RetrogeneDB ID: retro_nleu_2020

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397323.1:11649084..11649907(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000005626
• Aliases: None
• Description: None

Sequence

>retro_nleu_2020
GCAGCAGACACCCACTTAGGTGGCACCAACCTTGACTTCCAGATGGAACTGTACATGTACGAAAGGAAAAGTGATGGCAT
CTACATCCTAAATCTGAAAGGACCTGGGAGAAGCTTCTGCTGCAGCTCATGCCATTGTTGCCATTGAAAACCCTGCTGAT
GTCAGTGTCATAACCTCCAGGAATATCGGCCAGAGGGCCGTGCTGAAGTTTGCTGCTGCCACTGGAGCCACAGCAATTGC
TGGCCACTTCACTCCTGGAACCTTTACTAACCAGATCCAGGGAGCCTTCCAGGAGCCACAGCTTCTTGTGGTTACTGACC
GCAGGGTTGACCAACAGCCTCTCACAGAGGCATCTTATGTTAACTTTCCCACCATTGATCTGTGTCACACAGATTCTCCT
CTGCACTGTGTGAATATTGCCATCCTATGCAACAACACGGAAGCTCACTCAGTGGGTTTGATGTGGATGCTGCCCTGGGA
AGTTCTGCACATGCATGGTACCATTTCCCATGAACACCCGCGGGAGGTCATGCCTGATCTCTACTTCTACAGGGATCCTG
AAGAGACTGAAAAAGAAGAGCAGGCTGCTGCTGAAAAGCCTGTGACCAAGGAGGAATTTCAGGGTGAACAGACTGCTACA
GCTCCTGAGTCGACTGCTACTCAGCCTGAGGTTGGAGACTGGTCTGACGGCATGCGGTTGCCCTCTGTGCCTATTCAGCC
GTTCCCTACTGAAGACTGGAGCGCTCAGCCTGCCATGGAAGACTGGTCTGCAGCTCTCACTGCTCAGGCCACTGAATGGG
TAGGAGCAACCACTGAATGGTCT

Alignment

ORF - retro_nleu_2020 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.73 %
• Parental protein coverage: 93.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLK-RTWEKLLL-AARAIVAIENPADVSVISSRNTGQRAV
          AA.THLGGTNLDFQME.Y.Y.RKSDGIYI.NLK.RTWEKLLL.AA.AIVAIENPADVSVI.SRN.GQRAV
Retrocopy AADTHLGGTNLDFQMELYMYERKSDGIYILNLK<RTWEKLLL<AAHAIVAIENPADVSVITSRNIGQRAV

Parental  LKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYV
          LKFAAATGAT.IAG.FTPGTFTNQIQ.AF.EP.LLVVTD.R.D.QPLTEASYVN.PTI.LC.TDSPL..V
Retrocopy LKFAAATGATAIAGHFTPGTFTNQIQGAFQEPQLLVVTDRRVDQQPLTEASYVNFPTIDLCHTDSPLHCV

Parental  DIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEF
          .IAI.CNN..AHSVGLMW.ML..EVL.M.GTIS.EHP.EVMPDLYFYRDPEE.EKEEQAAAEK.VTKEEF
Retrocopy NIAILCNNTEAHSVGLMW-MLPWEVLHMHGTISHEHPREVMPDLYFYRDPEETEKEEQAAAEKPVTKEEF

Parental  QGEWTAPAPEFTATQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGATTDWS
          QGE.TA.APE.TATQPEV.DWS.G...PSVPIQ.FPTEDWSAQPA.EDWSAA.TAQATEWVGATT.WS
Retrocopy QGEQTATAPESTATQPEVGDWSDGMRLPSVPIQPFPTEDWSAQPAMEDWSAALTAQATEWVGATTEWS

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2020 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 243 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004183	1 retrocopy	retro_acar_140,
Ailuropoda melanoleuca	ENSAMEG00000008962	13 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	ENSCAFG00000005101	27 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	ENSCJAG00000009675	15 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	ENSDNOG00000004048	27 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	ENSECAG00000013062	5 retrocopies	retro_ecab_193, retro_ecab_453, retro_ecab_46, retro_ecab_592, retro_ecab_71,
Echinops telfairi	ENSETEG00000018160	4 retrocopies	retro_etel_1399, retro_etel_1665, retro_etel_1960, retro_etel_92,
Felis catus	ENSFCAG00000002739	22 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	ENSG00000168028	2 retrocopies	retro_hsap_107, retro_hsap_3015,
Loxodonta africana	ENSLAFG00000032009	5 retrocopies	retro_lafr_1234, retro_lafr_367, retro_lafr_806, retro_lafr_863, retro_lafr_997,
Mustela putorius furo	ENSMPUG00000002463	21 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	ENSMUSG00000032518	1 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	ENSPTRG00000022841	1 retrocopy	retro_ptro_14,
Pteropus vampyrus	ENSPVAG00000007794	19 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	ENSRNOG00000018645	27 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	ENSVPAG00000012307	4 retrocopies	retro_vpac_22, retro_vpac_293, retro_vpac_440, retro_vpac_553,