RetrogeneDB ID: retro_nleu_695

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397270.1:33800556..33801305(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX6
• Ensembl ID: ENSNLEG00000007372
• Aliases: None
• Description: None

Sequence

>retro_nleu_695
GTAGCAAAAGTTGATCATGTTCAGATTATAGTATTGGATGAGCAGGCAGATAAGTTGCTGTCACAGGATTTTGTTCAGAT
AATGGAGGATATTATTCTCATGCTACCTAAAAACAGGAAGATTTTACTACATTCTGCTACTTTCCCTCTTAGTGTACAGA
AGGTCATGAATTCCCACTTGCAGAAACCCTATGAGATTAACCTGATGTAGGAACTAACTCTAAAGGGAGTAACCCAGTAC
TATGCATGTGTAACTGAGCTCCAAAAAGTACACTGCCTCAACACACTTTTCTCCAGGCTTCAGATAAACCAGTCGATCAT
TTTCTGTAACTCCTCTCAGCCAGTTGAATTGCTAGCCAAGACTTCTCAACCAGGTTATTCTTGCTTCTATATTCATGCTA
AAATGAGGCAGGAACATCAAAATTGTGTATTTCGTGATTTCTGAAATGGCTTATGATGCAATCTTGTTTACACTGATCTG
TTTACACGAGGTATTGATATACAAGGTGTGAATGTGTTAATAAACTTTGATTTCCCAAAGCTGGCAGAGACCTATCTCCA
TCGTATTGGAAGATCAGGTAGCTTTGGTCACCTTGGCTTAGCCATCAGCTTGATCACTATTATGATCGCTTCAACCTGAA
AATTATTGAGGAGCAGCTGGGAACAGAAATGAAACCTATTCCAGGCAACATTGACAAGAGCCTGTGTGTGGCAGGATACC
ACAGCGAGCCTGTAGAGGATGAGAAGCCT

Alignment

ORF - retro_nleu_695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.7 %
• Parental protein coverage: 51.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VAKVDHVQMIVLDE-ADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLQKPYEINLME
          VAKVDHVQ.IVLDE.ADKLLSQDFVQIMEDIIL.LPKNR.ILL.SATFPLSVQK.MNSHLQKPYEINLM.
Retrocopy VAKVDHVQIIVLDEQADKLLSQDFVQIMEDIILMLPKNRKILLHSATFPLSVQKVMNSHLQKPYEINLM*

Parental  ELTLKGVTQYYAYVTERQKVHCLNTLFSRLQINQSIIFCNSSQRVELLAKKISQLGYSCFYIHAKMRQEH
          ELTLKGVTQYYA.VTE.QKVHCLNTLFSRLQINQSIIFCNSSQ.VELLA.K.SQ.GYSCFYIHAKMRQEH
Retrocopy ELTLKGVTQYYACVTELQKVHCLNTLFSRLQINQSIIFCNSSQPVELLA-KTSQPGYSCFYIHAKMRQEH

Parental  RNRVFHDFRNGLCRNLVCTDLFTRGIDIQAVNVVINFDFPKLAETYLHRIGRSGRFGHLGLAINLIT-YD
          .N.VF.DF.NGL..NLV.TDLFTRGIDIQ.VNV.INFDFPKLAETYLHRIGRSG.FGHLGLAI.LIT.Y.
Retrocopy QNCVFRDF*NGL*CNLVYTDLFTRGIDIQGVNVLINFDFPKLAETYLHRIGRSGSFGHLGLAISLIT<YY

Parental  DRFNLKSIEEQLGTEIKPIPSNIDKSLYVAEYHSEPVEDEKP
          DRFNLK.IEEQLGTE.KPIP.NIDKSL.VA.YHSEPVEDEKP
Retrocopy DRFNLKIIEEQLGTEMKPIPGNIDKSLCVAGYHSEPVEDEKP

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_695 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012442	1 retrocopy	retro_cfam_1347,
Callithrix jacchus	ENSCJAG00000013591	3 retrocopies	retro_cjac_1427, retro_cjac_1924, retro_cjac_379,
	ENSG00000110367	0 retrocopies
Gorilla gorilla	ENSGGOG00000016751	1 retrocopy	retro_ggor_955,
Macaca mulatta	ENSMMUG00000018651	2 retrocopies	retro_mmul_1300, retro_mmul_1826,
Mus musculus	ENSMUSG00000032097	1 retrocopy	retro_mmus_1896,
Nomascus leucogenys	ENSNLEG00000007372	1 retrocopy	retro_nleu_695 ,
Otolemur garnettii	ENSOGAG00000007978	1 retrocopy	retro_ogar_2861,
Pongo abelii	ENSPPYG00000003942	2 retrocopies	retro_pabe_1018, retro_pabe_2941,
Pan troglodytes	ENSPTRG00000004353	2 retrocopies	retro_ptro_2424, retro_ptro_838,
Rattus norvegicus	ENSRNOG00000012453	4 retrocopies	retro_rnor_2546, retro_rnor_2613, retro_rnor_900, retro_rnor_901,