RetrogeneDB ID: retro_nleu_2327

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397343.1:7476427..7477934(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPL
• Ensembl ID: ENSNLEG00000014696
• Aliases: None
• Description: None

Sequence

>retro_nleu_2327
GAGAACTACAGTGACCCACACAAAACCCCTGCCTCCCCAGTTGTCCACATTAGGGGCCTAATTGACGGTGTGGTGGAAGC
TGACCTTGTGGAGGCCTTGCAGGAGTTTGGACCCATCAGCTATGTGACGGTAACGCCTAAAAAGAGACAAGCACTGGTGG
AGTTTGAAGATGTGCTGGGGGCTTGCAACGCAGTGAACTACACAGCCGACAACCAAATACACATTGCCGGTCACCCAGCT
TTTGTCAACTACTCTACCAGCCAGAAGATCTCCCTCCGCGGGAACTCGGATGACTCCCGGAGAGTGAACACTGTGCTTCT
TTCCTTTATCATCCTGAACCCCATCTATTCGATCACCACGGATGTTCTTTACACTATTGGCAATCCTTGTGGCCCCTGTC
CCGAGAATTGCCATTTTCCCGGAAGAATGGAGTTTCAGGCCATGGTGGGAATTTGACTGTGTTCAAAGTGCCAGTGGGCC
AAGGCCTCACTCAGTGGGGCTGAAATCTATTCTGGCTGTTGCACTCTGAAGATCGAATACGCAAAGCCTGCATGCTTGAA
TGTGTTCAAGAATAATCAGGATACTTGGGACTATACAAACCCCAATCTCAGTGGACAAGGTGACCCTGGCAGCAACCCCA
ACAAACGCCAGAGGCAGCCCCCTCTCCTGGGAGATCACCCCACAGAATATGGAGGGCCCCACTGTGGGTATCACAGCCAT
TGCCATGATGAGGGCTACAGCCCCCCAGCCCCCGACCTCACTACGAAGGGAAAAGGATGGGTCTACCAGTGGGGGGGAGT
CGCTGTCGGGGCCCAAGTCGCTACGGCCCCCAGTATGGGCACCCCCCGCCCCCTCCCGACCACTCGAGCATGGCCCTCAC
TCCGACAGCCCTTTGCTCATGGTCTATGGTTTGGATCAATCTAAGATGAACTGTGACCAAGTCTTCAATGTCTTCTGCTT
GTATAGCAATGTGGAGAAGGTGAAATTCATGAAAAGCAAGCCGGGGGCCGCCATGGTGGAGATGGCTGATGGCTACACTG
TGGACCGGGCCACTACCCACCTCAGCAACAACTTCATGTTTGGGCAGAAGCTGAATGTCTGTCTCCAAGCAGCCAGCCAT
CAGCTCAGTCAGTCATGCGGGTTGGAAGTCAGGTCTTGCAGTTACAGAGACTTCAGTGAATCCCGAACAATGGGTTCCCC
ACTCCGGAGCGGGCAGCGAAGAACCGCATCCAGCACCCCAGCAGCAACGTGCTGCACCTCTCAACGCCCCGCTGGAGGTG
ACTGAGAACTTCTTTGAGATCTGCGATGAGCTGGGCGTGAAGCGTCCATCTTCTGTGACAGTATTCTCAGGCAAAAGTGA
GAGCAGCTCCTCTGGACTGCTGGAGTGGGAATCCAAGAGCGATGCCCTGGAGGCTCGGGGCTTCCTGAACCATTACCAGA
TGAAAAACCCAAATGGTCCATACCTTACTCTCTGAAGCTGTGTTTCTCCAACGCTCAGCATGCCTCC

Alignment

ORF - retro_nleu_2327 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.27 %
• Parental protein coverage: 84.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  ENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAAD
          ENY.DPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYV.V.PKKRQALVEFEDVLGACNAVNY.AD
Retrocopy ENYSDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVTVTPKKRQALVEFEDVLGACNAVNYTAD

Parental  NQIYIAGHPAFVNYSTSQKISRPGDSDDSRSVNSVLL-FTILNPIYSITTDVLYTICNPCGP-VQRIVIF
          NQI.IAGHPAFVNYSTSQKIS..G.SDDSR.VN.VLL.F.ILNPIYSITTDVLYTI.NPCGP.V.RI.IF
Retrocopy NQIHIAGHPAFVNYSTSQKISLRGNSDDSRRVNTVLLSFIILNPIYSITTDVLYTIGNPCGP>VPRIAIF

Parental  -RKNGV-QAMV-EFDSVQSA-QRAKASLNGADIYSGCCTLKIEYAKPTRLNVFKNDQDTWDYTNPNLSGQ
          .RKNGV.QAMV.EFD.VQSA.Q.AKASL.GA.IYSGCCTLKIEYAKP..LNVFKN.QDTWDYTNPNLSGQ
Retrocopy >RKNGV>QAMV>EFDCVQSA<QWAKASLSGAEIYSGCCTLKIEYAKPACLNVFKNNQDTWDYTNPNLSGQ

Parental  GDPGSNPNKRQRQPPLLGDHPAEYGGPHGGYHSHYHDE-GYGPPPP--HYEGRRMGPPVGGHR-RGPSRY
          GDPGSNPNKRQRQPPLLGDHP.EYGGPH.GYHSH.HDE.G..PP.P..HYEG.RMG.PVGG.R.RGPSRY
Retrocopy GDPGSNPNKRQRQPPLLGDHPTEYGGPHCGYHSHCHDE<GLQPPSPRPHYEGKRMGLPVGGSRCRGPSRY

Parental  GPQYGHPPPPPP-PPEYGPHADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMAD
          GPQYGHPPPPP..P.E.GPH.DSP.LMVYGLDQSKMNCD.VFNVFCLY.NVEKVKFMKSKPGAAMVEMAD
Retrocopy GPQYGHPPPPPD<PLEHGPHSDSPLLMVYGLDQSKMNCDQVFNVFCLYSNVEKVKFMKSKPGAAMVEMAD

Parental  GYAVDRAITHLNNNFMFGQKLNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESR-NNRFSTPEQAAKNRIQ
          GY.VDRA.THL.NNFMFGQKLNVC..........QS.GLE..SCSY.DFSESR.NN.F.TPE.AAKNRIQ
Retrocopy GYTVDRATTHLSNNFMFGQKLNVCL-QAASHQLSQSCGLEVRSCSYRDFSESR<NNGFPTPERAAKNRIQ

Parental  HP-SNVLHF-FNAPLEVTEENFFEICDELGVKRPSSVKVFSGKSERSSSGLLEWESKSDALETLGFLNHY
          HP.SNVLH...NAPLEVT.ENFFEICDELGVKRPSSV.VFSGKSE.SSSGLLEWESKSDALE..GFLNHY
Retrocopy HPSSNVLHL<LNAPLEVT-ENFFEICDELGVKRPSSVTVFSGKSESSSSGLLEWESKSDALEARGFLNHY

Parental  QMKNPNGPY-PYTLKLCFSTAQHAS
          QMKNPNGPY.PY.LKLCFS.AQHAS
Retrocopy QMKNPNGPY<PYSLKLCFSNAQHAS

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_2327 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000003779	1 retrocopy	retro_etel_886,
Nomascus leucogenys	ENSNLEG00000000864	1 retrocopy	retro_nleu_1834,
Nomascus leucogenys	ENSNLEG00000014696	1 retrocopy	retro_nleu_2327 ,
Pongo abelii	ENSPPYG00000009945	2 retrocopies	retro_pabe_1282, retro_pabe_3576,
Pan troglodytes	ENSPTRG00000010941	1 retrocopy	retro_ptro_1043,
Tupaia belangeri	ENSTBEG00000016563	1 retrocopy	retro_tbel_1340,