RetrogeneDB ID: | retro_cjac_847 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 11:39013130..39013516(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RAC2 | ||
| Ensembl ID: | ENSCJAG00000002144 | ||
| Aliases: | None | ||
| Description: | ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2) [Source:HGNC Symbol;Acc:9802] |
Retrocopy-Parental alignment summary:
>retro_cjac_847
TTTAACAATTACTCTGCCAATGTTATGGTAGATGGAAAACCGGTGAATCTGGGCTTATGGGATACAGCTGGACAAGAAAA
TTATGACATATTACGCCTCCTGTTCTATCCACAAACAGATGTGTTCTTAATTTGCTTTTCCCTTGTGAGTCCTGCATCAT
TTGAAAATGTGAGAGCATATCCTGAGGTGCGGCACCACTGTCCCAACACTACCATCATCCTAGTGGAAACTAAACTTGGT
ATTAGGGATGATAAGACACCATCAAGAAACTGAAGGAGAAGCTGACTCCCATCACCTATGAACAGGGTCTAGCCATGGCT
AAGGAGATCGGTGCTGTAAAATACTTGGCGTGCTCAGTGCTCACACAACGAGGCTTCAAGACTGTT
ORF - retro_cjac_847 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.45 % |
| Parental protein coverage: | 68.75 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | FDNYSANVMVDSKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASYENVRAKWFPEVRHHCP |
| F.NYSANVMVD.KPVNLGLWDTAGQE.YD.LR.L.YPQTDVFLICFSLVSPAS.ENVRA...PEVRHHCP | |
| Retrocopy | FNNYSANVMVDGKPVNLGLWDTAGQENYDILRLLFYPQTDVFLICFSLVSPASFENVRA--YPEVRHHCP |
| Parental | STPIILVGTKLDLRDDK-DTIEKLKEKKLAPITYPQGLALAKEIDSVKYLECSALTQRGLKTV |
| .T.IILV.TKL..RDDK.DTI.KLKE.KL.PITY.QGLA.AKEI..VKYL.CS.LTQRG.KTV | |
| Retrocopy | NTTIILVETKLGIRDDK<DTIKKLKE-KLTPITYEQGLAMAKEIGAVKYLACSVLTQRGFKTV |
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 | 1 .46 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .28 RPM |
| SRP051959_kidney | 0 .00 RPM | 1 .18 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .01 RPM |
| SRP051959_lung | 0 .00 RPM | 10 .10 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 26 .57 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .15 RPM |
| SRP051959_spleen | 0 .00 RPM | 8 .19 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_847 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_847 was not experimentally validated.