RetrogeneDB ID: | retro_vpac_406 | ||
Retrocopy location | Organism: | Alpaca (Vicugna pacos) | |
| Coordinates: | scaffold_16204:3283..3916(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | OTUD3 | ||
| Ensembl ID: | ENSVPAG00000010397 | ||
| Aliases: | None | ||
| Description: | OTU domain containing 3 [Source:HGNC Symbol;Acc:29038] |
Retrocopy-Parental alignment summary:
>retro_vpac_406
TATGACAGCGTCCGGAGGATCAACGACAACTCGGAAGCACCTGCGCACCTCCAGACTGATTTTCAGATGCTTCATCAAGA
TGAATCAAATAAAAGAGAGAAGATCAAGACAAAGGGAGTCGACTTTGAGGACGACCTGAAAGATGAAGTAGAAGACGCCG
TCCAGAAAGTCGGCAATGCAACTGGGTGTTCAGATTTTAATTTGATAGTCCAGAACCTGGAAGCTGAGAATTACAACATC
GAATCTGCGATAATTGCCATGCTCCAGATGAACCACGGGAGAAGAAATAATGCAGAGGAGAACCTTGAGTCCAGTGGCCG
AGTCCTGAAGCAGTGTGGCCCTTTATGGGAGGAGGATGGCAGTGGCACCAGAATCTTTGGAAATCAGGGCTTAAATGAAG
GCAGGACTGAAAACAATAAGGCACGGGCCAGCCCTACTGAAGAAAACAAAGCAAATAAAAACCAGCTCCCAAAGGTCACA
AACAGGCAGCGGCTAGAGAAGAACAAGCGGCAGGAGTAGCGGCATCGGCACAAAGCCCTGGAGGGCAGGGGCGGCCACAG
GGACGGCAGCAGGAGCGAAGCGGATGCGAGCGCTCAGGTCACCTTGGTGAAGACCTTCGCCGCTCTCACCATC
ORF - retro_vpac_406 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.28 % |
| Parental protein coverage: | 66.87 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | YDSVRRINDNSEAPAHLQTDFQMLHQDESNKREKIKTKGVDFEDDLKDEVEDAVQKVGNATGCSDFNLIV |
| YDSVRRINDNSEAPAHLQTDFQMLHQDESNKREKIKTKGVDFEDDLKDEVEDAVQKVGNATGCSDFNLIV | |
| Retrocopy | YDSVRRINDNSEAPAHLQTDFQMLHQDESNKREKIKTKGVDFEDDLKDEVEDAVQKVGNATGCSDFNLIV |
| Parental | QNLEAENYNIESAIIAMLQMNQGRRNNAEENLESSGRVLKQCGPLWEEDGSGTRIFGNQGLNAGRTENSK |
| QNLEAENYNIESAIIAMLQMN.GRRNNAEENLESSGRVLKQCGPLWEEDGSGTRIFGNQGLN.GRTEN.K | |
| Retrocopy | QNLEAENYNIESAIIAMLQMNHGRRNNAEENLESSGRVLKQCGPLWEEDGSGTRIFGNQGLNEGRTENNK |
| Parental | ARASPTEGNKANKNQLPKVTNRQRREQQRLEKKKRQEERHRHKALEGRGGPGDGSRSEADASAQVTLVKT |
| ARASPTE.NKANKNQLPKVTNRQR.E.....K......RH..KALEGRGG..DGSRSEADASAQVTLVKT | |
| Retrocopy | ARASPTEENKANKNQLPKVTNRQRLEK---NKRQE*RHRH--KALEGRGGHRDGSRSEADASAQVTLVKT |
| Parental | FAALSI |
| FAAL.I | |
| Retrocopy | FAALTI |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Vicugna pacos was not studied using RNA-Seq expression data.
Vicugna pacos was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_vpac_406 retrocopy.
Vicugna pacos was not studied using FANTOM5 data.
retro_vpac_406 was not experimentally validated.
Retrocopy orthology:
Vicugna pacos does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Vicugna pacos | ENSVPAG00000010397 | 1 retrocopy |
retro_vpac_406 ,
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