RetrogeneDB ID: | retro_cjac_599 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:106551790..106552266(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RPS5 | ||
| Ensembl ID: | ENSCJAG00000000304 | ||
| Aliases: | None | ||
| Description: | ribosomal protein S5 [Source:HGNC Symbol;Acc:10426] |
Retrocopy-Parental alignment summary:
>retro_cjac_599
ATGACCAAGTGGGAGACAGCAACACCAGAGGTGGCAGAGACCCCCAACATCAGCTCTTTGGGAAGTGGAGCACTGATGAT
GGGCAGATCAATGACATGTCCCTGCAGGATTACATTTCAGTGAGGAAGTATGCCAAGTACCTGCCTCACAGTGCAGGCCA
GTGTGCTGCCAAGCATTTCCACAAAACACAGTGCCCTATCATGGAGCACCTCACTACCTCCATGATGAAGCATGGCCACA
ACCATGACAAGAAGCCTATGACCATGCACACTGTCAAGCATGCCTTCGAGCTCATCCACCTGCCCAAGAGTGAGAACACT
CTTCAAGTCCTGGTGAATGCCATCAACAGTGATCTCTGGGAGGTCTCCACATGCATTGGGCGAGCCAAGACCACGAGATA
ACATACTGTGGCTGTGTCCCCCCTGCACAGCATGAATCAAGCCATCTGGCTGCTGTGCACAGGCACTTGTGAGGCT
ORF - retro_cjac_599 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 69.75 % |
| Parental protein coverage: | 78.92 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MTEWETAAPAVAETPDI-KLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKRFRKAQCPIV |
| MT.WETA.P.VAETP.I..LFGKWSTDD.QIND.SLQDYI.V..KYAKYLPHSAG..AAK.F.K.QCPI. | |
| Retrocopy | MTKWETATPEVAETPNI<QLFGKWSTDDGQINDMSLQDYISVR-KYAKYLPHSAGQCAAKHFHKTQCPIM |
| Parental | ERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSGPREDSTRIGRAGTVRRQAV |
| E.LT.SMM.HG.N..KK.MT...VKHAFE.IHL...EN.LQVLVNA.INS...E.ST.IGRA.T.R...V | |
| Retrocopy | EHLTTSMMKHGHNHDKKPMTMHTVKHAFELIHLPKSENTLQVLVNA-INSDLWEVSTCIGRAKTTR*HTV |
| Parental | DVSPLRRVNQAIWLLCTGAREA |
| .VSPL...NQAIWLLCTG..EA | |
| Retrocopy | AVSPLHSMNQAIWLLCTGTCEA |
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 | 87 .24 RPM |
| SRP051959_heart | 0 .00 RPM | 62 .78 RPM |
| SRP051959_kidney | 0 .00 RPM | 52 .71 RPM |
| SRP051959_liver | 0 .00 RPM | 101 .91 RPM |
| SRP051959_lung | 0 .00 RPM | 73 .32 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 123 .97 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 112 .09 RPM |
| SRP051959_spleen | 0 .00 RPM | 104 .37 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_599 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_599 was not experimentally validated.