RetrogeneDB ID: | retro_cjac_882 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 11:118341093..118341381(+) | ||
| Located in intron of: | ENSCJAG00000018709 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000035125 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DYNLRB1 | ||
| Ensembl ID: | ENSCJAG00000018199 | ||
| Aliases: | None | ||
| Description: | dynein, light chain, roadblock-type 1 [Source:HGNC Symbol;Acc:15468] |
Retrocopy-Parental alignment summary:
>retro_cjac_882
ATGGCAGAGGTGGAGGAGACACTGAAGCGACTTCAGAGCCAGAAGGGAGTGCAGGGAATCATCGTGGTGAACACAGAAGG
CATTTCCATCAAGAGCACTATGGACAACCCTACCACCACCCAGTATGCCAGCCTCATGCACAGCTTCATCCTGAAGGCAC
GGAGCACCGTGCGTGAAATCGACCCCCAGAACGATCTCACCTTCCTTCGAATTCGCTCCAAGAAAAATGAGATTATGGTT
GCACCAGATAAAGACTATTTCCTGATTGTGATTCAGAATCCAACCGAA
ORF - retro_cjac_882 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.96 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEVEETLKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVREIDPQNDLTFLR |
| MAEVEETLKRLQSQKGVQGIIVVNTEGI.IKSTMDNPTTTQYASLMHSFILKARSTVREIDPQNDLTFLR | |
| Retrocopy | MAEVEETLKRLQSQKGVQGIIVVNTEGISIKSTMDNPTTTQYASLMHSFILKARSTVREIDPQNDLTFLR |
| Parental | IRSKKNEIMVAPDKDYFLIVIQNPTE |
| IRSKKNEIMVAPDKDYFLIVIQNPTE | |
| Retrocopy | IRSKKNEIMVAPDKDYFLIVIQNPTE |
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 .20 RPM | 7 .81 RPM |
| SRP051959_heart | 0 .37 RPM | 6 .75 RPM |
| SRP051959_kidney | 0 .18 RPM | 10 .14 RPM |
| SRP051959_liver | 0 .11 RPM | 6 .41 RPM |
| SRP051959_lung | 0 .36 RPM | 8 .85 RPM |
| SRP051959_lymph_node | 0 .39 RPM | 9 .89 RPM |
| SRP051959_skeletal_muscle | 0 .07 RPM | 4 .02 RPM |
| SRP051959_spleen | 0 .38 RPM | 8 .70 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_882 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_882 was not experimentally validated.