RetrogeneDB ID: retro_nleu_697

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397270.1:37506658..37507728(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEX12
• Ensembl ID: ENSNLEG00000013933
• Aliases: None
• Description: None

Sequence

>retro_nleu_697
ATGGCTGAACACAGGCTCATCACGACTGCTTCTGTGGCTGTTGACCACCCATCCATCTTTGTGGTGGTGGCACAAGACAG
TTTAATGACAGCAGTGAGACTTGCTCTTCAGCATGTGTTCAAGGTTCTTGCAGAATCACACCCCACCCTCTATGGCTTCT
TGTGGAGGTGGTTTGATGAAATCTTTACTCTGCTACATCTCCTGCTGCAGCAGTATTATCTGTCTAGAACCAGTGCCTCA
TTTTCTGAAAACTTTTGTGGCTTAAAGAGAATAGTAATGGGGGACACTCACAAGTCTCACAGATTGGCTAGTGCTGGTCT
CCTAAAGAAGCAGCTTTGGAAATCAATTATGTTCCTGGTTCTTCTTTTCTATCTGAAAGTGAAGCTGGAGAAGCTGGTTT
CTAGCTGAGAAAAGAGGATGAATATTCTATTCATCCCCCTTATTCCAACTGGAAACGATTTTACAGACCCTTCCTGGCAG
CCTACCCATTTGTTAACATGGCCTGGGAAGGATGGTTTCTTGTACAACTTCAATACATCCTAGGAAAATCTCAGCATCAC
TCACCACTGCTGAAGCTGGCTGGAGTTCAGCTAGGTCGACTGACCATTCAGGATATACAAGCTCTGGAGCATAAACCAGC
TGAAGCCAGCATGATACAGCAATCAGCCAGCAGTGTTAGTGAAAAGATAAAGTTAGCTCTGAAGAAAGCTGTGAGGGGTG
TTGCCTTATCCCTGTCAACTGGCCTTTCTGTCCATGTATTCTTCTTGCAGTTCCTTGACTGGTGGTACTCATCTGAAAAC
CAAGAAACCATCAGGTCGTTGACTGCCCCGCCTACCCCACCACCACCTGTCCACCTAGACTATAACTCTGATTGTCCCCT
CTTACCCAAAATGCAGACTGTGTGCCCCTTGTGTTGTAAAACCCAGGTGAATGATACTATTCTTGCCACTTTTAGCTATG
TGTTTTGTTATGGCTGTGTGTTTCATTATGTGAGGAGTCACCAAGCTTGTCCCATTACAGGTTATCCAACAGAAGTACAA
CATCTGATTAAATTCTACTCCCGTGAGAAC

Alignment

ORF - retro_nleu_697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEHGAHITTASVADDQPSIFEVVAQDSLMTAVRPALQHVVKVLAESNPTHYGFLWRWFDEIFTLLDLLL
          MAEH...ITTASVA.D.PSIF.VVAQDSLMTAVR.ALQHV.KVLAES.PT.YGFLWRWFDEIFTLL.LLL
Retrocopy MAEHRL-ITTASVAVDHPSIFVVVAQDSLMTAVRLALQHVFKVLAESHPTLYGFLWRWFDEIFTLLHLLL

Parental  QQHYLSRTSASFSENFYGLKRIVMGDTHKSQRLASAGLPKQQLWKSIMFLVLLPYLKVKLEKLVSS-LRE
          QQ.YLSRTSASFSENF.GLKRIVMGDTHKS.RLASAGL.K.QLWKSIMFLVLL.YLKVKLEKLVSS.LR.
Retrocopy QQYYLSRTSASFSENFCGLKRIVMGDTHKSHRLASAGLLKKQLWKSIMFLVLLFYLKVKLEKLVSS<LRK

Parental  EDEYSIHPPSSRWKRFYRAFLAAYPFVNMAWEGWFLVQQLRYILGKAQHHSPLLRLAGVRLGRLTVQDIQ
          EDEYSIHPP.S.WKRFYR.FLAAYPFVNMAWEGWFLVQ.L.YILGK.QHHSPLL.LAGV.LGRLT.QDIQ
Retrocopy EDEYSIHPPYSNWKRFYRPFLAAYPFVNMAWEGWFLVQ-LQYILGKSQHHSPLLKLAGVQLGRLTIQDIQ

Parental  ALEHKPAKASMMQQPARSVSEKIKSALKKAVGGVALSLSTGLSVGVFFLQFLDWWYSSENQETIKSLTAL
          ALEHKPA.ASM.QQ.A.SVSEKIK.ALKKAV.GVALSLSTGLSV.VFFLQFLDWWYSSENQETI.SLTA.
Retrocopy ALEHKPAEASMIQQSASSVSEKIKLALKKAVRGVALSLSTGLSVHVFFLQFLDWWYSSENQETIRSLTAP

Parental  PTPPPPVHLEYNSDSPLLPKMKTVCPLCRKTRVNDTVLATSGYVFCYRCVFHYVRSHQACPITGYPTEVQ
          PTPPPPVHL.YNSD.PLLPKM.TVCPLC.KT.VNDT.LAT..............RSHQACPITGYPTEVQ
Retrocopy PTPPPPVHLDYNSDCPLLPKMQTVCPLCCKTQVNDTILATFXXXXXXXXXXXXXRSHQACPITGYPTEVQ

Parental  HLIKLYSPEN
          HLIK.YS.EN
Retrocopy HLIKFYSREN

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_697 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 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,