RetrogeneDB ID: | retro_cjac_2559 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:113532463..113532787(+) | ||
| Located in intron of: | ENSCJAG00000014988 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ATP5J | ||
| Ensembl ID: | ENSCJAG00000013803 | ||
| Aliases: | None | ||
| Description: | ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F6 [Source:HGNC Symbol;Acc:847] |
Retrocopy-Parental alignment summary:
>retro_cjac_2559
GTGATTCTTCAGAGGCTCTTCAGGTTCTCCTCTGTCATTTGGTCAGCAGTCTCGGTTCATTTGCAGAGAAACATTGGTGT
TACAGCAGTGTCATTAAATGAGGAACTTGATCCTGTACAGAAACTCTTTGTGGACAAGATTAGAGAATAGAAATCTAAGC
CACAGAAATCTGGAAGACCTGTTGATGCTGGTCCAGAATATCAGCAAGATCTGGAGAGGGAGCTTTTTAAACTCAAGCAA
ATGTTTGGTAAAGGAGACATGAATACCTTCCCCACCTTCAAATTTGAGGATCTCAAATTTGAAGTCTTTGATAAACCCCA
GGCC
ORF - retro_cjac_2559 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.26 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MILQRLFRFSSVIQSAVSVHLRRNIGVTAVAF-KELDPIQKLFVDKIREYKSKRQTAGGPVDTGPEYQQD |
| .ILQRLFRFSSVI.SAVSVHL.RNIGVTAV....ELDP.QKLFVDKIRE.KSK.Q..G.PVD.GPEYQQD | |
| Retrocopy | VILQRLFRFSSVIWSAVSVHLQRNIGVTAVSLNEELDPVQKLFVDKIRE*KSKPQKSGRPVDAGPEYQQD |
| Parental | LERELFKLKQMFGKGDMNTFPTFTFEDPKFEVFDKPPA |
| LERELFKLKQMFGKGDMNTFPTF.FED.KFEVFDKP.A | |
| Retrocopy | LERELFKLKQMFGKGDMNTFPTFKFEDLKFEVFDKPQA |
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 .07 RPM |
| SRP051959_heart | 0 .05 RPM | 30 .78 RPM |
| SRP051959_kidney | 0 .04 RPM | 22 .43 RPM |
| SRP051959_liver | 0 .04 RPM | 27 .18 RPM |
| SRP051959_lung | 0 .03 RPM | 12 .48 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 6 .64 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 33 .63 RPM |
| SRP051959_spleen | 0 .00 RPM | 9 .52 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2559 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2559 was not experimentally validated.