RetrogeneDB ID: retro_ptro_1043

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:31324126..31325618(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPL
• Ensembl ID: ENSPTRG00000010941
• Aliases: HNRNPL, HNRPL
• Description: None

Sequence

>retro_ptro_1043
AACTACCATGACCTGCACAAAACCCCTGCCTCCCCAGTTGCCCACATCAGGGGCCTGATTGACGATGTGGTGGAAGGTGA
CCTTGTGGAGGCCTTGCAGGAGTTTGCACCCATCAGCTATGGGGTGGTAATGCCTAAAAAGAGACAAGCGTTGGTGGAGG
TTGAAGATGTGTTGGGGGCTTGCAACTCCGTGAGCTACGCAGCCGACAACCAAATATACATTGCCGGTCACCCAGCTTTT
GTCAACTACTCTACCAGCCAGAAGATCTCCCTCCCCGGGGACTCCGATGACTCCCGGAGCGTGAACAGTGTGCTTCTCTT
TACCATCCTGAACCCCATTTATTCGATCACCGCGGATATTCTTTACACTATCTGTAATCCTTGTGGCCCTGTCCAGAGAA
TTATCATTTTCAAGAAGAATGGAGTTAAGGCGATGGTGGAATCTGACTCTGTTCAAAGTGCCCAGCGGGCCAAGGCCTCT
CTCAATGGGGCTGGTATCTATTCTGGCTGTTGCACTCTGAAGATGGAATACGCAAAGCCTACACGCTTGAATGTGTTCAA
GAATGATCAGGATACTTGGGACTACACAAACCCCAATCTCAGTGGACAAGGTGACCCTGGCAGCAACCCCAACAAACGCC
AGAGGCAGCCCCCTCTCCTGGGAGATCACCCCACAGAATATGGAGGGCCCCACGGTGGGTACCACAGCCATTACCATGAT
GAGGGCTACGGGCCCCCCCGACCTCACTACGAAGGGAGAAGGATGGGTCCACCAGTCGGGGGTCACTGTCGGGGCCCAAG
TCGCTACCGCCCCCAGTATGGGACCCCCCCACCCCCTCCCCCACCACCCGAGTATGGCCCTCACGCCGACAGCCCTGTGC
TCATGGTCTATGGCTTGCATCAATCTAAGATGAACTGTGACCTAGTCTTCAATGTCTTCTGCTTGTATGGCAATGTGGAG
AAGGTGAAATTCATGAAAAGCAAGCCGGGGGCGCCATGGTGGAGATGGCTGATGGCTACACTGTGGACCGGGTCATTACC
CACCTCAACAACAACTTCATGTTTGGGCAGAAGCTGAATGTCTTTGTCTCCAAGCAGCCAGCCATCATGCCCGGTCAGTC
ACACGGGTTGGAAGATGGGTCTTGCAGTTGCAAAGACTTCAGTGAATCCCGGAACAATCGGTTCTCCACCACAGAGCAGG
CAGCCAAGAACCGCATCCAGCACCCCAGCAACATGCTGCACTTCTTCAACGCCCCGCTGGAGGCGACCGAGGAGAACTCC
TTTGAGATCTATGATGAGCTGGGAGTGAAGCGGCCATCTTCTGTGAAAGTATTCTCAGGCAAAAGTGAGCGCAGCTCCTC
TGGACTGCTGGAATGGGAATCCAAGAGCGATGCCCTGGAGACTCCGGGCTTCCTGAACCATTACCAGATGAAAAACCCAA
TGGTCCATACCCTTACACTCTGAAGTTGTGTTTCTCCACCGCTCAGCACGCC

Alignment

ORF - retro_ptro_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.6 %
• Parental protein coverage: 84.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NYDDPHKTPASPVVHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQALVEFEDVLGACNAVNYAADN
          NY.D.HKTPASPV.HIRGLID.VVE.DLVEALQEF.PISY.VVMPKKRQALVE.EDVLGACN.V.YAADN
Retrocopy NYHDLHKTPASPVAHIRGLIDDVVEGDLVEALQEFAPISYGVVMPKKRQALVEVEDVLGACNSVSYAADN

Parental  QIYIAGHPAFVNYSTSQKISRPGDSDDSRSVNSVLLFTILNPIYSITTDVLYTICNPCGPVQRIVIFRKN
          QIYIAGHPAFVNYSTSQKIS.PGDSDDSRSVNSVLLFTILNPIYSIT.D.LYTICNPCGPVQRI.IF.KN
Retrocopy QIYIAGHPAFVNYSTSQKISLPGDSDDSRSVNSVLLFTILNPIYSITADILYTICNPCGPVQRIIIFKKN

Parental  GVQAMVEFDSVQSAQRAKASLNGADIYSGCCTLKIEYAKPTRLNVFKNDQDTWDYTNPNLSGQGDPGSNP
          GV.AMVE.DSVQSAQRAKASLNGA.IYSGCCTLK.EYAKPTRLNVFKNDQDTWDYTNPNLSGQGDPGSNP
Retrocopy GVKAMVESDSVQSAQRAKASLNGAGIYSGCCTLKMEYAKPTRLNVFKNDQDTWDYTNPNLSGQGDPGSNP

Parental  NKRQRQPPLLGDHPAEYGGPHGGYHSHYHDEGYGPPPPHYEGRRMGPPVGGHRRGPSRYGPQYGHPPPPP
          NKRQRQPPLLGDHP.EYGGPHGGYHSHYHDEGYGPP.PHYEGRRMGPPVGGH.RGPSRY.PQYG......
Retrocopy NKRQRQPPLLGDHPTEYGGPHGGYHSHYHDEGYGPPRPHYEGRRMGPPVGGHCRGPSRYRPQYGXXXXXX

Parental  PPPEYGPHADSPVLMVYGLDQSKMNCDRVFNVFCLYGNVEKVKFMKSKPGA-AMVEMADGYAVDRAITHL
          ...EYGPHADSPVLMVYGL.QSKMNCD.VFNVFCLYGNVEKVKFMKSKPGA.AMVEMADGY.VDR.ITHL
Retrocopy XXXEYGPHADSPVLMVYGLHQSKMNCDLVFNVFCLYGNVEKVKFMKSKPGA<AMVEMADGYTVDRVITHL

Parental  NNNFMFGQKLNVCVSKQPAIMPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAP
          NNNFMFGQKLNV.VSKQPAIMPGQS.GLEDGSCS.KDFSESRNNRFST.EQAAKNRIQHPSN.LHFFNAP
Retrocopy NNNFMFGQKLNVFVSKQPAIMPGQSHGLEDGSCSCKDFSESRNNRFSTTEQAAKNRIQHPSNMLHFFNAP

Parental  LEVTEENFFEICDELGVKRPSSVKVFSGKSERSSSGLLEWESKSDALETLGFLNHYQMKN-PNGPYPYTL
          LE.TEEN.FEI.DELGVKRPSSVKVFSGKSERSSSGLLEWESKSDALET.GFLNHYQMKN.PNGPYPYTL
Retrocopy LEATEENSFEIYDELGVKRPSSVKVFSGKSERSSSGLLEWESKSDALETPGFLNHYQMKN<PNGPYPYTL

Parental  KLCFSTAQHA
          KLCFSTAQHA
Retrocopy KLCFSTAQHA

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	5.17 RPM	115.79 RPM
SRP007412_cerebellum	1.90 RPM	184.87 RPM
SRP007412_heart	1.17 RPM	55.79 RPM
SRP007412_kidney	1.73 RPM	138.45 RPM
SRP007412_liver	0.75 RPM	114.83 RPM
SRP007412_testis	6.43 RPM	114.24 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1043 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1043 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	ENSPPYG00000009945	2 retrocopies	retro_pabe_1282, retro_pabe_3576,
Pan troglodytes	ENSPTRG00000010165	1 retrocopy	retro_ptro_928,
Pan troglodytes	ENSPTRG00000010941	1 retrocopy	retro_ptro_1043 ,
Tupaia belangeri	ENSTBEG00000016563	1 retrocopy	retro_tbel_1340,