RetrogeneDB ID: | retro_cjac_2512 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:32558512..32559942(+) | ||
| Located in intron of: | ENSCJAG00000011302 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PRAME | ||
| Ensembl ID: | ENSCJAG00000020319 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2512
GAGAGCCTGCTGAAGAATGAGGCCCTGGCCATCGCTGTCTTGGAGTTGCTCCCCAAAATTTTTTCCCGCCACTCTTCAGG
GCAGACTTTGACGGGAAACACAACCAGACTCTGAAGGCAATGGTGCAGGCCTGGCCCTTCACCTGCCTCCCTCTGGGAGT
GCTGATGAAGGGACAGCAGCTTCACGTGGAAACCTTCAAAGCTGTGCTTGAAGGAGTTGATGTGCTGCTTGCCCAGGAGG
TTCACCCCAGGAGGTGGACACTCAAAGTGCTGGATGTAGGAAAGCATTCTCATCAAGACTTCTGGACCATATGGTCTGGA
AAAAGGGTCAGTCTGCTCATTTCCAGAGCCAGAAGCAGCTCAGCCCATGAGAAAGAAGCGAAAATAGATGGTTTGAGCAC
AGAAGCAGAGAAGCCCTTTACTCCAAAAGATGTTCTCGTAGACCTGTCCCTCAAGGAAGGTGCCTATGATGAATTGTTCA
CCCACCTGATTGAGATAGTGAGGCGAAAGAAAGATGTACTACACCTGTGCTGTAAGAAGCTGAAGATTTTTTGCCATGCC
TGTGCAGAATATCAAGATGATCCTGAAAATGGTGCAGCTGGACTCTATTGAAGATTTGGAAGTGACTTGCACCTGGAAAC
TAACCTCCTTGGTGAAATTTTCTCCTCACCTGAGCCAGATAAGTAATCTATGTAGACTACTCCTCGCTCACATCCATCCA
TCTTCCTTCATTTCCCCAGAGAAGGAGGAGCAGTATATCGCCCAGTTCACCTCTCAGTTCCTCAGTCTCCACTGCCTCCA
GGAGCTCTACATGGACTCTTTATTTTTCCTCTGAGGCCGCCTGGATCAGTTGCTCAGATGCATGATGAACCCCTTGGAAA
CCCTTTCGATAACTAACTGCTGGCTTTCAGAAGAAGATGTGACACATCTGTCCTGGAGCCCCAGCATCAGTCAGCTGAGT
GTCTTGAGTCTAAGTGGGGTCATGCTGACCGAGATAAATCCCGAGCTCCTCCAAGCTCTGCTAGAGAGAACCTCCGCCAC
CCTCCAGGACCTGGACTTAGATGAGTGTGGGATCATGGATACTCAGCTCCTTATTCTTCTGCCTTCCCTGAGCCACTGCT
CCCAGCTTACCACCTTCAGCTTCTGCAGGAATCCCATCTCCATGTCTGTCCTGGAGAACCTCGTGCACCACATCATCGGA
TTGAATAATCTGAGCCACTTGCTGTATCCTGTCCGCATGGAGAGTTAGGAGGACGTCAATGGCACCCTCGACCTGGGGAG
ACTTGCCTATCTGCACACCAGGCTAGGGAGTTGCTGTGTGAATTGGGGTGGCCTGGCATGGTCTGGCTCAGTGCCAACTC
CTGTCCTCACTGTGGGGACAGAACCTTCTATGACCCAGATCCCATCCTGTGCCCCTGTTTCACGCCTGCC
ORF - retro_cjac_2512 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.03 % |
| Parental protein coverage: | 93.91 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | QSLLKNESLAIAALELLPR-ELFPPLFTAAFDGRHNKTLKAMVQAWPFTCLPLGVLMKGQQLHVETFKAV |
| .SLLKNE.LAIA.LELLP....FPPLF.A.FDG.HN.TLKAMVQAWPFTCLPLGVLMKGQQLHVETFKAV | |
| Retrocopy | ESLLKNEALAIAVLELLPK<NFFPPLFRADFDGKHNQTLKAMVQAWPFTCLPLGVLMKGQQLHVETFKAV |
| Parental | LDGVDVLLAQEVRPRRWKLKVLDLRKNSHQDFWTVWSGKRVSLCSFPEPEAAQPMRKKRKVDGSSTEAEQ |
| L.GVDVLLAQEV.PRRW.LKVLD..K.SHQDFWT.WSGKRVSL.............K..K.DG.STEAE. | |
| Retrocopy | LEGVDVLLAQEVHPRRWTLKVLDVGKHSHQDFWTIWSGKRVSLL-ISRARSSSAHEKEAKIDGLSTEAEK |
| Parental | RFIPIEVLVDLSLKEGAYDELFIHLIEIVRRKKDVLHLCCKKLKI-FAMPVQNIKMILKMVQLDSIEDLE |
| .F.P..VLVDLSLKEGAYDELF.HLIEIVRRKKDVLHLCCKKLKI.FAMPVQNIKMILKMVQLDSIEDLE | |
| Retrocopy | PFTPKDVLVDLSLKEGAYDELFTHLIEIVRRKKDVLHLCCKKLKI>FAMPVQNIKMILKMVQLDSIEDLE |
| Parental | VTCTWKLPTLAKFSPHLSQMSNLRRLLLAHIHPASFISPEKEEQFIAQFISQFLNLHCLEELYVDSLFFL |
| VTCTWKL..L.KFSPHLSQ.SNL.RLLLAHIHP.SFISPEKEEQ.IAQF.SQFL.LHCL.ELY.DSLFFL | |
| Retrocopy | VTCTWKLTSLVKFSPHLSQISNLCRLLLAHIHPSSFISPEKEEQYIAQFTSQFLSLHCLQELYMDSLFFL |
| Parental | RGHLDQLLRCMMNPLETLSITNCWLSEEDVTHLSQSPNISQLSVLSLSGVMLTEINPELLQALLERTSAT |
| .G.LDQLLRCMMNPLETLSITNCWLSEEDVTHLS.SP.ISQLSVLSLSGVMLTEINPELLQALLERTSAT | |
| Retrocopy | *GRLDQLLRCMMNPLETLSITNCWLSEEDVTHLSWSPSISQLSVLSLSGVMLTEINPELLQALLERTSAT |
| Parental | LQDLDLDECGIVDTQLLVLLPSLSHCSQLTTFSFCGNPISISVLESLVHHIIGLNNLSHVLYPVPVESFE |
| LQDLDLDECGI.DTQLL.LLPSLSHCSQLTTFSFC.NPIS.SVLE.LVHHIIGLNNLSH.LYPV..ES.E | |
| Retrocopy | LQDLDLDECGIMDTQLLILLPSLSHCSQLTTFSFCRNPISMSVLENLVHHIIGLNNLSHLLYPVRMES*E |
| Parental | DINGTLDLGRLAYLHTRL-RELLCELGRPGMVWLSATPCPHCGDRTFYDPDPILCPCFMPA |
| D.NGTLDLGRLAYLHTRL.RELLCELG.PGMVWLSA..CPHCGDRTFYDPDPILCPCF.PA | |
| Retrocopy | DVNGTLDLGRLAYLHTRL<RELLCELGWPGMVWLSANSCPHCGDRTFYDPDPILCPCFTPA |
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 | 1 .84 RPM | 0 .20 RPM |
| SRP051959_heart | 1 .26 RPM | 0 .19 RPM |
| SRP051959_kidney | 1 .06 RPM | 0 .18 RPM |
| SRP051959_liver | 0 .67 RPM | 0 .26 RPM |
| SRP051959_lung | 2 .10 RPM | 0 .31 RPM |
| SRP051959_lymph_node | 2 .44 RPM | 0 .32 RPM |
| SRP051959_skeletal_muscle | 0 .83 RPM | 0 .09 RPM |
| SRP051959_spleen | 2 .02 RPM | 0 .19 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2512 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2512 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2512 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000020319 | 2 retrocopies |
retro_cjac_1383, retro_cjac_2512 ,
|