RetrogeneDB ID: retro_nleu_1588

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397300.1:20067203..20069491(+)
• Located in intron of: ENSNLEG00000004981

Retrocopy information

• Ensembl ID: ENSNLEG00000005029
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HADHA
• Ensembl ID: ENSNLEG00000001616
• Aliases: None
• Description: None

Sequence

>retro_nleu_1588
ATGGTGGCCTGCCGGGCGACTGGCATCCTCAGCCGCTTCTCTGCCTTCAGGATCCTCCGCTCCCTAGGTTATATATGCCA
CAATTTTACAGGGTCTTCTGCTTTGCTGACCAGAACCCATATTAACTATGGAGTCAAAGGGGATGTGGCAGTTGTTCGAA
TTAACTCTCCCAATTCAAAGGTAAATACACTGAGTAAAGAGCCGCATTCAGAGTTCTCAAAAGTTATGAATGAAATCTGG
GCTAGTGATCAAATCAGAAGTGCCGTCCTTATCTAATCAAAGCCAGGCTGCTTTATTGCAGGTGCTGATATCAACATGTT
AGCTGCTTGCAAGACCCTTCAAGAAGTAACACAGCTATCACAAGAAGCACAGAGAATAGTTGAGAAACTTGAAAAGTCCA
CAAAGCCTATTGTGGCTGCCATCAATGGATCCTGCCTGGGAGGAGGACTTGAGCTTGCCATTTCATACCAATATAGAATA
GCAACAAAAGACAGAAAAACAGTATTAGGTACCCCTGAAGTCTTGCTGGGGGTCTTACCAGGAGCAGGAGGCACACAAAG
GTTGCCCAAAATGGTGGGTGTGCCTGCTGCTTTGGACGTGATGCTGACTGGTAGAAGCATTCATGCAGACAGGGCAAAGA
AAATGGGACTGGTTGACCAATTGGTGGAACCCCTGGGACCAGGACTAAAACCTCCAGCGGAACGGACATCGAATACCTAG
AAGAAGCTGCAATTACTTTCACCAAAGGACTAGCTGATAAGAAGATCTTTTCAAAGAGAGACAAGGGATTGGTGGAAAAT
GTGACAGCTTACGCCATGACTCTTCCATTTGTCAGGCAACAGGTTTACAAAAAAGTAGAAGAAAAAGTGCGAAAGCAGAC
TAAAGGCCTTTATCCTGTACCTCTGAAAATAACTGATGTGGTAAAGACTGGATTTGAGCAAGGGAGTGATGTCGGTTATC
TCTCTGAATCTCAGAAATTTGGAGAGCTTGTAATGACCAAAGAATCAAAGGCCTTGATGGGACTCTACCATGGTCAGGTC
CTGTGCAAGAAGAATAAATTTGGAGCTCTACAGAAGGATGTTAAGCATCTGGCTATTCTTGGTGCAGGGCTGATGGGAGC
AGGCATCGCCCAAGTCTCCATGGATAAGGGGCTAAAGACTATACTTAAAGATGCCACCCTCACTGTGCTAGACCGAGGAC
AGCAACAAGTGTTCAAAGGATTGAATGATAAAGTGAAGAAGAAAGCTCTGACATCATTTGAAAGGGATTCCATCTTCAGC
AACTTGACTGGGCAGCTTGATTATCAAGTTTTCGAAAAGGCCGACATGGTGATTGAAGCTGTGTTTGAGGACCTTAGTCT
TAAGCACGGAGTGCTAAAGGAAGTAGAAGCGGTGATTCCAGATCACCGTATCTTTGCCAGTAACACATCTGCTCTCCCAA
TCGGTGAAATTGCTGCTGTCAGCAAAAGACCTGAGAAGGTGATTGGCATGCACTACTTCTCTCCCGTGGACAAGATGCAG
CTGCTGGAGATTATCACGACCAAGAAAACTTCCAAAGACACCAGTGTTTCAGCTGTAGCAGTCGGACTCAAGCAGGGGAA
GGTCATCATTGAGGTTAAGGATGGACCTGGCTTCTATACTACCAGGTGTCTTGCGCCCATGATGTCTGAAGTAATCCGAA
TCCTCTAGGAAGGAGTTGACTCGAAGAAGATGGATTCCCTGACCACAAGCTTTGGCTTTCCTGTGGGGGCCGCCACACTG
GTGGATGAAGTTGGTGTGGATGTAGCGAAACATGTGGCGGAAGATCTGGGCAAAGTCTTTGGGGAGCGGTTTGGAGGCGG
AAACCCAGAACTGCTGACACAGATGGTGTCCAAGGGCTTCCTAGGTTGCAAGTCTGGGAAGGACTTTTACATCAGTCAGG
AGGGTGTGAAGAGGAAGGATTTGAATTCTGACATGGATAGTATTTTAGCGAGTCTGAAGCTGCCTCCTAAGTCTGAAGTC
TCGTCAGACGAAGACATCCAGTTCCACCTGGTGACAAGATTTGTGAATGAGGCAGTCATGTGCCTGCAAGAGGGGATCTT
GGCCACACCTGCAGAGGGAGACATTGGAGCCATCTTTGGGCTCGGCTTCGAGCCTTGTCTTGGAGGGCCTTTCCGCTTTG
TGGATCTGTATGGCGCCCAGAAGATAGTGGATGGGCTCAAGAAGTATGAAGCTGCCTATGGAAAACAGTTCACCCCATGC
CAGCTGCTAGCTGACCACGCTAACAGCCCTAACAAGAAGTTCTACCAG

Alignment

ORF - retro_nleu_1588 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVACRAIGILSRFSAFRILRSRGYICRNFTGSSALLTRTHINYGVKGDVAVIRINSPNSKVNTLSKELHS
          MVACRA.GILSRFSAFRILRS.GYIC.NFTGSSALLTRTHINYGVKGDVAV.RINSPNSKVNTLSKE.HS
Retrocopy MVACRATGILSRFSAFRILRSLGYICHNFTGSSALLTRTHINYGVKGDVAVVRINSPNSKVNTLSKEPHS

Parental  EFSEVMNEIWASDQIRSAVIISSKPGCFIAGADINMLAACKTLQEVTQLSQEAQRIVEKLEKSTKPIVAA
          EFS.VMNEIWASDQIRSAV.I.SKPGCFIAGADINMLAACKTLQEVTQLSQEAQRIVEKLEKSTKPIVAA
Retrocopy EFSKVMNEIWASDQIRSAVLI*SKPGCFIAGADINMLAACKTLQEVTQLSQEAQRIVEKLEKSTKPIVAA

Parental  INGSCLGGGLELAISCQYRIATKDRKTVLGTPEVLLGVLPGAGGTQRLPKMVGVPAALDMMLTGRSIRAD
          INGSCLGGGLELAIS.QYRIATKDRKTVLGTPEVLLGVLPGAGGTQRLPKMVGVPAALD.MLTGRSI.AD
Retrocopy INGSCLGGGLELAISYQYRIATKDRKTVLGTPEVLLGVLPGAGGTQRLPKMVGVPAALDVMLTGRSIHAD

Parental  RAKKMGLVDQLVEPLGPGLKPPEERT-MEYLEEVAITFAKGLADKKISPKRDKGLVEKLTAYAMTIPFVR
          RAKKMGLVDQLVEPLGPGLKPP.ERT..EYLEE.AITF.KGLADKKI..KRDKGLVE..TAYAMT.PFVR
Retrocopy RAKKMGLVDQLVEPLGPGLKPPAERT<IEYLEEAAITFTKGLADKKIFSKRDKGLVENVTAYAMTLPFVR

Parental  QQVYKKVEEKVRKQTKGLYPAPLKIIDVVKTGIEQGSDAGYLSESQKFGELVMTKESKALMGLYHGQVLC
          QQVYKKVEEKVRKQTKGLYP.PLKI.DVVKTG.EQGSD.GYLSESQKFGELVMTKESKALMGLYHGQVLC
Retrocopy QQVYKKVEEKVRKQTKGLYPVPLKITDVVKTGFEQGSDVGYLSESQKFGELVMTKESKALMGLYHGQVLC

Parental  KKNKFGAPQKDVKHLAILGAGLMGAGIAQVSVDKGLKTILKDATLTALDRGQQQVFRGLNDKVKKKALTS
          KKNKFGA.QKDVKHLAILGAGLMGAGIAQVS.DKGLKTILKDATLT.LDRGQQQVF.GLNDKVKKKALTS
Retrocopy KKNKFGALQKDVKHLAILGAGLMGAGIAQVSMDKGLKTILKDATLTVLDRGQQQVFKGLNDKVKKKALTS

Parental  FERDSIFSNLTGQLDYQGFEKADMVIEAVFEDLSLKHRVLKEVEAVIPDHCVFASNTSALPISEIAAVSK
          FERDSIFSNLTGQLDYQ.FEKADMVIEAVFEDLSLKH.VLKEVEAVIPDH..FASNTSALPI.EIAAVSK
Retrocopy FERDSIFSNLTGQLDYQVFEKADMVIEAVFEDLSLKHGVLKEVEAVIPDHRIFASNTSALPIGEIAAVSK

Parental  RPEKVIGMHYFSPVDKMQLLEIITTEKTSKDTSASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVI
          RPEKVIGMHYFSPVDKMQLLEIITT.KTSKDTS.SAVAVGLKQGKVII.VKDGPGFYTTRCLAPMMSEVI
Retrocopy RPEKVIGMHYFSPVDKMQLLEIITTKKTSKDTSVSAVAVGLKQGKVIIEVKDGPGFYTTRCLAPMMSEVI

Parental  RILQEGVDPKKLDSLTTSFGFPVGAATLVDEVGVDVAKHVAEDLGKVFGERFGGGNPELLTQMVSKGFLG
          RIL.EGVD.KK.DSLTTSFGFPVGAATLVDEVGVDVAKHVAEDLGKVFGERFGGGNPELLTQMVSKGFLG
Retrocopy RIL*EGVDSKKMDSLTTSFGFPVGAATLVDEVGVDVAKHVAEDLGKVFGERFGGGNPELLTQMVSKGFLG

Parental  RKSGKGFYIYQEGVKRKDLNSDMDSILASLKLPPKSEVSSDEDIQFRLVTRFVNEAVMCLQEGILATPAE
          .KSGK.FYI.QEGVKRKDLNSDMDSILASLKLPPKSEVSSDEDIQF.LVTRFVNEAVMCLQEGILATPAE
Retrocopy CKSGKDFYISQEGVKRKDLNSDMDSILASLKLPPKSEVSSDEDIQFHLVTRFVNEAVMCLQEGILATPAE

Parental  GDIGAVFGLGFPPCLGGPFRFVDLYGAQKIVDRLKKYEAAYGKQFTPCQLLADHANSPNKKFYQ
          GDIGA.FGLGF.PCLGGPFRFVDLYGAQKIVD.LKKYEAAYGKQFTPCQLLADHANSPNKKFYQ
Retrocopy GDIGAIFGLGFEPCLGGPFRFVDLYGAQKIVDGLKKYEAAYGKQFTPCQLLADHANSPNKKFYQ

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_1588 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 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006972	1 retrocopy	retro_dnov_1863,
Homo sapiens	ENSG00000084754	1 retrocopy	retro_hsap_958,
Gorilla gorilla	ENSGGOG00000004918	1 retrocopy	retro_ggor_772,
Macaca mulatta	ENSMMUG00000004380	2 retrocopies	retro_mmul_1987, retro_mmul_787,
Mustela putorius furo	ENSMPUG00000008546	1 retrocopy	retro_mputfur_705,
Nomascus leucogenys	ENSNLEG00000001616	2 retrocopies	retro_nleu_1588 , retro_nleu_772,
Nomascus leucogenys	ENSNLEG00000012951	1 retrocopy	retro_nleu_1738,
Pongo abelii	ENSPPYG00000012583	2 retrocopies	retro_pabe_2576, retro_pabe_817,
Pan troglodytes	ENSPTRG00000011732	2 retrocopies	retro_ptro_2109, retro_ptro_664,
Ictidomys tridecemlineatus	ENSSTOG00000001593	1 retrocopy	retro_itri_681,