RetrogeneDB ID: | retro_cjac_1274 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 14:42634715..42635002(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000006887 | |
| 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_1274
ATGGCAGAGGTGGAGGAGACCCTGAAGCGACTCAGAGCCAGAAGGGAGTGCACGGAATCACTGTGGTGAACACAGAAGGC
ATTCCCATCAAGAGCACCATGGACAACCCCACCACCACCCAATATGCCAGCCTCAGGCACAGCTTCATCCTGAAGGCACG
GAGTACCGTGCATGAAATCGACCCCCAGAATGATCTCCCCTTCCTTCAAATTCACTCCAAGAAAAATGAGATTATGGTTG
CACCAGATAAAGACTATTTCCTGATTGTGATTCAGAATCCAACTGAA
ORF - retro_cjac_1274 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.75 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAEVEETLKRL-QSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVREIDPQNDLTFL |
| MAEVEETLKRL.QSQKGV.GI.VVNTEGIPIKSTMDNPTTTQYASL.HSFILKARSTV.EIDPQNDL.FL | |
| Retrocopy | MAEVEETLKRL<QSQKGVHGITVVNTEGIPIKSTMDNPTTTQYASLRHSFILKARSTVHEIDPQNDLPFL |
| Parental | RIRSKKNEIMVAPDKDYFLIVIQNPTE |
| .I.SKKNEIMVAPDKDYFLIVIQNPTE | |
| Retrocopy | QIHSKKNEIMVAPDKDYFLIVIQNPTE |
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 .00 RPM | 7 .81 RPM |
| SRP051959_heart | 0 .00 RPM | 6 .75 RPM |
| SRP051959_kidney | 0 .04 RPM | 10 .14 RPM |
| SRP051959_liver | 0 .00 RPM | 6 .41 RPM |
| SRP051959_lung | 0 .02 RPM | 8 .85 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 9 .89 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 4 .02 RPM |
| SRP051959_spleen | 0 .00 RPM | 8 .70 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1274 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1274 was not experimentally validated.