RetrogeneDB ID: retro_pabe_218

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:9190184..9191819(+)
• Located in intron of: ENSPPYG00000000075

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD2
• Ensembl ID: ENSPPYG00000014354
• Aliases: None
• Description: 26S proteasome non-ATPase regulatory subunit 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R9I6]

Sequence

>retro_pabe_218
ATGGAGGAGGGAGGATGGGACAAGACGCTGGTACAGTCCCAGCAGCCCCCAGCGGCGGCCCCCAGCGGCACGGACGAGAA
GCCGAGCGGCAAGGAGCGGCGGGATGCCGGGGACAAGGACAAAGAACAGGAGCTGTCCAAGGAAGATAAACAGCTTCAAG
ATGAACTGGAGATGCTCGTGGAATGACTCGGGGAGAACGACATATCCCTGTATCGACCAGCGCTGGAGGAATTGCGAAGG
CAGATTTGTTCTTCTACAACTTCCATGACTTCAGTGCCCAAGCCTCTCAAATTTCTGCATCCACGCTATGGCAAACTGAA
GGAAATCTATGAGAACATGGCCCTGGGGAGAATAAGCGTTTTGCTGCTGACATCATCTCTGTTTTGGCCATGACCATGAG
TGGGGAGTGCGAGTGCCTCAAGTATCGGCTACTAGGCTCCCAGAAGGAATTGGCATCATGGGGTCATGAGTATGTCAGGC
ATCTGGCAGGAGAAGTGGCTAAGGAGCAGCAGGAGCTGGATGACGCAGAGAAGGTCCAGCAGGAGCCACTGCTCACTCTG
GTGAAGGAAATCGTCCTGTACAACATGGCCCACGACACAGAGCATGAGGCCTGCGACCTGCTTATGGAAATTGAGGAGGT
GGACATGCTGGAGAAGGACATTGATGAGAATGCATACACAAAGGTCTGCATTTATCTCACCAGTTGTGTGAATTACGTGT
CTGAGCCTGAGAACGCAGTCCTACTACGTTGTGCCCTGGGTGTGTTCTGAAAGTTTAGCCGCTTCCCTGAAGCTCTGAGA
TTGGCATTGATGCTCAATGACATGGAGCTGGTAGAAGACATCTTCACATCCTGCAAGGATATGGTAGTACGGAAACAGAT
GGCATTCATGCTAGGCTGGCATGGGGTGTTCCTGGAGCTGAGTGAAGATGTCGAGGAGTATGAGCACCTGACAGAGATCA
TGTCTAATGTACAGCTCAACAGCAACTTCTTGGCCTTAGCTCGGGAGCTGGACGTCATGGAGCCCAAGGTGCCTGATGAC
ATCTACAAAATCCACCTAGAGAACAACAGGTTTGGGGGTAGTGGCTCTCAGGTGGACTCTGCCCACATGAACTTGGCCTC
CTCTTTTGTGAATGGCTTTGTGAATGCAGCTTTTGTTTAAGACAAGCTGCTAACAGATGATGGCAACAAATGGCTTTACA
AGAACAAGGACCACGGAATGTTGAGTGCAGCTGCATCTGTTGGGATGCTGCTGCTGTGGGATGTGGATGGTGGCCTCATT
CAGATTGACAAGTAACCTGCACTCCTCTGAGGACTACATTAAGTCAGGAGTTCTTCTTGCCTGTGGCATAGTGAACTCTG
GAGTTCAGAATGAGTGTGTCCCTGCTCTGTGACTGCTTTCCGACTATGTTCTCCACAACAGCAACACCGTGAGACTTGGT
TCCACCCTTGGGTTAGGCTTGGCCTATGCTGGCTCAAATCACGAAGATGTCCTAACACTGCTGCTGCCTGTGATGGGAGA
TTCAGAGTCCAGCATGGAGGTGGCAGGTGTGACAGCTCTAGCCCATGGAATGATAGCAGTGGGGTCCTGCAATGGAGGTG
TAACTTCCACTATCCTTCAGACCATCAGGGAGAAG

Alignment

ORF - retro_pabe_218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.4 %
• Parental protein coverage: 60.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEEGGRDKAPVQPQQSPAAALGGTDEKPSGKERRDAGDKDKEQELSEEDKQLQDELEMLVERLGEKDTSL
          MEEGG.DK..VQ.QQ.PAAA..GTDEKPSGKERRDAGDKDKEQELS.EDKQLQDELEMLVE.LGE.D.SL
Retrocopy MEEGGWDKTLVQSQQPPAAAPSGTDEKPSGKERRDAGDKDKEQELSKEDKQLQDELEMLVE*LGENDISL

Parental  YRPALEELRRQIRSSTTSMTSVPKPLKFLRPHYGKLKEIYENMA-PGENKRFAADIISVLAMTMSGEREC
          YRPALEELRRQI.SSTTSMTSVPKPLKFL.P.YGKLKEIYENMA.PGENKRFAADIISVLAMTMSGE.EC
Retrocopy YRPALEELRRQICSSTTSMTSVPKPLKFLHPRYGKLKEIYENMA<PGENKRFAADIISVLAMTMSGECEC

Parental  LKYRLVGSQEELASWGHEYVRHLAGEVAKEWQELDDAEKVQREPLLTLVKEIIPYNMAHNAEHEACDLLM
          LKYRL.GSQ.ELASWGHEYVRHLAGEVAKE.QELDDAEKVQ.EPLLTLVKEI..YNMAH..EHEACDLLM
Retrocopy LKYRLLGSQKELASWGHEYVRHLAGEVAKEQQELDDAEKVQQEPLLTLVKEIVLYNMAHDTEHEACDLLM

Parental  EIEQVDMLEKDIDENAYAKVCLYLTSCVNYVPEPENSALLRCALGVFRKFSRFPEALRLALMLNDMELVE
          EIE.VDMLEKDIDENAY.KVC.YLTSCVNYV.EPEN..LLRCALGVF.KFSRFPEALRLALMLNDMELVE
Retrocopy EIEEVDMLEKDIDENAYTKVCIYLTSCVNYVSEPENAVLLRCALGVF*KFSRFPEALRLALMLNDMELVE

Parental  DIFTSCKDVVVQKQMAFMLGRHGVFLELSEDVEEYEDLTEIMSNVQLNSNFLALARELDIMEPKVPDDIY
          DIFTSCKD.VV.KQMAFMLG.HGVFLELSEDVEEYE.LTEIMSNVQLNSNFLALARELD.MEPKVPDDIY
Retrocopy DIFTSCKDMVVRKQMAFMLGWHGVFLELSEDVEEYEHLTEIMSNVQLNSNFLALARELDVMEPKVPDDIY

Parental  KTHLENNRFGGSGSQVDSARMNLASSFVNGFVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAASLGMILL
          K.HLENNRFGGSGSQVDSA.MNLASSFVNGFVNAAF..DKLLTDDGNKWLYKNKDHGMLSAAAS.GM.LL
Retrocopy KIHLENNRFGGSGSQVDSAHMNLASSFVNGFVNAAFV*DKLLTDDGNKWLYKNKDHGMLSAAASVGMLLL

Parental  WDVDGGLTQIDK-YLYSSEDYIKSGALLACGIVNSGVRNECDPALALLSDYVLHNSNTMRLGSIFGLGLA
          WDVDGGL.QIDK..L.SSEDYIKSG.LLACGIVNSGV.NEC.PAL.LLSDYVLHNSNT.RLGS..GLGLA
Retrocopy WDVDGGLIQIDK>NLHSSEDYIKSGVLLACGIVNSGVQNECVPAL*LLSDYVLHNSNTVRLGSTLGLGLA

Parental  YAGSNREDVLTLLLPVMGDSKSSMEVAGVTALACGMIAVGSCNGDVTSTILQTIMEK
          YAGSN.EDVLTLLLPVMGDS.SSMEVAGVTALA.GMIAVGSCNG.VTSTILQTI.EK
Retrocopy YAGSNHEDVLTLLLPVMGDSESSMEVAGVTALAHGMIAVGSCNGGVTSTILQTIREK

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	0.28 RPM	168.30 RPM
SRP007412_cerebellum	0.24 RPM	125.74 RPM
SRP007412_heart	0.06 RPM	89.92 RPM
SRP007412_kidney	0.10 RPM	101.63 RPM
SRP007412_liver	0.06 RPM	66.77 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_218 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_218 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_218 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_531
Pan troglodytes	retro_ptro_397
Gorilla gorilla	retro_ggor_486

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000175166	1 retrocopy	retro_hsap_531,
Gorilla gorilla	ENSGGOG00000027136	1 retrocopy	retro_ggor_486,
Mus musculus	ENSMUSG00000006998	2 retrocopies	retro_mmus_209, retro_mmus_3247,
Nomascus leucogenys	ENSNLEG00000006305	1 retrocopy	retro_nleu_1786,
Pongo abelii	ENSPPYG00000014354	1 retrocopy	retro_pabe_218 ,
Pan troglodytes	ENSPTRG00000015689	1 retrocopy	retro_ptro_397,