RetrogeneDB ID: | retro_cjac_1460 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 16:28713961..28714315(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AKIRIN1 | ||
| Ensembl ID: | ENSCJAG00000002309 | ||
| Aliases: | None | ||
| Description: | akirin 1 [Source:HGNC Symbol;Acc:25744] |
Retrocopy-Parental alignment summary:
>retro_cjac_1460
ACCTCACCGCCGAGTCTGCAGCAGCCCGCCCTGCCCGGCAGCGAGCGGCGCCTTCCAACTCCGGAGCAAATTTTTCAGAA
CATGAAACAAGAATATAGTCGTTACCAGAGGTGGAGACATTTAGAAGTTGTTCTTAATCAGAGTGAGGCTTGTGCCTCGA
AAAGTCAGCCTCACTCCTCAGCACTCACAGCACCTAGCTCTCCAGGTTCCTCATGGATGAAGAAGAACCATCCCATCTCT
ACCCTCCGACAAGTTGGAATCGTATGTGAGCGTCCCTTAAAAGACTATGGAGATAAGATTCGGGAGCAAATTCTCACTAC
CAAACTAGCAGAACAATATGAATCTTTTGTGAAA
ORF - retro_cjac_1460 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.6 % |
| Parental protein coverage: | 62.69 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | TPPPSLQQPAPPGSERRLPTPEQIFQNIKQEYSRYQRWRHLEVVLNQSEACASESQPHSSALTAPSSPGS |
| T.PPSLQQPA.PGSERRLPTPEQIFQN.KQEYSRYQRWRHLEVVLNQSEACAS.SQPHSSALTAPSSPGS | |
| Retrocopy | TSPPSLQQPALPGSERRLPTPEQIFQNMKQEYSRYQRWRHLEVVLNQSEACASKSQPHSSALTAPSSPGS |
| Parental | SWMKKDQPTFTLRQVGIICERLLKDYEDKIREEYEQILNTKLAEQYESFVK |
| SWMKK..P..TLRQVGI.CER.LKDY.DKIRE...QIL.TKLAEQYESFVK | |
| Retrocopy | SWMKKNHPISTLRQVGIVCERPLKDYGDKIRE---QILTTKLAEQYESFVK |
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 | 12 .80 RPM |
| SRP051959_heart | 0 .00 RPM | 9 .88 RPM |
| SRP051959_kidney | 0 .00 RPM | 14 .89 RPM |
| SRP051959_liver | 0 .00 RPM | 11 .70 RPM |
| SRP051959_lung | 0 .00 RPM | 17 .03 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 18 .86 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 10 .26 RPM |
| SRP051959_spleen | 0 .04 RPM | 17 .94 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1460 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1460 was not experimentally validated.