RetrogeneDB ID: retro_nleu_1735

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397306.1:12916981..12918027(-)
• Located in intron of: ENSNLEG00000006457

Retrocopy information

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

Parental gene information

• Parental gene symbol: UTP6
• Ensembl ID: ENSNLEG00000011009
• Aliases: None
• Description: None

Sequence

>retro_nleu_1735
CAACTGCTGGACTTTGCCAAAGGTCTACAAAAAGAAATTTATGATGACCCTCAGGCTCTACACACAGATGATCTTCTCAC
TTGGGATTATGTGGCAAGGTAAGAATTAGAGATCGAGTCACAGACAGGAGAAGAGCAGCCTACAATGAAATAAGACAAAG
CAGAGGAGGGCCAGAAGGAGGAGAGATACTGTACCGTATATGAAGAGGCAGTGAAGACTCTGTCAAGGGAGGCCATGTGG
AAGTGTTACATCACCTTTTGCTTGGAAAGATTTACTAAGAAGACAAATAGTGGGTTCCTCAGAGGGAAGAAGTTGGAAAG
AACCATGACTGCATTCAGAAGGGCACATGAACTCAAGCTTCTGCCAGAATTCCAATACAAGCAGTTGACTTGAGTTGTTG
CTGTGCCATAACTTCCTGAGGAAAGCTCTGGAGGTGGCAGTAGCTGGGACTGAATTGTTTAGAGACTCTGGGACAATGTG
GCAGATGAAGGTACATGTGCTGATTGACTCAAACAGCCCTGACGTAGCCATGCTTTTTGAAGAAGACTTTGTGCACCTGA
AACTCCAGGTTTGTCTACCATTGTGGACTTCTTGGCAGAGTGGAGCGAAGGTGCCAAAAGCCAAGACGACACCGAGGCAA
TCTTTAAGACAGTTCTCTTAGCTGTCACAGGTGCCAACTCAGTAACCCTGAAGGATAAGTACCCGGATTGGGCTTATCAA
CATGGTGGCTACAAAAAAGCCAGAGCTGTGTATAAAAGTTTACAGAACAGCCATCCATTTTCAGTTGACTTTTTCAGGAA
AATGATTCAGTTTAAAAACAGCAAGAATCCTGCAAGATGGTGAACATAAGAGAATATTATGAGAAGGCTTTGAGAAAGTT
TGGATCTGTAGATTCTGATCTTTGGATGGATTATATCAAGGAACCACTGAACCACCCCCTTGGTAGACCTGAAAACTGCA
GACAGATCTACTGGCAAGCAATGGAAATGTTGCAGGGAGAGTCAGCAGAGGCGTCTGTAGCTAAACATGCTATGCATCAG
ACTGGC

Alignment

ORF - retro_nleu_1735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.32 %
• Parental protein coverage: 58.39 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QLFDFAKDLQKEIYDDLQALHTERIPR-DYVARQELEIESQT-EEQPTTKQAKAVEVSRKEERCCAVYEE
          QL.DFAK.LQKEIYDD.QALHT......DYVAR.ELEIESQT.EEQPT.K..KA.E...KEER.C.VYEE
Retrocopy QLLDFAKGLQKEIYDDPQALHTDDLLTWDYVAR*ELEIESQTGEEQPTMK*DKAEE-GQKEERYCTVYEE

Parental  AVKTLPTEAMWKCYITFCLERLTKKSNSGFLRGKRLERTMTVFRKAHELKLLSECQYKQL-IVSLLCHNL
          AVKTL..EAMWKCYITFCLER.TKK.NSGFLRGK.LERTMT.FR.AHELKLL.E.QYKQL....LLCHN.
Retrocopy AVKTLSREAMWKCYITFCLERFTKKTNSGFLRGKKLERTMTAFRRAHELKLLPEFQYKQL>LELLLCHNF

Parental  LREALEVAVAGTELFRDSGTMWQLKLRVLIESKSPDIAMLFEEAFVHLKPQVCLPLWISW-AEWSEGAKS
          LR.ALEVAVAGTELFRDSGTMWQ.K..VLI.S.SPD.AMLFEE.FVHLK.QVCLPLW.SW.AEWSEGAKS
Retrocopy LRKALEVAVAGTELFRDSGTMWQMKVHVLIDSNSPDVAMLFEEDFVHLKLQVCLPLWTSW<AEWSEGAKS

Parental  QEDTEAVFKKALLAVIGADSVTLKNKYLDWAYRSGGYKKARAVFKSLQESRPFSVDFFRKMIQFE-KEQE
          Q.DTEA.FK..LLAV.GA.SVTLK.KY.DWAY..GGYKKARAV.KSLQ.S.PFSVDFFRKMIQF..K.QE
Retrocopy QDDTEAIFKTVLLAVTGANSVTLKDKYPDWAYQHGGYKKARAVYKSLQNSHPFSVDFFRKMIQFK<KQQE

Parental  SCNMANVREYYERALREFGSADSDLWMDYMKEELNHPLGRPENCGQIYWRAMKMLQGESAEAFVAKHAMH
          SC.M.N.REYYE.ALR.FGS.DSDLWMDY.KE.LNHPLGRPENC.QIYW.AM.MLQGESAEA.VAKHAMH
Retrocopy SCKMVNIREYYEKALRKFGSVDSDLWMDYIKEPLNHPLGRPENCRQIYWQAMEMLQGESAEASVAKHAMH

Parental  QTG
          QTG
Retrocopy QTG

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_1735 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015612	1 retrocopy	retro_btau_368,
Nomascus leucogenys	ENSNLEG00000011009	2 retrocopies	retro_nleu_1734, retro_nleu_1735 ,