RetrogeneDB ID:

retro_opri_1218

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_9723:14886..15510(-)
Located in intron of:None
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_1218
TTATCTAATGAGGAGAGGAACCTCCTCTCTGTTGCCTATAAAAATGTCATAGGAGCCCGAAGGTCATCATGGAGGGTTGT
CTCAAGCATAGAGCAAAAGAACGAAGGTGCTGAGAACAAGCAGCAGATGGCTCATGGATACAGGGAGAAAATTGAGAGTG
AGCTAAGAGATACCTGTAAGGGTGTGCTGTCTCTTTTGGAAAAGTTCTTAATCCTCAATGCTTCACAAGCAGAGCAAAGT
CTTCTATTTGAAAATGAAAGGAAACTACTGCCGTTACCTGGCCGAGGTCGCTGCTAGTGACGACAAGCAGGAGATTGTGA
ACCCGTCCCAACAGGCATACCAACAAGCTTTTGAAATCAGCTAAACAGAGATGCAGCCCATGCATCCCATCTGATTGAAC
CTGGCCCTTAACTTCTCTGTGTTCTATTACAAGATTCTGAATTCCCCCGAAAAAACACCTGCTCTGTGGCAAAGATGGCT
TTTGATGAAACCATTGCTGAACTTGATACTTTAAGTGAAGAGTCATACAAAGACAGCACACTAATAATGCAGTTACTGAG
AGACAACTTGACATTGTGGGCATCTGATACCCAAGGAGGTGAAGCTGAAGGAGAAGGAGGGGAA

ORF - retro_opri_1218 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.11 %
Parental protein coverage: 92.86 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalLSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTEGAEKKQQMAREYREKIETELRDICNDVLSLLE-KF
LSNEERNLLSVAYKNV.GARRSSWRVVSSIEQK.EGAE.KQQMA..YREKIE.ELRD.C..VLSLLE.K.
RetrocopyLSNEERNLLSVAYKNVIGARRSSWRVVSSIEQKNEGAENKQQMAHGYREKIESELRDTCKGVLSLLE<KV
ParentalLIPNASQA-ESKVFYLKMKGDYYRYLAEVAAGDDKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALN
L.P.......SKVFYLKMKG.Y.RYLAEVAA.DDK..IV..SQQAYQ.AFEIS..EMQP.HPI.L.LALN
RetrocopyLNPQCFTS<QSKVFYLKMKGNYCRYLAEVAASDDKQEIVNPSQQAYQQAFEIS*TEMQPMHPI*LNLALN
ParentalFSVFYYEILNSPEKACSL-AKTAF-DEAIAELDTLSEESYKDSTLIMQLLRDLTXXXXXXXXXXXEAGEG
FSVFYY.ILNSPEK...L..K..F.DE.IAELDTLSEESYKDSTLIMQLLRD...............GEG
RetrocopyFSVFYYKILNSPEKTPAL>GKDGF>DETIAELDTLSEESYKDSTLIMQLLRDNLTLWASDTQGGEAEGEG
ParentalGE
GE
RetrocopyGE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ochotona princeps was not studied using ChIP-Seq data.

EST - click to see more details

Ochotona princeps was not studied using EST data.

TSS - click to see more details

Ochotona princeps was not studied using FANTOM5 data.

Lab - click to see more details

retro_opri_1218 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
retro_acar_25, retro_acar_44,
Bos taurus ENSBTAG000000002364 retrocopies
retro_btau_1482, retro_btau_635, retro_btau_68, retro_btau_910,
Canis familiaris ENSCAFG000000005806 retrocopies
retro_cfam_1302, retro_cfam_1521, retro_cfam_158, retro_cfam_1840, retro_cfam_233, retro_cfam_465,
Callithrix jacchus ENSCJAG000000158445 retrocopies
retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
Dasypus novemcinctus ENSDNOG0000000167210 retrocopies
retro_dnov_1007, retro_dnov_117, retro_dnov_1354, retro_dnov_1579, retro_dnov_1769, retro_dnov_1907, retro_dnov_1993, retro_dnov_2588, retro_dnov_892, retro_dnov_99,
Ficedula albicollis ENSFALG000000058601 retrocopy
retro_falb_13,
Gallus gallus ENSGALG000000107251 retrocopy
retro_ggal_3,
Gorilla gorilla ENSGGOG000000221339 retrocopies
retro_ggor_1092, retro_ggor_1754, retro_ggor_211, retro_ggor_2379, retro_ggor_2997, retro_ggor_2998, retro_ggor_3020, retro_ggor_499, retro_ggor_544,
Monodelphis domestica ENSMODG000000061588 retrocopies
retro_mdom_1589, retro_mdom_1664, retro_mdom_1763, retro_mdom_1815, retro_mdom_1875, retro_mdom_1958, retro_mdom_255, retro_mdom_446,
Mus musculus ENSMUSG000000222853 retrocopies
retro_mmus_163, retro_mmus_2187, retro_mmus_744,
Oryctolagus cuniculus ENSOCUG000000007342 retrocopies
retro_ocun_1091, retro_ocun_248,
Ochotona princeps ENSOPRG00000000276 3 retrocopies
retro_opri_1218 , retro_opri_218, retro_opri_967,
Ochotona princeps ENSOPRG000000118362 retrocopies
retro_opri_56, retro_opri_924,
Pongo abelii ENSPPYG000000187917 retrocopies
retro_pabe_103, retro_pabe_1242, retro_pabe_2047, retro_pabe_3417, retro_pabe_3740, retro_pabe_556, retro_pabe_89,
Pelodiscus sinensis ENSPSIG000000037031 retrocopy
retro_psin_13,
Sarcophilus harrisii ENSSHAG000000126712 retrocopies
retro_shar_126, retro_shar_409,
Sus scrofa ENSSSCG000000060622 retrocopies
retro_sscr_222, retro_sscr_35,
Taeniopygia guttata ENSTGUG000000120781 retrocopy
retro_tgut_4,




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