RetrogeneDB ID: retro_nleu_1453

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397294.1:8690251..8692024(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPF4B
• Ensembl ID: ENSNLEG00000011291
• Aliases: None
• Description: None

Sequence

>retro_nleu_1453
ACACAACCTCAAGATGATATCCTCAATAGAGGTGAAAGATCAAAAGATGCCAGCCCCATTAATAGGTGGTCTCCTACCTG
AAGAAGTAGATCTCCCATTAAAAAGAGGTCTCGTTCCCCACTCAGGCGTAACACAAAAATCATGTCTCCAAGAAGAAGAA
GCAGGTCTCCTCGGAAAAGGGACAGAGGTTGGAGGAGCAGATCACGCTTGAGAAGGTGTTCTCGATCATGGGGCAGTCAT
AGATGAAGGAGCAGAAGCAAAGTAAAGGAAGATAAATTTAAAGGAAGTGTTTCTGAAGGCATGAAAGTTGAGCAGGAATC
TTTGTCTGATGATAACCTTGAAGATTTTGATGTGGGGGAAGAAGATGAAGAAGCCCTAATAGAAGAGAAGAATCCAAAGG
CAGGCAATTGTTCAGAAATACAAATATCTTGCTGAAGATAGCAATATGTCTGTGTCATCTGAACCAAGCATCCCCCAGAG
CAGTATGAAAACATGATCACCTTCTCCAGATGACATTCTGGAGTGAGTAGCTGCTGATGTTAAAGAGTATGAACAGGAAA
ATGTTGATACATTTCAGGCCTCAGTGAAAGCCAAGCACAATCTAATGACAGTTGAAGAGAATAATAGTTCATCTCAGAAG
TTGTTGGCACTTGATATGTTTTACAGAATCTGATGATGTTTGCTGACTATTTTGATTGTGCTTGTCTTTGGGTTGCTGGC
AATGGATAAGATTCAAAGAGAATCCCAACCCCAGAGATAACTGGACTGATGCAGAAGGCTATTATCATGTGCACATAAGT
GAAGTCCTGGATAAATGTTACAATGTGTATGGCTACACCGGGCAAGGTGTGTTCAGTAATGTTTTATGAGCCAGAGTTAA
TGCAAGAGCCAACCAAGAAGTGGCTGTAAAGGTCATCAGAGACAATGAGCTCATGCAGAAGACTTGTTTAAAAGAACTAG
AGTTCTTGAAAGAATTTGATGCTGATCCTGATGACAAACTTCATTGTCTGCGACCCTTCAGGCGCTTCTATCACAAACAG
CATCTCTGTCTCATATTCGAGCCTCTCAGTATGAACTTATGAGAGATGTTAAAAAAATATGATAAAGATACTGGTTTTCA
TATTAAAGCTGTAAGATCCCATAGTCAGCAGTTTTTCCTGGCATTGAAACTCCTTAAAAGATGTGATATCCTACATGCAG
ACAACAAGCCAGATAGTATCCTGGTTAATCATCAAAAACTATTTTAAAGCTTTGCAATTTGGGGTTGGCTTCACATGTTG
CGGATAATGACATTATACCTTATCTTGTCAGTAGATTTTATCGTGCTCTTGAAATCATCATAGGTAAATGCTGTGACTAC
GGTATAGATATGTGGTCAGTAGGTTGCACCTTATACAAACTCTATACTGGAAAAATTTTATTTCCTGGCAACACCAATAA
CTATATGTTGAAGCTTGTGATGAATCTCAAAGGAAAGATGCCAAATGAGATGATTCAAAAGGTGTATTCAAAGATCAGCA
TTTTGATCAGAATCTCAACTTCATTTACATAGAAGTTGATAAAGTAACAGACAGGGAGAAAGTTACTGTTATGAGCACAA
TTAATCCAACTAAGGACCTATTGGCTAACTTGATTGGGTGCCAGATACTTCCTGAAGACCAACGTAAGAAAGTATACCAG
CTAAAGGACTTGTTGGACCAGATTCTAATGTTGGGCCTAGCTAGATGAATTAGCATCAACCAGGCCCTGCAGCATGCCTT
CATCCAGGAAAAA

Alignment

ORF - retro_nleu_1453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.36 %
• Parental protein coverage: 58.95 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TRPRDDILSRRERSKDASPINRWSPTRRRSRSPIRRRSRSPLRRSR---SPRRRSRSPRRRDRGRRSRSR
          T.P.DDIL.R.ERSKDASPINRWSPT.R.SRSPI..RSRSPLRR.....SPRRRSRSPR.RDRG.RSRSR
Retrocopy TQPQDDILNRGERSKDASPINRWSPT*R-SRSPIKKRSRSPLRRNTKIMSPRRRSRSPRKRDRGWRSRSR

Parental  LRRRSRSRGARRRRSRSKVKEDKFKGSLSEGMKVEQESSSDDNLEDFDVEEEDEEALIEQ-RRIQRQAIV
          LRR.SRS.G..R.RSRSKVKEDKFKGS.SEGMKVEQES.SDDNLEDFDV..E..E......RRIQRQAIV
Retrocopy LRRCSRSWGSHR*RSRSKVKEDKFKGSVSEGMKVEQESLSDDNLEDFDVG-EEDEEALIE>RRIQRQAIV

Parental  QKYKYLAEDSNMSVPSEPSSPQSSTRTRSPSPDDILERVAADVKEYERENVDTFEASVKAKHNLMTVEQN
          QKYKYLAEDSNMSV.SEPS.PQSS..T.SPSPDDILE.VAADVKEYE.ENVDTF.ASVKAKHNLMTVE.N
Retrocopy QKYKYLAEDSNMSVSSEPSIPQSSMKT*SPSPDDILE*VAADVKEYEQENVDTFQASVKAKHNLMTVEEN

Parental  NGSSQKKLLAPDMF-TESDDMFAAYFDSARLRAAGIGKD-FKENPNLRDNWTDAEGYYRVNIGEVLDKRY
          N.SSQK.LLA.DMF......MFA.YFD.A.L..AG.G.D.FKENPN.RDNWTDAEGYY.V.I.EVLDK.Y
Retrocopy NSSSQK-LLALDMF<LQNLMMFADYFDCACLWVAGNG*D<FKENPNPRDNWTDAEGYYHVHISEVLDKCY

Parental  NVYGYTGQGVFSNVVRARDNARANQEVAVKIIRNNELMQKTGLKELEFLKKLNDADPDDKFHCLRLFRHF
          NVYGYTGQGVFSNV..AR.NARANQEVAVK.IR.NELMQKT.LKELEFLK...DADPDDK.HCLR.FR.F
Retrocopy NVYGYTGQGVFSNVL*ARVNARANQEVAVKVIRDNELMQKTCLKELEFLKEF-DADPDDKLHCLRPFRRF

Parental  YHKQHLCLVFEPLSMNLREVLKKYGKDVGLHIKAVRSYSQQLFLALKLLKRCNILHADIKPDNILVNE-S
          YHKQHLCL.FEPLSMNL.E.LKKY.KD.G.HIKAVRS.SQQ.FLALKLLKRC.ILHAD.KPD.ILVN..S
Retrocopy YHKQHLCLIFEPLSMNL*EMLKKYDKDTGFHIKAVRSHSQQFFLALKLLKRCDILHADNKPDSILVNH<S

Parental  KTILKLCDFGSASHVADNDITPYLVSRFYRAPEIIIGKSYDYGIDMWSVGCTLYELYTGKILFPGKTNNH
          KTILKLC..G.ASHVADNDI.PYLVSRFYRA.EIIIGK..DYGIDMWSVGCTLY.LYTGKILFPG.TNN.
Retrocopy KTILKLCNLGLASHVADNDIIPYLVSRFYRALEIIIGKCCDYGIDMWSVGCTLYKLYTGKILFPGNTNNY

Parental  MLKLAMDLKGKMPNKMIRK-GVFKDQHFDQNLNFMYIEVDKVTEREKVTVMSTINPTKDLLADLIGCQRL
          MLKL.M.LKGKMPN.MI.K.GVFKDQHFDQNLNF.YIEVDKVT.REKVTVMSTINPTKDLLA.LIGCQ.L
Retrocopy MLKLVMNLKGKMPNEMIQK<GVFKDQHFDQNLNFIYIEVDKVTDREKVTVMSTINPTKDLLANLIGCQIL

Parental  PEDQRKKVHQLKDLLDQILMLDPAKRISINQALQHAFIQEK
          PEDQRKKV.QLKDLLDQILML..A..ISINQALQHAFIQEK
Retrocopy PEDQRKKVYQLKDLLDQILMLGLAR*ISINQALQHAFIQEK

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_1453 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000112739	1 retrocopy	retro_hsap_4212,
Gorilla gorilla	ENSGGOG00000006422	1 retrocopy	retro_ggor_2821,
Myotis lucifugus	ENSMLUG00000005901	1 retrocopy	retro_mluc_259,
Monodelphis domestica	ENSMODG00000009756	1 retrocopy	retro_mdom_1114,
Nomascus leucogenys	ENSNLEG00000011291	1 retrocopy	retro_nleu_1453 ,
Nomascus leucogenys	ENSNLEG00000012062	2 retrocopies	retro_nleu_2126, retro_nleu_3112,
Pan troglodytes	ENSPTRG00000017683	1 retrocopy	retro_ptro_2859,