RetrogeneDB ID: retro_nleu_772

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397272.1:31472079..31473910(-)
• Located in intron of: ENSNLEG00000006506

Retrocopy information

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

Parental gene information

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

Sequence

>retro_nleu_772
GCCATTTTATGCCAATACAGAATAGCAACAAAAGACAGAAAAACAGTATTCGGTGCTCCTGAAGTCTTGCTGGGGATCTT
ACCAGGAGCAGGAGGGACACAAAGGCTGCCCAAAATGGTGGGTGTGCCTGCTGCTTTTGACATGATGCTGGCTGGTAGAA
ACATTCGTGCAGACAGGGCAAGGAAAATGGGACTGGTTGACCAATTGGTGGAATCTCTGGGACCAGGACTAAAACTTCCA
GAAGAATGGACAATCAAATACCTAGAAGAAGTCACAATTACTTTCCCAAAGGACTAGCTGATAAGAAGATCTCTCCACAG
AGAGACAAGGGATTGGTGGAAAAATTAACAGGGTATGCCATGACTATTCCATTTGTCAGGCAACAGATTTACAAAAAAGT
GGAAGAAAAAGTGTGAAAGCGGACTAAAGGGCTTTATCCCACACCTCTGAAAATAACTGATGTGGTAAAGACTGGAATTG
AGCAAGGGAGTGATGCTGGTTATCTCTCTGAATTTCAGAAATTTGGAGAGCTTGCAATGACCAAAGAATCAAAGGCCTTG
ATGGGACTCTACCAGGGTCAGGTCCTGTGCAAGAAGAATACATCTGGAGCTCCACAGAAGGATGTTAAGCATTTGGCTAT
TCCTGGTGCAGGGATGATGGGAGCAGGCATTGCCCAAGTCTCCGTGGATAAGGGGCGAAAGACTATACTTAAAGATGCCA
CACTCACTGGGCTAGGCCGAGGACAGCAACAAGTGTTCAAAGGATTGAATGATAAAGTAAAGAACAAAGCTCTAACATCA
TTTGAAAGGGATTCCATCTTCAGCAACTTGACTGGGAAGCTTGATTACCAAGGTTTTGAAAGACAGACATGGTGATGGAT
GCTGTGTTCGAGGACCTTAGTTTTAAGCACAGAGTGCTAAAGGAAGTAGAAGCAGTGATTCCAGATCACTGTGTCTTTGC
CAGTAACACATCTCCTCTCCCAATAAGTGAAATCGCTGCTGTCAGCAAAAGACCTGAGAAGGTGATTGGCAGGCACTACT
TCTCTCCCGCAGACAAGACGCAGCTGCTGGAGATGATCACAACCGAGAAGACTTCCAAAGACACCAGTGCTTCAGCTGTA
GCAGTCAGTCTCAAGCAGGGAAAGGTCATCATTGTGGTTAAGGATGGACCTGGCTTCTATACCACCAGGTGTCTTGCACC
CATGATGTCTGAAGTCATCTGAATCCTCCAGGAAAGAGTTGACCTGAAGAAGCTGGATTCCCTGACCACAAGCCTTGGCT
TTCCTGTGGGTGCCGCCACACTGGTGGATGAAGTTGGTGTGGATGTAGCGAAACATGTGGCGGAGGATCTGGGCAAAGCC
TTTGGGGAGCAGTTTGGAGGTGGAAACCCAGAACTGCTGACACAGATGGTGTCCAAGGGCTTCCTAGGTCGCAAGTCTGG
GAAGGGCTTTTCCATCTATCAGGAGAGTGTGAAGAGTAAGAATTTGAATTCTGACATGGATAGTATTTTAGCAAGTCTGA
AGATGCCTCCTAAGTCTGAAGTCTCCTCAGATGAAGACATCCAGTTCCGCCTGGTGACAAGATTTGTGAATGAGGCAGTC
ACGTGCCTGCAAGAGGGGATCTTGGCCACACCTACAGAGCAAGACATTGGAGCCATCTTCGGGCTCAGCTTCCCACCTTG
TCCTGGAGAGCCTTTCTGCTTTGCGGATCTGTATGAAGCCCAGAAGATAGTGGACCGGCTCAAGAAGTATGAGGCTGCCT
ATGGAAAAAAGTTCACCCCAAGCCAGCTGCTAGCTGACCACGCTAACAGCCCTAACAAGAAGTTTTACCAG

Alignment

ORF - retro_nleu_772 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.58 %
• Parental protein coverage: 80.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AISCQYRIATKDRKTVLGTPEVLLGVLPGAGGTQRLPKMVGVPAALDMMLTGRSIRADRAKKMGLVDQLV
          AI.CQYRIATKDRKTV.G.PEVLLG.LPGAGGTQRLPKMVGVPAA.DMML.GR.IRADRA.KMGLVDQLV
Retrocopy AILCQYRIATKDRKTVFGAPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLAGRNIRADRARKMGLVDQLV

Parental  EPLGPGLKPPEERTMEYLEEVAITFAK-GLADKKISPKRDKGLVEKLTAYAMTIPFVRQQVYKKVEEKVR
          E.LGPGLK.PEE.T..YLEEV.ITF.K.GLADKKISP.RDKGLVEKLT.YAMTIPFVRQQ.YKKVEEKV.
Retrocopy ESLGPGLKLPEEWTIKYLEEVTITFPK<GLADKKISPQRDKGLVEKLTGYAMTIPFVRQQIYKKVEEKV*

Parental  KQTKGLYPAPLKIIDVVKTGIEQGSDAGYLSESQKFGELVMTKESKALMGLYHGQVLCKKNKFGAPQKDV
          K.TKGLYP.PLKI.DVVKTGIEQGSDAGYLSE.QKFGEL.MTKESKALMGLY.GQVLCKKN..GAPQKDV
Retrocopy KRTKGLYPTPLKITDVVKTGIEQGSDAGYLSEFQKFGELAMTKESKALMGLYQGQVLCKKNTSGAPQKDV

Parental  KHLAILGAGLMGAGIAQVSVDKGLKTILKDATLTALDRGQQQVFRGLNDKVKKKALTSFERDSIFSNLTG
          KHLAI.GAG.MGAGIAQVSVDKG.KTILKDATLT.L.RGQQQVF.GLNDKVK.KALTSFERDSIFSNLTG
Retrocopy KHLAIPGAGMMGAGIAQVSVDKGRKTILKDATLTGLGRGQQQVFKGLNDKVKNKALTSFERDSIFSNLTG

Parental  QLDYQGFE-KADMVIEAVFEDLSLKHRVLKEVEAVIPDHCVFASNTSALPISEIAAVSKRPEKVIGMHYF
          .LDYQGFE.K.DMV..AVFEDLS.KHRVLKEVEAVIPDHCVFASNTS.LPISEIAAVSKRPEKVIG.HYF
Retrocopy KLDYQGFE<KTDMVMDAVFEDLSFKHRVLKEVEAVIPDHCVFASNTSPLPISEIAAVSKRPEKVIGRHYF

Parental  SPVDKMQLLEIITTEKTSKDTSASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKK
          SP.DK.QLLE.ITTEKTSKDTSASAVAV.LKQGKVIIVVKDGPGFYTTRCLAPMMSEVI.ILQE.VD.KK
Retrocopy SPADKTQLLEMITTEKTSKDTSASAVAVSLKQGKVIIVVKDGPGFYTTRCLAPMMSEVI*ILQERVDLKK

Parental  LDSLTTSFGFPVGAATLVDEVGVDVAKHVAEDLGKVFGERFGGGNPELLTQMVSKGFLGRKSGKGFYIYQ
          LDSLTTS.GFPVGAATLVDEVGVDVAKHVAEDLGK.FGE.FGGGNPELLTQMVSKGFLGRKSGKGF.IYQ
Retrocopy LDSLTTSLGFPVGAATLVDEVGVDVAKHVAEDLGKAFGEQFGGGNPELLTQMVSKGFLGRKSGKGFSIYQ

Parental  EGVKRKDLNSDMDSILASLKLPPKSEVSSDEDIQFRLVTRFVNEAVMCLQEGILATPAEGDIGAVFGLGF
          E.VK.K.LNSDMDSILASLK.PPKSEVSSDEDIQFRLVTRFVNEAV.CLQEGILATP.E.DIGA.FGL.F
Retrocopy ESVKSKNLNSDMDSILASLKMPPKSEVSSDEDIQFRLVTRFVNEAVTCLQEGILATPTEQDIGAIFGLSF

Parental  PPCLGGPFRFVDLYGAQKIVDRLKKYEAAYGKQFTPCQLLADHANSPNKKFYQ
          PPC.G.PF.F.DLY.AQKIVDRLKKYEAAYGK.FTP.QLLADHANSPNKKFYQ
Retrocopy PPCPGEPFCFADLYEAQKIVDRLKKYEAAYGKKFTPSQLLADHANSPNKKFYQ

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_772 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,