RetrogeneDB ID: | retro_cjac_2548 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:102584995..102585371(+) | ||
| 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: | ENSCJAG00000012116 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2548
GAAGAGAGCTTTACTCTGTCCTTCTCAGCCTCTGATGCAGAAATTGACACGATGGTTGCATAATTAGAGGACATTATCAT
GGATGACAAGTTCCATTTATTACAGAGAAACTTCATAGAAAAGTACTACCTGGAGTTTTGAAAATACAGAAGCGAATAAA
CTCACCTACATGCCTAGTTTTAATAAGTATATTTTTTTGGAGAGAAAATATGATGAAGAATAGCAGAAGATTCCTGGATT
CAACACTGCAGTTTTCACAACTACATTACAGCATCATAAAGGTGAAGTGGCTGGTAACATATTCGACATGCTGCCCACCT
TTACTGATGTTTTAGCTTTTACAGAAATGCTTTTGGACTACAGAGCAGAAAAGGAA
ORF - retro_cjac_2548 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 72.87 % |
| Parental protein coverage: | 79.01 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | EESFALSFSSASDAEFDAVVGYLEDIIMDDKFQLLQRNFMDKYYLEF-EDTEENKLTYTPIFNEYISLVE |
| EESF.LSFS.ASDAE.D..V..LEDIIMDDKF.LLQRNF..KYYLEF.E.TE.NKLTY.P.FN.YI.L.. | |
| Retrocopy | EESFTLSFS-ASDAEIDTMVA*LEDIIMDDKFHLLQRNFIEKYYLEF>ENTEANKLTYMPSFNKYIFLER |
| Parental | KYVEEQLLERIPGFNMAAFTVTLQHHRDEVAGDIFDMLLTFTDFLAFKEMFLDYRAEKE |
| KY.EE.....IPGFN.A.FT.TLQHH..EVAG.IFDML.TFTD.LAF.EM.LDYRAEKE | |
| Retrocopy | KYDEE*--QKIPGFNTAVFTTTLQHHKGEVAGNIFDMLPTFTDVLAFTEMLLDYRAEKE |
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 | 5 .59 RPM |
| SRP051959_heart | 0 .00 RPM | 8 .37 RPM |
| SRP051959_kidney | 0 .00 RPM | 8 .39 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .86 RPM |
| SRP051959_lung | 0 .00 RPM | 11 .22 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 6 .89 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 4 .45 RPM |
| SRP051959_spleen | 0 .00 RPM | 5 .86 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2548 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2548 was not experimentally validated.