RetrogeneDB ID: retro_pabe_3576

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:16689011..16690509(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPL
• Ensembl ID: ENSPPYG00000009945
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein L [Source:HGNC Symbol;Acc:5045]

Sequence

>retro_pabe_3576
AAGAACTACGATGACCCGCACAAAACCCCTGCCTCCCCAGTTGTCCACATCAGGGGCCTGATTGAGGGTGTGGTGGAAGC
TGACCTTGTGGAGGACTTGCAGGAGTTTGGACCCATCAGCTCTGTGGTGGTAATGCCTAAAAAGAGACAAGCACTGGTGG
AGTTTGAAGATGTGTTGGGGGCTTGCAACGCAGTGAGCTACGCAGCCGACAACCAAATATGCATTGCCGATCACCCAGCT
TTTGTCAACTACTCTACCATCCAGAAGATCTCCCACCCCGGGGACTCGGATGACTCCCGGAGCGTGAACAGTGTGCTTCT
CTTTACCATCCTGAACCCCATTTATTCGATCACCACGGATGTTCTTTACGCTATCTGTAATCCTTGTGGCCCTGTCCAGA
GAATTGTCATTTTCAGGAAGAATGGAGTTCAGGCGATGGTGGAATTCGACTCTGTTCAAAGTGCCCAGTGGGCCAAGGCC
TCTCTCAATGGGGCTGATATCTATTCTGGCTGTTGTGCTCTGAAGATGGAATACGCAAAGCCTACACGCTTGAATGTGTT
CAAGAGTGATCAGGATACTTGGGACTACACAAACCCCAATCTCAGTGGACAAGGTGATCCTGGCAGCAACCCCAACAAAC
GCCAGAGGCAGCCCCCTCTCCTGGGAGATCACCCAGCAGAATATGGAGGGCCCCACGGTGGATACCACAGCCATTACCAT
GATGAGGGCTACGGCCCCGCACCCCTCACTACTAAGGGAGAAGGATGGGTCCACCAGTGGGGGGTCACCGTCGGGGCCCA
AGTCGCTACGGCCCCCAGTATGGGCACCCCCCCACCCCCTCCCCCACCACCCGAGTATGGCCCTCACGCCCACAGCCCTG
TGCTGGTGGTCTATGGCTTGGATCAATCTAAGATGAACTGTGACCGAGTCTTCAATGTCTTCTGCTTGTATGGCAATGTG
GAGAAGGTGAAATTCATGAAAAGCAAGCCGGGGGCCGCCATGGTGGAGATGGCTGATGGCTACGCTGTGGACCGGGCCAT
TACCCACCTCAACAACAACTTCATGTTTGGGCAGAAGCTGAATGTCTGTGTCTCCAAGCAGCCAGCCATCATGCCCGGTC
AGTCATACGGGTTGGAAGACGGGTCTTGCAGTTACAAAGACTTCAGTGAATCCCAGAACAATCGGTTCTCCACCCCAGAG
CAGGCAGCCAAGAACCGCATCCAGCACCCCAGCAACGTGCTGCATTTCTTCAACACCCCGCTGGAGGTGACTGAGGAGAA
CTTCTTTGAGATCTGCGATGAGCTTGGAGTGAAACGGCCATCTTCTGTGAAAGTATTCTCAGCAAAAGTGAGCGCAGCTC
CTCTGGACTGCTGGAGTGGGAATCCAAGAGCGATGCCCTGGAGACTCTGGGCTTCCTGAACCATTACCAGATGAAAAACC
CAATGGTCCATACCCTTACACTCTGAAGTTGTGTTTCTCCACCGCTCAGCACGCCTCC

Alignment

ORF - retro_pabe_3576 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.87 %
• Parental protein coverage: 84.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAAD
          .NYDDPHKTPASPVVHIRGLI.GVVEADLVE.LQEFGPIS.VVVMPKKRQALVEFEDVLGACNAV.YAAD
Retrocopy KNYDDPHKTPASPVVHIRGLIEGVVEADLVEDLQEFGPISSVVVMPKKRQALVEFEDVLGACNAVSYAAD

Parental  NQIYIAGHPAFVNYSTSQKISRPGDSDDSRSVNSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRK
          NQI.IA.HPAFVNYST.QKIS.PGDSDDSRSVNSVLLFTILNPIYSITTDVLY.ICNPCGPVQRIVIFRK
Retrocopy NQICIADHPAFVNYSTIQKISHPGDSDDSRSVNSVLLFTILNPIYSITTDVLYAICNPCGPVQRIVIFRK

Parental  NGVQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKPTRLNVFKNDQDTWDYTNPNLSGQGDPGSN
          NGVQAMVEFDSVQSAQ.AKASLNGADIYSGCC.LK.EYAKPTRLNVFK.DQDTWDYTNPNLSGQGDPGSN
Retrocopy NGVQAMVEFDSVQSAQWAKASLNGADIYSGCCALKMEYAKPTRLNVFKSDQDTWDYTNPNLSGQGDPGSN

Parental  PNKRQRQPPLLGDHPAEYGGPHGGYHSHYHDEGYGPPP-PHYEGRRMGPPVGGHRRGPSRYGPQYGHPPP
          PNKRQRQPPLLGDHPAEYGGPHGGYHSHYHDEGYGP.P.PHY.GRRMGPPVGGHRRGPSRY.........
Retrocopy PNKRQRQPPLLGDHPAEYGGPHGGYHSHYHDEGYGPAP<PHY*GRRMGPPVGGHRRGPSRYXXXXXXXXX

Parental  PPPPPEFFPHADSP-VLMVYGLDQSKMNCDRVFNVFC-YGNVEKVKFMKSKPGAAMVEMADGYAVDRAIT
          ........P....P.VL.VYGLDQSKMNCDRVFNVFC.YGNVEKVKFMKSKPGAAMVEMADGYAVDRAIT
Retrocopy XXXXXXVWPSRPQP>VLVVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAIT

Parental  HLNNNFMFGQKLNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFN
          HLNNNFMFGQKLNVCVSKQPAIMPGQSYGLEDGSCSYKDFSES.NNRFSTPEQAAKNRIQHPSNVLHFFN
Retrocopy HLNNNFMFGQKLNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESQNNRFSTPEQAAKNRIQHPSNVLHFFN

Parental  APLEVTEENFFEICDELGVKRPSSVKVFS-GKSERSSSGLLEWESKSDALETLGFLNHYQMKN-PNGPYP
          .PLEVTEENFFEICDELGVKRPSSVKVFS..KSERSSSGLLEWESKSDALETLGFLNHYQMKN.PNGPYP
Retrocopy TPLEVTEENFFEICDELGVKRPSSVKVFS<SKSERSSSGLLEWESKSDALETLGFLNHYQMKN<PNGPYP

Parental  YTLKLCFSTAQHAS
          YTLKLCFSTAQHAS
Retrocopy YTLKLCFSTAQHAS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	1.16 RPM	133.75 RPM
SRP007412_cerebellum	1.58 RPM	100.32 RPM
SRP007412_heart	0.54 RPM	41.93 RPM
SRP007412_kidney	1.16 RPM	104.64 RPM
SRP007412_liver	0.92 RPM	72.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3576 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3576 has 0 orthologous retrocopies within eutheria group .

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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	ENSNLEG00000014696	1 retrocopy	retro_nleu_2327,
Pongo abelii	ENSPPYG00000009289	1 retrocopy	retro_pabe_1122,
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,