RetrogeneDB ID:

retro_opri_1014

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_57541:3481..4076(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL3
Ensembl ID:ENSOPRG00000013088
Aliases:None
Description:ribosomal protein L3 [Source:HGNC Symbol;Acc:10332]


Retrocopy-Parental alignment summary:






>retro_opri_1014
ACCATGGGCGAGAAGCTGGGTTGGACCTGGGAACGTCTGGAGCACCAGATGCGGATGAGCCACATGTTGGGGTATGCCGA
GATGATCGTCATCTGCACGATTAAGGGCAAGGACTACAAAAGGGTCACGAGCCGCTGGGGCCACAACAAGCTGCCACACA
AAACTCACTTAGGCCTGTGCAAGATGGCTTGCGTGGGGCTTGCCATCCTGCTTGGGTAGCCTTCTCCATGGTGCCAGCAG
GACAAAAAGGCTACCATTACTGCATGGAGATCAACTAGAATATCTGCAAGGTTAGACAGAGCTACCTGATCAAGGGTGGC
AATCTAATAAAGAACAAAGCCTCCACTATGACCTGTCCTTACAAGAGCATCAGCCCTCTGGGTGGCTTGGTCCGTTGTGC
TAGAATGACCAATTATTTTGTCATGCTGAAAGGCTGTGTGGTGGGGACCAAGAAGCAGTACTCACTCTGTGCCAGTTCTT
GTGAGTGTATACTAGTTGATGGGCTCTGGAGAAGATTGAGCTCAAGTTCATTGACACCACCAAATTTGAGCATGGTGGCT
TCCAGACTGTGAAGAAGACAGCATCAATGGGACCA

ORF - retro_opri_1014 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.46 %
Parental protein coverage: 50.5 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIG-AW
T..EKL.W..ERLE.Q.......G..EMI.VI...KGK.YK.VTSRW...KLP.KTH.GL.K.AC.G.A.
RetrocopyTMGEKLGWTWERLEHQMRMSHMLGYAEMI-VICTIKGKDYKRVTSRWGHNKLPHKTHLGLCKMACVG<AC
ParentalHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVT
HPA.VAFS...AGQKGYH...EIN..I.K..Q.YLIK.G.LIKN.AST......KSI.PLGG.V.....T
RetrocopyHPAWVAFSMVPAGQKGYHYCMEIN*NICKVRQSYLIKGGNLIKNKAST-MTCPYKSISPLGGLVRCARMT
ParentalNDFVMLKGCVVGTKKR-VLTLRKSLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTVEEKKAFMGP
N.FVMLKGCVVGTKK..VLTL...L.V.T...ALEKI.LKFIDTT.KF.HG.FQTV..K.A.MGP
RetrocopyNYFVMLKGCVVGTKKQ<VLTLCQFL*VYTS*WALEKIELKFIDTT-KFEHGGFQTV-KKTASMGP

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_1014 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 27 parental genes, and 143 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000108531 retrocopy
retro_amel_1115,
Bos taurus ENSBTAG000000032283 retrocopies
retro_btau_1644, retro_btau_281, retro_btau_341,
Canis familiaris ENSCAFG000000013461 retrocopy
retro_cfam_97,
Callithrix jacchus ENSCJAG000000162766 retrocopies
retro_cjac_1198, retro_cjac_1972, retro_cjac_2157, retro_cjac_2264, retro_cjac_3079, retro_cjac_823,
Dasypus novemcinctus ENSDNOG000000011214 retrocopies
retro_dnov_1359, retro_dnov_1641, retro_dnov_652, retro_dnov_788,
Erinaceus europaeus ENSEEUG000000146612 retrocopies
retro_eeur_488, retro_eeur_557,
Echinops telfairi ENSETEG000000113805 retrocopies
retro_etel_1646, retro_etel_2199, retro_etel_2212, retro_etel_657, retro_etel_972,
Felis catus ENSFCAG000000058201 retrocopy
retro_fcat_1809,
Homo sapiens ENSG000001003169 retrocopies
retro_hsap_1341, retro_hsap_2403, retro_hsap_2529, retro_hsap_3328, retro_hsap_3448, retro_hsap_3638, retro_hsap_3889, retro_hsap_4081, retro_hsap_4749,
Gorilla gorilla ENSGGOG0000000232610 retrocopies
retro_ggor_1043, retro_ggor_1295, retro_ggor_1582, retro_ggor_1822, retro_ggor_2329, retro_ggor_2616, retro_ggor_2713, retro_ggor_2736, retro_ggor_2955, retro_ggor_36,
Macropus eugenii ENSMEUG0000000978926 retrocopies
retro_meug_1045, retro_meug_118, retro_meug_1210, retro_meug_1403, retro_meug_1452, retro_meug_1492, retro_meug_1516, retro_meug_1554, retro_meug_1589, retro_meug_1604, retro_meug_1698, retro_meug_1856, retro_meug_2150, retro_meug_2151, retro_meug_221, retro_meug_367, retro_meug_412, retro_meug_461, retro_meug_592, retro_meug_677, retro_meug_683, retro_meug_831, retro_meug_851, retro_meug_886, retro_meug_889, retro_meug_898,
Microcebus murinus ENSMICG000000158321 retrocopy
retro_mmur_1307,
Myotis lucifugus ENSMLUG000000237111 retrocopy
retro_mluc_810,
Macaca mulatta ENSMMUG000000100294 retrocopies
retro_mmul_1170, retro_mmul_149, retro_mmul_2334, retro_mmul_973,
Monodelphis domestica ENSMODG000000095392 retrocopies
retro_mdom_380, retro_mdom_408,
Mustela putorius furoENSMPUG000000132713 retrocopies
retro_mputfur_1284, retro_mputfur_199, retro_mputfur_774,
Mus musculus ENSMUSG0000006003630 retrocopies
retro_mmus_1148, retro_mmus_1158, retro_mmus_1164, retro_mmus_1165, retro_mmus_1167, retro_mmus_1183, retro_mmus_1238, retro_mmus_1239, retro_mmus_1240, retro_mmus_1241, retro_mmus_1242, retro_mmus_1243, retro_mmus_1244, retro_mmus_1245, retro_mmus_1246, retro_mmus_1465, retro_mmus_1548, retro_mmus_2231, retro_mmus_2275, retro_mmus_2276, retro_mmus_2474, retro_mmus_2501, retro_mmus_2547, retro_mmus_2849, retro_mmus_3125, retro_mmus_3215, retro_mmus_3422, retro_mmus_3467, retro_mmus_361, retro_mmus_897,
Nomascus leucogenys ENSNLEG000000152342 retrocopies
retro_nleu_1038, retro_nleu_1449,
Oryctolagus cuniculus ENSOCUG000000277124 retrocopies
retro_ocun_105, retro_ocun_179, retro_ocun_1893, retro_ocun_558,
Otolemur garnettii ENSOGAG000000000327 retrocopies
retro_ogar_1264, retro_ogar_1679, retro_ogar_2096, retro_ogar_2122, retro_ogar_2448, retro_ogar_3431, retro_ogar_960,
Ochotona princeps ENSOPRG00000013088 3 retrocopies
retro_opri_1004, retro_opri_1014 , retro_opri_432,
Procavia capensis ENSPCAG000000106421 retrocopy
retro_pcap_115,
Pongo abelii ENSPPYG0000001183710 retrocopies
retro_pabe_1113, retro_pabe_1861, retro_pabe_2167, retro_pabe_2743, retro_pabe_2985, retro_pabe_3170, retro_pabe_3318, retro_pabe_3349, retro_pabe_3696, retro_pabe_3761,
Pteropus vampyrus ENSPVAG000000032042 retrocopies
retro_pvam_1220, retro_pvam_1390,
Rattus norvegicus ENSRNOG000000168962 retrocopies
retro_rnor_1333, retro_rnor_731,
Sarcophilus harrisii ENSSHAG000000032122 retrocopies
retro_shar_154, retro_shar_662,
Tupaia belangeri ENSTBEG000000059891 retrocopy
retro_tbel_939,


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