RetrogeneDB ID: retro_ptro_839

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:90138073..90139139(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEX12
• Ensembl ID: ENSPTRG00000009020
• Aliases: None
• Description: None

Sequence

>retro_ptro_839
ATGGCTGAACACAGGCTCACATCACGACTGCTTCTGTGGCTGTTGACCAGCCATCCATCTTTGCGGTGGTAGCACAAGAC
AGTTTAATGACAGCAGTGAGACTTGCTCGTCAGCATGTGTTCAAGGTTCTTGCAGAATCACATCCCACCCACTATGGCTT
CTTGTGGAGGTGGTTTGATGAAATCTTTACTGTGCTACGTCTTCTGCTCCAGCAGTATTATCTGTCTAGAACCAGTGCCT
CATTTTCTGAAAACTTTTGTGGCTTGAAGAGAATAGTAATGGGGGACACTCACAAGTGTCACAGATTGGCTAGTGCTGGT
CTCCTAAAGGAGCAGCTTTGGAAATCAATTATGTCCCTGGTTCTTCTTTTCTATCTGAAAGTGAAGCTGGAGAAGCTGGT
TTCTAGCTGAGAGAAGAGGATGAATATTCTATTCATCCCCCTTCTTCCAACTGGAAATGATTTTACAGACCCTTCCTGGC
AGCCTACCCATTTGTTAACATGGCCTAGGAAGGATGGTTTCTTGTACAACTTCGATACATCCTAGGAAAATCTCAGCATC
ACTCACCACTGCTGAAGCTGGCTGGAGTTCAGCTAGGTCAACTGACAGTTGAGGATATACAAGCTCTGGAGCATAGACCA
GCTGAAGCCAGCATGATACAGCAACCAGCCAGAAGTGTTAGTGAGAAGATTAAGTCAGCTCTGAAGAAAGCTGTGAGGGA
TGTTGCCTTTTCCCTGTCTACTGGCCTTTCTGTCAGTGCATTCTTCTTCCAGTTCCTTGACTGGTGGTGCTCATCTGAAA
ACCAAGAAACCATCAAGTCATTGACTGCCCCGCCTACTCCACCACCACCTGTCCACCTAGACTATAACTCTGATTGTCCC
CTCTTACCCAAAATGCAGACTGTGTGCCCCTTGTGTTGTAAAACCCAGGTGAATGATACTGTTCTTGCCACTTTTAGCTA
TGTGTTTCATTACGGCTGTGTGTTTCATTATATGAGTCACCAAGCTTGTCCCATTACAGGTTATCCAACAGAAGTACATC
TGATTAAATTCTACTCCCCTGAGAAC

Alignment

ORF - retro_ptro_839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.04 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEHG-AHFTAASVADDQPSIFEVVAQDSLMTAVRPALQHVVKVLAESNPTHYGFLWRWFDEIFTLLDLL
          MAEH..AH.T.ASVA.DQPSIF.VVAQDSLMTAVR.A.QHV.KVLAES.PTHYGFLWRWFDEIFT.L.LL
Retrocopy MAEHR<AHITTASVAVDQPSIFAVVAQDSLMTAVRLARQHVFKVLAESHPTHYGFLWRWFDEIFTVLRLL

Parental  LQQHYLSRTSASFSENFYGLKRIVMGDTHKSQRLASAGLPKQQLWKSIMFLVLLPYLKVKLEKLVSS-LR
          LQQ.YLSRTSASFSENF.GLKRIVMGDTHK..RLASAGL.K.QLWKSIM.LVLL.YLKVKLEKLVSS.LR
Retrocopy LQQYYLSRTSASFSENFCGLKRIVMGDTHKCHRLASAGLLKEQLWKSIMSLVLLFYLKVKLEKLVSS<LR

Parental  EEDEYSIHPPSSRWKRFYRAFLAAYPFVNMAWEGWFLVQQLRYILGKAQHHSPLLRLAGVQLGRLTVQDI
          EEDEYSIHPPSS.WK.FYR.FLAAYPFVNMA.EGWFLVQ.LRYILGK.QHHSPLL.LAGVQLG.LTV.DI
Retrocopy EEDEYSIHPPSSNWK*FYRPFLAAYPFVNMA*EGWFLVQ-LRYILGKSQHHSPLLKLAGVQLGQLTVEDI

Parental  QALEHKPAKASMMQRPARSVSEKIKSALKKAVGGVALSLSTGLSVGVFFLQFLDWWYSSENQETIKSLTA
          QALEH.PA.ASM.Q.PARSVSEKIKSALKKAV..VA.SLSTGLSV..FF.QFLDWW.SSENQETIKSLTA
Retrocopy QALEHRPAEASMIQQPARSVSEKIKSALKKAVRDVAFSLSTGLSVSAFFFQFLDWWCSSENQETIKSLTA

Parental  LPTPPPPVHLDYNSDSPLLPKMKTVCPLCRKTRVNDTVLATSGYVFCYRCVFHYVRSHQACPITGYPTEV
          .PTPPPPVHLDYNSD.PLLPKM.TVCPLC.KT.VNDTVLAT..YVF.Y.CVFHY..SHQACPITGYPTEV
Retrocopy PPTPPPPVHLDYNSDCPLLPKMQTVCPLCCKTQVNDTVLATFSYVFHYGCVFHYM-SHQACPITGYPTEV

Parental  QHLIKLYSPEN
          .HLIK.YSPEN
Retrocopy -HLIKFYSPEN

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	0.00 RPM	7.38 RPM
SRP007412_cerebellum	0.00 RPM	6.99 RPM
SRP007412_heart	0.00 RPM	6.56 RPM
SRP007412_kidney	0.03 RPM	8.19 RPM
SRP007412_liver	0.00 RPM	4.94 RPM
SRP007412_testis	0.00 RPM	14.23 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_839 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_839 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_839 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_957

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000003330	1 retrocopy	retro_ggor_957,
Macaca mulatta	ENSMMUG00000006047	1 retrocopy	retro_mmul_749,
Monodelphis domestica	ENSMODG00000019129	1 retrocopy	retro_mdom_557,
Nomascus leucogenys	ENSNLEG00000013933	1 retrocopy	retro_nleu_697,
Pan troglodytes	ENSPTRG00000009020	1 retrocopy	retro_ptro_839 ,