RetrogeneDB ID: | retro_cjac_2364 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:106422077..106422455(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRAPPC6A | ||
| Ensembl ID: | ENSCJAG00000012869 | ||
| Aliases: | None | ||
| Description: | trafficking protein particle complex 6A [Source:HGNC Symbol;Acc:23069] |
Retrocopy-Parental alignment summary:
>retro_cjac_2364
GGACAGAAGATGAGCCTGTTGATCCTGGAGAGCATGGATTTCTGCGTGAGCCAGGTTCTAGGCGAGAGACTGCCCCAGGA
GATGCTCATCTCAGGGAGGAGCTATGTGGCCTCAAATTCCTATGCAAAACCCTGTGGGTGGCTGTGTTCCAACAGCTGAA
CGGCCTGTGCACCAATTACATACTTTTTGCAGGACAACAGCTTCCCCTCCTCATCCCGATGGCCTTGGGCCTGCAGAATC
TGGAGTAAGCACCCAAGTTCCTGGCTTCACTTGTGGCCTGTGCGTGGCACCCTCAGTACCCTGGGCATAGAGAGTTTGGT
CACTGCCCCTGTGGCAACCCTGACTGCTTGTAAGCTCCCAGTGATAATCTGGAAATCT
ORF - retro_cjac_2364 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.7 % |
| Parental protein coverage: | 75.72 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | GQNMNLSVLESVGFRVGQALGERLPREMLA-FREELDVLKFLCKDLWLAIFQKQMDSLRTNHQGTYVLQD |
| GQ.M.L..LES..F.V.Q.LGERLP.EML...REEL..LKFLCK.LW.A.FQ.Q...L.TN......... | |
| Retrocopy | GQKMSLLILESMDFCVSQVLGERLPQEMLI<LREELCGLKFLCKTLWVAVFQ-QLNGLCTNY---ILFAG |
| Parental | NSFPLLLPMAAGLQYLEEAPKFLA-FTCGL-LRGALCTLGIESVVTASVAALPGCKFQVVIQNS |
| ...PLL.PMA.GLQ.LE.APKFLA.FTCGL..RG.L.TLGIES.VTA.VA.L..CK..V.I..S | |
| Retrocopy | QQLPLLIPMALGLQNLE*APKFLA<FTCGL<VRGTLSTLGIESLVTAPVATLTACKLPVIIWKS |
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 .04 RPM | 1 .84 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .77 RPM |
| SRP051959_kidney | 0 .09 RPM | 10 .87 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .91 RPM |
| SRP051959_lung | 0 .05 RPM | 1 .25 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .65 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 1 .22 RPM |
| SRP051959_spleen | 0 .00 RPM | 1 .81 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2364 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2364 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2364 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000012869 | 1 retrocopy |
retro_cjac_2364 ,
|
| Macaca mulatta | ENSMMUG00000022932 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000010109 | 1 retrocopy |