RetrogeneDB ID:

retro_onil_38

Retrocopy
location
Organism:Tilapia (Oreochromis niloticus)
Coordinates:GL831156.1:852919..853477(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:zgc:66127
Ensembl ID:ENSONIG00000012248
Aliases:None
Description:zgc:66127 [Source:ZFIN;Acc:ZDB-GENE-040426-1546]


Retrocopy-Parental alignment summary:






>retro_onil_38
AAACTTTGTAAGCTTTTTGTCGGGGGATTGAACGTGGAGACCACCGATGAAGGCCTCCGCAAGTACTTCGAGCAGTATGG
CACCCTTAGCGACTGCGTGGTGGTCATGAACCAACAGCTCGGACGTTCCCGCTGTTTCGGTTTCATCACCTACTCCACGC
CGGAGGAGGCCGACGCAGCAATGGCCGCTAAGCCACATGTCGTCGAAGGCAACAACGTGGAGGTGAAAAGGGCCATAGCG
CGAGAGGATGCCAACAACCCGGACATACTCGCCAATGTAAAGAAAATCTTCGTTGGCGGCGTGAAAGACCACATCGTTGA
GGAGAACCTGACCGAGTACTTCTCGCAATTCGGCGCGGTGGAGAAGGCCGAGATCATCTCCGACAAGCAAACCGGCAGGA
AGAGAGGCTTCGGCTTTGTCTTCTTCGAGGATACCGACTCCGCCACCAAAGCAGTCCTGACCAAATACCACACCATCAAC
GGGAACAAGGTGGAGGTGAAAAAGGCTCTAACCAAGCAGGAAATGTCCGCCAGCGGCCGGGGAGGAAGGGGTCGAGGG

ORF - retro_onil_38 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.45 %
Parental protein coverage: 54.23 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQLRKLFIGGLSFETTDESLRAHFEQWGTLTDCVVMRDPNSKRSRGFGFVTYSSVQEVDAAMSARPHKVDG
.L.KLF.GGL..ETTDE.LR..FEQ.GTL.DCVV.......RSR.FGF.TYS...E.DAAM.A.PH.V.G
RetrocopyKLCKLFVGGLNVETTDEGLRKYFEQYGTLSDCVVVMNQQLGRSRCFGFITYSTPEEADAAMAAKPHVVEG
ParentalRVVEPKRAVSREDSNRPGAHITVKKIFVGGIKEDTEESHLRDYFQQFGKIEVIDIMTDRNTGKKRGFAFV
..VE.KRA..RED.N.P.....VKKIFVGG.K....E..L..YF.QFG..E...I..D..TG.KRGF.FV
RetrocopyNNVEVKRAIAREDANNPDILANVKKIFVGGVKDHIVEENLTEYFSQFGAVEKAEIISDKQTGRKRGFGFV
ParentalTFDDHDSVDRIVIQKYHTINSHNCEVRKALTKQEMQSAGMGMGMRG
.F.D.DS....V..KYHTIN....EV.KALTKQEM...G.G...RG
RetrocopyFFEDTDSATKAVLTKYHTINGNKVEVKKALTKQEMSASGRGGRGRG

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






RNA-Seq - click to see more details

Oreochromis niloticus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Oreochromis niloticus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_onil_38 retrocopy.

TSS - click to see more details

Oreochromis niloticus was not studied using FANTOM5 data.

Lab - click to see more details

retro_onil_38 was not experimentally validated.

Retrocopy orthology:
Oreochromis niloticus 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 28 parental genes, and 291 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000007173 retrocopies
retro_amel_1726, retro_amel_547, retro_amel_925,
Bos taurus ENSBTAG0000000155320 retrocopies
retro_btau_1019, retro_btau_1065, retro_btau_1268, retro_btau_1378, retro_btau_1379, retro_btau_1437, retro_btau_1455, retro_btau_1657, retro_btau_1673, retro_btau_283, retro_btau_337, retro_btau_403, retro_btau_462, retro_btau_516, retro_btau_519, retro_btau_589, retro_btau_602, retro_btau_677, retro_btau_715, retro_btau_822,
Canis familiaris ENSCAFG0000000658016 retrocopies
retro_cfam_1080, retro_cfam_1081, retro_cfam_1170, retro_cfam_1323, retro_cfam_1616, retro_cfam_1844, retro_cfam_2017, retro_cfam_2128, retro_cfam_360, retro_cfam_564, retro_cfam_702, retro_cfam_803, retro_cfam_839, retro_cfam_855, retro_cfam_892, retro_cfam_937,
Cavia porcellus ENSCPOG000000209721 retrocopy
retro_cpor_1078,
Dasypus novemcinctus ENSDNOG000000092287 retrocopies
retro_dnov_1059, retro_dnov_1670, retro_dnov_1944, retro_dnov_2081, retro_dnov_250, retro_dnov_320, retro_dnov_374,
Equus caballus ENSECAG000000086761 retrocopy
retro_ecab_74,
Felis catus ENSFCAG000000101509 retrocopies
retro_fcat_1574, retro_fcat_1742, retro_fcat_1867, retro_fcat_382, retro_fcat_474, retro_fcat_712, retro_fcat_781, retro_fcat_844, retro_fcat_888,
Homo sapiens ENSG0000013548657 retrocopies
retro_hsap_1021, retro_hsap_1042, retro_hsap_1082, retro_hsap_1240, retro_hsap_1276, retro_hsap_1282, retro_hsap_1287, retro_hsap_1481, retro_hsap_158, retro_hsap_1584, retro_hsap_1613, retro_hsap_1638, retro_hsap_1711, retro_hsap_1899, retro_hsap_1933, retro_hsap_2002, retro_hsap_2029, retro_hsap_2091, retro_hsap_2096, retro_hsap_2197, retro_hsap_2347, retro_hsap_2379, retro_hsap_2636, retro_hsap_2640, retro_hsap_2668, retro_hsap_2718, retro_hsap_2857, retro_hsap_291, retro_hsap_2917, retro_hsap_2944, retro_hsap_3049, retro_hsap_3055, retro_hsap_332, retro_hsap_3343, retro_hsap_3393, retro_hsap_3432, retro_hsap_3439, retro_hsap_3449, retro_hsap_3549, retro_hsap_3745, retro_hsap_3756, retro_hsap_3757, retro_hsap_394, retro_hsap_3979, retro_hsap_4011, retro_hsap_4084, retro_hsap_414, retro_hsap_4218, retro_hsap_4282, retro_hsap_437, retro_hsap_4747, retro_hsap_482, retro_hsap_4883, retro_hsap_668, retro_hsap_84, retro_hsap_845, retro_hsap_924,
Gorilla gorilla ENSGGOG000000030406 retrocopies
retro_ggor_1006, retro_ggor_1010, retro_ggor_1221, retro_ggor_1738, retro_ggor_2041, retro_ggor_950,
Loxodonta africana ENSLAFG000000295875 retrocopies
retro_lafr_1202, retro_lafr_1208, retro_lafr_192, retro_lafr_747, retro_lafr_961,
Myotis lucifugus ENSMLUG000000006483 retrocopies
retro_mluc_2503, retro_mluc_342, retro_mluc_82,
Macaca mulatta ENSMMUG000000129895 retrocopies
retro_mmul_1031, retro_mmul_1427, retro_mmul_1726, retro_mmul_187, retro_mmul_1871,
Mustela putorius furoENSMPUG000000046201 retrocopy
retro_mputfur_34,
Mustela putorius furoENSMPUG000000057352 retrocopies
retro_mputfur_1378, retro_mputfur_653,
Mus musculus ENSMUSG000000464343 retrocopies
retro_mmus_1861, retro_mmus_410, retro_mmus_543,
Nomascus leucogenys ENSNLEG0000001765934 retrocopies
retro_nleu_1011, retro_nleu_1090, retro_nleu_1257, retro_nleu_130, retro_nleu_132, retro_nleu_1497, retro_nleu_1630, retro_nleu_1648, retro_nleu_166, retro_nleu_167, retro_nleu_1695, retro_nleu_1739, retro_nleu_1774, retro_nleu_1802, retro_nleu_1875, retro_nleu_190, retro_nleu_2040, retro_nleu_2222, retro_nleu_2304, retro_nleu_2324, retro_nleu_2378, retro_nleu_2690, retro_nleu_2742, retro_nleu_2852, retro_nleu_32, retro_nleu_366, retro_nleu_458, retro_nleu_587, retro_nleu_601, retro_nleu_645, retro_nleu_648, retro_nleu_708, retro_nleu_825, retro_nleu_987,
Oryctolagus cuniculus ENSOCUG000000133501 retrocopy
retro_ocun_1675,
Otolemur garnettii ENSOGAG000000297073 retrocopies
retro_ogar_1721, retro_ogar_205, retro_ogar_2321,
Oreochromis niloticus ENSONIG00000012248 1 retrocopy
retro_onil_38 ,
Ochotona princeps ENSOPRG0000000610710 retrocopies
retro_opri_1183, retro_opri_338, retro_opri_349, retro_opri_424, retro_opri_456, retro_opri_597, retro_opri_753, retro_opri_782, retro_opri_79, retro_opri_843,
Procavia capensis ENSPCAG000000018675 retrocopies
retro_pcap_111, retro_pcap_162, retro_pcap_377, retro_pcap_424, retro_pcap_435,
Pongo abelii ENSPPYG000000258504 retrocopies
retro_pabe_1765, retro_pabe_2285, retro_pabe_3492, retro_pabe_3835,
Pteropus vampyrus ENSPVAG000000003229 retrocopies
retro_pvam_1133, retro_pvam_1230, retro_pvam_1313, retro_pvam_1370, retro_pvam_196, retro_pvam_300, retro_pvam_453, retro_pvam_643, retro_pvam_859,
Rattus norvegicus ENSRNOG0000003683917 retrocopies
retro_rnor_1001, retro_rnor_1322, retro_rnor_1658, retro_rnor_1770, retro_rnor_1786, retro_rnor_1846, retro_rnor_1987, retro_rnor_2194, retro_rnor_2482, retro_rnor_2551, retro_rnor_2619, retro_rnor_2657, retro_rnor_2881, retro_rnor_2944, retro_rnor_2945, retro_rnor_2965, retro_rnor_2969,
Sus scrofa ENSSSCG000000002883 retrocopies
retro_sscr_354, retro_sscr_355, retro_sscr_861,
Ictidomys tridecemlineatus ENSSTOG000000065518 retrocopies
retro_itri_1291, retro_itri_1567, retro_itri_190, retro_itri_354, retro_itri_439, retro_itri_446, retro_itri_456, retro_itri_515,
Tupaia belangeri ENSTBEG0000000823830 retrocopies
retro_tbel_1219, retro_tbel_156, retro_tbel_162, retro_tbel_1643, retro_tbel_1830, retro_tbel_1967, retro_tbel_2192, retro_tbel_2195, retro_tbel_2211, retro_tbel_2330, retro_tbel_261, retro_tbel_2666, retro_tbel_2673, retro_tbel_2703, retro_tbel_276, retro_tbel_2774, retro_tbel_2787, retro_tbel_2970, retro_tbel_3473, retro_tbel_3976, retro_tbel_3995, retro_tbel_4266, retro_tbel_4271, retro_tbel_453, retro_tbel_4653, retro_tbel_4729, retro_tbel_692, retro_tbel_70, retro_tbel_79, retro_tbel_839,
Tursiops truncatus ENSTTRG0000000450527 retrocopies
retro_ttru_1202, retro_ttru_1223, retro_ttru_1251, retro_ttru_1331, retro_ttru_1362, retro_ttru_156, retro_ttru_157, retro_ttru_1678, retro_ttru_1732, retro_ttru_1806, retro_ttru_1813, retro_ttru_1874, retro_ttru_221, retro_ttru_311, retro_ttru_479, retro_ttru_599, retro_ttru_605, retro_ttru_607, retro_ttru_620, retro_ttru_63, retro_ttru_678, retro_ttru_708, retro_ttru_812, retro_ttru_882, retro_ttru_902, retro_ttru_926, retro_ttru_981,


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