RetrogeneDB ID: retro_pabe_277

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:97089581..97090361(+)
• Located in intron of: ENSPPYG00000000781

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD8
• Ensembl ID: ENSPPYG00000009931
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 [Source:HGNC Symbol;Acc:9566]

Sequence

>retro_pabe_277
GTGAACAGTGCAGCCGGTGCCTTGAGCTCCGGGCCCAAGGCGACCTAGGGCCCTGTCCTGCAGGCTGCGGACGGGAAGTA
CAAGCAACTCAAGGGCGAGTGGAACCGTAAAAGCCCCAATCTTAGCAAGCGCAGGGAAGAGCTGGGCCGCCTCAAGCTAG
TTCTTCTGGAGCTCAACTTCTTGCCAACCACAGGGACCAAGCTGACCAAACAGTAGCTCATTCCGGCCCGTGACATACTG
AAGATCGGGGCCAGTGGAGCATCCTATGCAAGGTCATCCCCTCCTTCCAGCGCCACATGACCCAGCTCAAATGCTGCTAC
TTTGATTACAAGGAACAGCTTCCCCAGTCGCCTACATGCACCAGCTCTTGGGCCTCAACCTCCTCTTCCTGCTGTCCCAA
AAGCGGGTGGCTGAGTTCCACATGGAGCTGGAGTGGCTGCCTGCCAAGGACATCCAGACCAATGTCTACACCAAAAACCC
TGTGTCCCTGGAGCAATACCTGATGGAGGGGAGCTACAACAAAGTGTTCCTGGCCAAGGGTAACATCCTCGCCAGGAGCT
ACACTGTCTTCATCGACATCCTGCTTGACACTATCAGGGATGAGATCGCCGGGTGCATCAAGAAAGCCTATGAGAAAATC
CCTTTTACCGAGGCCACCAGATCCTCTTCTTCAACACACCCAAAAAGATGACCGACTACACCAAGAAGTGAGGGTGGGTC
CCGGGCCCCAACAACTAATATAGTTTTGCCAGCCAGCAGCAGGAGCCAGAAGACACTACC

Alignment

ORF - retro_pabe_277 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.23 %
• Parental protein coverage: 74.57 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VNGAAGFSSSGPAATSGAVLQAATGMYEQLKGEWNRKSPNLSKCGEELGRLKLVLLELNFLPTTGTKLTK
          VN.AAG..SSGP.AT.G.VLQAA.G.Y.QLKGEWNRKSPNLSK..EELGRLKLVLLELNFLPTTGTKLTK
Retrocopy VNSAAGALSSGPKAT*GPVLQAADGKYKQLKGEWNRKSPNLSKRREELGRLKLVLLELNFLPTTGTKLTK

Parental  QQLILARDILEIGA-QWSILRKDIPSFERYMAQLKCYYFDYKEQLPES-AYMHQLLGLNLLFLLSQNRVA
          Q.LI.ARDIL.IGA.QWSIL.K.IPSF.R.M.QLKC.YFDYKEQLP.S.AYMHQLLGLNLLFLLSQ.RVA
Retrocopy Q*LIPARDILKIGA<QWSILCKVIPSFQRHMTQLKCCYFDYKEQLPQS<AYMHQLLGLNLLFLLSQKRVA

Parental  EFHTELERLPAKDIQTNVYIKHPVSLEQYLMEGSYNKVFLAKGNIPAESYTFFIDILLDTIRDEIAGCIE
          EFH.ELE.LPAKDIQTNVY.K.PVSLEQYLMEGSYNKVFLAKGNI.A.SYT.FIDILLDTIRDEIAGCI.
Retrocopy EFHMELEWLPAKDIQTNVYTKNPVSLEQYLMEGSYNKVFLAKGNILARSYTVFIDILLDTIRDEIAGCIK

Parental  KAYEKILFTEATR-ILFFNTPKKMTDYAKKRGWVLGPNNYYSFASQQQKPEDTT
          KAYEKI.FTEATR.ILFFNTPKKMTDY.KK.GWV.GPNN.YSFASQQQ.PEDTT
Retrocopy KAYEKIPFTEATR<ILFFNTPKKMTDYTKK*GWVPGPNN*YSFASQQQEPEDTT

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	34.34 RPM
SRP007412_cerebellum	1.46 RPM	27.00 RPM
SRP007412_heart	1.48 RPM	17.46 RPM
SRP007412_kidney	4.81 RPM	33.01 RPM
SRP007412_liver	3.49 RPM	26.62 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_277 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_277 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_277 has 0 orthologous retrocopies within eutheria group .

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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	ENSG00000099341	1 retrocopy	retro_hsap_456,
Monodelphis domestica	ENSMODG00000013151	1 retrocopy	retro_mdom_58,
Nomascus leucogenys	ENSNLEG00000016876	1 retrocopy	retro_nleu_878,
Pongo abelii	ENSPPYG00000009931	1 retrocopy	retro_pabe_277 ,
Pan troglodytes	ENSPTRG00000010926	1 retrocopy	retro_ptro_343,
Ictidomys tridecemlineatus	ENSSTOG00000014464	1 retrocopy	retro_itri_10,