RetrogeneDB ID: retro_ptro_397

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:219462355..219463991(-)
• Located in intron of: ENSPTRG00000002157

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD2
• Ensembl ID: ENSPTRG00000015689
• Aliases: None
• Description: None

Sequence

>retro_ptro_397
ATGGACGAGGGAGGATGGGACAAGACGCTGGTGCAGTCCCAGCAGCCCCCAGCGGCGGCCCCCAGCGGCATGGATGAGAA
GCCAAGCGGCAAGGAGCGGCGGGATGCCGGGGACAAGGACAAAGAACAGGAGCTGTCTGAGGAAGATAAACAGCTTCAAG
ATGAACTGGAGATGCTCGTGGAATGACTCGGGGAGAAGGACACATCCCTGTATCGACCAGCGCTGGAGGAAATGCGAAGG
CAGATTCGTTCTTCTACAACTTCCATGACGTTGGTGACCAAGCCTCTCAAATTTCTGCGTCCACACTATGGCAAACTGAA
GGAAATCTATGAGAACGTGGCCCCTGGGGAGAATGAGCATTTTGCTGCTGACATCATCTCTGTTTTGTGCATGACCATGA
GTGGGGAGTGCGAGTGCCTCAAGTATCGGCTAGTAGGCTCCCAGAAGGAATTGGCATCATGGAGTCATGAGTATGTCAGG
CACCTGGCAGGAGAAGTGGCTAAGGAGTGGCAGGAGCTGGATGATGCGGAGAAGGTCTAGCAGGAGCCACTGCTCACTCT
GGTGAAGGAAATCGTCCCCTACAACATGGCCCACGACGCAGAGCATGAGGCCTGCGACCTACTTATGGAAATTGAGCAGG
TGGACATGCTGGAGAAGGACATTGATGAGAATGCATACACAAAGGTCTGCCTTTATCTCACCAGTTGTGTGAATTACGTG
TCTGAGTCTGAGAACTCAGTCCTACTGCGTTGTGCCCTGGGTGTGTTCTGAAAGTTTAGCCGCTTCCCTAAAGCTCTGAG
ATTGGCATTGATGCGCAATGACATGGAGCTGGTAGAAGACATCTTCACATCCTGCAAGGATGTGGTAGTACAGAAACAGA
TGGCATTCATGCTAGGCTGGCATGGGGTGTTCCTGGAGCTGAGTGAAGATGTCGAGGAGTATGAGCACCTGACAGAGATC
ATGTCCAATGTACAGCTCAACAGCAACTTCTTGGCCTTAGCTCGGGAGCTGGACATCATGGAGCCCAAGGTGCCTGATGA
CATCTACAAAACCCACCTAGAGAACAACAGGTTTGGGGGCAGTGGCTCTCAGGTGGACTCTGCCCGCATGAACCTGGCCT
TCTCTTTTGTGAATGGCTTTGTGAATGCAGCTTTTGTTTAAGACAAGCTGCTAACAGATGATGGCAACAAATGGCTTTAC
AAGAACAAGGACCATGGAATGTTGAGTGCAGCTGCATCTGTTGGGATGCTGCTGCTGTGGGATGTGGATGGTGGCCTCAT
TCAGATTGACAAGTAACCTGTACTCCTCTGAGGACTACATTAAGTCAGGAATTCTTCTTGCCTGTGGCATAGTGAACTCT
GGGGTCTGGAATGAGTGTGTCCCTGCTCTGGGACTGCTTTCAGACTATGTTCTCCACAACAGCAACACCATGAGACTTGG
TTCCATCTTTGGGCTAGGCTTGGCCTATGCTGGCTCAAATCATGAAGATGTCCTAACACTGCTGCTGCCTGTGATGGGAG
ATTCAAAGTCCAGCATGGAGGTGGCAGGTGTGACAGCTCTAGCCTGTGGAATGATAGCAGTGGGGTCCTGCAATGGAGAT
GTAACTTCCACTATCCTTCAGACCATCAGGGAGAAG

Alignment

ORF - retro_ptro_397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.76 %
• Parental protein coverage: 60.02 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MEEGGRDKAPVQPQQSPAAAPGGTDEKPSGKERRDAGDKDKEQELSEEDKQLQDELEMLVERLGEKDTSL
          M.EGG.DK..VQ.QQ.PAAAP.G.DEKPSGKERRDAGDKDKEQELSEEDKQLQDELEMLVE.LGEKDTSL
Retrocopy MDEGGWDKTLVQSQQPPAAAPSGMDEKPSGKERRDAGDKDKEQELSEEDKQLQDELEMLVE*LGEKDTSL

Parental  YRPALEELRRQIRSSTTSMTSVPKPLKFLRPHYGKLKEIYENMAPGENKRFAADIISVLAMTMSGERECL
          YRPALEE.RRQIRSSTTSMT.V.KPLKFLRPHYGKLKEIYEN.APGEN..FAADIISVL.MTMSGE.ECL
Retrocopy YRPALEEMRRQIRSSTTSMTLVTKPLKFLRPHYGKLKEIYENVAPGENEHFAADIISVLCMTMSGECECL

Parental  KYRLVGSQEELASWGHEYVRHLAGEVAKEWQELDDAEKVQREPLLTLVKEIVPYNMAHNAEHEACDLLME
          KYRLVGSQ.ELASW.HEYVRHLAGEVAKEWQELDDAEKV..EPLLTLVKEIVPYNMAH.AEHEACDLLME
Retrocopy KYRLVGSQKELASWSHEYVRHLAGEVAKEWQELDDAEKV*QEPLLTLVKEIVPYNMAHDAEHEACDLLME

Parental  IEQVDMLEKDIDENAYAKVCLYLTSCVNYVPEPENSALLRCALGVFRKFSRFPEALRLALMLNDMELVED
          IEQVDMLEKDIDENAY.KVCLYLTSCVNYV.E.ENS.LLRCALGVF.KFSRFP.ALRLALM.NDMELVED
Retrocopy IEQVDMLEKDIDENAYTKVCLYLTSCVNYVSESENSVLLRCALGVF*KFSRFPKALRLALMRNDMELVED

Parental  IFTSCKDVVVQKQMAFMLGRHGVFLELSEDVEEYEDLTEIMSNVQLNSNFLALARELDIMEPKVPDDIYK
          IFTSCKDVVVQKQMAFMLG.HGVFLELSEDVEEYE.LTEIMSNVQLNSNFLALARELDIMEPKVPDDIYK
Retrocopy IFTSCKDVVVQKQMAFMLGWHGVFLELSEDVEEYEHLTEIMSNVQLNSNFLALARELDIMEPKVPDDIYK

Parental  THLENNRFGGSGSQVDSARMNLASSFVNGFVNAAFGQDKLLTDDGNKWLYKNKDHGMLSAAASLGMILLW
          THLENNRFGGSGSQVDSARMNLA.SFVNGFVNAAF..DKLLTDDGNKWLYKNKDHGMLSAAAS.GM.LLW
Retrocopy THLENNRFGGSGSQVDSARMNLAFSFVNGFVNAAFV*DKLLTDDGNKWLYKNKDHGMLSAAASVGMLLLW

Parental  DVDGGLTQIDK-YLYSSEDYIKSGALLACGIVNSGVRNECDPALALLSDYVLHNSNTMRLGSIFGLGLAY
          DVDGGL.QIDK..LYSSEDYIKSG.LLACGIVNSGV.NEC.PAL.LLSDYVLHNSNTMRLGSIFGLGLAY
Retrocopy DVDGGLIQIDK>NLYSSEDYIKSGILLACGIVNSGVWNECVPALGLLSDYVLHNSNTMRLGSIFGLGLAY

Parental  AGSNREDVLTLLLPVMGDSKSSMEVAGVTALACGMIAVGSCNGDVTSTILQTIMEK
          AGSN.EDVLTLLLPVMGDSKSSMEVAGVTALACGMIAVGSCNGDVTSTILQTI.EK
Retrocopy AGSNHEDVLTLLLPVMGDSKSSMEVAGVTALACGMIAVGSCNGDVTSTILQTIREK

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	0.64 RPM	181.41 RPM
SRP007412_cerebellum	0.36 RPM	166.98 RPM
SRP007412_heart	0.00 RPM	167.82 RPM
SRP007412_kidney	0.08 RPM	152.88 RPM
SRP007412_liver	0.07 RPM	133.23 RPM
SRP007412_testis	0.42 RPM	282.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_397 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_397 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_397 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_531
Gorilla gorilla	retro_ggor_486
Pongo abelii	retro_pabe_218

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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 ,