RetrogeneDB ID: retro_nleu_1738

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397306.1:17446432..17447262(-)
• Located in intron of: ENSNLEG00000006658

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADH
• Ensembl ID: ENSNLEG00000012951
• Aliases: None
• Description: None

Sequence

>retro_nleu_1738
ATGATGGTCATCAGCATCACACAGGTTGCTGCAGTGACTGGCCACACAGTAGTGTTGCTAGACCAGACAGAGGACATCTT
GGCAAAATATAAAGAGGGAATTGAGAAAAGCCTTAGGAAAGTGACAAAGAAGTTGTTTGTAGAAAACACTAAGGCTGCTG
ATGAATTTGTGGAGAAAACCCTAAGCAGCATATCAACCAGCACAGATGCAATATCCGTAGTCCACAGCACAGACCTGGTG
GTAGAGGCCATTGTAGAAAATCTAAAGGTGAAAATCAAGCTCTCCAAGAGGTTGGACAAGTTTGTTGCTGAACATACAAC
TTTGCCAGCAACACTTCCTCTTTGCAAATTACAAGCATAGCCAATGCTACCACCAAACAAGACCAATTTGCTGGCCTCCA
TTTACTCAACCCAGTGCCCCTGATGAAATTTGTAGAGGTCTTTAAAACACCAATGGCCACCCAAAAGACATTTGAATCTT
TGGTAAACTTGAGCAAAACCCTGGGAAAGCATCCTGTTTCTTGCAAGGACACTCCTGGGTTTATTGTCAGCTGTCTCAGG
ATTCAACACCTCATGGAAGCAGTCAGGCTGCATGAATGAGGTGACGTATCCAAGGAAAACACTGACACTGCTATGAAGTT
AGGAGCCAGGTACCCCATCGACTCACTTGAGCTTCTAGATTACGTTGGGCTGGATTCTGTGCAGTTCATCATGGATGGAT
GGCATGAAATAGATACAAGGAACCCCATATTTCAGCCCAGCCCATCCTTAAAAAAGCTGATGGCAGAGAAGAAGCTTGGC
AAGAAGTCTGGAGAAGGATTTTACAAATAC

Alignment

ORF - retro_nleu_1738 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.9 %
• Parental protein coverage: 88.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSSIATSTDA
          .M...I.QVAA.TGHTVVL.DQTEDILAK.K.GIE.SLRKV.KK.F.EN.KA.DEFVEKTLSSI.TSTDA
Retrocopy MMVISITQVAAVTGHTVVLLDQTEDILAKYKEGIEKSLRKVTKKLFVENTKAADEFVEKTLSSISTSTDA

Parental  ASVVHSTDLVVEAIVENLKVKNELFKRLDKFAAEHTI-FASNTSSLQITSIANATTRQDRFAGLHFFNPV
          .SVVHSTDLVVEAIVENLKVK..L.KRLDKF.AEHT..FASNTSSLQITSIANATT.QD.FAGLH..NPV
Retrocopy ISVVHSTDLVVEAIVENLKVKIKLSKRLDKFVAEHTT<FASNTSSLQITSIANATTKQDQFAGLHLLNPV

Parental  PVMKLVEVIKTPMTSQKTFESLIDFSKALGKHPVSCKDTPGFIVNRLLVPYLMEAIRLYERGDASKEDID
          P.MK.VEV.KTPM..QKTFESL...SK.LGKHPVSCKDTPGFIV..L....LMEA.RL.E.GD.SKE..D
Retrocopy PLMKFVEVFKTPMATQKTFESLVNLSKTLGKHPVSCKDTPGFIVSCLRIQHLMEAVRLHE*GDVSKENTD

Parental  TAMKLGAGYPMGPFELLDYVGLDTTKFIVDGWHEMDAENPLHQPSPSLNKLVAENKFGKKTGEGFYKY
          TAMKLGA.YP....ELLDYVGLD...FI.DGWHE.D..NP..QPSPSL.KL.AE.K.GKK.GEGFYKY
Retrocopy TAMKLGARYPIDSLELLDYVGLDSVQFIMDGWHEIDTRNPIFQPSPSLKKLMAEKKLGKKSGEGFYKY

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_1738 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002049	2 retrocopies	retro_btau_1111, retro_btau_1685,
Callithrix jacchus	ENSCJAG00000015938	1 retrocopy	retro_cjac_772,
Echinops telfairi	ENSETEG00000013807	1 retrocopy	retro_etel_1694,
Felis catus	ENSFCAG00000022260	1 retrocopy	retro_fcat_1225,
Homo sapiens	ENSG00000138796	1 retrocopy	retro_hsap_1571,
Gorilla gorilla	ENSGGOG00000004423	1 retrocopy	retro_ggor_1196,
Macaca mulatta	ENSMMUG00000023254	1 retrocopy	retro_mmul_2217,
Nomascus leucogenys	ENSNLEG00000001616	2 retrocopies	retro_nleu_1588, retro_nleu_772,
Nomascus leucogenys	ENSNLEG00000012951	1 retrocopy	retro_nleu_1738 ,
Pongo abelii	ENSPPYG00000014986	1 retrocopy	retro_pabe_1296,
Pan troglodytes	ENSPTRG00000016351	1 retrocopy	retro_ptro_1058,