RetrogeneDB ID: | retro_cjac_1962 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:133657083..133657404(-) | ||
| Located in intron of: | ENSCJAG00000016802 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RBX1 | ||
| Ensembl ID: | ENSCJAG00000004763 | ||
| Aliases: | None | ||
| Description: | ring-box 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:9928] |
Retrocopy-Parental alignment summary:
>retro_cjac_1962
ATGGCGGCAGCAATGGATGTGGATACCCCGAGTGGCACCACCAGCGATGCGGGAAAGTGCTTTGAAGTGAAAAAGGGGAA
TGCAATAGCCCTCTGGGCCTGGGATATTGTGGTTGATAACTGTGCCATCTGCAGGAACCACATTATGGACCTTTGCATAG
AATGTCAAGCTAACTAGGCATCTGCTACTTCAGAAGAGTGTACCGTTGCATGGGGAGTCTGTAACCATGCTTTTCACTTC
CACTGCATCGCTCCCTGGCTCAAAACATGATAGGTGTGTCCACTGGACAACAGAGAGTGGGAATTCCAGAAGTATGGACA
C
ORF - retro_cjac_1962 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.81 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTV |
| MAAAMDVDTPSGT.S.AGK..FEVKK.NA.ALWAWDIVVDNCAICRNHIMDLCIECQAN.ASATSEECTV | |
| Retrocopy | MAAAMDVDTPSGTTSDAGKC-FEVKKGNAIALWAWDIVVDNCAICRNHIMDLCIECQAN*ASATSEECTV |
| Parental | AWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH |
| AWGVCNHAFHFHCI..WLKT..VCPLDNREWEFQKYGH | |
| Retrocopy | AWGVCNHAFHFHCIAPWLKT**VCPLDNREWEFQKYGH |
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 .91 RPM | 7 .61 RPM |
| SRP051959_heart | 0 .65 RPM | 11 .51 RPM |
| SRP051959_kidney | 1 .00 RPM | 12 .22 RPM |
| SRP051959_liver | 0 .35 RPM | 8 .47 RPM |
| SRP051959_lung | 1 .02 RPM | 10 .09 RPM |
| SRP051959_lymph_node | 1 .44 RPM | 11 .03 RPM |
| SRP051959_skeletal_muscle | 0 .44 RPM | 10 .37 RPM |
| SRP051959_spleen | 0 .95 RPM | 13 .17 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1962 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1962 was not experimentally validated.