RetrogeneDB ID: retro_ptro_260

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:215414667..215415915(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039463
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACO2
• Ensembl ID: ENSPTRG00000014428
• Aliases: None
• Description: aconitase 2, mitochondrial [Source:HGNC Symbol;Acc:118]

Sequence

>retro_ptro_260
TCCTGTGCTGGCATGGCGACAATCTGCAACATGGGCGCAGAAATTGGGGCCACCACTTCCGTGTTCCTTTACAACCACAG
GATGAGGAAGTACCTAAGCAAGACCGGCCGGACAGACATTGCCAATCTAGCTGATGAATTCCAGGATCACTTGGTGCCTG
ACCCTGGCTGCCATTATGACCAACTAATTGAAATTAACCTCAGTGAGCTGAAGCCGCACATCAATGGGCCCTTCACCCCC
GACCAGGCTCACCCTGTGGCAGAAGTGGGCAAGGTGGCAGAGAAGGAAGGATGGCCTCTGGACATCCGAGTAGGTCTGAT
TGGTACCTGCAACAGTTAAAGCTATGAAGATCCCGGGCGCTCAGCAGCTGTGGCCAAGCAGGCACTGGCCCATGACCTCA
AGTGCAAGTCCCACTTCACCATCACTCCAGGCTCCGAGCAGATCCGCGCCACCATTGAGTGGGACAGCTACGCACAGATT
TTGAGGAATGTGGGTGGCATCGTCCTGGCCAATGCTTGTGGCCCCTGCATTGGCCGCGGGGACACGAAGGACATCAAGAA
GGGGAAGAAGTACACAATCGTCACCTCCTACAACAGGAACTTCACGGGCTGCAATGACGCGAACCCTGAGACCCATGTCT
TCGTCACGTCCCCAGAGATTGTCACAGCCCTGGCCATTGTGGGAATCCTCAAGTTCAACCCAGAGACCAACTACCTGATG
GGCAAAGATAGGAAGAAGTTCAAGCTAGAGGCTCCGGATGCAGACGACCTTCCCCAAGCGGAGTTTGACCCAGGGCAGGA
CCCCTACCAGCACCCCCCACAGGACAGCAGTGGCCAGCACGTGGATGTGAGCCCCACTAGCCAGCGCCTGCAGCTCCTGG
AGGCTTTTGACAAGTGGGATAGCAAGGACCTGGAGGACCTGCAGATACTCATCAAGGTCAAAGGGAAGTGTACTACTGAC
CACATCTTGGCTGCTGGCCCCTGGCTCAAGTTTTGTGGGCGCTTGGACAACATCTCCAACAACCTGCTGACTGGTGCCAT
CAACATTGAAAACAGCCAGGCCAACTCCGTGTGCAGTGCCGTCACCCAGGAGTTTGGCCCCGTCCCTGACACTGCCCGCT
ACTACAAGAAACATGGCATCAGGTGGGTGGTGATCGGGGACGAGAACTCGAGCCAGGAGCACGCAGTGCTGGAGCCTCCC
CACCTCTGGGGCCGGGCCATCATCACCAAGAGCTTTGCCAGGATCCAC

Alignment

ORF - retro_ptro_260 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.14 %
• Parental protein coverage: 58.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRSGMATICNMGAEIGATTSVFPYNHRMKKYLSKTGREDIANLADEFKDHLVPDPGCHYDQLIEINLSEL
          S..GMATICNMGAEIGATTSVF.YNHRM.KYLSKTGR.DIANLADEF.DHLVPDPGCHYDQLIEINLSEL
Retrocopy SCAGMATICNMGAEIGATTSVFLYNHRMRKYLSKTGRTDIANLADEFQDHLVPDPGCHYDQLIEINLSEL

Parental  KPHINGPFTPDLAHPVAEVGKVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFT
          KPHINGPFTPD.AHPVAEVGKVAEKEGWPLDIRVGLIG.C...SYED.GRSAAVAKQALAH.LKCKS.FT
Retrocopy KPHINGPFTPDQAHPVAEVGKVAEKEGWPLDIRVGLIGTCNS*SYEDPGRSAAVAKQALAHDLKCKSHFT

Parental  ITPGSEQIRATIERDGYAQILRDLGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDANPE
          ITPGSEQIRATIE.D.YAQILR..GGIVLANACGPCIG..D.KDIKKG.K.TIVTSYNRNFTG.NDANPE
Retrocopy ITPGSEQIRATIEWDSYAQILRNVGGIVLANACGPCIGRGDTKDIKKGKKYTIVTSYNRNFTGCNDANPE

Parental  THAFVTSPEIVTALAIAGTLKFNPETDYLTGTDGKKFRLEAPDADELPKAEFDPGQDTYQHPPKDSSGQH
          TH.FVTSPEIVTALAI.G.LKFNPET.YL.G.D.KKF.LEAPDAD.LP.AEFDPGQD.YQHPP.DSSGQH
Retrocopy THVFVTSPEIVTALAIVGILKFNPETNYLMGKDRKKFKLEAPDADDLPQAEFDPGQDPYQHPPQDSSGQH

Parental  VDVSPTSQRLQLLEPFDKWDGKDLEDLQILIKVKGKCTTDHISAAGPWLKFRGHLDNISNNLLIGAINIE
          VDVSPTSQRLQLLE.FDKWD.KDLEDLQILIKVKGKCTTDHI.AAGPWLKF.G.LDNISNNLL.GAINIE
Retrocopy VDVSPTSQRLQLLEAFDKWDSKDLEDLQILIKVKGKCTTDHILAAGPWLKFCGRLDNISNNLLTGAINIE

Parental  NGKANSVRNAVTQEFGPVPDTARYYKKHGIRWVVIGDENYGEGSSREHAALEPRHLGGRAIITKSFARIH
          N..ANSV..AVTQEFGPVPDTARYYKKHGIRWVVIGDEN....SS.EHA.LEP.HL.GRAIITKSFARIH
Retrocopy NSQANSVCSAVTQEFGPVPDTARYYKKHGIRWVVIGDEN----SSQEHAVLEPPHLWGRAIITKSFARIH

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	0.21 RPM	208.56 RPM
SRP007412_cerebellum	0.50 RPM	114.25 RPM
SRP007412_heart	0.61 RPM	292.60 RPM
SRP007412_kidney	0.50 RPM	280.84 RPM
SRP007412_liver	0.16 RPM	50.90 RPM
SRP007412_testis	0.21 RPM	37.83 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_260 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_260 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_260 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_324

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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,