RetrogeneDB ID: retro_nleu_1131

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397282.1:3067852..3069452(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MIPEP
• Ensembl ID: ENSNLEG00000013401
• Aliases: None
• Description: None

Sequence

>retro_nleu_1131
AAAACTAGGCAAGTGGCCTAACTGTTTATGTTTGATTTTGAAATTAGTGGAATCCACCTAGACAAAGAAAAGTGTAAAAG
AGCAGTGGACCTTAATGTTAAAATCTTAGATTTGAGTAGTACATGTCTTATGGCAAACAACTTTCCCAACAAGATTGAGA
AGCATCTCTTACAAGAACACATTCACCATAACTTTTATCTGATGGGGATCGTATCATAATTGATGGTCTCCATGCAGAAG
CACCAGGCGACTTGGTGTGAGAAGCTGCTTATAAAATTTTTCTTTATCCCTATACTGGTCAATTAAAATGTTTAGAAGAG
TAGCTCAGCAACAGAGATCCTCTGCAAAAGTTGGTAGTGTATTCCGTGTTTTCCAACAGGGCTCTCCAAGGAACAATAGT
TAAAATTCAGAAACTGTCATCCAGTTCCTTGAGAAACTCTCTGACAAACTTTCCGAAAGAACTCGAAAAGATTTTGAGAT
GATATGAGGGATGAAAATGAAACAGAATTCTCAAAATTCCAAAGTAATGCCTTGGGACCCCTGCTACCACAGTGGTGTGA
TTCATGCACAAAGGTATAATATTGAGCCTGGCTTATATTGCCTGTTTTTCTCCCTTGGAGCATGCAGGGAAGGCCTGAAT
ATTTGGCTTAACAAACGGTTGGGGATTTCCTTATGTGCAGAGTAGCCTGCAAAAGGAGAGGTATGGTGTGAAGATGTCTG
AAAACTGGCCCTCATTCATGAATCTGAAGGACTGTCAGAGTGCATTTACTTTGATTTTTTTCAGCAAGCAGACAAACCAC
ATCAGGATTGCCATTTTACAATCCATGGAGGCAGATGAAAGGACAACAGAGACTATCAACTCCCAGTCATGGTTCTTATG
CTGAATCTTCCCCATTCCTCAAGTTCACCAACTTTGCTAACTCCTGGAATGATGGAAAATCTTGTCCACAAAATGGGACA
TGCTATGCTTTCAATGCTAAGATGTACTTGTTACTAACACATCACTGGAACCAGGTGCCCCACTGATTTTGCAGAGGTTC
CTTCTATTCTAATAGAGTACTTTGCAAATGATTATCGAGTAAACAATTTGCCAGACAAAATTAGAATGGGCAGCCACTGC
CAAAAAAATATGGTGTCTCAGCTTTGTGAATCTAAAAAGCTTTGTGCTGTAGCTGATATGAAACTTTAGGTCTTTTATGC
CACTCTGGATCAAATCTACCATGGGAGGCATCCCCTGAGGAATTCAACCACAGACATTCTCAAGGAAACACAAGAGACAT
TCTGTGGCTTACCATATGTTCCAAATACTGCCTGGAAGCTGCGGATCACCTACCTCGTGGGCTATACTGCCAAATATTAC
TCTTACCTCATGTCTAGGGCAGTCACTTCCATGGTTTGGAAGGAATGTTTTCTACAAAATCCTTTCAACAGGGTCACCAT
GGAGTGCTATTGCAGGGAGATGCTGGCCCACAGTGGAGGCAAGAAGCCCATGCTCATGGTTGAAGGTGTGTTTCAGAAGT
GCCCTTCTATTGATTACTTTGTAAGTGCCCTTGTTTCTGACTTGGATCTGGACTTTTAAACTTTTGTCATGGATTCTGAA

Alignment

ORF - retro_nleu_1131 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.44 %
• Parental protein coverage: 75.18 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ETRRVAELFMFDFEISGIHLDKEKRKRAVDLNVKILDLSSTFLMGTNFPNKIEKHLLPEHIRRNF-TSVG
          .TR.VA.LFMFDFEISGIHLDKEK.KRAVDLNVKILDLSST.LM..NFPNKIEKHLL.EHI..NF..S.G
Retrocopy KTRQVA*LFMFDFEISGIHLDKEKCKRAVDLNVKILDLSSTCLMANNFPNKIEKHLLQEHIHHNF<LSDG

Parental  DHIIIDGLHAESPDDLVREAAYKIFLYPNAGQLKCLEELLSSRDLLAKLVGYSTFSHRALQGTIAK-NPE
          D.IIIDGLHAE.P.DLV.EAAYKIFLYP..GQLKCLEE.LS.RD.L.KLV.YS.FS.RALQGTI.K.N.E
Retrocopy DRIIIDGLHAEAPGDLV*EAAYKIFLYPYTGQLKCLEE*LSNRDPLQKLVVYSVFSNRALQGTIVK<NSE

Parental  TVMQFLEKLSDKLSERTLKDFQMIRGMKMKLNPQNSEVMPWDPPYYSGVIRAERYNIEPSLYCPFFSLGA
          TV.QFLEKLSDKLSERT.KDF.MI.GMKMK.N.QNS.VMPWDP.Y.SGVI.A.RYNIEP.LYC.FFSLGA
Retrocopy TVIQFLEKLSDKLSERTRKDFEMI*GMKMKQNSQNSKVMPWDPCYHSGVIHAQRYNIEPGLYCLFFSLGA

Parental  CMEGLNILLNRLLGISLYAEQPARGEVWSEDVRKLAVVHESEGLLGYIYCDFFQRADKPHQDCHFTIRGG
          C.EGLNI.LN..LGISL.AE.PA.GEVW.EDV.KLA..HESEGL...IY.DFFQ.ADKPHQDCHFTI.GG
Retrocopy CREGLNIWLNKRLGISLCAE*PAKGEVWCEDV*KLALIHESEGLSECIYFDFFQQADKPHQDCHFTIHGG

Parental  RLKEDGDYQLPVVVLMLNLPRSSKSSPTLLTPGMMENLFHEMGHAMHSMLGRTRYQHVTGTRCPTDFAEV
          R.K...DYQLPV.VLMLNLP.SS.SSPTLLTPGMMENL.H.MGHAM.SML..T.Y.H.TGTRCPTDFAEV
Retrocopy R*KDNRDYQLPVMVLMLNLPHSS-SSPTLLTPGMMENLVHKMGHAMLSMLRCTCY*HITGTRCPTDFAEV

Parental  PSILMEYFANDYRVVN-QFARHYQTGQPLPK-NMVSRLCESKKVCAAADMQLQVFYATLDQIYHGKHPLR
          PSIL.EYFANDYR.VN.QFAR....GQPLPK.NMVS.LCESKK.CA.ADM.L.VFYATLDQIYHG.HPLR
Retrocopy PSILIEYFANDYR-VN<QFARQN*NGQPLPK>NMVSQLCESKKLCAVADMKL*VFYATLDQIYHGRHPLR

Parental  NSTTDILKETQEKFYGLPYVPNTAWQLRFSHLVGYGAKYYSYLMSRAVASMVWKECFLQDPFNRAAGERY
          NSTTDILKETQE.F.GLPYVPNTAW.LR...LVGY.AKYYSYLMSRAV.SMVWKECFLQ.PFNR...E.Y
Retrocopy NSTTDILKETQETFCGLPYVPNTAWKLRITYLVGYTAKYYSYLMSRAVTSMVWKECFLQNPFNRVTMECY

Parental  RREMLAHGGGREPMLMVEGMLQKCPSVDDFVSALVSDLDLDFETFLMDSE
          .REMLAH.GG..PMLMVEG..QKCPS.D.FVSALVSDLDLDF.TF.MDSE
Retrocopy CREMLAHSGGKKPMLMVEGVFQKCPSIDYFVSALVSDLDLDF*TFVMDSE

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_1131 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000027001	1 retrocopy	retro_hsap_3891,
Gorilla gorilla	ENSGGOG00000009424	1 retrocopy	retro_ggor_2619,
Macaca mulatta	ENSMMUG00000006942	1 retrocopy	retro_mmul_1732,
Nomascus leucogenys	ENSNLEG00000013401	1 retrocopy	retro_nleu_1131 ,
Pongo abelii	ENSPPYG00000005207	1 retrocopy	retro_pabe_3172,
Sus scrofa	ENSSSCG00000009290	1 retrocopy	retro_sscr_415,
Sus scrofa	ENSSSCG00000025544	1 retrocopy	retro_sscr_414,