RetrogeneDB ID: retro_nleu_1767

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397308.1:5644090..5645633(+)
• 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_1767
GGTGCAATTGTGGAATACCATGGGCCCGGCGTAGACTCCATCTCCTGTGCTGGCATGGCGAAATCTGCAACATGGGTGCA
GAAATTGGGGCCACCACTTCCGTGTTCCCTTACAACCACAGGATGAGGAAGTACCTAAGCAAGACCGGCCAGACAGACAT
TGCCGGTCTAGCTGATGAATTCCAGGATCACTTGGTGCCTGACCCTGGCTGCTGTTATGACCAACTAATTGAAATTAACC
TCAGTGAGCTGAAGCCACACATCAATGGGCCCTTCACCCCTGATAAGGCTCACCCTGTGGCAGAAGTGGGCAAGGTGGCA
GAGAAGGAAGGATGGCCTCTGGACATCCGAGTGGGTCTGATTGGTACCTGCAACAATTAAAGCTATGAAGATCCGGGGCA
CTCAGCAGCTGTGGCCAAGCAGGCACTGGCCCATGACCTCAGGTGCAAGTCCCACTTCACCATCACTCCAGGCTCCGAGC
AGATCCACGCCACCATTGAGCGGGACAGCTACACACAGATCTTGAGGAATGTGGGCGGCATCGTCCTGGCCAATGCTTGT
GGCCTCTGCATTGGCCACTGGGACATGAAGGACATCAAGAAGGGGAAGAAGAACACGATCGTCACCTCCTACAACAGGAA
CTTCACGGCCACAACAACACAGACCCCAAGACCCATGCCTTCGTCACGTCCCCAGAGATTGTCACAGCCCTGGCCATTGC
GGGAATCCTCAAGTTCAACCCAGAGACCAACTACCTGACAGGCAAGGATGGGAAGAAGTTCAAGCTGGAGCCTCCGGATG
CAGATGAGCTTCCCCAAGCAGAGTTTGGCCCAGGGCAGGGCACCTACCAGCACCCCCTACAGGACAGCAGTGGCCAGCAC
GTGGATGTGAGCCCCACCAGCCAGCGCCTGCAGCTCCTGGAGCGTTTTGACAAGTGGGATGGCAGGGACCTGGCGGACCT
GCAGATCGTCATCCAGGTCAGAGGGAAGTGTACTTCTGACCGCATCTCGGCTGCTGGCCCCTGGCTCAAGTTTTGTGGGC
ACTTGGACAACATTTCCAACAACCTGCTCATTGGTGCCATCAACATTGAAAACAGCCAGTCCAACTCCGTGTGCAGTGCC
GTCACCCAGGAGTTTGGCCCCGTCCCTGCCACTGCCCGCTGCTGCAAGAAACATGGCATCAGGTGGGTGGTGATTGGGGA
CAAGAACTCGAGCCGGGAGCACGCAGCGCTGGAGCCTCACCGCCTCTGGGGCCGGGCCATCATCACCGAGAGCTTTGCCA
GGATCCATGAGACCAACCTGAAGAAGCAGGGCCTGCTGCCCCTGACCTTTGCTGACCCAGCCGACTACAGCAAGGTTCAC
CCTGTGGACAAGCTGACCATTCAGGGCCTGAAGGACTTCGCCCCTGACACGCCCCTGAAGTTCATCATCAAGCACCCCGA
TGGGACCCAGGAGACCATCCTCCTGAACCACACCTTCAACAAGATGCGGATCAAGTGGTTCTGTGCCAGCAGTGCCCTCA
ACAGAATGAAGGAGCTGCAGCAG

Alignment

ORF - retro_nleu_1767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.88 %
• Parental protein coverage: 66.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GAIMEYHGPGVDSISCTGMAT-ICNMGAEIGATTSVFPYNHRMKKYLSKTGRADIANLADEFKDHLVPDP
          GAI.EYHGPGVDSISC.GMA..ICNMGAEIGATTSVFPYNHRM.KYLSKTG..DIA.LADEF.DHLVPDP
Retrocopy GAIVEYHGPGVDSISCAGMAK<ICNMGAEIGATTSVFPYNHRMRKYLSKTGQTDIAGLADEFQDHLVPDP

Parental  GCHYDQLIEINLSELKPHINGPFTPDLAHPVAEVGRVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVA
          GC.YDQLIEINLSELKPHINGPFTPD.AHPVAEVG.VAEKEGWPLDIRVGLIG.C.N.SYED.G.SAAVA
Retrocopy GCCYDQLIEINLSELKPHINGPFTPDKAHPVAEVGKVAEKEGWPLDIRVGLIGTCNN*SYEDPGHSAAVA

Parental  KQALAHGLKCKSQFTITPGSEQIRATIERDGYAQILRDLGGIVLANACGPCIGQWDRKDIKKGEKNTIVT
          KQALAH.L.CKS.FTITPGSEQI.ATIERD.Y.QILR..GGIVLANACG.CIG.WD.KDIKKG.KNTIVT
Retrocopy KQALAHDLRCKSHFTITPGSEQIHATIERDSYTQILRNVGGIVLANACGLCIGHWDMKDIKKGKKNTIVT

Parental  SYNRNFT-GRNDANPETHAFVTSPEIVTALAIAGTLKFNPETDYLTGTDGKKFKLEAPDADELPKVEFDP
          SYNRNFT.G.N...P.THAFVTSPEIVTALAIAG.LKFNPET.YLTG.DGKKFKLE.PDADELP..EF.P
Retrocopy SYNRNFT<GHNNTDPKTHAFVTSPEIVTALAIAGILKFNPETNYLTGKDGKKFKLEPPDADELPQAEFGP

Parental  GQDTYQHPPKDSSGQHVDVSPTSQRLQLLEPFDKWDGKDLEDLQILIKVKGKCTTDHISAAGPWLKFRGH
          GQ.TYQHP..DSSGQHVDVSPTSQRLQLLE.FDKWDG.DL.DLQI.I.V.GKCT.D.ISAAGPWLKF.GH
Retrocopy GQGTYQHPLQDSSGQHVDVSPTSQRLQLLERFDKWDGRDLADLQIVIQVRGKCTSDRISAAGPWLKFCGH

Parental  LDNISNNLLIGAINIENGKANSVRNAVTQEFGPVPDTARYYKKHGIRWVVIGDENYGEGSSREHAALEPR
          LDNISNNLLIGAINIEN...NSV..AVTQEFGPVP.TAR..KKHGIRWVVIGD.N....SSREHAALEP.
Retrocopy LDNISNNLLIGAINIENSQSNSVCSAVTQEFGPVPATARCCKKHGIRWVVIGDKN----SSREHAALEPH

Parental  HLGGRAIITKSFARIHETNLKKQGLLPLTFADPADYNKIHPVDKLTIQGLKDFTPGKPLKCIIKHPNGTQ
          .L.GRAIIT.SFARIHETNLKKQGLLPLTFADPADY.K.HPVDKLTIQGLKDF.P..PLK.IIKHP.GTQ
Retrocopy RLWGRAIITESFARIHETNLKKQGLLPLTFADPADYSKVHPVDKLTIQGLKDFAPDTPLKFIIKHPDGTQ

Parental  ETILLNHTFNETQIEWFRAGSALNRMKELQQ
          ETILLNHTFN...I.WF.A.SALNRMKELQQ
Retrocopy ETILLNHTFNKMRIKWFCASSALNRMKELQQ

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_1767 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,