RetrogeneDB ID: retro_nleu_728

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397271.1:34353153..34355644(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PHF15
• Ensembl ID: ENSNLEG00000008110
• Aliases: None
• Description: None

Sequence

>retro_nleu_728
ATGGAAGAGAAGAGGCGAAAATACTCCATCAGCAGTGACAACTCTGACACCACTGACAGTCATGCGACATCTACATCCGC
ATCAAGATGCTCCGAACTTCCCAGTAGCACCAAGTCAGGCTGGCCCCGACAGAATGAAAAGAAGCCCTCCGAGGTTTTCC
AGACAGACTTGATCACAGCCATGAAGATCCCGGACTCATACCCGCTCAGCCCAGTTGACTACTACATCCTGGCAGACCCA
TGGCGACAGGAATGGGAGAAAGGTGTGCAGGTGCATGCCGGGCAGAGGCCATCCCAGAGCCCATGTTGAGGATCCTCCCA
CAACTGGAAGGCCCCCCTGCCCAGGCATCCCTGAGCAGCACACTTGGTGAGGGCTCCCAGTCTGATTGGCCAGGGGGCAG
CCGCTATGACTCGGACGAGATTGACGCCTACTGGCTGGAGCTCATCAACTTGGAGCTTAAGGAGATAGAGAGGCCGGAGC
TGGATGAGCTGACATTAGAGCGTGTGGTGGAGGAACTGGAGACCCTGTGCCACCAGAATATGGCCAGAGCCATTGAGACG
CAGGAGGGGCTGGGCATCGAGTATGACGAGGATGTTGTCTGCGACGTGTGTCGCTCTCCTGAGGGCGAGGATGGCAACAA
GATGGTCTTCTGTGACAAGTGCAATGTCTGTGTGCATCAGGCATGCTACATGATCCTCAGGGTGCCCACGGGCAGCTGGC
TGTGCCAGACGTGTACCCTGGGTGTCCAGCCAAAGTGCCTGCCCTGCCCCAAGTGAGGAGGAGCCTTGAAGCCCACCAGA
AGTGGGACCAAGTGGGTGCACATCAGCTGTGCCCTATGGATTCCTGAGGTCAGCATCGGCTGCCCAGAGAAGATGGAGCC
CATCACCAAGATCTCGCATATCCCAGCCAGCTGCTGGGCTCTGTCCTGCAGCCTCTGCAAGGAATGCACAGGCACCTGCA
TCCAGTGTTCCATGCCTTCGTGCGTCACAGTGTTCCATGTCACATGCGCCTTTGACCACGGCCTGGAAATGCGGACTATA
TTAGCAGACAATGATGAGGTCAAGTTCAAGTCATTCTGCCAGGAGCACAGTGACGGGGGCCCACGTAATGAGCCCACATC
TGAGCCTGCGAAGCCCAGCCAGGCTGGCAAGGACCTGGAAAAGGTGACCCTGCACAAGCAGCGGCTGCAGCAGATAGAGG
AGGACTTCTATGAGCTGGTGGAGCCGGCTGAGGTGGCTGAGCGTCTGGACCTGGCTGAGGCGTTAGTCGACTTCATCTAC
CAGTACTGGAAGCTGAAGAGGAAAGCCAACGCCAACCAGCCGCTGCTGACCCCCAACACTGACAAGGTGGACAGCCTGGC
CCAGCAGGAGCAGGACGTCCTCTACTGCTGCCTGAAGCTCTTCACCCATCTGTAGCAAGACCTAGAGAGGGTTAGAAATC
TGTGCTACATGGTGACAAGGCACGAGAGAACGAAACACGCCATCTGCAAACTCCAGGAGCAGATATTCCACCTGCAGATG
AAACTTATTGAACAGGATCTGTGTCGAGAGCGGTCTGGAAGAAGAGCAAAGGGCAAGAAGAGTGACTCGAAGAGAAAGGG
CTGCGAGGGTTCCCAGGGCAGCACTGAGAAGAAAGAGAAAGTGAAGGCGGGGCCTGACTCAGTCCTGGGGCAGCTGGGCC
TGTCCACCTCATTCCCCATCGATGGCACCTTCTTCAACAGCTGGCTGGCACAGTCGATACAGATCACAGCAGAGAACATG
GCCATGAGCGAGTGGCTGCTGAACAGTGGGCACCGTGAGGACCCTGCTCTAGGGCTGCTGTCAGAGGAGCTGCTGCAGGA
CAAGGAGACACTGCTCAGCTTCATGCGGGACCCCTCGCTGCGACCTGGCGACCCTGCTAGGAAGGCCCGAGGCCGCACCC
GCCTGCCTGCCAAGAAGAAACCACCACCACCACCACTGCAGGACAGGCCTGGTTGACGGACGACTCTAGACAAAGTCCCC
AAGAAGACCTGGGGCCAGGAGGCAGGCAGCGGCAAGGGGGGTTAAGGGCCACCTACCGGGAAGCCACCACGTCGGACATC
TCACTTGCCGTCCAGCCCTGCAGCCGGGGACTGTCCCATCCTAGCCGCCCCTGAAAGCCCCCCACCACTGGCCCCTGAGA
CCCTGGACGCGGCAGCCTCAGTAGCTGCTGACTCAGATGTCCAAGTGCCTGGCCCTGCAGCGAGCCCTAAGCCTTTGGGC
CGGCTCTGGCCACCCCGTGAGAACAAGGTAACCCGGAGATTGCCGGGTGCCAGGCCTGATGTTGGGATGGGACCACCTTC
AGCTGTGGCTGAGAGGCCCAAGGTCAGCCTGCATTTTGACACTGAGACTGATGGCTACTTCTCTGATGGGGAGATGAGCG
ACTCAGATGTAGAGGCCGAGGACGGTGGGGTGAAGCAGGGTCCCGGGAGGTAGGGGCAGAAGAGGTAGTCCACATGGGTG
TACTAGCCTCC

Alignment

ORF - retro_nleu_728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.63 %
• Parental protein coverage: 94.89 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEEKRRKYSISSDNSDTTDSHATSTSASRCSKLPSSTKSGWPRQNEKKPSEVFRTDLITAMKIPDSYQLS
          MEEKRRKYSISSDNSDTTDSHATSTSASRCS.LPSSTKSGWPRQNEKKPSEVF.TDLITAMKIPDSY.LS
Retrocopy MEEKRRKYSISSDNSDTTDSHATSTSASRCSELPSSTKSGWPRQNEKKPSEVFQTDLITAMKIPDSYPLS

Parental  PDDYYILADPWRQEWEKGVQVPAG-AEAIPEPVVRILPPLEGPPAQASPSSTTLGEGSQPDWPGGSRYDL
          P.DYYILADPWRQEWEKGVQV.AG.AEAIPEP..RILP.LEGPPAQAS.SST.LGEGSQ.DWPGGSRYD.
Retrocopy PVDYYILADPWRQEWEKGVQVHAG<AEAIPEPMLRILPQLEGPPAQASLSST-LGEGSQSDWPGGSRYDS

Parental  DEIDAYWLELINSELKEMERPELDELTLERVLEELETLCHQNMARAIETQEGLGIEYDEDVVCDVCRSPE
          DEIDAYWLELIN.ELKE.ERPELDELTLERV.EELETLCHQNMARAIETQEGLGIEYDEDVVCDVCRSPE
Retrocopy DEIDAYWLELINLELKEIERPELDELTLERVVEELETLCHQNMARAIETQEGLGIEYDEDVVCDVCRSPE

Parental  GEDGNEMVFCDKCNVCVHQACYGILKVPTGSWLCRTCALGVQPKCLLCPKRGGALKPTRSGTKWVHVSCA
          GEDGN.MVFCDKCNVCVHQACY.IL.VPTGSWLC.TC.LGVQPKCL.CPK.GGALKPTRSGTKWVH.SCA
Retrocopy GEDGNKMVFCDKCNVCVHQACYMILRVPTGSWLCQTCTLGVQPKCLPCPK*GGALKPTRSGTKWVHISCA

Parental  LWIPEVSIGCPEKMEPITKISHIPASRWALSCSLCKECTGTCIQCSMPSCVTAFHVTCAFDHGLEMRTLL
          LWIPEVSIGCPEKMEPITKISHIPAS.WALSCSLCKECTGTCIQCSMPSCVT.FHVTCAFDHGLEMRT.L
Retrocopy LWIPEVSIGCPEKMEPITKISHIPASCWALSCSLCKECTGTCIQCSMPSCVTVFHVTCAFDHGLEMRTIL

Parental  ADNDEVKFKSFCQEHSDGGPRNEPTSEPAEPSQAGEDLEKVTLRKQRLQQLEEDFYELVEPAEVAEPWDK
          ADNDEVKFKSFCQEHSDGGPRNEPTSEPA.PSQAG.DLEKVTL.KQRLQQ.EEDFYELVEPAEVAE..D.
Retrocopy ADNDEVKFKSFCQEHSDGGPRNEPTSEPAKPSQAGKDLEKVTLHKQRLQQIEEDFYELVEPAEVAERLDL

Parental  LDCL-GYLLLSRELRKNPNANQPLLTPKTDEVDNLAQQEQDVLYRRLKLFTHLRQDLERVRNLCYMVTRR
          ...L.........L....NANQPLLTP.TD.VD.LAQQEQDVLY..LKLFTHL.QDLERVRNLCYMVTR.
Retrocopy AEALVDFIYQYWKLKRKANANQPLLTPNTDKVDSLAQQEQDVLYCCLKLFTHL*QDLERVRNLCYMVTRH

Parental  ERTKHAICKLQEQIFHLQMKLIEQDLCRERSGRRAKGKKSDSKRKGCEGSKGSTEKKEKVKAGPDSVLGQ
          ERTKHAICKLQEQIFHLQMKLIEQDLCRERSGRRAKGKKSDSKRKGCEGS.GSTEKKEKVKAGPDSVLGQ
Retrocopy ERTKHAICKLQEQIFHLQMKLIEQDLCRERSGRRAKGKKSDSKRKGCEGSQGSTEKKEKVKAGPDSVLGQ

Parental  LAGLSTSFPIDGTFFNSWLAQSVQITAENMAMSEWPLNNGHREDPAPGLLSEELLQDEETLLSFMRDPSL
          L.GLSTSFPIDGTFFNSWLAQS.QITAENMAMSEW.LN.GHREDPA.GLLSEELLQD.ETLLSFMRDPSL
Retrocopy L-GLSTSFPIDGTFFNSWLAQSIQITAENMAMSEWLLNSGHREDPALGLLSEELLQDKETLLSFMRDPSL

Parental  RPGDPARKARGRTRLPAKKKPPPPPPPPPQDGPGSRTTPDKAPKKTWGQDAGSGKGGQGPPTRKPPRRTS
          RPGDPARKARGRTRLPAKKKPPPPP....QD.PG.RTT.DK.PKKTWGQ.AGSGKGG.GPPT.KPPRRT.
Retrocopy RPGDPARKARGRTRLPAKKKPPPPP---LQDRPG*RTTLDKVPKKTWGQEAGSGKGG*GPPTGKPPRRT-

Parental  SHLPSSPAAGDCPILAAPESPPPLAPETLDEAASIAADSDVQVPGPAASPKPLGRLRPPRESKATRRLPG
          SHLPSSPAAGDCPILAAPESPPPLAPETLD.AAS.AADSDVQVPGPAASPKPLGRL.PPRE.K.TRRLPG
Retrocopy SHLPSSPAAGDCPILAAPESPPPLAPETLDAAASVAADSDVQVPGPAASPKPLGRLWPPRENKVTRRLPG

Parental  ARPDAGMGPPSAVAERPKVSLHFDTETDGYFSDGEMSDSDVEAEDGGVQRGP-REAGAEEVVRMGVLAS
          ARPD.GMGPPSAVAERPKVSLHFDTETDGYFSDGEMSDSDVEAEDGGV..GP.RE.GAEEVV.MGVLAS
Retrocopy ARPDVGMGPPSAVAERPKVSLHFDTETDGYFSDGEMSDSDVEAEDGGVKQGP<REVGAEEVVHMGVLAS

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_728 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000008110	1 retrocopy	retro_nleu_728 ,