RetrogeneDB ID: | retro_cjac_561 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:81426985..81427671(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TGFB2 | ||
| Ensembl ID: | ENSCJAG00000012931 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_561
AGCACACTCGATATGGACCAGTTCATGCGCAAGAGGATCGAGGCGATCCGCGGGCAGATCCTGAGCAAGCTGAAGCTTAC
CAGACCCCCAGAAGACTATCCTGAGCCCGAGGAAGTCCCCCCGGAGGTGATTTCCATCTACAACAGCACCAGGGACTTGT
CCAGGAGAAGGTGAGCCGGAGGCCTGCCACCTGCAAGCGCGAGAGGAGCGACGAGGAGTACTACGCCAAGGAGGTTTACA
AAATAGACACGCCGCCCTTCTTCCCCTCCGAAAATGCCATCCCGCCCACTTTCTACAGACCCGACTTCAGAATTGTCCGA
TTTGATGTCTCAGCAATGGAGAAGAATGCTTCCAATTTGGTGAAAGCAGAGTTCAGAGTCTTTCGTTTGCAGAACCCAAA
AGCCAGAGTGCCTGAACAACGGATCGAGCTGTATCAGATTCTCAAGTCCAAAGATTGAACATCTCTAACCCAGCGCTACA
TCAACAGCAAAGTTGTGAAAACAAGAGCAGAAGGCGAATGGTTCTCTTTTGATGTAACTGATGCTGTTCATGAATGGCTT
CACCATAAAGACAGGAATCTGGGGTTTAAAATAAGCTTACACTGTCCCTGTTGTACTTTTGTACCATCTAATAATTACAT
CATCCCAAATAAAAGCGAAGAACTAGAAGCAAGATTTGCAGACTTG
ORF - retro_cjac_561 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.48 % |
| Parental protein coverage: | 55.31 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | STLDMDQFMRKRIEAIRGQILSKLKLTSPPEDYPEPEEVPPEVISIYNSTRDL-LQEKASRRAAACERER |
| STLDMDQFMRKRIEAIRGQILSKLKLT.PPEDYPEPEEVPPEVISIYNSTRDL..QEK.SRR.A.C.RER | |
| Retrocopy | STLDMDQFMRKRIEAIRGQILSKLKLTRPPEDYPEPEEVPPEVISIYNSTRDL<VQEKVSRRPATCKRER |
| Parental | SDEEYYAKEVYKIDMPPFFPSENAIPPTFYRPYFRIVRFDVSAMEKNASNLVKAEFRVFRLQNPKARVPE |
| SDEEYYAKEVYKID.PPFFPSENAIPPTFYRP.FRIVRFDVSAMEKNASNLVKAEFRVFRLQNPKARVPE | |
| Retrocopy | SDEEYYAKEVYKIDTPPFFPSENAIPPTFYRPDFRIVRFDVSAMEKNASNLVKAEFRVFRLQNPKARVPE |
| Parental | QRIELYQILKSKDLTSPTQRYIDSKVVKTRAEGEWLSFDVTDAVHEWLHHKDRNLGFKISLHCPCCTFVP |
| QRIELYQILKSKD.TS.TQRYI.SKVVKTRAEGEW.SFDVTDAVHEWLHHKDRNLGFKISLHCPCCTFVP | |
| Retrocopy | QRIELYQILKSKD*TSLTQRYINSKVVKTRAEGEWFSFDVTDAVHEWLHHKDRNLGFKISLHCPCCTFVP |
| Parental | SNNYIIPNKSEELEARFAGI |
| SNNYIIPNKSEELEARFA.. | |
| Retrocopy | SNNYIIPNKSEELEARFADL |
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 | 3 .90 RPM |
| SRP051959_heart | 0 .00 RPM | 16 .38 RPM |
| SRP051959_kidney | 0 .00 RPM | 7 .52 RPM |
| SRP051959_liver | 0 .00 RPM | 1 .00 RPM |
| SRP051959_lung | 0 .00 RPM | 9 .19 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 1 .87 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 6 .90 RPM |
| SRP051959_spleen | 0 .00 RPM | 2 .96 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_561 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_561 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_561 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000012931 | 1 retrocopy |
retro_cjac_561 ,
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