RetrogeneDB ID: retro_nleu_609

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397268.1:8033426..8034898(-)
• Located in intron of: ENSNLEG00000003727

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX50
• Ensembl ID: ENSNLEG00000011631
• Aliases: None
• Description: None

Sequence

>retro_nleu_609
AGAAAAGATCTACCAAATGGAAAATATTGATGAATATGAAAAAAATATCAAAGCAAGTATCATCCTTAGATAGTTTTACT
CATAAATCAAGTGATAATAAACTAGAGGAGACCTTACCATGTGAACAGAAAGAAGGAGCCTTCTCCTATTTCCATATTTC
TGAAGAGACTGTAAAGCTTCTGAAAGATCAAAGGGTAACATATCTCTTTCCTATTCAAGTTAGAACCTTGTCCTGTATAT
GAAGGAAAAGACTTAATAGCTCGAGCATGGACAGGAACAGGAAAGACATTCTTTTTTGCCATCCCCTTGATTGAAAGACT
CCAAAGAAATCAAGAAACAATTTTTAAAAAGCTGCTCACCAAAGGTACTTGTTTTGGCTCCAACAAGGGAACTGGCAAAT
CAGGCAGCCAAAGACTTCAAAGACAAAACTAGGAAACTCAGCATCGTGTGTTTTTATGGTAGAACACCATATCAAAGCCA
AATTAATCATATGCGAAATGGTATTGACATCTTGGTTGGAACCCCTGGTCATATCAAAGATCATCTGCAGAGTGGCTGAT
TGGATCTTTCTAAACTGTGCCATGTTGTGCTTGATGAAGTGGATCAAACGTTAGATTTAGATTTTGATGAACAAGTTGAA
GATATGATTCACAAATCCTACAAAACTGAATCTGAAGACCATCCTGAGACTTTACTTTTTTCTGCAACTTGCCCACAGTG
GGTATAAAAGTTGCAAAAAAAATACATAAAATCCAGATATGAACAGGTTGACCTTGTTGGAAAAATGACTCAAAAGGCTG
CAACTACTGTGGGACACTTGGCCATTCAGTGTCATTGGTCTCAGAGGCCAGAAGTTATTGGAGATGTCCTTCAAGTCTAC
GGTGGGTCTAAATGGAGGGCTAGTATTTTCTGTGAGACCAAGAAGAATGTAACTGAAATGGCCATGAATCCACACATAAA
ACAGAATGCCCAGTATTTACATGGGGACATTATACAGTCACAAAGAGAAATTACACTAAAAGGCTTCAGAGAAGATAGTT
TTAAAGTTTTGGTGGCAACCAACGTGGCTGCCCGTAGTTTGCACATTCCTGAAGTAGACCTGGTGACTCAACATTCTCCT
CCTCAGGATGCTGAGGCCTGTATCCATCCTCTGGATGCACAGATAGAGCTGGACAGGGATATGTATATGTTTTTATCAAA
CAAGAGAAAGAGATCAACTAAGATATGTGGAACAAAAAGCAGGAATTACTTTTAAATGTGTAGGTGTTCCTTCTACAATG
GATTTAGTTAAATCTAAAAGCATGGATACCATCAGGTTTCTGACTTCCGTTTCTTATGCTGCTGTTGATTTTCTCTGACC
ATCAGCTCAGAGACTGATAGAAGAGAAAGGGGCAGTGGATGCATTGGCTGCAATTTTAGCCCACATTTCTGGTGCATCAA
GTTTTGAACCACGATCTTTGATCGCCTCTGAT

Alignment

ORF - retro_nleu_609 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.32 %
• Parental protein coverage: 66.76 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RKDLPNG-DIDEYEKK-SKRVSSLDTSTHKSSDNKLEETLTREQKEGAFSNFPISEETIKLLKGRGVTYL
          RKDLPNG..IDEYEK..SK.VSSLD..THKSSDNKLEETL..EQKEGAFS.F.ISEET.KLLK...VTYL
Retrocopy RKDLPNG>NIDEYEKN>SKQVSSLDSFTHKSSDNKLEETLPCEQKEGAFSYFHISEETVKLLKDQRVTYL

Parental  FPIQVKTFGPVYEGKDLIAQARTGTGKTFSFAIP-LIERLQRNQETI-KKSRSPKVLVLAPTRELANQVA
          FPIQV.T.......K.L.........K...F..P.LIERLQRNQETI..KS.SPKVLVLAPTRELANQ.A
Retrocopy FPIQVRTLSCI*R-KRLNSSSMDRNRKDILFCHP>LIERLQRNQETI>LKSCSPKVLVLAPTRELANQAA

Parental  KDFKDITRKLSVACFYGGTSYQSQINHIRNGIDILVGTPGRIKDHLQSGRLDLSKLRHVVLDEVDQMLDL
          KDFKD.TRKLS..CFYG.T.YQSQINH.RNGIDILVGTPG.IKDHLQSG.LDLSKL.HVVLDEVDQ.LDL
Retrocopy KDFKDKTRKLSIVCFYGRTPYQSQINHMRNGIDILVGTPGHIKDHLQSG*LDLSKLCHVVLDEVDQTLDL

Parental  GFAEQVEDIIHESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYEQVDLVGKMTQKAATTVEHLAIQ
          .F.EQVED.IH.SYKT.SED.P.TLLFSATCPQWV.K....Y.KSRYEQVDLVGKMTQKAATTV.HLAIQ
Retrocopy DFDEQVEDMIHKSYKTESEDHPETLLFSATCPQWV*KLXXXYIKSRYEQVDLVGKMTQKAATTVGHLAIQ

Parental  CHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQCLHGDIAQSQREITLKGFREGS
          CHWSQRP.VIGDVLQVY.GS..RA.IFCETKKNVTEMAMNPHIKQNAQ.LHGDI.QSQREITLKGFRE.S
Retrocopy CHWSQRPEVIGDVLQVYGGSKWRASIFCETKKNVTEMAMNPHIKQNAQYLHGDIIQSQREITLKGFREDS

Parental  FKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIH-RSGRTGRAGRTGICICF-YQPRERGQLRYVEQK
          FKVLVATNVAAR.L.IPEVDLV.Q.SPPQD.E..IH..SG.T.RAG..G....F.YQ.RER.QLRYVEQK
Retrocopy FKVLVATNVAARSLHIPEVDLVTQHSPPQDAEACIH<SSGCTDRAGQ-GYVYVF<YQTRERDQLRYVEQK

Parental  AGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEKGAVDALAAALAHISGASSFE
          AGITFK.VGVPSTMDLVKSKSMD.IR.L.SVSYAAVDF..PSAQRLIEEKGAVDALAA.LAHISGASSFE
Retrocopy AGITFKCVGVPSTMDLVKSKSMDTIRFLTSVSYAAVDFL*PSAQRLIEEKGAVDALAAILAHISGASSFE

Parental  PRSLITSD
          PRSLI.SD
Retrocopy PRSLIASD

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_609 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018844	1 retrocopy	retro_cjac_1298,
Homo sapiens	ENSG00000107625	2 retrocopies	retro_hsap_2089, retro_hsap_2866,
Macaca mulatta	ENSMMUG00000001006	1 retrocopy	retro_mmul_982,
Mus musculus	ENSMUSG00000020076	1 retrocopy	retro_mmus_3362,
Nomascus leucogenys	ENSNLEG00000001209	1 retrocopy	retro_nleu_1094,
Nomascus leucogenys	ENSNLEG00000011631	2 retrocopies	retro_nleu_1300, retro_nleu_609 ,
Otolemur garnettii	ENSOGAG00000001844	2 retrocopies	retro_ogar_1492, retro_ogar_555,
Pongo abelii	ENSPPYG00000002390	3 retrocopies	retro_pabe_2007, retro_pabe_2369, retro_pabe_2418,
Pan troglodytes	ENSPTRG00000002562	2 retrocopies	retro_ptro_1536, retro_ptro_1938,