RetrogeneDB ID: retro_pabe_1282

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:30605839..30607336(-)
• 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_1282
AAGAACTACGATGACCCGCACAAAACCCCTGCCTCCCCAGTTTTCCACATCAGGGGCCTGATTGAGGGTGTGGTGGAAGC
TGACCTTGTGGAGGCCTTGCAGGAGTTTGGACCCATCAGCTCTGTGGTGGTAATGCCTAAAAAGAGACAAGCACTGGTGG
AGTTTGAAGATGTGTTGGGGGCTTGCAACGCAGTGAGCTACGCAGCCGACAACCAAATATGCATTGCCGATCACCCAGCT
TTTGTCAACTACTCTACCATCCAGAAGATCTCCCGCCCCGGGGACTCGGATGACTCCCGGAGTGTGAACAGTGTGCTTCT
CTTTACCATCCTGAACCCCATTTATTCGATCACCACGGATGTTCTTTACACTATCTGTAATCCTTGTGGCCCTGTCCAGA
GAATTGTCATTTTCAGGAAGAATGGAGTTCAGGCGATGGTGGAATTCGACTCTGTTCAAAGTGCCCAGTGGGCCAAGGCC
TCTCTCAATGGGGCTGATATCTATTCTGGCTTTTGTGCTCTGAAGATGGAATATGCAAAGCCTACACGCTTGAATGTGTT
CAAGAGTGATCAGGATACTTGGGACTACACAAACCCCAATCTCAGTGGACAAGGTGACCCTGGCAGCAACCCCAAGAAAC
GCCAGAGGCAGCCCCCTCTCCTGGGAGATCACCCAGCAGAATATGGAGGGCCCCACGGTGGATACCACAGCCATTACCAT
GATGAGGGCTACGGCCCCCCACCCCTCACTACGAAGGGAGAAGGATGGGTCCACCAGTGGGGGGTCACCGTTGGGGCCCA
AGTCGCTATGGCCCCCAGTATGGGCACCCCCCACCCCCTCCCCCACCACCCGAGGATGGCCCTCACGCCCACAGCCCTGT
GCTTGTGGTCTATGGCTTGGATCAATCTAAGATGAACTGTAACCGAGTCTTCAATGTCTTCTGCTTGTATGGCAATGTGG
AGAAGGTGAAATTCATGAAAAGCAAGCCGGGGGCCGCCATGATGGAGATGGCTGATGGCTACGCTGTGGACCGGGCCATT
ACCCACCTCAACAATAACTTCATGTTTGGGCAGAAGCTGAATGTCCGTGTCTCCAAGCAGCCAGCCATCATGCCCGGTCA
GTCATACGGGTTGGAAGACGGGTCTTGCAGTTACAAAGACTTCAGTGAATCCCAGAACAATCGGTTCTCCACCCCAGAGC
AGGCAGCCAAGAACCGCATCCAGCACCCCAGCAACGTGCTGCATTTCTTCAACACCCCGCTGGAGGTGACTGAGGAGAAC
TTCTTTGAGATCTGCGATGAGCTTGGAGTGAAACGGCCACCTTCTGTGAAAGTATTCTCAGCAAAAGTGAGCGCAACTCC
TCTGGACTGCTGGAGTGGGAATCCAAGAGCGATGCCCCGGAGACTCTGGGCTTCCTGAACCATTACCAGATGAAAAACCC
AATGGTCCATACCCCTACACTCTGAAGTTGTGTTTCTCCACCGCTCAGAACGCCTCC

Alignment

ORF - retro_pabe_1282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.66 %
• Parental protein coverage: 84.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ENYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAAD
          .NYDDPHKTPASPV.HIRGLI.GVVEADLVEALQEFGPIS.VVVMPKKRQALVEFEDVLGACNAV.YAAD
Retrocopy KNYDDPHKTPASPVFHIRGLIEGVVEADLVEALQEFGPISSVVVMPKKRQALVEFEDVLGACNAVSYAAD

Parental  NQIYIAGHPAFVNYSTSQKISRPGDSDDSRSVNSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRK
          NQI.IA.HPAFVNYST.QKISRPGDSDDSRSVNSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRK
Retrocopy NQICIADHPAFVNYSTIQKISRPGDSDDSRSVNSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRK

Parental  NGVQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKPTRLNVFKNDQDTWDYTNPNLSGQGDPGSN
          NGVQAMVEFDSVQSAQ.AKASLNGADIYSG.C.LK.EYAKPTRLNVFK.DQDTWDYTNPNLSGQGDPGSN
Retrocopy NGVQAMVEFDSVQSAQWAKASLNGADIYSGFCALKMEYAKPTRLNVFKSDQDTWDYTNPNLSGQGDPGSN

Parental  PNKRQRQPPLLGDHPAEYGGPHGGYHSHYHDEGYGPPP-PHYEGRRMGPPVGGHRRGPSRYGPQYGHPPP
          P.KRQRQPPLLGDHPAEYGGPHGGYHSHYHDEGYGPPP.PHYEGRRMGPPVGGHR.GPSRY.........
Retrocopy PKKRQRQPPLLGDHPAEYGGPHGGYHSHYHDEGYGPPP<PHYEGRRMGPPVGGHRWGPSRYXXXXXXXXX

Parental  PPPPPEFFPHADSPVLMVYGLDQSKMNCDRVFNVFC-YGNVEKVKFMKSKPGAAMVEMADGYAVDRAITH
          .....E..PHA.SPVL.VYGLDQSKMNC.RVFNVFC.YGNVEKVKFMKSKPGAAM.EMADGYAVDRAITH
Retrocopy XXXXXEDGPHAHSPVLVVYGLDQSKMNCNRVFNVFCLYGNVEKVKFMKSKPGAAMMEMADGYAVDRAITH

Parental  LNNNFMFGQKLNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNA
          LNNNFMFGQKLNV.VSKQPAIMPGQSYGLEDGSCSYKDFSES.NNRFSTPEQAAKNRIQHPSNVLHFFN.
Retrocopy LNNNFMFGQKLNVRVSKQPAIMPGQSYGLEDGSCSYKDFSESQNNRFSTPEQAAKNRIQHPSNVLHFFNT

Parental  PLEVTEENFFEICDELGVKRPSSVKVFS-GKSERSSSGLLEWESKSDALETLGFLNHYQMKN-PNGPYPY
          PLEVTEENFFEICDELGVKRP.SVKVFS..KSER.SSGLLEWESKSDA.ETLGFLNHYQMKN.PNGPYPY
Retrocopy PLEVTEENFFEICDELGVKRPPSVKVFS<SKSERNSSGLLEWESKSDAPETLGFLNHYQMKN<PNGPYPY

Parental  TLKLCFSTAQHAS
          TLKLCFSTAQ.AS
Retrocopy TLKLCFSTAQNAS

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	0.17 RPM	133.75 RPM
SRP007412_cerebellum	0.12 RPM	100.32 RPM
SRP007412_heart	0.12 RPM	41.93 RPM
SRP007412_kidney	0.20 RPM	104.64 RPM
SRP007412_liver	0.12 RPM	72.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1282 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1282 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1282 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,