RetrogeneDB ID:

retro_opri_218

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_3720:421822..422501(-)
Located in intron of:ENSOPRG00000001046
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:YWHAZ
Ensembl ID:ENSOPRG00000000276
Aliases:None
Description:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide [Source:HGNC Symbol;Acc:12855]


Retrocopy-Parental alignment summary:






>retro_opri_218
GACTTGGCAGCCCACATGAAGTCTGTAACCCAGCAAGGAGCTGAGTTATCTAATGAGAGGAGCCTCCTCTCCATTGCCTA
TTAAAAATGTCATAGGAGACTATAGGTCATCATGGAGGGTCGTCTCAAGTGTTGAGCAAAACACCGAAGGTGCTGAGAAA
AAGCAGCAGATGATTCGTGAATACAGGGAGAAAGTTGAGACTGAGCTAAGAGATATTTGCAACGATGTAGTGTGTCTTTT
GGAAAATTTCTTGATCCCCAATGCTTCACAAGCAGCGAACAAGGTCTTCTGTTTGAAAATGAAAGGAGGCTAATGCCGTT
TACCTGGCTGAGGTCACCGCTGGTGACCTGGTGACGACAAGAAGGGGATTGTGGATCAGTCACAACAGGCATACCAAGAT
GCTTTTCAAATCAGCAAAAAGGAGATGCAGCCAACATAGTCCATCAGATCGGGTCTGGCCCTTAACTTCTCTGTGTTCTA
TTACGAGATTCTGAATTCCCCAGGAAAAGCCTGCTCTCTGGCGAAGACGGCTTTCAATGAAGCCCTTGCTGAACTTAATA
CGTTAAGTGAAGAGTCATACAAAGACAGCATGCTAATAATGCAGCTACTGAGAGACAGCTTGACATTGTGAACATCTGAT
ACCCAAGGAGATGAAGCTCGAGCAGAAGAAGGGGAAAAT

ORF - retro_opri_218 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.26 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalDMAACMKSVTEQGAELSNEERNLLSVAY-KNVVGARRSSWRVVSSIEQKTEGAEKKQQMAREYREKIETE
D.AA.MKSVT.QGAELSNE.R.LLS.AY.KNV.G..RSSWRVVSS.EQ.TEGAEKKQQM.REYREK.ETE
RetrocopyDLAAHMKSVTQQGAELSNE-RSLLSIAY>KNVIGDYRSSWRVVSSVEQNTEGAEKKQQMIREYREKVETE
ParentalLRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYR-YLAEVAAGD---DKKGIVDQSQQAYQEAFEI
LRDICNDV..LLE.FLIPNASQA..KVF.LKMKG...R.YLAEV.AGD......G............F..
RetrocopyLRDICNDVVCLLENFLIPNASQAANKVFCLKMKGG*CR>YLAEVTAGDLVTTRRGLWISHNRHTKMLFKS
ParentalSKK-EMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEESYKDSTLIMQLLRDL
.K..EMQPT..IR.GLALNFSVFYYEILNSP.KACSLAKTAF.EA.AEL.TLSEESYKDS.LIMQLLRD.
RetrocopyAKR<EMQPT*SIRSGLALNFSVFYYEILNSPGKACSLAKTAFNEALAELNTLSEESYKDSMLIMQLLRDS
ParentalTXXXXXXXXXXXEAGEGGEN
...............E.GEN
RetrocopyLTL*TSDTQGDEARAEEGEN

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_218 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 18 parental genes, and 69 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086942 retrocopies
Bos taurus ENSBTAG000000002364 retrocopies
Canis familiaris ENSCAFG000000005806 retrocopies
Callithrix jacchus ENSCJAG000000158445 retrocopies
Dasypus novemcinctus ENSDNOG0000000167210 retrocopies
Ficedula albicollis ENSFALG000000058601 retrocopy
Gallus gallus ENSGALG000000107251 retrocopy
Gorilla gorilla ENSGGOG000000221339 retrocopies
Monodelphis domestica ENSMODG000000061588 retrocopies
Mus musculus ENSMUSG000000222853 retrocopies
Oryctolagus cuniculus ENSOCUG000000007342 retrocopies
Ochotona princeps ENSOPRG00000000276 3 retrocopies
retro_opri_1218, retro_opri_218 , retro_opri_967,
Ochotona princeps ENSOPRG000000118362 retrocopies
Pongo abelii ENSPPYG000000187917 retrocopies
Pelodiscus sinensis ENSPSIG000000037031 retrocopy
Sarcophilus harrisii ENSSHAG000000126712 retrocopies
Sus scrofa ENSSSCG000000060622 retrocopies
Taeniopygia guttata ENSTGUG000000120781 retrocopy



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