RetrogeneDB ID: | retro_cjac_3985 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286472.1:95146..95485(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000037786 | ||
| Aliases: | C5H17orf61, TMEM256 | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3985
ATGGCAAGGCCAGTGGCAGCTTTCTGCAGCCTGGGTACTTTGTCCAGAGCTGCAGCCTTAGGCTTGGCCTCCTAAGGCAT
GCCTGGCGCCCAATCCCCAGATGCCTACGGAAAGGAGCTCTTTGACAAGGCCAACAAATACCACTTCTTCCACAGCCTGG
CCCTGTTAGGGGTGCCCCATTGCAGAAAGCCCCTCTGGGCTGGGTTACTGCTAGCTTCCGGAACGACCTTATTCTGCACC
AGCTTTTACTACTAGGCTCTGAGTGGAGACCCCAGAATCCAGACTTTGACCCCAGCGGGAGGGACCCTGCTACTCTTGGG
CTGGCTTGCCTTGGCTCTT
ORF - retro_cjac_3985 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.5 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MARPAAAFRRLGALSGAAALGLASYGAHGAQFPDAYGKELFDKANKHHFFHSLALLGVPHCRKPLWAGLL |
| MARP.AAF..LG.LS.AAALGLAS.G..GAQ.PDAYGKELFDKANK.HFFHSLALLGVPHCRKPLWAGLL | |
| Retrocopy | MARPVAAFCSLGTLSRAAALGLAS*GMPGAQSPDAYGKELFDKANKYHFFHSLALLGVPHCRKPLWAGLL |
| Parental | LASGTTLFCTSFYYQALSGDPSIQTLAPAGGTLLLLGWLALAL |
| LASGTTLFCTSFYY.ALSGDP.IQTL.PAGGTLLLLGWLALAL | |
| Retrocopy | LASGTTLFCTSFYY*ALSGDPRIQTLTPAGGTLLLLGWLALAL |
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 .02 RPM | 8 .30 RPM |
| SRP051959_heart | 0 .00 RPM | 4 .72 RPM |
| SRP051959_kidney | 0 .02 RPM | 15 .29 RPM |
| SRP051959_liver | 0 .00 RPM | 8 .84 RPM |
| SRP051959_lung | 0 .02 RPM | 3 .97 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 4 .86 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 9 .35 RPM |
| SRP051959_spleen | 0 .04 RPM | 5 .80 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3985 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3985 was not experimentally validated.