RetrogeneDB ID:

retro_opri_56

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:GeneScaffold_1470:241173..241889(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOPRG00000016417
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:YWHAB
Ensembl ID:ENSOPRG00000011836
Aliases:None
Description:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide [Source:HGNC Symbol;Acc:12849]


Retrocopy-Parental alignment summary:






>retro_opri_56
ATGGAGAGAGCCCATCTGATCCAGAAGGCCAAGTTGGCCGAGCAGGCTGAGCGCTACGAGGACATGGCAGGCTTCATGAA
GGGTGCCGTGGAAAAGGGCGAGGAGCTTTCCTGTGAGGAGCGAAACCTGCTCTCAGTGGCCTACAAGAACGTCGTGGGCG
GCCAGAGGGCTGCCTGGAGGGTCCTGTCTAGCATTGAGCAGAAAAGCACCGAGGAAGGCTCAGAAGAGCAGGGCCCCGAA
GTGCGTGAGTACCGGGAGAAGGTGGAGACGGAGCTCCGGGGTGTGTGCGACACCGTGCTGGGCCTGCTGGACACCCACCT
CATCAAGGAGGCCGGCGACGCCGAGAGCCGGGTCTTCTACCTGAAGATGAAGGGAGACTACTACCGCTACCTGGCCGAGG
TGGCCACCGGCGATGACAAGAAACGCATCATCGACTCCGCCCGGTCGGCCTACCAGGAGGCCATGGACATCAGCAAGAAG
GAGATGCCGCCCACCAACCCCATCCGCCTGGGCCTGGCCCTGAACTTTTCCGTCTTCCACTATGAGATTGCCAACAGCCC
CGAGGAGGCCATCACGCTGGCCAAGACCACTTTCGACGAAGCCATGGCTGACCTGCACACCCTCAGCGAGTACTCCTACA
AAGACAGCACCCTCATCATGCAGCTGCTGCGAGACAACCTGACGCTGTGACAGCCGACAACGCCGGAGAAGAGGGC

ORF - retro_opri_56 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.25 %
Parental protein coverage: 96.34 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKT-
M....L.QKAKLAEQAERY.DMA..MK...E.G.ELS.EERNLLSVAYKNVVG..R..WRV.SSIEQK..
RetrocopyMERAHLIQKAKLAEQAERYEDMAGFMKGAVEKGEELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKST
Parental-ERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLILNATQPESKVFYLKMKGDYFRYLSEVASGDNK
.E..E.......EYREK.E.EL...C..VL.LLD..LI..A...ES.VFYLKMKGDY.RYL.EVA.GD.K
RetrocopyEEGSEEQGPEVREYREKVETELRGVCDTVLGLLDTHLIKEAGDAESRVFYLKMKGDYYRYLAEVATGDDK
ParentalQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNE
.........AYQEA..ISKKEM.PT.PIRLGLALNFSVF.YEI.NSPE.A..LAKT.FDEA.A.L.TL.E
RetrocopyKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAITLAKTTFDEAMADLHTLSE
ParentalESYKDSTLIMQLLRDNLTL-WTSENQGDEG
.SYKDSTLIMQLLRDNLTL..T..N.G.EG
RetrocopyYSYKDSTLIMQLLRDNLTL<VTADNAGEEG

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_56 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 26 parental genes, and 142 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000117961 retrocopy
retro_acar_8,
Choloepus hoffmanni ENSCHOG0000000578215 retrocopies
retro_chof_1049, retro_chof_1325, retro_chof_1630, retro_chof_1670, retro_chof_1975, retro_chof_22, retro_chof_2221, retro_chof_2350, retro_chof_2423, retro_chof_2619, retro_chof_326, retro_chof_352, retro_chof_487, retro_chof_707, retro_chof_971,
Callithrix jacchus ENSCJAG000000176642 retrocopies
retro_cjac_1002, retro_cjac_2214,
Dipodomys ordii ENSDORG0000000106414 retrocopies
retro_dord_235, retro_dord_236, retro_dord_255, retro_dord_256, retro_dord_258, retro_dord_259, retro_dord_262, retro_dord_263, retro_dord_332, retro_dord_442, retro_dord_545, retro_dord_681, retro_dord_725, retro_dord_9,
Echinops telfairi ENSETEG000000099674 retrocopies
retro_etel_1221, retro_etel_1380, retro_etel_1536, retro_etel_1705,
Homo sapiens ENSG000001669134 retrocopies
retro_hsap_4160, retro_hsap_4841, retro_hsap_622, retro_hsap_855,
Gorilla gorilla ENSGGOG000000045802 retrocopies
retro_ggor_2795, retro_ggor_699,
Microcebus murinus ENSMICG000000009737 retrocopies
retro_mmur_1044, retro_mmur_1100, retro_mmur_1288, retro_mmur_1576, retro_mmur_27, retro_mmur_305, retro_mmur_979,
Myotis lucifugus ENSMLUG000000063191 retrocopy
retro_mluc_871,
Macaca mulatta ENSMMUG000000132063 retrocopies
retro_mmul_1061, retro_mmul_236, retro_mmul_673,
Monodelphis domestica ENSMODG000000162002 retrocopies
retro_mdom_1557, retro_mdom_212,
Nomascus leucogenys ENSNLEG000000066432 retrocopies
retro_nleu_42, retro_nleu_422,
Oryctolagus cuniculus ENSOCUG000000030021 retrocopy
retro_ocun_273,
Otolemur garnettii ENSOGAG000000089093 retrocopies
retro_ogar_122, retro_ogar_1243, retro_ogar_2934,
Ochotona princeps ENSOPRG000000002763 retrocopies
retro_opri_1218, retro_opri_218, retro_opri_967,
Ochotona princeps ENSOPRG00000011836 2 retrocopies
retro_opri_56 , retro_opri_924,
Pongo abelii ENSPPYG000000110415 retrocopies
retro_pabe_3453, retro_pabe_3454, retro_pabe_3519, retro_pabe_3520, retro_pabe_692,
Pan troglodytes ENSPTRG0000001352912 retrocopies
retro_ptro_1010, retro_ptro_1686, retro_ptro_2390, retro_ptro_2828, retro_ptro_2887, retro_ptro_3125, retro_ptro_3201, retro_ptro_3225, retro_ptro_412, retro_ptro_453, retro_ptro_594, retro_ptro_965,
Pteropus vampyrus ENSPVAG000000126621 retrocopy
retro_pvam_157,
Sarcophilus harrisii ENSSHAG000000112411 retrocopy
retro_shar_483,
Sus scrofa ENSSSCG000000073811 retrocopy
retro_sscr_506,
Ictidomys tridecemlineatus ENSSTOG000000037331 retrocopy
retro_itri_1214,
Tupaia belangeri ENSTBEG0000000280647 retrocopies
retro_tbel_1038, retro_tbel_1272, retro_tbel_1460, retro_tbel_1472, retro_tbel_1572, retro_tbel_1653, retro_tbel_1664, retro_tbel_2127, retro_tbel_2128, retro_tbel_2229, retro_tbel_2246, retro_tbel_228, retro_tbel_2371, retro_tbel_2373, retro_tbel_2379, retro_tbel_2397, retro_tbel_2512, retro_tbel_2536, retro_tbel_2540, retro_tbel_2542, retro_tbel_2583, retro_tbel_2584, retro_tbel_2615, retro_tbel_2617, retro_tbel_3502, retro_tbel_3554, retro_tbel_3604, retro_tbel_3642, retro_tbel_3743, retro_tbel_390, retro_tbel_3989, retro_tbel_3993, retro_tbel_40, retro_tbel_4101, retro_tbel_4121, retro_tbel_4338, retro_tbel_4447, retro_tbel_4456, retro_tbel_4459, retro_tbel_4510, retro_tbel_4514, retro_tbel_4604, retro_tbel_4664, retro_tbel_4690, retro_tbel_5, retro_tbel_705, retro_tbel_854,
Tarsius syrichta ENSTSYG000000065374 retrocopies
retro_tsyr_1065, retro_tsyr_1473, retro_tsyr_1637, retro_tsyr_2084,
Tursiops truncatus ENSTTRG000000076151 retrocopy
retro_ttru_762,
Vicugna pacos ENSVPAG000000050233 retrocopies
retro_vpac_396, retro_vpac_516, retro_vpac_9,


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