RetrogeneDB ID: retro_pabe_733

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:106716176..106716806(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR2E
• Ensembl ID: ENSPPYG00000009305
• Aliases: None
• Description: DNA-directed RNA polymerases I, II, and III subunit RPABC1 [Source:RefSeq peptide;Acc:NP_001126823]

Sequence

>retro_pabe_733
ATGGACGACGAGGAGGAGAGGTACCAGCTCTGGAAAATCCGCAAGACCTTCATGCAGCTGTGCCATGACCGTGGCTACCT
AGTGACCTAGGACGAGCTTGACCAGACACGGAAGGAGTTCAAAGCCCAGTTCGGGGACAAGCCAACTGAGGGGCAGCCAT
GGTGCACGGACCTCACCACGCTGGTGGCCCACAGTGATGACCCCACCGACGAGATGTTTGTGTTCTTTCCAGAGGAGCCC
AAGGTGGGCATCAAGACCCTCAATGTGTACCGCCAGCACATGCAGCAGGAGAACATCACGCGGGTCCTCATCATGGTGCA
GCAGGGCATGACGCCCTCCACCAAGTAGTGCCTGGTCGACATGGCTCCCAAGTACGTCATGGAGCAGTTTCTGCAGCAGA
AGTTGCTCATCAACATCACAGAGCACAAGCTAGTCCCTGAGTACGTTGTCATGACCAAGGAGGAGGTGACAGTGCTGTTG
GCCCGATATAAGCTCCGAGAGAACCAGCTGCCCAGGATCCAGGCGGGGGACGCCGTGGCGCGCTACTTTGGGATAAAGCA
TGGGCAGGTAGTGAAGATCATCCGGCCCAGCAAGACGGCGGGCAGGTACCTCACCTACCGGCTGGTGCAG

Alignment

ORF - retro_pabe_733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.25 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDELDQTLEEFKAQFGDKPSEGRPRRTDLTVLVAHNDDPTD
          MDDEEE.Y.LWKIRKT.MQLCHDRGYLVT.DELDQT..EFKAQFGDKP.EG.P..TDLT.LVAH.DDPTD
Retrocopy MDDEEERYQLWKIRKTFMQLCHDRGYLVT*DELDQTRKEFKAQFGDKPTEGQPWCTDLTTLVAHSDDPTD

Parental  QMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINIT
          .MFVFFPEEPKVGIKT..VY.Q.MQ.ENITR.LI.VQQGMTPS.K..LVDMAPKY..EQFLQQ.LLINIT
Retrocopy EMFVFFPEEPKVGIKTLNVYRQHMQQENITRVLIMVQQGMTPSTK*CLVDMAPKYVMEQFLQQKLLINIT

Parental  EHEFYPSWHVTLALSSIFLTLLRSKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLV
          EH...P...V..........L.R.KLRENQLPRIQAGD.VARYFGIK.GQVVKIIRPS.TAGRY.TYRLV
Retrocopy EHKLVPE-YVVMTKEEVTVLLARYKLRENQLPRIQAGDAVARYFGIKHGQVVKIIRPSKTAGRYLTYRLV

Parental  Q
          Q
Retrocopy Q

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	3.87 RPM	87.58 RPM
SRP007412_cerebellum	3.28 RPM	32.95 RPM
SRP007412_heart	1.02 RPM	24.75 RPM
SRP007412_kidney	3.98 RPM	91.15 RPM
SRP007412_liver	2.17 RPM	45.05 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_733 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_733 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_733 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_822

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000099817	1 retrocopy	retro_hsap_822,
Myotis lucifugus	ENSMLUG00000013193	1 retrocopy	retro_mluc_1636,
Monodelphis domestica	ENSMODG00000005494	1 retrocopy	retro_mdom_1725,
Mustela putorius furo	ENSMPUG00000008953	1 retrocopy	retro_mputfur_1524,
Nomascus leucogenys	ENSNLEG00000001207	1 retrocopy	retro_nleu_255,
Pongo abelii	ENSPPYG00000009305	1 retrocopy	retro_pabe_733 ,