RetrogeneDB ID:

retro_opri_481

Retrocopy
location
Organism:Southern American pika (Ochotona princeps)
Coordinates:scaffold_135:6655..7067(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOPRG00000001957
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_opri_481
ATGTCGAAGTGAGGACGTGGCGGGTCCTCCAGCACCAAGTTTCGCATTTCCCTGGGTCTCCTCGTGGGTGTTAACTGTGC
GGACAACATAGGAGCCAAAAACCTCTACATCATCTCCATGAAGGGGATCAAGGCACGGCTGAATAGGCTCCCTGCCGCCA
GCGTCCAGGACATGGTGATGGCCACAGTCAAGAGAGGCAAGCCAGAGCTGCGGAAGAAGGAACTTCCAGCCATGGTAATT
CGACAATGAAAGTCATATAGAAGAAAAGCTGGTGTTTCTTTACTTTGAAGATAATGCAGGAGTCATAATAAACAACAAAG
GCGAGATGGAAGGTTCTACCATCACTGGACCAGTTGCAAAGGAGTATGCAGACTTGTGGCCCAGGATTGCATCCAGCACA
GGCAGTATCGCC

ORF - retro_opri_481 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80. %
Parental protein coverage: 99.28 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSKRGRGGSSGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGVGDMVMATVKKGKP
MSK.GRGGSS..KFRISLGL.VG...NCADN.GAKNLYIIS.KGIK.RLNRLPAA.V.DMVMATVK.GKP
RetrocopyMSK*GRGGSSSTKFRISLGLLVG--VNCADNIGAKNLYIISMKGIKARLNRLPAASVQDMVMATVKRGKP
ParentalELRKKVHPAVVIRQRKSYRRKDGVFL-FEDNAGVIVNNKGEMKGSAIAGPVAKECADLWPRI-SNAGSIA
ELRKK..PA.VIRQ.KSYRRK.GV.L.FEDNAGVI.NNKGEM.GS.I.GPVAKE.ADLWPRI.S..GSIA
RetrocopyELRKKELPAMVIRQ*KSYRRKAGVSL>FEDNAGVIINNKGEMEGSTITGPVAKEYADLWPRIASSTGSIA

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_481 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 30 parental genes, and 172 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000042686 retrocopies
retro_amel_1791, retro_amel_226, retro_amel_308, retro_amel_880, retro_amel_918, retro_amel_990,
Bos taurus ENSBTAG000000032295 retrocopies
retro_btau_1588, retro_btau_349, retro_btau_65, retro_btau_953, retro_btau_974,
Canis familiaris ENSCAFG000000289551 retrocopy
retro_cfam_118,
Choloepus hoffmanni ENSCHOG000000091539 retrocopies
retro_chof_1290, retro_chof_1583, retro_chof_1599, retro_chof_1610, retro_chof_2422, retro_chof_2565, retro_chof_520, retro_chof_872, retro_chof_95,
Callithrix jacchus ENSCJAG000000083119 retrocopies
retro_cjac_1129, retro_cjac_1483, retro_cjac_2283, retro_cjac_2598, retro_cjac_2639, retro_cjac_2772, retro_cjac_2885, retro_cjac_3128, retro_cjac_3831,
Cavia porcellus ENSCPOG000000100022 retrocopies
retro_cpor_1212, retro_cpor_263,
Dipodomys ordii ENSDORG000000013723 retrocopies
retro_dord_366, retro_dord_475, retro_dord_530,
Felis catus ENSFCAG0000001450210 retrocopies
retro_fcat_1022, retro_fcat_1431, retro_fcat_1707, retro_fcat_1708, retro_fcat_1959, retro_fcat_242, retro_fcat_296, retro_fcat_716, retro_fcat_756, retro_fcat_859,
Homo sapiens ENSG000001256919 retrocopies
retro_hsap_2211, retro_hsap_2213, retro_hsap_2522, retro_hsap_3581, retro_hsap_3708, retro_hsap_3710, retro_hsap_4042, retro_hsap_4106, retro_hsap_556,
Gorilla gorilla ENSGGOG000000250829 retrocopies
retro_ggor_1574, retro_ggor_1744, retro_ggor_1746, retro_ggor_2416, retro_ggor_2508, retro_ggor_256, retro_ggor_2710, retro_ggor_2757, retro_ggor_504,
Latimeria chalumnae ENSLACG000000044301 retrocopy
retro_lcha_16,
Loxodonta africana ENSLAFG000000284504 retrocopies
retro_lafr_274, retro_lafr_305, retro_lafr_375, retro_lafr_440,
Macropus eugenii ENSMEUG000000011882 retrocopies
retro_meug_1717, retro_meug_515,
Myotis lucifugus ENSMLUG000000156739 retrocopies
retro_mluc_1262, retro_mluc_1523, retro_mluc_1598, retro_mluc_1792, retro_mluc_184, retro_mluc_2051, retro_mluc_2410, retro_mluc_447, retro_mluc_560,
Macaca mulatta ENSMMUG000000045029 retrocopies
retro_mmul_1598, retro_mmul_1705, retro_mmul_1955, retro_mmul_2366, retro_mmul_2391, retro_mmul_384, retro_mmul_928, retro_mmul_930, retro_mmul_935,
Monodelphis domestica ENSMODG000000126343 retrocopies
retro_mdom_1949, retro_mdom_527, retro_mdom_916,
Mustela putorius furoENSMPUG000000150752 retrocopies
retro_mputfur_1138, retro_mputfur_1324,
Mus musculus ENSMUSG0000007141510 retrocopies
retro_mmus_1146, retro_mmus_1430, retro_mmus_2153, retro_mmus_2297, retro_mmus_2319, retro_mmus_2826, retro_mmus_3603, retro_mmus_3704, retro_mmus_583, retro_mmus_657,
Nomascus leucogenys ENSNLEG000000006427 retrocopies
retro_nleu_1506, retro_nleu_181, retro_nleu_2056, retro_nleu_2337, retro_nleu_2988, retro_nleu_574, retro_nleu_8,
Ornithorhynchus anatinus ENSOANG000000012301 retrocopy
retro_oana_76,
Oryctolagus cuniculus ENSOCUG000000139156 retrocopies
retro_ocun_1027, retro_ocun_1196, retro_ocun_1270, retro_ocun_1919, retro_ocun_251, retro_ocun_482,
Otolemur garnettii ENSOGAG000000124457 retrocopies
retro_ogar_1050, retro_ogar_1645, retro_ogar_1695, retro_ogar_2250, retro_ogar_277, retro_ogar_3145, retro_ogar_539,
Ochotona princeps ENSOPRG00000001957 10 retrocopies
retro_opri_1079, retro_opri_1216, retro_opri_137, retro_opri_14, retro_opri_178, retro_opri_202, retro_opri_224, retro_opri_481 , retro_opri_639, retro_opri_684,
Pongo abelii ENSPPYG0000000850110 retrocopies
retro_pabe_2083, retro_pabe_2085, retro_pabe_2951, retro_pabe_3145, retro_pabe_3147, retro_pabe_3316, retro_pabe_3340, retro_pabe_3362, retro_pabe_455, retro_pabe_512,
Pan troglodytes ENSPTRG000000090799 retrocopies
retro_ptro_1467, retro_ptro_164, retro_ptro_1677, retro_ptro_1679, retro_ptro_2428, retro_ptro_2512, retro_ptro_2513, retro_ptro_2738, retro_ptro_417,
Pteropus vampyrus ENSPVAG000000022772 retrocopies
retro_pvam_488, retro_pvam_890,
Rattus norvegicus ENSRNOG0000000410710 retrocopies
retro_rnor_1195, retro_rnor_1539, retro_rnor_1622, retro_rnor_2445, retro_rnor_2483, retro_rnor_2688, retro_rnor_2981, retro_rnor_347, retro_rnor_498, retro_rnor_941,
Sus scrofa ENSSSCG000000215903 retrocopies
retro_sscr_1115, retro_sscr_135, retro_sscr_332,
Ictidomys tridecemlineatus ENSSTOG000000142792 retrocopies
retro_itri_122, retro_itri_1577,
Vicugna pacos ENSVPAG000000056942 retrocopies
retro_vpac_29, retro_vpac_634,


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