RetrogeneDB ID: | retro_cjac_2212 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:20413604..20413840(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000033635 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_2212
ATGGTGCACAAACACATTTATTATTCTACAAATCTGACGACGAGGAGTTTGAGTATCAGCATGTCATGCTAGCCAAGGAC
ATAGCCAAGCTGGTCCCTAAAACCCATTTGATGTCTGAATCTGAATAGAGGAATCTTGGCGTTCAGCAGAGTCACGGATG
GATCCATTATATGATCCTTGAACCAGAACCTCACATCTTACTGTTCCAGCACGCGCTACCCAAGAAGCCAAAAGAA
ATGGTGCACAAACACATTTATTATTCTACAAATCTGACGACGAGGAGTTTGAGTATCAGCATGTCATGCTAGCCAAGGAC
ATAGCCAAGCTGGTCCCTAAAACCCATTTGATGTCTGAATCTGAATAGAGGAATCTTGGCGTTCAGCAGAGTCACGGATG
GATCCATTATATGATCCTTGAACCAGAACCTCACATCTTACTGTTCCAGCACGCGCTACCCAAGAAGCCAAAAGAA
ORF - retro_cjac_2212 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.25 % |
| Parental protein coverage: | 100. % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSHKQIYYSD-KYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILLF |
| M.HK.IYYS..K.DDEEFEY.HVML.KDIAKLVPKTHLMSESE.RNLGVQQS.GW.HYMI.EPEPHILLF | |
| Retrocopy | MVHKHIYYST<KSDDEEFEYQHVMLAKDIAKLVPKTHLMSESE*RNLGVQQSHGWIHYMILEPEPHILLF |
| Parental | RRPLPKKPKK |
| ...LPKKPK. | |
| Retrocopy | QHALPKKPKE |
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 | 5 .79 RPM |
| SRP051959_heart | 0 .00 RPM | 2 .19 RPM |
| SRP051959_kidney | 0 .00 RPM | 1 .73 RPM |
| SRP051959_liver | 0 .00 RPM | 3 .44 RPM |
| SRP051959_lung | 0 .00 RPM | 1 .64 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .42 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .50 RPM |
| SRP051959_spleen | 0 .00 RPM | 4 .92 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2212 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2212 was not experimentally validated.