RetrogeneDB ID: retro_nleu_1486

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397296.1:7961003..7962142(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FDPS
• Ensembl ID: ENSNLEG00000012099
• Aliases: None
• Description: None

Sequence

>retro_nleu_1486
TACTATGAAACATCCTGGAAGTCTATTAAAGGGTCATGCAGACCTGCATCCAGGAACAGAGCCCTTTGCTCCTCCCTCAG
AATGAATGGAGACCAGAAATCAGATGTTTATGCCCAAGAAAAGTAGGATTTTGTTCAGCACTTCTCCCAGATTATTAGGG
TGCTGACTAAGGATGAGATGGGGTACCCAGAGACAGGAGATGCTATTGCCCGGCTCAAGGAGGTCCTGGAGTACAATGCC
ATTGGAGGCAAGTATCACCCAGGTTTGACGGTGCTAGTAGTGTTCCAGGAGCCGGTGGAGCCAGGGAAACAGGATGCTGA
TAGTCTCCAATGGGCCCTGACTGTGGACTGGTGTGTGGAACTGCTGCAAGCTTTCTTCCTGGTGGCAGATGACATCATGG
ATTCATCCTTCACCTGTCGGGGACAGATCTGCTGGTATCAGAAGCTGGGCATGGATTTAGATGCCATCAATGATGCTATC
CTTCTGGAAGCATGTATCTACCACCTGCTGAAGATCTATTGCCGGGAGCAGCCCTATTACCTGAACCTGACTGAGCTCTT
CCTGCAGAGTTCCTATCAGACTGAGATTAGGCAGACCCTGGACCTCATCACAGCCCGCCAGGGCAATGTGGATCTTGGCA
GATTCACTGAAAAGAGGCACGAATCTATTGTCAAGTACAAGACAGCTTTCTACTCCTTCTACCTTCCTGTAGCTGCAGCC
ATGTACATGGCAGGAATTGCTGGCAAGAAGGAGCACGCCAATGCCAAGAAGATCCTGCTGGGGATGGGAGAGTTCTTTCA
GGTTCAGGATGATTACCTTGACCTCTTTGGGGACCCCAGTGTGACCGGCAAAGTTGGCACTGACATCCAGGACAACAAAT
GCAGCTGGCTGGTGGTTCAGTGTCTGCAACAGGCTACTCCATAACAGTACCAGATCCTGAAGGAAAATTCAGGCAGAAGG
AAGCCGAGAAGATGGCCTGGGTGAAGGCACTGTATGAGGAGCTGGATCTGCCAGCCGTTTTCTTGCAATATGAGGAAGAC
ACTTACAGTCACATTATGGGTCTCATTGAACAGTACGCAGCGCCCCTGCCCCCAGCCATCTTTCTGGGGCTTGCGCGCAA
AATCTACAAGCAGAAAAAG

Alignment

ORF - retro_nleu_1486 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.72 %
• Parental protein coverage: 90.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YPVLAWHSARCWCQAWTEEPRALCSSLRMNGDQKSDVYAQEKQDFVQHFSQIVRVLTEDEMGHPETGDAI
          Y....W.S....C.......RALCSSLRMNGDQKSDVYAQEK.DFVQHFSQI.RVLT.DEMG.PETGDAI
Retrocopy YYETSWKSIKGSCRPASRN-RALCSSLRMNGDQKSDVYAQEK*DFVQHFSQIIRVLTKDEMGYPETGDAI

Parental  ARLKEVLEYNAIGGKYHRGLAVVVAFRELVEPRKQDADSLQRAWTVGWCVELXXXXLLVADDIMDSSLTR
          ARLKEVLEYNAIGGKYH.GL.V.V.F.E.VEP.KQDADSLQ.A.TV.WCVEL.....LVADDIMDSS.T.
Retrocopy ARLKEVLEYNAIGGKYHPGLTVLVVFQEPVEPGKQDADSLQWALTVDWCVELLQAFFLVADDIMDSSFTC

Parental  RGQICWYQKPGVGLDAINDANLLEACVYRLLKLYCREQPYYLNLIELFLQSSYQTEIGQTLDLITAPQGN
          RGQICWYQK.G..LDAINDA.LLEAC.Y.LLK.YCREQPYYLNL.ELFLQSSYQTEI.QTLDLITA.QGN
Retrocopy RGQICWYQKLGMDLDAINDAILLEACIYHLLKIYCREQPYYLNLTELFLQSSYQTEIRQTLDLITARQGN

Parental  VDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAMYMAGIDGEKEHTNAKKILLEMGEFFQIQDDYLDLFGDP
          VDL.RFTEKR..SIVKYKTAFYSFYLP.AAAMYMAGI.G.KEH.NAKKILL.MGEFFQ.QDDYLDLFGDP
Retrocopy VDLGRFTEKRHESIVKYKTAFYSFYLPVAAAMYMAGIAGKKEHANAKKILLGMGEFFQVQDDYLDLFGDP

Parental  SVTGKIGTDIQDNKCSWLVVQCLQRATPEQYQILKENYG-QKEAEKVARVKALYEELDLPAVFLQYEEDS
          SVTGK.GTDIQDNKCSWLVVQCLQ.ATP.QYQILKEN.G.QKEAEK.A.VKALYEELDLPAVFLQYEED.
Retrocopy SVTGKVGTDIQDNKCSWLVVQCLQQATP*QYQILKENSG<QKEAEKMAWVKALYEELDLPAVFLQYEEDT

Parental  YSHIMALIEQYAAPLPPAIFLGLARKIYKRKK
          YSHIM.LIEQYAAPLPPAIFLGLARKIYK.KK
Retrocopy YSHIMGLIEQYAAPLPPAIFLGLARKIYKQKK

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_1486 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 10 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008364	11 retrocopies	retro_cjac_1066, retro_cjac_1217, retro_cjac_1395, retro_cjac_157, retro_cjac_2011, retro_cjac_2081, retro_cjac_2161, retro_cjac_299, retro_cjac_4154, retro_cjac_44, retro_cjac_70,
Echinops telfairi	ENSETEG00000001154	6 retrocopies	retro_etel_1770, retro_etel_1818, retro_etel_2179, retro_etel_730, retro_etel_743, retro_etel_990,
Homo sapiens	ENSG00000160752	6 retrocopies	retro_hsap_1519, retro_hsap_1558, retro_hsap_1560, retro_hsap_3871, retro_hsap_3872, retro_hsap_502,
Microcebus murinus	ENSMICG00000007468	1 retrocopy	retro_mmur_1148,
Macaca mulatta	ENSMMUG00000023144	3 retrocopies	retro_mmul_1190, retro_mmul_2152, retro_mmul_565,
Nomascus leucogenys	ENSNLEG00000012099	6 retrocopies	retro_nleu_1486 , retro_nleu_1727, retro_nleu_2301, retro_nleu_2405, retro_nleu_2595, retro_nleu_2692,
Pongo abelii	ENSPPYG00000000747	3 retrocopies	retro_pabe_1290, retro_pabe_1329, retro_pabe_235,
Pan troglodytes	ENSPTRG00000001422	9 retrocopies	retro_ptro_1028, retro_ptro_1048, retro_ptro_1049, retro_ptro_2637, retro_ptro_2638, retro_ptro_2639, retro_ptro_2940, retro_ptro_2995, retro_ptro_377,
Rattus norvegicus	ENSRNOG00000043377	3 retrocopies	retro_rnor_1175, retro_rnor_153, retro_rnor_2897,
Ictidomys tridecemlineatus	ENSSTOG00000004475	1 retrocopy	retro_itri_488,