RetrogeneDB ID: | retro_cjac_3993 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286683.1:5507..6494(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FBLN5 | ||
| Ensembl ID: | ENSCJAG00000017963 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_3993
GATGAAGGCAACCAGTGTGTGGATGTGGACAAGTGTGCAACAGATTCCCACCAGTGCAACTCTACCCAGATCTGTATCAA
CAATGAAGGCGGGTACACCTGCTCCTGCACCGATGGATACTGGCTACTGGAAGGCCAGTGCTTAGATATTGATGAATGTC
ACTATGGTTACTGCCAGCAGCTCTGTGTGAATGTTCCTTGATCCTACTCTTGTACATGCAACCCTGGTTTTACCCTCAAT
GAGGATGGAAGGTCTTGCCAAGATGTGAACGAGTGTGTAACTGAGAGCCCCTGTGTGCAAACCTGCGTCAACACCTATGC
CTCTTTCGTCTGCCACTGTGACCCGGGATATGAACTTGAGGAAGATGGTGTTCACTGCAGTGATGTGGACGAGTGTAGCT
TCTCTGAGTTCCTCTGCCAACATGAATGTGTGAACCAGCCTGGCACATATTTCTGCTCCTGCCCTTCAGGCTACATCCTA
CTGGATGACAACCAAAGCTGCCAGGATATCAATGAATGTGAGCACAGAAACCACACATGCAACCTGCAGCAGACTTGCTA
CAATTTACAAGGGGGCTTCAAATGCATTGACCCCATCCGCTGTGAGGAGCCTTATCTGAGGATCAATGATAACCGCTGTA
TGTGTCCTGCTGAGAACCCTGGCTGCAGAGACCAGCCCTTTACCATCTTGTACCTGGACGTGGATGTGGTGTCAGGACAC
TCTGTTCCCGCTGACATCTTCCAAATGCAAGCCACGACCTGCTACCCTGGGGCCTATTACATTTTCCAGATCAACTCTGG
GAATGAGGGCAGAGAATTTTATGTGCAGCAAACGGGCCCCATCAGCACCACCCTAGTGATGACGCGCCCCATCAAAGGGC
CCCAGGAAATCCAGTTGGACTTGGAAATGATCACTGTCAACACTGTCATCAACTTCAGAGGCAGCTCTGTGATCCGACTG
TGGATATATGTGTCGCAATACCCATTC
ORF - retro_cjac_3993 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.1 % |
| Parental protein coverage: | 60.37 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | DEGNQCVDVDECATDSHQCNPTQICINTEGGYTCSCTDGYWLLEGQCLDIDECRYGYCQQLCANVPGSYS |
| DEGNQCVDVD.CATDSHQCN.TQICIN.EGGYTCSCTDGYWLLEGQCLDIDEC.YGYCQQLC.NVP.SYS | |
| Retrocopy | DEGNQCVDVDKCATDSHQCNSTQICINNEGGYTCSCTDGYWLLEGQCLDIDECHYGYCQQLCVNVP*SYS |
| Parental | CTCNPGFTLNEDGRSCQDVNECATENPCVQTCVNTYGSFICRCDPGYEPEEDGVHCSDMDECSFSEFLCQ |
| CTCNPGFTLNEDGRSCQDVNEC.TE.PCVQTCVNTY.SF.C.CDPGYE.EEDGVHCSD.DECSFSEFLCQ | |
| Retrocopy | CTCNPGFTLNEDGRSCQDVNECVTESPCVQTCVNTYASFVCHCDPGYELEEDGVHCSDVDECSFSEFLCQ |
| Parental | HECVNQPGTYFCSCPPGYILLDDNRSCQDINECEHRNHTCNLQQTCYNLQGGFKCIDPIRCEEPYLRISD |
| HECVNQPGTYFCSCP.GYILLDDN.SCQDINECEHRNHTCNLQQTCYNLQGGFKCIDPIRCEEPYLRI.D | |
| Retrocopy | HECVNQPGTYFCSCPSGYILLDDNQSCQDINECEHRNHTCNLQQTCYNLQGGFKCIDPIRCEEPYLRIND |
| Parental | NRCMCPAENPGCRDQPFTILYRDMDVVSGRSVPADIFQMQATTRYPGAYYIFQIKSGNEGREFYMRQTGP |
| NRCMCPAENPGCRDQPFTILY.D.DVVSG.SVPADIFQMQATT.YPGAYYIFQI.SGNEGREFY..QTGP | |
| Retrocopy | NRCMCPAENPGCRDQPFTILYLDVDVVSGHSVPADIFQMQATTCYPGAYYIFQINSGNEGREFYVQQTGP |
| Parental | ISATLVMTRPIKGPREIQLDLEMITVNTVINFRGSSVIRLRIYVSQYPF |
| IS.TLVMTRPIKGP.EIQLDLEMITVNTVINFRGSSVIRL.IYVSQYPF | |
| Retrocopy | ISTTLVMTRPIKGPQEIQLDLEMITVNTVINFRGSSVIRLWIYVSQYPF |
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 | 2 .20 RPM |
| SRP051959_heart | 0 .02 RPM | 52 .32 RPM |
| SRP051959_kidney | 0 .27 RPM | 30 .11 RPM |
| SRP051959_liver | 0 .09 RPM | 0 .50 RPM |
| SRP051959_lung | 0 .02 RPM | 14 .67 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .35 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 5 .98 RPM |
| SRP051959_spleen | 0 .02 RPM | 23 .84 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3993 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3993 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3993 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 38 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000017963 | 3 retrocopies |
retro_cjac_3822, retro_cjac_3823, retro_cjac_3993 ,
|
| Callithrix jacchus | ENSCJAG00000037941 | 35 retrocopies |
retro_cjac_3343, retro_cjac_3355, retro_cjac_3369, retro_cjac_3372, retro_cjac_3389, retro_cjac_3391, retro_cjac_3423, retro_cjac_3425, retro_cjac_3430, retro_cjac_3445, retro_cjac_3456, retro_cjac_3474, retro_cjac_3476, retro_cjac_3477, retro_cjac_3487, retro_cjac_3491, retro_cjac_3543, retro_cjac_3545, retro_cjac_3547, retro_cjac_3549, retro_cjac_3566, retro_cjac_3583, retro_cjac_3598, retro_cjac_3609, retro_cjac_3616, retro_cjac_3622, retro_cjac_3633, retro_cjac_3641, retro_cjac_3656, retro_cjac_3672, retro_cjac_3674, retro_cjac_3677, retro_cjac_3682, retro_cjac_3733, retro_cjac_3736,
|