RetrogeneDB ID: | retro_cjac_2937 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:118280728..118280928(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | PDCD5 | ||
| Ensembl ID: | ENSCJAG00000018410 | ||
| Aliases: | None | ||
| Description: | programmed cell death 5 [Source:HGNC Symbol;Acc:8764] |
Retrocopy-Parental alignment summary:
>retro_cjac_2937
GTAAGTAACTTGGCACTTGTAAAGCCTGAAAAAACGCAAGCAGTAGAGAATTACCTTATACAGATGGCAAGATATGGACA
AATAAGTGAGATGGTATCAAACAAGGTTTAATGGAAATCCTTAAAAAAGTAAGCCAGCAAACAGAAAAGACAACAGCAGT
GAAATTCAACAGAAGAAAGGTAATGGACTCTGATGAAGAT
GTAAGTAACTTGGCACTTGTAAAGCCTGAAAAAACGCAAGCAGTAGAGAATTACCTTATACAGATGGCAAGATATGGACA
AATAAGTGAGATGGTATCAAACAAGGTTTAATGGAAATCCTTAAAAAAGTAAGCCAGCAAACAGAAAAGACAACAGCAGT
GAAATTCAACAGAAGAAAGGTAATGGACTCTGATGAAGAT
ORF - retro_cjac_2937 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.71 % |
| Parental protein coverage: | 53.6 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LSNLALVKPEKTKAVENYLIQMARYGQISEKVS-EQGLIEILKKVSQQTEKTTTVKFNRRKVMDSDED |
| .SNLALVKPEKT.AVENYLIQMARYGQISE.VS..QGL.EILKKVSQQTEKTT.VKFNRRKVMDSDED | |
| Retrocopy | VSNLALVKPEKTQAVENYLIQMARYGQISEMVS<KQGLMEILKKVSQQTEKTTAVKFNRRKVMDSDED |
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 | 9 .10 RPM |
| SRP051959_heart | 0 .04 RPM | 15 .91 RPM |
| SRP051959_kidney | 0 .00 RPM | 12 .67 RPM |
| SRP051959_liver | 0 .00 RPM | 11 .72 RPM |
| SRP051959_lung | 0 .00 RPM | 12 .01 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 17 .85 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 13 .95 RPM |
| SRP051959_spleen | 0 .00 RPM | 15 .63 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2937 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2937 was not experimentally validated.