RetrogeneDB ID: retro_nleu_1776

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397308.1:11512301..11513504(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BECN1
• Ensembl ID: ENSNLEG00000011840
• Aliases: None
• Description: None

Sequence

>retro_nleu_1776
GCCCCGGCGCCCACCTCCAGTCAGGCTGAGCCAGGAGACACCCGGGAGCCCGGCGCCACCACCAGGGAGGTGACAGACGC
TGAGGAGAAACAGGACGGTGCCTCTAGCAGACCCCTTCCAGGTGATGGCAGTGCGTCCAAGTACCATGCCAACATCTTCA
CCCTGCTGGGGGAGCTTGGCGCCATGCATATGCTCAGTAGCATCCAGAAGGCAGCTGGTGACATTTTTGACATAGTCTCT
GGCCAAGAAGTTGTGGACTATCCCCTGTGTGAAGAATGCACCGACAGTCTTTTAGAGCAGCTGGACAACCAGCTCGCTGT
CACAGAAGCTGAGAGTCAGAACTACCAACGCTGCCTGGAGACCGGGGAGCTGGCGACCAGCGAGGATGAGATGGCGGCGC
TGCGGGCGGAGCTGCGGGACCTGGAGCTGGAGGAGGCCAGGCTGGTGCAGGAGCTGGAGGATGTGGACAGGAACAATGCA
AGAGCAGCGGCGGATCTCGAGGCAGCCCAGGCAGAGGCTGCGGAGCTGGACCAGCAGGAGAGGCAGTACGACAGGGACTA
CAGTGCCTTGAAGTGGCAGCAGCTGGAACTGCTTGACCAGCTGGGGAACGTGGAGAACCAGCTACAATATGCCACGGTCC
AGATGGACCGGCTGAAGGAAATCAACTGTTTCACCGCCGCGTTTGAGATCTGGTTGGAGGGCCCCTTGGGCGTCATCAAT
AACTTCAGGTTGGGCCGCCTCCCCACTGTCCCTGTGGGCTGGAATGAGATTAACACTGCCTGGGGACAGGCGGCTTTGCT
GCTCCTTGCCCTGGCCAATGCAATTGGACTGCAGTTTCAGCGGTATCGACTCATCCCCTGCGGAAACCATTCGTATCTGA
AGTCTTTAACAGAGGACCGGACTGAGCTGCCGTTGTTCTGTTATGGGGGGCAGGATGTTTTCCTCAATAACAAGTTTGAC
CGCGCCATGGTGGCCTTCCTGGACTGCATGCAGCAGTTCAAGGAAGAGGCTGAGAAGGGTGAGCTGGGCCTCTGTCTGCC
CTACAGGATCCAGGTGGAGACAGGCCTGCTGGAGGACGTTAGCGGCCGAGGGGAATGCTATTCCATCAGAACCCATCTGA
ACACGCAGGAGCTGTGGACGAAGGCACTCAAGTTCCTGCTTATAAATTTCCAGTGGAGTCTCGTCTGGGTTGCCTCAAGG
TAT

Alignment

ORF - retro_nleu_1776 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.27 %
• Parental protein coverage: 89.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APLLTTAQAKPGETQEEETNSGEEPFIETPRQDGVSRRFIPPARMMSTESANSFTLIGEASDGGTMENLS
          AP..T..QA.PG.T.E......E....E...QDG.S.R..P.....S...AN.FTL.GE....G.M..LS
Retrocopy APAPTSSQAEPGDTREPGATTREVTDAEE-KQDGASSRPLPGDGSASKYHANIFTLLGEL---GAMHMLS

Parental  RRLKVTGDLFDIMSGQTDVDHPLCEECTDTLLDQLDTQLNVTENECQNYKRCLEILE-QMNEDDSEQLQM
          ...K..GD.FDI.SGQ..VD.PLCEECTD.LL.QLD.QL.VTE.E.QNY.RCLE..E....ED....L..
Retrocopy SIQKAAGDIFDIVSGQEVVDYPLCEECTDSLLEQLDNQLAVTEAESQNYQRCLETGELATSEDEMAALRA

Parental  ELKELALEEERLIQELEDVEKNRKIVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDELKSVEN
          EL..L.LEE.RL.QELEDV..N....A..LE..QAEA..LDQ.E.QY.R.YS..K.QQLEL.D.L..VEN
Retrocopy ELRDLELEEARLVQELEDVDRNNARAAADLEAAQAEAAELDQQERQYDRDYSALKWQQLELLDQLGNVEN

Parental  QMRYAQMQLDKLKKTNVFNATFHIWHSGQFGTINNFRLGRLPSVPVEWNEINAAWGQTVLLLHALANKMG
          Q..YA..Q.D.LK..N.F.A.F.IW..G..G.INNFRLGRLP.VPV.WNEIN.AWGQ..LLL.ALAN..G
Retrocopy QLQYATVQMDRLKEINCFTAAFEIWLEGPLGVINNFRLGRLPTVPVGWNEINTAWGQAALLLLALANAIG

Parental  LKFQRYRLVPYGNHSYLESLTDKSKELPLYCSGGLRFFWDNKFDHAMVAFLDCVQQFKEEVEKGETRFCL
          L.FQRYRL.P.GNHSYL.SLT....ELPL.C.GG...F..NKFD.AMVAFLDC.QQFKEE.EKGE...CL
Retrocopy LQFQRYRLIPCGNHSYLKSLTEDRTELPLFCYGGQDVFLNNKFDRAMVAFLDCMQQFKEEAEKGELGLCL

Parental  PYRMDVEKGKIEDTGGSGGSYSIKTQFNSEEQWTKALKFMLTNLKWGLAWVSSQF
          PYR..VE.G..ED..G.G..YSI.T..N..E.WTKALKF.L.N..W.L.WV.S..
Retrocopy PYRIQVETGLLEDVSGRGECYSIRTHLNTQELWTKALKFLLINFQWSLVWVASRY

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_1776 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006867	1 retrocopy	retro_amel_16,
Bos taurus	ENSBTAG00000019914	1 retrocopy	retro_btau_226,
Dipodomys ordii	ENSDORG00000000956	1 retrocopy	retro_dord_675,
Felis catus	ENSFCAG00000013136	1 retrocopy	retro_fcat_62,
Homo sapiens	ENSG00000126581	1 retrocopy	retro_hsap_335,
Macropus eugenii	ENSMEUG00000011700	1 retrocopy	retro_meug_600,
Macaca mulatta	ENSMMUG00000029971	1 retrocopy	retro_mmul_81,
Monodelphis domestica	ENSMODG00000015064	1 retrocopy	retro_mdom_1778,
Mus musculus	ENSMUSG00000035086	1 retrocopy	retro_mmus_390,
Nomascus leucogenys	ENSNLEG00000011840	1 retrocopy	retro_nleu_1776 ,
Oryctolagus cuniculus	ENSOCUG00000015964	3 retrocopies	retro_ocun_1021, retro_ocun_1732, retro_ocun_218,
Procavia capensis	ENSPCAG00000014049	1 retrocopy	retro_pcap_345,
Pan troglodytes	ENSPTRG00000022819	1 retrocopy	retro_ptro_268,
Sorex araneus	ENSSARG00000000367	1 retrocopy	retro_sara_136,
Sus scrofa	ENSSSCG00000017386	1 retrocopy	retro_sscr_75,
Ictidomys tridecemlineatus	ENSSTOG00000012612	1 retrocopy	retro_itri_25,
Tursiops truncatus	ENSTTRG00000011716	1 retrocopy	retro_ttru_595,