RetrogeneDB ID: | retro_cjac_1479 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 16:73723694..73724078(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GNPNAT1 | ||
| Ensembl ID: | ENSCJAG00000007154 | ||
| Aliases: | None | ||
| Description: | glucosamine-phosphate N-acetyltransferase 1 [Source:HGNC Symbol;Acc:19980] |
Retrocopy-Parental alignment summary:
>retro_cjac_1479
ATACTGGGTCAGCTGACAGAGACTGGAGTTGTGAACCCTGAATGATTTATGAAAAGTTTTGAGCATATGAAGAAATCTGG
GGATTATCATGTTACAGTTGTGGAAGATGCAACTCTAGGACAGATTGTTGCCACAGCCACTCTGATAATAGAACACAGAC
TCATCCACTCCTGTTCTAAGAGAGGAAGAGTAGATGTTATCATTAATAATGAATGCAGAGGAAAGCAGCTGGGCAAGTTT
TTCTCATCAATCCTTACTTTGCTAAGCTAAAAACTGAACTGTTAAAATATGCCCCTTGAATTTCTACCACAAACTATTGG
TTTGTACAAAAAGTTTGGTTATATTGTATCTGAAGAAAACCACACAGTCTGGAGGTTTCTAAAG
ORF - retro_cjac_1479 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.97 % |
| Parental protein coverage: | 70.11 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VLGQLTETGVVSPEQFMKSFEHMKKSGDYYVTVVEDVTLGQIVATATLIIEHKFIHSCAKRGRVEDVVVS |
| .LGQLTETGVV.PE.FMKSFEHMKKSGDY.VTVVED.TLGQIVATATLIIEH..IHSC.KRGRV.DV... | |
| Retrocopy | ILGQLTETGVVNPE*FMKSFEHMKKSGDYHVTVVEDATLGQIVATATLIIEHRLIHSCSKRGRV-DVIIN |
| Parental | DECRGKQLGKLLLSTLTLLSKKLNCYKITLECLPQNVGFYKKFGYTVSEENYMCRRFLK |
| .ECRGKQLGK...S.LTLLS.KLNC....LE.LPQ..G.YKKFGY.VSEEN....RFLK | |
| Retrocopy | NECRGKQLGKFFSSILTLLS*KLNC*NMPLEFLPQTIGLYKKFGYIVSEENHTVWRFLK |
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 | 21 .85 RPM |
| SRP051959_heart | 0 .07 RPM | 8 .82 RPM |
| SRP051959_kidney | 0 .00 RPM | 14 .24 RPM |
| SRP051959_liver | 0 .00 RPM | 33 .62 RPM |
| SRP051959_lung | 0 .00 RPM | 10 .12 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 12 .37 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 5 .85 RPM |
| SRP051959_spleen | 0 .00 RPM | 10 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1479 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1479 was not experimentally validated.