RetrogeneDB ID: retro_nleu_1519

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397297.1:14704692..14706373(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACO2
• Ensembl ID: ENSNLEG00000015482
• Aliases: None
• Description: aconitase 2, mitochondrial [Source:HGNC Symbol;Acc:118]

Sequence

>retro_nleu_1519
ATGGCGCTCTACAGCCTACTGGTTACCTGGCTGTAGAAAGCTCTGGGTGTGCAGCAGTACCATGTGACCTCAGTCCTGTG
CCAACAGGCCAAGGTGGCGATGAGCCACTTTGAGCCCAAGTACATCCACTATGACCTGCTAGAGAACATTAACATTGTTC
GCAAACAATTTAACTGGCCTCTGACCCTCTCGGAGAAGATCGTGTATGGACACCTGGATGACCCTGCCAGCCAGGAAATC
GAGTGGAGCAAGACGTACCTGCAGCAGCGGTCAGACAGTGTGGCCATGCAGGATGCAACGGCCCAGATGGCCATGCTGCA
GTTCATCAGCAGCAGGCTCCCAAGGTGACTGTGCCGTCCACCATCCACTGTGACCATCTGATTGAGGCCCAGCTCGGGAG
TGAGAAAGACCTGCACCGGCCCAAGGACATCAACCACAAAGTTTATAATTTCCTGGCAACTGGAAGTGTCAAATATGGCA
TGGGCTTCTGGAAGCCTGGATCTGGAATCATTCACCAGATTATTCTGGAAAACCGTGAATACCCTGGGGTTCTTCTGATT
GACACTGACTCCCACACCCCCAGTGGTGGCAGCCTGCAGGGCATCTGCATTGGAGTTGGGGGTGCTGAGCTGTGGATATC
ATGACTGGGATCCCCTGGGAGCTGAAGTGACCCAAGGTGATTGGTGTGAAGGTGATGGGCTCCCTCTCCGGTTGGACCTC
ACCCAAAGATGAGATCCTGAAGGTGGCAGGCATCCTCACAGTGAAAGGTGGCACAGGTGCAATCATGGAATACCACAGGC
CTGGTGTAGACTCCATCTCCTGCACTGGCATGGCGACAGTCTGCAACATGGGTGCAGAAATTGGGGCCACCACTTCCGTG
TTCTCTCACAACCTCAGGATGAAGAAGTACCTGAGCAAGACCTGCTGGGCATACATTGCCAATCTAGCTGATGAATTCAA
GGATCACTTGGTGCCTGACCCTGGCTGCCATTATGACCAACTAATTGAAGTTAACCTCAGTGAACTGAAGCTGCACATCA
ATGGGCCCTTCACCCCTGACCTGGCTCACCCGGTGGTAGAAGTTGGCAAGGTGGCAAAGAAGGAAGAATGGCCTCTGGAC
ATCTGAGTGGGTCTGATTGGCAGCTGCACCAATTTAAGCTATGAAGATATGGGGCGCTTAGCAGCTGTGGTCAAGCAGGC
ACTGGCCCATGGCCTCAAGTGCAAGTCCCAGTTCACTATCACTCCATGCTCTGAGCACATCCGTGTCTCCACTGAGCGGG
ATGGCTATGGACAGACCTTGAGGGATGTGGGCAGCATCGTCCTGGCCAATGCTTGTGGCCCTTGCATTGGCCAGTCGGAC
AGAAAGGACATCAAGAAGCGGGAGAAGAACATAATTGTCACCTCCTACAACAGGAACTTCACGGGCCACGATGACACGAA
TCCCGAGACCCATGCCTTCATCACGTCCCCAGAGACTGTCACAGCCCTGGCCAGTGCGGGAACCCTCAAGTTCAACCCAG
AGACCGACTACCTGACAGGCAAAGATGGCAAGAAGTTCAAGCTGGAGGCTCCGGATGCAGATGAGCTTCCCCAAGCGGAG
CTTGGCTCGGGGCAGGACACCTACCAGCACCCCCGCACGGGATACCACTGACCACATCTCGGCTGCTGGCCTCTGGCTCA
A

Alignment

ORF - retro_nleu_1519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 72.18 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPYSLLVTRLQKALGVRQYHVASVLCQRAKVAMSHFEPNEYIHYDLLEKNINIVRKRMNRPLTLSEKIV
          MA.YSLLVT.L.KALGV.QYHV.SVLCQ.AKVAMSHFEP..YIHYDLLE.NINIVRK..N.PLTLSEKIV
Retrocopy MALYSLLVTWL*KALGVQQYHVTSVLCQQAKVAMSHFEP-KYIHYDLLE-NINIVRKQFNWPLTLSEKIV

Parental  YGHLDDPASQEIERGKSYLRLRPDRVAMQDVTAQMAMLQFISSGLP-KVAVPSTIHCDHLIEAQVGGEKD
          YGHLDDPASQEIE..K.YL..R.D.VAMQD.TAQMAMLQFISS.LP.KV.VPSTIHCDHLIEAQ.G.EKD
Retrocopy YGHLDDPASQEIEWSKTYLQQRSDSVAMQDATAQMAMLQFISSRLP<KVTVPSTIHCDHLIEAQLGSEKD

Parental  LRRAKDINQEVYNFLATAGAKYGVGFWKPGSGIIHQIILENYAYPGVLLIGTDSHTPNGGGLGGICIGVG
          L.R.KDIN..VYNFLAT...KYG.GFWKPGSGIIHQIILEN..YPGVLLI.TDSHTP.GG.L.GICIGVG
Retrocopy LHRPKDINHKVYNFLATGSVKYGMGFWKPGSGIIHQIILENREYPGVLLIDTDSHTPSGGSLQGICIGVG

Parental  GAD-AVDVMAGIPWELKCPKVIGVKLTGSLSGWSSPKDVILKVAGILTVKGGTGAIMEYHGPGVDSISCT
          GA..AVD.M.GIPWELK.PKVIGVK..GSLSGW.SPKD.ILKVAGILTVKGGTGAIMEYH.PGVDSISCT
Retrocopy GAE<AVDIMTGIPWELK*PKVIGVKVMGSLSGWTSPKDEILKVAGILTVKGGTGAIMEYHRPGVDSISCT

Parental  GMATICNMGAEIGATTSVFPYNHRMKKYLSKTGRADIANLADEFKDHLVPDPGCHYDQLIEINLSELKPH
          GMAT.CNMGAEIGATTSVF..N.RMKKYLSKT..A.IANLADEFKDHLVPDPGCHYDQLIE.NLSELK.H
Retrocopy GMATVCNMGAEIGATTSVFSHNLRMKKYLSKTCWAYIANLADEFKDHLVPDPGCHYDQLIEVNLSELKLH

Parental  INGPFTPDLAHPVAEVGRVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFTITP
          INGPFTPDLAHPV.EVG.VA.KE.WPLDI.VGLIGSCTN.SYEDMGR.AAV.KQALAHGLKCKSQFTITP
Retrocopy INGPFTPDLAHPVVEVGKVAKKEEWPLDI*VGLIGSCTNLSYEDMGRLAAVVKQALAHGLKCKSQFTITP

Parental  GSEQIRATIERDGYAQILRDLGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDANPETHA
          .SE.IR...ERDGY.Q.LRD.G.IVLANACGPCIGQ.DRKDIKK.EKN.IVTSYNRNFTG..D.NPETHA
Retrocopy CSEHIRVSTERDGYGQTLRDVGSIVLANACGPCIGQSDRKDIKKREKNIIVTSYNRNFTGHDDTNPETHA

Parental  FVTSPEIVTALAIAGTLKFNPETDYLTGTDGKKFKLEAPDADELPKVEFDPGQDTYQHPPKDSSGQHVDV
          F.TSPE.VTALA.AGTLKFNPETDYLTG.DGKKFKLEAPDADELP..E...GQDTYQHP.......H...
Retrocopy FITSPETVTALASAGTLKFNPETDYLTGKDGKKFKLEAPDADELPQAELGSGQDTYQHPRTGYH*PHLGC

Parental  SPTSQ
          .P..Q
Retrocopy WPLAQ

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_1519 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100412	2 retrocopies	retro_hsap_2583, retro_hsap_324,
Myotis lucifugus	ENSMLUG00000002472	1 retrocopy	retro_mluc_2566,
Macaca mulatta	ENSMMUG00000001454	2 retrocopies	retro_mmul_647, retro_mmul_694,
Mus musculus	ENSMUSG00000022477	1 retrocopy	retro_mmus_535,
Nomascus leucogenys	ENSNLEG00000015482	2 retrocopies	retro_nleu_1519 , retro_nleu_1767,
Pongo abelii	ENSPPYG00000011871	1 retrocopy	retro_pabe_1903,
Pan troglodytes	ENSPTRG00000014428	1 retrocopy	retro_ptro_260,
Drosophila melanogaster	FBgn0010100	1 retrocopy	retro_dmel_56,