RetrogeneDB ID: retro_pabe_1903

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:29765237..29766923(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACO2
• Ensembl ID: ENSPPYG00000011871
• Aliases: None
• Description: aconitase 2, mitochondrial [Source:HGNC Symbol;Acc:118]

Sequence

>retro_pabe_1903
ATGGTGCCCTACAGCCCACTGGTTACCTGGCTGCAGAAAGCTCTGGGTGTGCAGCAGTACCATGTGGCATCAGTCCTGTG
CCAACGGGCCAAGGTGGCGATGAGCCACTTTGAGCCTAAGTACATCCACTATGACCTGCTAGAGAAGAACATTAACATTG
TTCACAAACGATTGAACCGGTCTCTGACCCTCTCGGAGAAAATCGTGTATGGACACCTGGATGACCCCGCCAGCCAGGAA
ATCGAGCGGGGCAGGATGTACCTGCAGCAGTGGACAGACAGCGCGACCATGCAGGATAGATGGCCCAGATGGCCATGCTG
CAGTTCATCAGCAGCAGGCTCCCAAGGTGACCATGCCAACCACCATCCACTGTGACCATCTGATTGAGGCCCAGCTCGGT
CGGGCGTGAGAAAGACCTGCACCAGGCCAAGGACATCAACCACAAAGTTTGTAATTTCCTGGCAACTGGAAGTGTCAAAT
ATGGCGTGAGCTTCTGGAAGCCTGGATCTGGAATCATTCACCAGATTATTCTGGAAAACTATGACTACCCTGGGATTCTT
CTGATTGGCACTGACTCCCACACCCCCAATGGTGGCAGCCTGGGGGGCATCTGCATTGGAGTTGGGGGTGCCAAGCTGTG
GATTTCATGACTGGCATCCCCTGGGAGCTGAAGTGCCCTAAGGTGATTGGTGTGAAGCTGATGGGCTCCCTCTCTGGTTG
GACCTCACCCAAAGATGTGATCCTGAAGGTGGCAGGAATCCTCACCATGAAAAGTGGCGAAGGTGCAATTGTGGAATACC
ATGGGCCTGGTGTAGACTCCATCTCCTGCACTGGCATGGCTACAGTCTGCAAAATGGGCTCAGAAATTGGGGCCACCACT
TCCGTGTTCCGTTACAACCTCAGGATGAAGAAATACCTGAGCAAGACCTGCCAGGTAGACATTGCCAATCTAGCTGATGA
ATTCAAAGATCACTTGGTGCCTGACCCTGGGTGCCATTATGACCAACTAATTGAAGTTAACCTCAGTGAACTGAAGCTGC
ACATCAATGGGCCCTTCACCCCTGACCTGGCTCACCTTGTGGCAGAAGTGGGCAAGGTGGCAGGGAAGGAAGAATGGCCT
CTGGACATCTGAGTGGGTCTGTGGGGCAGCTGCACCAATTCAAGCTATGAAGATATGGGGCACTCAGCAGCTGTGGCCAA
GCAGGAACTGGGCCATGGCCTCAAGTGCAAGACCCAGTTCACTATCACTCCATGGTCTGAGCAGATCTGTGCCTCCATTG
AGTGGGATGGCTATGCACAGACCTTGAGGGATGTGGGCAGCATTGTCCTGGTCAATGCTTGTGGCCCCTGCATTGGCCAG
TCGGACAGAAAGGACATCAAGAAGCGGGAGAAGAACATAATTGTCACCTTCTACAACAGGAACTTCACAGGCCACAACGA
CACGAACCCGAGACCCATGACTTCATCATGTACCCAGAGACTGTCACAGCCCTGGCCATTGTGGGAACCCTCAAGTTCAA
CCCAGAGACCAACTACCTGACAGGCAAGGATGGCAAGAAGTTCAAGCTGGAGGCTCTGGATGCAGATGAGCTTCCCCAAG
CAGAGTTTGGCCCAGGGCAGGACACCTACCAGCACCCCCGCACGGGGTACCACTGACCACATCTCAGCTGCTGGCCCCTG
GCTCAA

Alignment

ORF - retro_pabe_1903 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.23 %
• Parental protein coverage: 72.18 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAPYSLLVTRLQKALGVRQYHVASVLCQRAKVAMSHFEPNEYIHYDLLEKNINIVRKRLNRPLTLSEKIV
          M.PYS.LVT.LQKALGV.QYHVASVLCQRAKVAMSHFEP..YIHYDLLEKNINIV.KRLNR.LTLSEKIV
Retrocopy MVPYSPLVTWLQKALGVQQYHVASVLCQRAKVAMSHFEP-KYIHYDLLEKNINIVHKRLNRSLTLSEKIV

Parental  YGHLDDPTSQEIERGKSYLRLRPDRVAMQDA-TAQMAMLQFISSGLPK--VAVPSTIHCDHLIEAQVGGE
          YGHLDDP.SQEIERG..YL....D...MQD...AQMAMLQFISS.LP......PST.....L....VG.E
Retrocopy YGHLDDPASQEIERGRMYLQQWTDSATMQDR<MAQMAMLQFISSRLPR*PCQPPSTVTI*-LRPSSVGRE

Parental  KDLRRAKDINQEVYNFLATAGAKYGVGFWKPGSGIIHQIILENYAYPGVLLIGTDSHTPNGGGLGGICIG
          KDL..AKDIN..V.NFLAT...KYGV.FWKPGSGIIHQIILENY.YPG.LLIGTDSHTPNGG.LGGICIG
Retrocopy KDLHQAKDINHKVCNFLATGSVKYGVSFWKPGSGIIHQIILENYDYPGILLIGTDSHTPNGGSLGGICIG

Parental  VGGA-DAVDVMAGIPWELKCPKVIGVKLTGSLSGWSSPKDVILKVAGILTVKGGTGAIMEYHGPGVDSIS
          VGGA..AVD.M.GIPWELKCPKVIGVKL.GSLSGW.SPKDVILKVAGILT.K.G.GAI.EYHGPGVDSIS
Retrocopy VGGA<QAVDFMTGIPWELKCPKVIGVKLMGSLSGWTSPKDVILKVAGILTMKSGEGAIVEYHGPGVDSIS

Parental  CTGMATICNMGAEIGATTSVFPYNHRMKKYLSKTGRADIANLADEFKDHLVPDPGCHYDQLIEINLSELK
          CTGMAT.C.MG.EIGATTSVF.YN.RMKKYLSKT...DIANLADEFKDHLVPDPGCHYDQLIE.NLSELK
Retrocopy CTGMATVCKMGSEIGATTSVFRYNLRMKKYLSKTCQVDIANLADEFKDHLVPDPGCHYDQLIEVNLSELK

Parental  PHINGPFTPDLAHPVAEVGKVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFTI
          .HINGPFTPDLAH.VAEVGKVA.KE.WPLDI.VGL.GSCTNSSYEDMG.SAAVAKQ.L.HGLKCK.QFTI
Retrocopy LHINGPFTPDLAHLVAEVGKVAGKEEWPLDI*VGLWGSCTNSSYEDMGHSAAVAKQELGHGLKCKTQFTI

Parental  TPGSEQIRATIERDGYAQILRDLGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDAN-PE
          TP.SEQI.A.IE.DGYAQ.LRD.G.IVL.NACGPCIGQ.DRKDIKK.EKN.IVT.YNRNFTG.ND.N.PE
Retrocopy TPWSEQICASIEWDGYAQTLRDVGSIVLVNACGPCIGQSDRKDIKKREKNIIVTFYNRNFTGHNDTN<PE

Parental  THAFVTSPEIVTALAIAGTLKFNPETDYLTGTDGKKFKLEAPDADELPEAEFDPGQDTYQHPPNDSSGQH
          TH.F...PE.VTALAI.GTLKFNPET.YLTG.DGKKFKLEA.DADELP.AEF.PGQDTYQHP.......H
Retrocopy THDFIMYPETVTALAIVGTLKFNPETNYLTGKDGKKFKLEALDADELPQAEFGPGQDTYQHPRTGYH*PH

Parental  VDVSPTSQ
          ....P..Q
Retrocopy LSCWPLAQ

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.17 RPM	299.56 RPM
SRP007412_cerebellum	0.00 RPM	140.21 RPM
SRP007412_heart	0.03 RPM	364.31 RPM
SRP007412_kidney	0.13 RPM	233.29 RPM
SRP007412_liver	0.00 RPM	72.43 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1903 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1903 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1903 has 0 orthologous retrocopies within eutheria group .

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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,