RetrogeneDB ID: | retro_opri_612 | ||
Retrocopy location | Organism: | Southern American pika (Ochotona princeps) | |
| Coordinates: | scaffold_19360:5155..5635(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FAM107B | ||
| Ensembl ID: | ENSOPRG00000004614 | ||
| Aliases: | None | ||
| Description: | family with sequence similarity 107, member B [Source:HGNC Symbol;Acc:23726] |
Retrocopy-Parental alignment summary:
>retro_opri_612
GAGCGAGCCCGGGAGGCAGCCGCATGCCTTTGTGTGCACCAAGACGGCCCACTGGAGGCTGACCCTTCGGACCCCTACCT
CATCATGAGAAACATCATGGCGGAGCCTAACTACACGGACTACGACAACCCTGAGCTGATCAGACCCCAGAAGCTCATCA
ATACGATCAAGATGTCCCGGAACCACCAGGACCTGCACAGAGAGCTGCTGATGAATCAGAAAAGAGGTCTTCCCCCTCAG
AATAAACCTGAATTGCAGAAAGTGATGGAAAAGAGAAAAGAAGACCAAGTAATAAAGCAGAAGGAAGAAGAAGCATAAAA
GAAGTCTGACTTAGAACTGTTAAAACGCTAGCAGAAGTTGGAACAGCTTGAACTTGAGAAGCAGAAATTGCAAGAAGAGC
AAGAAAATGCCCCGGAGTTTGTGAAAGTGAAAGGCAATCTCAGGAGAACAGGCCAGGAAGTAGCCCAAGCCCAGGAGTCC
ORF - retro_opri_612 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.04 % |
| Parental protein coverage: | 54.75 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EELQEETKCLELQQKMISDGPLEADPSDPYLIPRSIMAEPDYTDDDNPELIRPQKLINPVKTSRNHQDLH |
| E...E...CL...Q....DGPLEADPSDPYLI.R.IMAEP.YTD.DNPELIRPQKLIN..K.SRNHQDLH | |
| Retrocopy | ERAREAAACLCVHQ----DGPLEADPSDPYLIMRNIMAEPNYTDYDNPELIRPQKLINTIKMSRNHQDLH |
| Parental | RELLMNQKRGLAPQNKPELQKVMEKRKRDQVIKQKEEEAQKKKSDLEIELLKRQQKLEQLELEKQKLQEE |
| RELLMNQKRGL.PQNKPELQKVMEKRK.DQVIKQKEEEA.KK......ELLKR.QKLEQLELEKQKLQEE | |
| Retrocopy | RELLMNQKRGLPPQNKPELQKVMEKRKEDQVIKQKEEEA*KKS---DLELLKR*QKLEQLELEKQKLQEE |
| Parental | QENAPEFVKVKGNLRRTGQEVAQAQES |
| QENAPEFVKVKGNLRRTGQEVAQAQES | |
| Retrocopy | QENAPEFVKVKGNLRRTGQEVAQAQES |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ochotona princeps was not studied using RNA-Seq expression data.
Ochotona princeps was not studied using ChIP-Seq data.
Ochotona princeps was not studied using EST data.
Ochotona princeps was not studied using FANTOM5 data.
retro_opri_612 was not experimentally validated.
Retrocopy orthology:
Ochotona princeps 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 | |
|---|---|---|---|
| Ochotona princeps | ENSOPRG00000004614 | 1 retrocopy |
retro_opri_612 ,
|