAAGAAAATGATAAGTGAAATTGATAAGGAAGGG
ACAGGAAAAATGAACTTTGGTGACTTTTTAACTGTGATGACCCAGAAAATGTCTGAGAAAGATACCAAAGAAGAAATCCT
AAAAGCTTTCAAGCTCTTTGATGATGATGAAACTGGGAAGATTTCGTTCAAAAATCTGAAACACATGGCCAAGGAGTTGG
GTGAGAACCTGACTGATGAGGAGCTGCAGGAAATGACTGATGAAGCTGATCGAGATGGAGATGGAGAGATCAGTGAGCAA
GAGTTCCTGCGCATCATGAAAAAGACCAGCCTTTAA
ORF - retro_cjac_106 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.74 % |
| Parental protein coverage: | 99.42 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MASSFKKANMASSAQRKRMSPKPELTEEQKQEIREAFDLFDADGTGSIDVKELKVAMRALGFEPKKEEIK |
| MAS.FKKANMASSAQ..RMSPKPELTEEQKQEIREAFDLFDADGTGSIDVKELKVA.R.LGFEPKKEEIK | |
| Retrocopy | MASNFKKANMASSAQQNRMSPKPELTEEQKQEIREAFDLFDADGTGSIDVKELKVATRSLGFEPKKEEIK |
| Parental | KMISEIDKEGTGKMNFGDFLTVMTQKMSEKDTKEEILKAFKLFDDDETGKISFKNLKRVAKELGENLTDE |
| KMISEIDKEGTGKMNFGDFLTVMTQKMSEKDTKEEILKAFKLFDDDETGKISFKNLK..AKELGENLTDE | |
| Retrocopy | KMISEIDKEGTGKMNFGDFLTVMTQKMSEKDTKEEILKAFKLFDDDETGKISFKNLKHMAKELGENLTDE |
| Parental | ELQEMIDEADRDGDGEVSEQEFLRIMKKTSL |
| ELQEM.DEADRDGDGE.SEQEFLRIMKKTSL | |
| Retrocopy | ELQEMTDEADRDGDGEISEQEFLRIMKKTSL |
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 | 1 .06 RPM | 4 .95 RPM |
| SRP051959_heart | 0 .53 RPM | 6 .31 RPM |
| SRP051959_kidney | 0 .69 RPM | 14 .44 RPM |
| SRP051959_liver | 0 .45 RPM | 7 .04 RPM |
| SRP051959_lung | 1 .07 RPM | 13 .23 RPM |
| SRP051959_lymph_node | 1 .53 RPM | 6 .28 RPM |
| SRP051959_skeletal_muscle | 0 .57 RPM | 6 .07 RPM |
| SRP051959_spleen | 1 .13 RPM | 7 .56 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_106 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_106 was not experimentally validated.