RetrogeneDB ID:

retro_nleu_540

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397267.1:12502798..12503373(+)
Located in intron of:ENSNLEG00000002668
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL19
Ensembl ID:ENSNLEG00000000748
Aliases:None
Description:Ribosomal protein L19 [Source:UniProtKB/TrEMBL;Acc:G1QJ16]


Retrocopy-Parental alignment summary:






>retro_nleu_540
AGGCTTCAGAAGAGGCTTGCCTCTAGTGTCCTCTGCTGTGGCAAAAAGAAGATCTGGCTGGACACCAATGAGACCAATGA
AATCGGCCATGCCAACTCCTGTCAGCAGATCCAGAAGCTGATCAAAGATGGGCTGATTATCCATAAGCCTGTGACTGTCC
GTTCCTGGGCTCACTGCCAGAAAAGCACCTTGGCCTGCCAGAAGGGCAGGTACATGGGCATAGGTAAACAAAAAGGGTAC
AGCCAATACTCAAATGCCAGAGAAGGTAACCTGGGTGAGGAGAATAGGAATTCTGCATCAGCTGCTCAAAGATACTGTGA
ATCTAAAAAGACTGATCACCACATGTATCACAGCCTGTACCTGAAGGTAAAGGGGAGTGTGTTCAAAAACAGGTGGATTC
TCATGGAACACATCCACCTGCTGAAGGCACAAAGGCCCACAAGACGCTCCTGGCTGACCAGGCAGAGGCCTGCTGGTCTA
AGATCAAGGAAGCATGTAAGTACCATGAAGAGCGCCTCCAGGCCAAGAAGGAAGAGAGCATCAAGACTTTGTCCAATGAG
GAAGAGACGAGGAAA

ORF - retro_nleu_540 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.82 %
Parental protein coverage: 97.95 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRARCRKNTLARRKGR
RLQKRLASSVL.CGKKK.WLD.NETNEI..ANS.QQI.KLIKDGLII.KPVTV.S.A.C.K.TLA..KGR
RetrocopyRLQKRLASSVLCCGKKKIWLDTNETNEIGHANSCQQIQKLIKDGLIIHKPVTVRSWAHCQKSTLACQKGR
ParentalHMGIGK-RKGTANARMPKKVTWMRKMRILRRKLQ-VVEFK-KIDRHMYHSLYLKVKGNVFKNKRILMEHI
.MGIGK..KGTAN..MP.KVTW.R...IL...L...V..K.K.D.HMYHSLYLKVKG.VFKN..ILMEHI
RetrocopyYMGIGK>KKGTANTQMPEKVTWVRRIGILHQLLKDTVNLK<KTDHHMYHSLYLKVKGSVFKNRWILMEHI
ParentalHKLKAD-KARKKLLADQAEARRSKTKEARKRREERLQAKKEEIIKTLSKEEETKK
H.LKA..KA.K.LLADQAEA..SK.KEA.K..EERLQAKKEE.IKTLS.EEET.K
RetrocopyHLLKAQ<KAHKTLLADQAEACWSKIKEACKYHEERLQAKKEESIKTLSNEEETRK

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






RNA-Seq - click to see more details

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Nomascus leucogenys was not studied using ChIP-Seq data.

EST - click to see more details

Nomascus leucogenys was not studied using EST data.

TSS - click to see more details

Nomascus leucogenys was not studied using FANTOM5 data.

Lab - click to see more details

retro_nleu_540 was not experimentally validated.

Retrocopy orthology:
Nomascus leucogenys 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 300 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000041215 retrocopies
retro_amel_1195, retro_amel_1663, retro_amel_451, retro_amel_531, retro_amel_889,
Bos taurus ENSBTAG000000020605 retrocopies
retro_btau_1241, retro_btau_1254, retro_btau_1371, retro_btau_1480, retro_btau_761,
Canis familiaris ENSCAFG0000001649314 retrocopies
retro_cfam_1011, retro_cfam_1647, retro_cfam_1767, retro_cfam_1799, retro_cfam_1892, retro_cfam_2082, retro_cfam_2129, retro_cfam_328, retro_cfam_357, retro_cfam_486, retro_cfam_851, retro_cfam_909, retro_cfam_932, retro_cfam_940,
Choloepus hoffmanni ENSCHOG000000060237 retrocopies
retro_chof_1041, retro_chof_1065, retro_chof_1135, retro_chof_1930, retro_chof_2567, retro_chof_338, retro_chof_993,
Callithrix jacchus ENSCJAG000000085204 retrocopies
retro_cjac_131, retro_cjac_220, retro_cjac_32, retro_cjac_64,
Dasypus novemcinctus ENSDNOG000000197427 retrocopies
retro_dnov_1478, retro_dnov_1897, retro_dnov_2, retro_dnov_2170, retro_dnov_2431, retro_dnov_691, retro_dnov_720,
Dipodomys ordii ENSDORG000000043301 retrocopy
retro_dord_105,
Equus caballus ENSECAG000000250806 retrocopies
retro_ecab_104, retro_ecab_319, retro_ecab_351, retro_ecab_456, retro_ecab_497, retro_ecab_905,
Homo sapiens ENSG0000010829821 retrocopies
retro_hsap_1085, retro_hsap_1802, retro_hsap_2072, retro_hsap_2157, retro_hsap_2209, retro_hsap_2406, retro_hsap_2651, retro_hsap_2679, retro_hsap_2850, retro_hsap_3012, retro_hsap_3155, retro_hsap_3274, retro_hsap_3401, retro_hsap_3885, retro_hsap_3933, retro_hsap_399, retro_hsap_3991, retro_hsap_4219, retro_hsap_4680, retro_hsap_4774, retro_hsap_739,
Loxodonta africana ENSLAFG000000182573 retrocopies
retro_lafr_1045, retro_lafr_479, retro_lafr_88,
Macropus eugenii ENSMEUG0000001390010 retrocopies
retro_meug_1047, retro_meug_1201, retro_meug_1226, retro_meug_1256, retro_meug_1262, retro_meug_1486, retro_meug_1878, retro_meug_2108, retro_meug_2155, retro_meug_82,
Microcebus murinus ENSMICG000000026635 retrocopies
retro_mmur_1213, retro_mmur_231, retro_mmur_469, retro_mmur_520, retro_mmur_678,
Myotis lucifugus ENSMLUG0000001255511 retrocopies
retro_mluc_1149, retro_mluc_1473, retro_mluc_1694, retro_mluc_2032, retro_mluc_2034, retro_mluc_2398, retro_mluc_2400, retro_mluc_2616, retro_mluc_573, retro_mluc_887, retro_mluc_890,
Macaca mulatta ENSMMUG000000042352 retrocopies
retro_mmul_283, retro_mmul_63,
Monodelphis domestica ENSMODG000000126932 retrocopies
retro_mdom_53, retro_mdom_750,
Mustela putorius furoENSMPUG000000150415 retrocopies
retro_mputfur_1221, retro_mputfur_1248, retro_mputfur_1479, retro_mputfur_357, retro_mputfur_688,
Mus musculus ENSMUSG0000001740425 retrocopies
retro_mmus_1174, retro_mmus_1235, retro_mmus_1248, retro_mmus_1273, retro_mmus_1323, retro_mmus_1397, retro_mmus_1591, retro_mmus_1614, retro_mmus_1699, retro_mmus_1700, retro_mmus_1877, retro_mmus_1885, retro_mmus_1964, retro_mmus_2301, retro_mmus_2688, retro_mmus_2749, retro_mmus_2967, retro_mmus_3110, retro_mmus_3187, retro_mmus_3310, retro_mmus_341, retro_mmus_3413, retro_mmus_507, retro_mmus_571, retro_mmus_600,
Nomascus leucogenys ENSNLEG00000000748 19 retrocopies
retro_nleu_1182, retro_nleu_1570, retro_nleu_1602, retro_nleu_1620, retro_nleu_1889, retro_nleu_2171, retro_nleu_2236, retro_nleu_2284, retro_nleu_2335, retro_nleu_2430, retro_nleu_2446, retro_nleu_2538, retro_nleu_2695, retro_nleu_2702, retro_nleu_2735, retro_nleu_3116, retro_nleu_479, retro_nleu_540 , retro_nleu_656,
Ochotona princeps ENSOPRG000000070922 retrocopies
retro_opri_1220, retro_opri_987,
Procavia capensis ENSPCAG000000152281 retrocopy
retro_pcap_141,
Pongo abelii ENSPPYG0000000849220 retrocopies
retro_pabe_1546, retro_pabe_1687, retro_pabe_1709, retro_pabe_1815, retro_pabe_2177, retro_pabe_2300, retro_pabe_2320, retro_pabe_2496, retro_pabe_2625, retro_pabe_2799, retro_pabe_2800, retro_pabe_3166, retro_pabe_3278, retro_pabe_3299, retro_pabe_3513, retro_pabe_3635, retro_pabe_3829, retro_pabe_4, retro_pabe_973, retro_pabe_980,
Pan troglodytes ENSPTRG0000000908622 retrocopies
retro_ptro_1180, retro_ptro_1385, retro_ptro_1642, retro_ptro_1676, retro_ptro_1786, retro_ptro_1806, retro_ptro_1930, retro_ptro_2036, retro_ptro_2214, retro_ptro_2279, retro_ptro_2311, retro_ptro_2645, retro_ptro_2709, retro_ptro_2865, retro_ptro_2998, retro_ptro_305, retro_ptro_3109, retro_ptro_3179, retro_ptro_467, retro_ptro_525, retro_ptro_673, retro_ptro_737,
Pteropus vampyrus ENSPVAG000000084989 retrocopies
retro_pvam_1191, retro_pvam_1332, retro_pvam_183, retro_pvam_244, retro_pvam_468, retro_pvam_792, retro_pvam_914, retro_pvam_918, retro_pvam_950,
Rattus norvegicus ENSRNOG0000000474137 retrocopies
retro_rnor_1029, retro_rnor_1039, retro_rnor_1295, retro_rnor_1338, retro_rnor_1405, retro_rnor_1440, retro_rnor_1449, retro_rnor_1478, retro_rnor_1512, retro_rnor_1525, retro_rnor_1558, retro_rnor_1577, retro_rnor_1765, retro_rnor_1766, retro_rnor_1795, retro_rnor_1814, retro_rnor_1860, retro_rnor_1885, retro_rnor_1905, retro_rnor_1907, retro_rnor_1970, retro_rnor_1981, retro_rnor_208, retro_rnor_2169, retro_rnor_2522, retro_rnor_2536, retro_rnor_2708, retro_rnor_2773, retro_rnor_2783, retro_rnor_2921, retro_rnor_2943, retro_rnor_326, retro_rnor_426, retro_rnor_434, retro_rnor_464, retro_rnor_465, retro_rnor_829,
Sarcophilus harrisii ENSSHAG000000164824 retrocopies
retro_shar_159, retro_shar_287, retro_shar_317, retro_shar_415,
Sus scrofa ENSSSCG000000175093 retrocopies
retro_sscr_1108, retro_sscr_398, retro_sscr_913,
Ictidomys tridecemlineatus ENSSTOG000000111205 retrocopies
retro_itri_1174, retro_itri_1180, retro_itri_1330, retro_itri_178, retro_itri_200,
Tupaia belangeri ENSTBEG0000000807731 retrocopies
retro_tbel_1024, retro_tbel_1150, retro_tbel_1200, retro_tbel_1248, retro_tbel_1507, retro_tbel_1620, retro_tbel_173, retro_tbel_1752, retro_tbel_1791, retro_tbel_1826, retro_tbel_1942, retro_tbel_199, retro_tbel_2166, retro_tbel_2529, retro_tbel_2558, retro_tbel_2687, retro_tbel_2751, retro_tbel_2855, retro_tbel_3256, retro_tbel_3347, retro_tbel_3493, retro_tbel_3758, retro_tbel_4501, retro_tbel_4606, retro_tbel_4631, retro_tbel_759, retro_tbel_799, retro_tbel_835, retro_tbel_867, retro_tbel_957, retro_tbel_988,
Tarsius syrichta ENSTSYG0000000869810 retrocopies
retro_tsyr_1164, retro_tsyr_1267, retro_tsyr_1310, retro_tsyr_1330, retro_tsyr_1770, retro_tsyr_1916, retro_tsyr_540, retro_tsyr_713, retro_tsyr_782, retro_tsyr_93,
Tursiops truncatus ENSTTRG000000066874 retrocopies
retro_ttru_1131, retro_ttru_1132, retro_ttru_1389, retro_ttru_1804,


Copyright © RetrogeneDB 2014-2017