RetrogeneDB ID: | retro_cjac_2394 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:160000164..160000485(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | YKT6 | ||
| Ensembl ID: | ENSCJAG00000008053 | ||
| Aliases: | None | ||
| Description: | YKT6 v-SNARE homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:16959] |
Retrocopy-Parental alignment summary:
>retro_cjac_2394
CTGAGCAGCCTCAGTGTCCTCTACGAAGGTGAGCCCAAGGCAGTGCCGCCCAAAGCCACTTACGATAATGTGGCTTCCTT
CAGTTTCTCCCAGAGGTCCAGTGTTCAAGAAGTCATGACCTTCATGAGTCAACTGGCTGAGGAGGGGTCATGCAAAGGCA
TTAGATCGTCAGTCAAAGAACAAGGCTTCGTGTGCCATGTCCATGTCCGGAATGACGGTCTTGCAGGTGTGGCCATTGCT
GACAATGAACGCCCATCCCAGGTAGCCTGTACCTGAATGGAGTACTTACTAGATGAATTCTCCAAGCAAGTCAACAGGCT
C
ORF - retro_cjac_2394 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.29 % |
| Parental protein coverage: | 53.54 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LYSLSVLYKGDAKVVLLKAAHD-VSSFSFFQRSSVQEFMTFTSQLIVERSSKGTRASVKEQDYLCHVYVR |
| L.SLSVLY.G..K.V..KA..D.V.SFSF.QRSSVQE.MTF.SQL..E.S.KG.R.SVKEQ...CHV.VR | |
| Retrocopy | LSSLSVLYEGEPKAVPPKATYDNVASFSFSQRSSVQEVMTFMSQLAEEGSCKGIRSSVKEQGFVCHVHVR |
| Parental | NDSLAGVVIADNEYPSRVAFTLLEKVLDEFSKQVDRI |
| ND.LAGV.IADNE.PS.VA.T..E..LDEFSKQV.R. | |
| Retrocopy | NDGLAGVAIADNERPSQVACT*MEYLLDEFSKQVNRL |
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 | 28 .00 RPM |
| SRP051959_heart | 0 .00 RPM | 22 .15 RPM |
| SRP051959_kidney | 0 .00 RPM | 24 .87 RPM |
| SRP051959_liver | 0 .00 RPM | 11 .70 RPM |
| SRP051959_lung | 0 .00 RPM | 22 .40 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 17 .19 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 23 .83 RPM |
| SRP051959_spleen | 0 .00 RPM | 18 .21 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2394 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2394 was not experimentally validated.