RetrogeneDB ID: retro_ptro_1102

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 16:46202788..46203428(+)
• Located in intron of: ENSPTRG00000008089

Retrocopy information

• Ensembl ID: ENSPTRG00000040515
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMB8
• Ensembl ID: ENSPTRG00000018022
• Aliases: None
• Description: Proteasome subunit beta type [Source:UniProtKB/TrEMBL;Acc:H2QSR8]

Sequence

>retro_ptro_1102
ATCAAAATGCTTCATGGAATCACCACCCTGGTCTTCAAGTTCTGGCATGGAGTCACAGTTGCAGCAGACTATAGGGCTGC
AGTGGGTGCTTACATTGCCTCCAGATGGTAAAGAAGGTGACAGAGATCAACCCCTACCCGAAGCCATCATGGCTAGGGGC
ACAGGGAACTGTAGCTTCTGAGAATGGCTGTTGGCTCGGCAAAGTCAAATGTATGAGCTTTGAAATAAGGAATGCATCCC
TGTAACAGCTGCCTCCAAGCTGCTTGCCAACATATTGTATCAGTACAAAGGCATGGGGCTGTCCATGGGCAACATGATCT
GTGGCTGGGATAGGAGAGGCCCTGGCCTCTGCTACATGGACACTGAAGGGAATCAGATCTCAGGGGCCACCTTCTCTGTA
GGTTCTGGCTCTGTGTATGCTTATGGGGTTATGAATCAGGGCTATTCCTGTAACCTGGAAATGGAGCAGGCCTATGATCT
GGCCCATGAGGTAAGCTACCAAGCCATCTACCAAGCCACCTGCATAGTTGCCTACTCAGGAGGTGCTGCTAACCTCTACC
ACATGCAGGAGGATGGCTGGATCCAAGTCTCCAGTGACAATGCAGTTGATCTTCATGACAAGTATGATGGATCTACCCAG

Alignment

ORF - retro_ptro_1102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.85 %
• Parental protein coverage: 76.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IEMAHGTTTLAFKFQHGVIAAVDSRASAGSYISAL-RVNKVIEIN-PYLLGTMSGSAADCQYWERLLAKE
          I.M.HG.TTL.FKF.HGV..A.D.RA..G.YI.....V.KV.EIN.P.....M......C...E.LLA..
Retrocopy IKMLHGITTLVFKFWHGVTVAADYRAAVGAYIASR<MVKKVTEIN<PLPEAIMARGTGNCSF*EWLLARQ

Parental  CRLYYLRNGERISVSAASKLLSNMMCQYRGMGLSMGSMICGWDKKGPGLYYVDEHGTRLSGNMFSTGSGN
          ...Y.L.N.E.I.V.AASKLL.N...QY.GMGLSMG.MICGWD..GPGL.Y.D..G...SG..FS.GSG.
Retrocopy SQMYEL*NKECIPVTAASKLLANILYQYKGMGLSMGNMICGWDRRGPGLCYMDTEGNQISGATFSVGSGS

Parental  TYAYGVMDSGYRPNLSPEEAYDLGR----RAIAYATHRDSYSGGVVNMYHMKEDGWVKVESTDVSDLLHQ
          .YAYGVM..GY..NL..E.AYDL.......AI..AT....YSGG..N.YHM.EDGW..V.S....DL...
Retrocopy VYAYGVMNQGYSCNLEMEQAYDLAHEVSYQAIYQATCIVAYSGGAANLYHMQEDGWIQVSSDNAVDLHDK

Parental  YREANQ
          Y....Q
Retrocopy YDGSTQ

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	0.20 RPM	6.13 RPM
SRP007412_cerebellum	2.33 RPM	14.45 RPM
SRP007412_heart	1.52 RPM	30.43 RPM
SRP007412_kidney	2.72 RPM	151.92 RPM
SRP007412_liver	4.22 RPM	381.98 RPM
SRP007412_testis	1.69 RPM	1.58 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1102 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1102 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002026	1 retrocopy	retro_amel_27,
Bos taurus	ENSBTAG00000003039	1 retrocopy	retro_btau_11,
Canis familiaris	ENSCAFG00000000829	1 retrocopy	retro_cfam_75,
Equus caballus	ENSECAG00000018887	1 retrocopy	retro_ecab_18,
Felis catus	ENSFCAG00000023131	1 retrocopy	retro_fcat_30,
Loxodonta africana	ENSLAFG00000003213	1 retrocopy	retro_lafr_65,
Microcebus murinus	ENSMICG00000015254	1 retrocopy	retro_mmur_33,
Myotis lucifugus	ENSMLUG00000013876	1 retrocopy	retro_mluc_285,
Monodelphis domestica	ENSMODG00000014366	1 retrocopy	retro_mdom_179,
Otolemur garnettii	ENSOGAG00000013830	1 retrocopy	retro_ogar_256,
Procavia capensis	ENSPCAG00000016741	1 retrocopy	retro_pcap_21,
Pan troglodytes	ENSPTRG00000018022	2 retrocopies	retro_ptro_1102 , retro_ptro_97,
Pteropus vampyrus	ENSPVAG00000002800	1 retrocopy	retro_pvam_20,
Sus scrofa	ENSSSCG00000026951	1 retrocopy	retro_sscr_90,
Tupaia belangeri	ENSTBEG00000007794	1 retrocopy	retro_tbel_2055,
Tarsius syrichta	ENSTSYG00000007730	1 retrocopy	retro_tsyr_1639,