RetrogeneDB ID: retro_ggor_957

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 13:72898105..72899174(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEX12
• Ensembl ID: ENSGGOG00000003330
• Aliases: None
• Description: None

Sequence

>retro_ggor_957
ATGGCTGAACACAGGCTCACATCACGACTGCTTCTGTGGCTGTTGACCAGCCATCCATCTTTGCGGTGGTAGCACAAGAC
AGTTTAATGACAGCAGTGAGACTTGCTCATCAGCATGTGTTCAAGGTTCTTGCAAAATCACACCCCACCCACTATGGCTT
CTTGTGGAGGTGGTTTGATGAAATCTTTACTCTGCTACATCTCCTGCTCCAGCAGTATTATCTGTCTAGAACCAGTGCCC
CATTTTCTGAAATCTTTTGTGGCTTGAAGAGAATAGTAATGGGGGACACTCACAATTCTCACAGATTGGCTAGTGCTGGT
CTCCTAAAGGAGCAGCTTTGGAAATCAATTATGTCCCTGGTTCTTCTTTTCTATCTGAAAGTGAAGCTGGAGAAGCTGGT
TTCTAGCTGAGAGAAGAGGATGAATATTCTATTCATCCCCCTTCTTCCAACTGGAAATGATTTTACAGACCCTTCCTGGC
AGCCTACCCATTTGTTAACATGGCCTGGGAAGGATGGTTTCTTGTACAACTTCGATACATCCTAGGAAAATCTCAGCATC
ACTCACCACTGCTGAAGCTGGCTGGAGTTCAGCTAGGTCGACTGACAGTTGAGGATATACAAGCTCTGGAGCATAGACCA
GCTGAAGCCAGCATGATACAGCAACCAGCCAGAAGTGTTAGTGAGAAGATAAAGTCAGCTCTGAAGAAGGCTGTGAGGGA
TGTTGCCTTTTCCCTGTCTACTGGCCTTTCTGTCAGTGTATTCTTCTTGCAGTTCCTTGACTGGTGGTGCTCATCTGAAA
ACCAAGAAACCATCAAGTCATTGACTGCCCCGCCTACTCCACCACCACCTGTCCACCTAGACTATAACTCTGATTGTCCC
CTCTTACCCAAAATGCAGACTGTGTGCCCCTTGTGTTGTAAAACCCAGGTGATTGATACTGTTCTTGCCACTTTTAGCTA
TGTGTTTCATTACGGCTGTGTGTTTCATTATATGAGGAGTCACCAAGCTTGTCCCATTACAGGTTATCCAACAGAAGTAC
ATCTGATTAAATTCTACTCCCCTGAGAAC

Alignment

ORF - retro_ggor_957 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEHG-AHFTAASVADDQPSIFEVVAQDSLMTAVRPALQHVVKVLAESNPTHYGFLWRWFDEIFTLLDLL
          MAEH..AH.T.ASVA.DQPSIF.VVAQDSLMTAVR.A.QHV.KVLA.S.PTHYGFLWRWFDEIFTLL.LL
Retrocopy MAEHR<AHITTASVAVDQPSIFAVVAQDSLMTAVRLAHQHVFKVLAKSHPTHYGFLWRWFDEIFTLLHLL

Parental  LQQHYLSRTSASFSENFYGLKRIVMGDTHKSQRLASAGLPKQQLWKSIMFLVLLPYLKVKLEKLVSS-LR
          LQQ.YLSRTSA.FSE.F.GLKRIVMGDTH.S.RLASAGL.K.QLWKSIM.LVLL.YLKVKLEKLVSS.LR
Retrocopy LQQYYLSRTSAPFSEIFCGLKRIVMGDTHNSHRLASAGLLKEQLWKSIMSLVLLFYLKVKLEKLVSS<LR

Parental  EEDEYSIHPPSSRWKRFYRAFLAAYPFVNMAWEGWFLVQQLRYILGKAQHHSPLLRLAGVQLGRLTVQDI
          EEDEYSIHPPSS.WK.FYR.FLAAYPFVNMAWEGWFLVQ.LRYILGK.QHHSPLL.LAGVQLGRLTV.DI
Retrocopy EEDEYSIHPPSSNWK*FYRPFLAAYPFVNMAWEGWFLVQ-LRYILGKSQHHSPLLKLAGVQLGRLTVEDI

Parental  QALEHKPAKASMMQQPARSVSEKIKSALKKAVGGVALSLSTGLSVGVFFLQFLDWWYSSENQETIKSLTA
          QALEH.PA.ASM.QQPARSVSEKIKSALKKAV..VA.SLSTGLSV.VFFLQFLDWW.SSENQETIKSLTA
Retrocopy QALEHRPAEASMIQQPARSVSEKIKSALKKAVRDVAFSLSTGLSVSVFFLQFLDWWCSSENQETIKSLTA

Parental  LPTPPPPVHLDYNSDSPLLPKMKTVCPLCRKTRVNDTVLATSGYVFCYRCVFHYVRSHQACPITGYPTEV
          .PTPPPPVHLDYNSD.PLLPKM.TVCPLC.KT.V.DTVLAT..YVF.Y.CVFHY.RSHQACPITGYPTEV
Retrocopy PPTPPPPVHLDYNSDCPLLPKMQTVCPLCCKTQVIDTVLATFSYVFHYGCVFHYMRSHQACPITGYPTEV

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	13.00 RPM
SRP007412_cerebellum	0.00 RPM	10.09 RPM
SRP007412_heart	0.00 RPM	3.19 RPM
SRP007412_kidney	0.00 RPM	7.73 RPM
SRP007412_liver	0.00 RPM	9.79 RPM
SRP007412_testis	0.00 RPM	10.88 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_957 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_957 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_839

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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,