RetrogeneDB ID: | retro_cjac_1440 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 15:98402746..98403122(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | TXNDC12 | ||
| Ensembl ID: | ENSCJAG00000021581 | ||
| Aliases: | None | ||
| Description: | thioredoxin domain containing 12 (endoplasmic reticulum) [Source:HGNC Symbol;Acc:24626] |
Retrocopy-Parental alignment summary:
>retro_cjac_1440
AAGATGCAGTCAGTTCCTAGCAGTTTGCCCCTGATGGTGATTATTCATAAGTCATGGTGTGGAGCTTGCAATGCTTGAAA
GCCCAAATTTGCAGAACCTCTAGAAATTTCAGAACTTTCTCATAGTTTTGTTACGGTAAACCTTGAGGATGAAGGAGGAC
GCAAGGATGAGGATTTTGCCCTGATAGAGTTATATTTCACACATCGTTTGTTTGGATCCCAGTGGTAAGGCGCATCCTGA
AATCATCAATGAGAATGGAAACTGCAGCTGCAAGTATTTCTACATCAGTGCCGAGCAAGTTGTTCAGGGGATGAAGGAAG
CTCAGGAAAGGCTGATGGGTGATGCCTTCAGAAAGAAACGTCTTGATAATGATTTG
AAGATGCAGTCAGTTCCTAGCAGTTTGCCCCTGATGGTGATTATTCATAAGTCATGGTGTGGAGCTTGCAATGCTTGAAA
GCCCAAATTTGCAGAACCTCTAGAAATTTCAGAACTTTCTCATAGTTTTGTTACGGTAAACCTTGAGGATGAAGGAGGAC
GCAAGGATGAGGATTTTGCCCTGATAGAGTTATATTTCACACATCGTTTGTTTGGATCCCAGTGGTAAGGCGCATCCTGA
AATCATCAATGAGAATGGAAACTGCAGCTGCAAGTATTTCTACATCAGTGCCGAGCAAGTTGTTCAGGGGATGAAGGAAG
CTCAGGAAAGGCTGATGGGTGATGCCTTCAGAAAGAAACGTCTTGATAATGATTTG
ORF - retro_cjac_1440 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.44 % |
| Parental protein coverage: | 73.26 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | KKEAAASGLPLMVIIHKSWCGACKALKPKFAESTEISELSHNFVMVNLEDEEEPKDEDFS-PDG-GYIPR |
| K.....S.LPLMVIIHKSWCGAC.A.KPKFAE..EISELSH.FV.VNLEDE...KDEDF..PD...YI.. | |
| Retrocopy | KMQSVPSSLPLMVIIHKSWCGACNA*KPKFAEPLEISELSHSFVTVNLEDEGGRKDEDFA<PDR<SYISH |
| Parental | ILFLDPSGKVHPEIINENGNPSYKYFYVSAEQVVQGMKEAQERLTGDAFREKHLEDEL |
| I..LDPSGK.HPEIINENGN.S.KYFY.SAEQVVQGMKEAQERL.GDAFR.K.L...L | |
| Retrocopy | IVCLDPSGKAHPEIINENGNCSCKYFYISAEQVVQGMKEAQERLMGDAFRKKRLDNDL |
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 | 10 .96 RPM |
| SRP051959_heart | 0 .09 RPM | 7 .40 RPM |
| SRP051959_kidney | 0 .02 RPM | 13 .38 RPM |
| SRP051959_liver | 0 .09 RPM | 20 .10 RPM |
| SRP051959_lung | 0 .07 RPM | 9 .84 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 8 .15 RPM |
| SRP051959_skeletal_muscle | 0 .11 RPM | 8 .34 RPM |
| SRP051959_spleen | 0 .02 RPM | 10 .88 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1440 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1440 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1440 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 | ENSCJAG00000021581 | 2 retrocopies |
retro_cjac_1369, retro_cjac_1440 ,
|