RetrogeneDB ID: | retro_opri_431 | ||
Retrocopy location | Organism: | Southern American pika (Ochotona princeps) | |
| Coordinates: | scaffold_11825:23440..24252(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSOPRG00000011575 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | LACC1 | ||
| Ensembl ID: | ENSOPRG00000013275 | ||
| Aliases: | None | ||
| Description: | laccase (multicopper oxidoreductase) domain containing 1 [Source:HGNC Symbol;Acc:26789] |
Retrocopy-Parental alignment summary:
>retro_opri_431
AGGGAATTTGAGACTGATACAATCCCATCATGGCTGCCTCATTATATACTATTAACAAAAATCAATGAAAAAATCTGAGC
AGTATTAATGTCATTCTCCCCTTGCATTGGAAAGCATCAATGAAAGCCTTTATTGTCCACCTCTTCACTGATGTTTACAA
TTTTAAGTTTGAAGATTTACAGATGACTTCAAAGGACAGCTTTTTGAAACAATCGCCCGAAGTAAATGTGATGACAGCTC
AAAAACTAGAAGAAATCCAGAATGAGATAGAAATGTATTTGAGTAGTTTGCCAGCACTAAAGGGAGAATTAACTATTATC
ACATCTGCTTTGATCCCAGATATTTTCACACATGGATTTACAACAAGAACAGGTGGCATATCTTACGTACCAACCCTTAG
CTCATTCAATCTCTTCAGTAGTTCCAAAAGGAGAGATCCCAAGGCAGTTGTTCAAGAAACTCTATATAGATTGGCAAATA
CTATGGGATTTAATATGAAGAAATTTTACTGGATAAGGACTGATCATGGTAGTGATGTCTGGATTATGGGAAGAAAGAAA
CCTGCATCTTTTGACGGAATAACTACAAATCAGAGAGGAGTCACAACAGCAGCCCTTGCTGCTGACTGTATCCCTATAGT
TTTTGCAGATCCTGTCAAAAAAGCATGTGGAGTTGATCACGCTGGTTGGAAGGGTACTTTGTTAGGTGTTGCAATGGCCA
TGGTACATACTATGATAACAGAGTATGGCTGTCATTTGGAAGATATTATTGCTGTGCTGGAACTTTCGGTAGGACCTTGC
TATTTTACTCTG
ORF - retro_opri_431 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.78 % |
| Parental protein coverage: | 62.88 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | RESETAN-NPIMGAS-YTINQKIDEKNLSSIKIVVPLHRKALMKAFIDHLFTDVYDFEFEDLQMTSKESF |
| RE.ET...NPIM.AS.YTIN.K...KNLSSI....PLH.KA.MKAFI.HLFTDVY.F.FEDLQMTSK.SF | |
| Retrocopy | REFETDT<NPIMAASLYTIN-KNQ*KNLSSINVILPLHWKASMKAFIVHLFTDVYNFKFEDLQMTSKDSF |
| Parental | LKQSPEVNMITAQKLEEIQNEIETYLSSLPALKGELTIITSPLIPNIFTHGFTTRTGGISYIPTLSSFNL |
| LKQSPEVN..TAQKLEEIQNEIE.YLSSLPALKGELTIITS.LIP.IFTHGFTTRTGGISY.PTLSSFNL | |
| Retrocopy | LKQSPEVNVMTAQKLEEIQNEIEMYLSSLPALKGELTIITSALIPDIFTHGFTTRTGGISYVPTLSSFNL |
| Parental | FSSSKRRDPKAVVQENLRRLANTAGFNVKKFYRIKTDHANAVWIMGRKEPASYDGITTNQRGVTIAALGA |
| FSSSKRRDPKAVVQE.L.RLANT.GFN.KKFY.I.TDH...VWIMGRK.PAS.DGITTNQRGVT.AAL.A | |
| Retrocopy | FSSSKRRDPKAVVQETLYRLANTMGFNMKKFYWIRTDHGSDVWIMGRKKPASFDGITTNQRGVTTAALAA |
| Parental | DCIPIVFADPVKKACGVAHAGWKGTLLGVAMATVHAMITEYGCRLEDIIVVLGPSVGPCCFTL |
| DCIPIVFADPVKKACGV.HAGWKGTLLGVAMA.VH.MITEYGC.LEDII.VL..SVGPC.FTL | |
| Retrocopy | DCIPIVFADPVKKACGVDHAGWKGTLLGVAMAMVHTMITEYGCHLEDIIAVLELSVGPCYFTL |
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_431 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000011253 | 1 retrocopy | |
| Ochotona princeps | ENSOPRG00000013275 | 1 retrocopy |
retro_opri_431 ,
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