RetrogeneDB ID: | retro_cjac_3664 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | ACFV01193355.1:2794..3301(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | WDR83 | ||
| Ensembl ID: | ENSCJAG00000005272 | ||
| Aliases: | None | ||
| Description: | WD repeat domain 83 [Source:HGNC Symbol;Acc:32672] |
Retrocopy-Parental alignment summary:
>retro_cjac_3664
ATGGCTTTCCCTGAGCCAAAGCCGCGGCCACCGGAGCTGCCGCAGAAACGGTTGAAGACTCTGGACTGCGGGCAAGGGGC
AGTGCCAGCCGTACGATTTAACGTGGATGGCAATTACTGCCTGGCGTGCGGCAGCGACAAGACCCTGAAACTGTGGAACC
CACTTCGGGGAACGCTGCTGCGGACGTACAGCGGCCACGGCTACGAGGTGCTGGATGCGGCCGGCTCCTTTGACAACAGC
CTCTGCTCCGGCGGCGGCGGAGACAAGGCGGTGGTCCTGTGGGATGTGGCATCGGGGCAGGTCGTGCGCAAATTCCGGGG
CCACGCAGGGAAGGTGAACACGGTGCAGTTTAATGAAGAGGCCACAGTTATCCCGTCCGGCTCTATTGATTCCAGTATCC
GCTGTTGGGACTGCCGCTCACGGAGGCCTGAGCCAGTGCAGACGCTGGATGAGGCCAGAGATGGCGTGTCCAGTGTGGAG
GTGTCAGACCACGAGATCCTGGCAGGG
ORF - retro_cjac_3664 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.27 % |
| Parental protein coverage: | 53.65 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAFPEPKPRPPELPQKRLKTLDCGQGAVRAVRFNVDGNYCLTCGSDKTLKLWNPLRGTLLRTYSGHGYEV |
| MAFPEPKPRPPELPQKRLKTLDCGQGAV.AVRFNVDGNYCL.CGSDKTLKLWNPLRGTLLRTYSGHGYEV | |
| Retrocopy | MAFPEPKPRPPELPQKRLKTLDCGQGAVPAVRFNVDGNYCLACGSDKTLKLWNPLRGTLLRTYSGHGYEV |
| Parental | LDAAGSFDNSSLCSGGGDKAVVLWDVASGQVVRKFRGHAGKVNTVQFNEEATVILSGSIDSSIRCWDCRS |
| LDAAGSFDNS....GGGDKAVVLWDVASGQVVRKFRGHAGKVNTVQFNEEATVI.SGSIDSSIRCWDCRS | |
| Retrocopy | LDAAGSFDNSLCSGGGGDKAVVLWDVASGQVVRKFRGHAGKVNTVQFNEEATVIPSGSIDSSIRCWDCRS |
| Parental | RRPEPVQTLDEARDGVSSVKVSDHEILAG |
| RRPEPVQTLDEARDGVSSV.VSDHEILAG | |
| Retrocopy | RRPEPVQTLDEARDGVSSVEVSDHEILAG |
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 .11 RPM | 0 .22 RPM |
| SRP051959_heart | 0 .02 RPM | 0 .26 RPM |
| SRP051959_kidney | 0 .04 RPM | 0 .49 RPM |
| SRP051959_liver | 0 .56 RPM | 0 .35 RPM |
| SRP051959_lung | 0 .44 RPM | 0 .37 RPM |
| SRP051959_lymph_node | 0 .50 RPM | 0 .84 RPM |
| SRP051959_skeletal_muscle | 0 .09 RPM | 0 .44 RPM |
| SRP051959_spleen | 0 .38 RPM | 0 .25 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3664 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3664 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3664 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000005272 | 1 retrocopy |
retro_cjac_3664 ,
|
| Callithrix jacchus | ENSCJAG00000010123 | 1 retrocopy |