RetrogeneDB ID: | retro_cjac_3482 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01181484.1:11309..12111(-) | ||
| 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: | ENSCJAG00000015967 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3482
TCATCCCACTGCCATGTGACCCTCAGTTCCTCAGAGACAGTGAGTGAGCTCAACTCTCAGGCTATCATTCACACTCAGCG
TGAAAAGGCAGCAGATTCACTACCAAGGGAGAAACTGGCCCCCAGGAATGGCTCCCCAACATCTCAAAAGTCTAGGCCTC
GTAGAAAGAAATATCCTCCGCTGCCATGCAGCGAAGGGGAGCCTCTGATGCTGCCCCCTCCCTTACAGCTGGGGTTCCAG
ATCACTGCTGAAGACCTGGACCTGGAGAAGGAGGCGACGCTCCGGGGCATTAATAGTGCACTTCGGGGTGAGGTCAAGGC
CATCTGGGACTGTAGAGCCTCACAGCCTTCACAAGCTTTGTCCTCACCTGCAACAGGGACTACTTGTCTGCCTGCTGTCC
CTGAAGCACCCAGCATGGATGCACATCAGCAGACTCACAAGTCCCAACAGTACCTGGACCACCTGTCCCTCCTAGCATCT
GCTGCAGGGGACCCCTCTAGACCTGCTGTGTCTGGGAGGAAGCACCGCTCATCAGGCCCCCTGTTCTCCTAAGAGCCCCT
TCCTGACACCACTTCACACTCCCGGGACACAGCCCAGGTCACCTCCCTGATTCCTGCCCCCTTCCCAGCTCCACGTGCGG
ACTGCAGCCTGAGAAGCGCAAGGCCTGGCACTTCTGCTGCTGCAGCTGCCGCAGGGGCCCTTACCCCCTCTACATGGAAC
CCTTCATGGGGGGCCCCACCGAGTGGAGGGCAAAGAGGCCCCTCACATCCCTGGGCCTCAGCCACAGCTGCAGCAGGTGC
CC
ORF - retro_cjac_3482 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.78 % |
| Parental protein coverage: | 66.58 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SSHCHVTLSSSKTVSEDNSQAVSQAVIHTQGEKAADAPPGEKLAPRNGSPTYQESRPCRRKFPLLPRRQR |
| SSHCHVTLSSS.TVSE.N....SQA.IHTQ.EKAAD..P.EKLAPRNGSPT.Q.SRP.R.K.P.LP.... | |
| Retrocopy | SSHCHVTLSSSETVSELN----SQAIIHTQREKAADSLPREKLAPRNGSPTSQKSRPRRKKYPPLPCSEG |
| Parental | EPLMLPPPLQLGYRVTAEDMDLEKEAGIQCINSALQGEVKAIRDCRASQPSQALSSPATGSS-PPAVPKV |
| EPLMLPPPLQLG...TAED.DLEKEA....INSAL.GEVKAI.DCRASQPSQALSSPATG....PAVP.. | |
| Retrocopy | EPLMLPPPLQLGFQITAEDLDLEKEATLRGINSALRGEVKAIWDCRASQPSQALSSPATGTTCLPAVPEA |
| Parental | PSMDAHQQTHKSQQYLGHLSLLASAAGDPSRPAVSGRKRRSSGPLFSYSYPLPDTPSHPRDTAQVTSLIP |
| PSMDAHQQTHKSQQYL.HLSLLASAAGDPSRPAVSGRK.RSSGPLFS...PLPDT.SH.RDTAQVTSLIP | |
| Retrocopy | PSMDAHQQTHKSQQYLDHLSLLASAAGDPSRPAVSGRKHRSSGPLFS*E-PLPDTTSHSRDTAQVTSLIP |
| Parental | APFPAPRADCSLRSPRPGTSAAAAAAGALTPSTWNPSWGS-HRVEGKEAPHIPGPQPQLQQVP |
| APFPAPRADCSLRS.RPGTSAAAAAAGALTPSTWNPSWG..HRVEGKEAPHIPGPQPQLQQVP | |
| Retrocopy | APFPAPRADCSLRSARPGTSAAAAAAGALTPSTWNPSWGA>HRVEGKEAPHIPGPQPQLQQVP |
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 | 0 .00 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .00 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .02 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .00 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3482 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3482 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3482 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000002950 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000015967 | 2 retrocopies |
retro_cjac_3482 , retro_cjac_645,
|