RetrogeneDB ID:

retro_nleu_1564

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397299.1:11744784..11745399(-)
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:ENSNLEG00000005626
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_1564
ATGTCCAAAGCCCTTGATGTCCTGCAAATGAAAGAGAAGGATGTTCTTAAGTTTTTTGCTGCAGGAACCAATTTAGGTGG
AAACAACCTTGACTTCAAAATGGAACAGTACACCTATGAGAGGAAAAGTGATGGCATCTACATCATAAATATGAGGAGGA
CCTGGGAGAAGCTTCTGCTGGCAGCTTGTGTCTTTGTTGCCACTGAAAACTCTGCTGATGTCCATGTCATATCCTCCAAG
AATACTAGCCAATGGGCCTTGCTAAAGTTTGCTGCTGCCATTGAAGCTACTCCTATTACTTGCTACTTCACTGAAAATGT
CACTAACCAGATCCAGATGGTCTTTTGGAAGCCATGGGTTCTGATGGTTACTGAGCCCAGGGTTGACCACCATCCTCTCA
TAGAGGCATCTTATGGTAACCTGCCTACCACTGGTTTGTGTGACACAGATTCTCCTCTGCACTATGTGGACATTGCCATC
CCATGCAACAACAAGGGAACTCACTTAGTGGGTTTTATGTGATGGATGCTGGCCTGGGAAATGGTTTGCATGCATGGCAC
CATTTCCTGTGAACACCTATGAGGGGTTATGCCTGATCTCTACTTCTACAGAGAT

ORF - retro_nleu_1564 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.84 %
Parental protein coverage: 69.83 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAARAIVAIEN
MS.ALDVLQMKE.DVLKF.AAGT.LGG.NLDF.MEQY.Y.RKSDGIYIIN..RTWEKLLLAA...VA.EN
RetrocopyMSKALDVLQMKEKDVLKFFAAGTNLGGNNLDFKMEQYTYERKSDGIYIINMRRTWEKLLLAACVFVATEN
ParentalPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASYV
.ADV.VISS.NT.Q.A.LKFAAA..ATPI...FT....TNQIQ..F..P..L.VT.PR.DH.PL.EASY.
RetrocopySADVHVISSKNTSQWALLKFAAAIEATPITCYFTENV-TNQIQMVFWKPWVLMVTEPRVDHHPLIEASYG
ParentalNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRD
NLPT..LC.TDSPL.YVDIAIPCNNKG.H.VG.M.WMLA.E...M.GTIS.EH...VMPDLYFYRD
RetrocopyNLPTTGLCDTDSPLHYVDIAIPCNNKGTHLVGFM*WMLAWEMVCMHGTISCEHL*GVMPDLYFYRD

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_1564 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 17 parental genes, and 243 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000041831 retrocopy
retro_acar_140,
Ailuropoda melanoleuca ENSAMEG0000000896213 retrocopies
retro_amel_1091, retro_amel_1276, retro_amel_1357, retro_amel_1432, retro_amel_1446, retro_amel_1497, retro_amel_1634, retro_amel_1817, retro_amel_1857, retro_amel_196, retro_amel_430, retro_amel_808, retro_amel_943,
Canis familiaris ENSCAFG0000000510127 retrocopies
retro_cfam_1046, retro_cfam_1109, retro_cfam_1173, retro_cfam_1189, retro_cfam_1263, retro_cfam_1288, retro_cfam_1366, retro_cfam_1373, retro_cfam_1435, retro_cfam_1511, retro_cfam_1534, retro_cfam_1545, retro_cfam_1555, retro_cfam_1679, retro_cfam_1770, retro_cfam_1814, retro_cfam_1957, retro_cfam_1990, retro_cfam_2140, retro_cfam_512, retro_cfam_820, retro_cfam_828, retro_cfam_854, retro_cfam_928, retro_cfam_957, retro_cfam_980, retro_cfam_994,
Callithrix jacchus ENSCJAG0000000967515 retrocopies
retro_cjac_1113, retro_cjac_1572, retro_cjac_1595, retro_cjac_2265, retro_cjac_2438, retro_cjac_2500, retro_cjac_2502, retro_cjac_2750, retro_cjac_2897, retro_cjac_305, retro_cjac_3160, retro_cjac_4124, retro_cjac_53, retro_cjac_732, retro_cjac_958,
Dasypus novemcinctus ENSDNOG0000000404827 retrocopies
retro_dnov_1022, retro_dnov_108, retro_dnov_1099, retro_dnov_1219, retro_dnov_1372, retro_dnov_1431, retro_dnov_1614, retro_dnov_184, retro_dnov_1913, retro_dnov_1974, retro_dnov_1987, retro_dnov_1988, retro_dnov_2067, retro_dnov_2200, retro_dnov_2224, retro_dnov_2309, retro_dnov_2339, retro_dnov_2469, retro_dnov_2480, retro_dnov_375, retro_dnov_42, retro_dnov_456, retro_dnov_465, retro_dnov_663, retro_dnov_800, retro_dnov_895, retro_dnov_940,
Equus caballus ENSECAG000000130625 retrocopies
retro_ecab_193, retro_ecab_453, retro_ecab_46, retro_ecab_592, retro_ecab_71,
Echinops telfairi ENSETEG000000181604 retrocopies
retro_etel_1399, retro_etel_1665, retro_etel_1960, retro_etel_92,
Felis catus ENSFCAG0000000273922 retrocopies
retro_fcat_1119, retro_fcat_1127, retro_fcat_1239, retro_fcat_1353, retro_fcat_1595, retro_fcat_1668, retro_fcat_1694, retro_fcat_1720, retro_fcat_1758, retro_fcat_1804, retro_fcat_1807, retro_fcat_1861, retro_fcat_1970, retro_fcat_239, retro_fcat_258, retro_fcat_384, retro_fcat_391, retro_fcat_551, retro_fcat_682, retro_fcat_722, retro_fcat_793, retro_fcat_906,
Homo sapiens ENSG000001680282 retrocopies
retro_hsap_107, retro_hsap_3015,
Loxodonta africana ENSLAFG000000320095 retrocopies
retro_lafr_1234, retro_lafr_367, retro_lafr_806, retro_lafr_863, retro_lafr_997,
Mustela putorius furoENSMPUG0000000246321 retrocopies
retro_mputfur_1045, retro_mputfur_1143, retro_mputfur_1194, retro_mputfur_1227, retro_mputfur_1311, retro_mputfur_1318, retro_mputfur_1427, retro_mputfur_1502, retro_mputfur_1558, retro_mputfur_1584, retro_mputfur_288, retro_mputfur_358, retro_mputfur_423, retro_mputfur_477, retro_mputfur_515, retro_mputfur_560, retro_mputfur_576, retro_mputfur_712, retro_mputfur_733, retro_mputfur_932, retro_mputfur_953,
Mus musculus ENSMUSG000000325181 retrocopy
retro_mmus_219,
Nomascus leucogenys ENSNLEG00000005626 49 retrocopies
retro_nleu_1204, retro_nleu_1277, retro_nleu_1278, retro_nleu_1462, retro_nleu_1564 , retro_nleu_1607, retro_nleu_1635, retro_nleu_1719, retro_nleu_1769, retro_nleu_1837, retro_nleu_1885, retro_nleu_1924, retro_nleu_1983, retro_nleu_2020, retro_nleu_2035, retro_nleu_2036, retro_nleu_2172, retro_nleu_2289, retro_nleu_2298, retro_nleu_2343, retro_nleu_2450, retro_nleu_254, retro_nleu_2579, retro_nleu_2624, retro_nleu_2650, retro_nleu_2662, retro_nleu_2693, retro_nleu_275, retro_nleu_2837, retro_nleu_2849, retro_nleu_2912, retro_nleu_3057, retro_nleu_3060, retro_nleu_307, retro_nleu_309, retro_nleu_3098, retro_nleu_310, retro_nleu_336, retro_nleu_339, retro_nleu_508, retro_nleu_591, retro_nleu_598, retro_nleu_705, retro_nleu_718, retro_nleu_740, retro_nleu_877, retro_nleu_883, retro_nleu_925, retro_nleu_950,
Pan troglodytes ENSPTRG000000228411 retrocopy
retro_ptro_14,
Pteropus vampyrus ENSPVAG0000000779419 retrocopies
retro_pvam_1189, retro_pvam_1249, retro_pvam_1335, retro_pvam_1403, retro_pvam_1406, retro_pvam_1443, retro_pvam_1446, retro_pvam_396, retro_pvam_499, retro_pvam_532, retro_pvam_548, retro_pvam_60, retro_pvam_635, retro_pvam_650, retro_pvam_789, retro_pvam_889, retro_pvam_896, retro_pvam_898, retro_pvam_98,
Rattus norvegicus ENSRNOG0000001864527 retrocopies
retro_rnor_1004, retro_rnor_1114, retro_rnor_1119, retro_rnor_1213, retro_rnor_1301, retro_rnor_1396, retro_rnor_1481, retro_rnor_1634, retro_rnor_1778, retro_rnor_1840, retro_rnor_1886, retro_rnor_2068, retro_rnor_2153, retro_rnor_2329, retro_rnor_2384, retro_rnor_2444, retro_rnor_2553, retro_rnor_2554, retro_rnor_2589, retro_rnor_2637, retro_rnor_2649, retro_rnor_2701, retro_rnor_2810, retro_rnor_2912, retro_rnor_2958, retro_rnor_645, retro_rnor_702,
Vicugna pacos ENSVPAG000000123074 retrocopies
retro_vpac_22, retro_vpac_293, retro_vpac_440, retro_vpac_553,


Copyright © RetrogeneDB 2014-2017