RetrogeneDB ID: retro_pabe_2512

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:39039277..39039983(-)
• Located in intron of: ENSPPYG00000014663

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSME2
• Ensembl ID: ENSPPYG00000005684
• Aliases: None
• Description: proteasome (prosome, macropain) activator subunit 2 (PA28 beta) [Source:HGNC Symbol;Acc:9569]

Sequence

>retro_pabe_2512
GCCAAGCCTTGTGGTGGGTGCCTGAGCAGGAAGGCCGGCACCCAGGTGCATGTCTTCAGGCAAGAGCTTTCCCAAGAAGC
CAAGGAATTCCTCTACAGATTCTTGCCACAGAAAATCATACACCCGCATAGGCCTTGCAAAAGGATTCCCTCATTGTAGC
TGCCTGACCTCCCTCTGGGCCCCACTGGACATCCCCATCCCAGAACCCCCACCCAAGGATGAGGTGGAAACAGAGAGGCA
GGAGAAGAAAGAAGTCCTTGAGTGTGGATTTCTCCCTGGGAATGAGAAGGTCCTGTCGCTGCTTGCCATGGTTAAGTCAG
AAGTCTGGATTCTCAAAGAGAAATGCATCTGGTGATCACATGGATCCAGCACCTGATCCCCAAGACTGAGGATGGAAATG
ATTTGGGGGAGCAATCCAGGAGAAGGTGCTGGAGAGGGTGAATGCAGTTAAGATCAAAGTGGAAGCCTTCCAGACAACCA
TTTCCAAATACTCCTCAGAACACGGGGATGCTGTGGCCAAGGCCTCCAAGGAGACCCCTGTAATGGATTACCAGGCGTTG
GTGCAAAAGTGAGATAAGACGGCCTATGGGGAGGTCAAGGCCAGGGTACTGGACCTGAAGGCCTTCTGTGCTGAGCTTTA
TCATATCATCAGCACCAACCTGGAGAAAACCGCAACCCAAAGGGTGAAGAGAAACCATCTGTGTAC

Alignment

ORF - retro_pabe_2512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.37 %
• Parental protein coverage: 99.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  AKPCGVRLSGEARKQVEVFRQNLFQEAEEFLYRFLPQKIIYLNQ-LLQEDSLNVAD-LTSLRAPLDIPIP
          AKPCG..LS..A..QV.VFRQ.L.QEA.EFLYRFLPQKII......LQ.DSL.VA..LTSL.APLDIPIP
Retrocopy AKPCGGCLSRKAGTQVHVFRQELSQEAKEFLYRFLPQKIIHPHR<ALQKDSLIVAA<LTSLWAPLDIPIP

Parental  DPPPKDDEMETDKQEKKEVPKCGFLPGNEKVLSLLALVKPEVWTLKEKCI-LVITWIQHLIPKIEDGND-
          .PPPKD.E.ET..QEKKEV..CGFLPGNEKVLSLLA.VK.EVW.LKEKCI.LVITWIQHLIPK.EDGND.
Retrocopy EPPPKD-EVETERQEKKEVLECGFLPGNEKVLSLLAMVKSEVWILKEKCI<LVITWIQHLIPKTEDGND<

Parental  FGVAIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDYRALVHERDEAAYGELRAMVL
          FG.AIQEKVLERVNAVK.KVEAFQTTISKY.SE.GDAVAKASKET.VMDY.ALV...D..AYGE..A.VL
Retrocopy FGGAIQEKVLERVNAVKIKVEAFQTTISKYSSEHGDAVAKASKETPVMDYQALVQK*DKTAYGEVKARVL

Parental  DLRAFYAELYHIISSNLEKIV-NPKGEEKPSMY
          DL.AF.AELYHIIS.NLEK...NPKGEEKPS.Y
Retrocopy DLKAFCAELYHIISTNLEKTA<NPKGEEKPSVY

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	0.06 RPM	21.07 RPM
SRP007412_cerebellum	0.00 RPM	21.77 RPM
SRP007412_heart	0.06 RPM	18.15 RPM
SRP007412_kidney	0.07 RPM	78.89 RPM
SRP007412_liver	0.03 RPM	76.93 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2512 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2512 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2512 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3033
Pan troglodytes	retro_ptro_2046
Gorilla gorilla	retro_ggor_2093
Macaca mulatta	retro_mmul_1940

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007167	3 retrocopies	retro_cjac_233, retro_cjac_322, retro_cjac_71,
Homo sapiens	ENSG00000100911	4 retrocopies	retro_hsap_1200, retro_hsap_2999, retro_hsap_3033, retro_hsap_3222,
Gorilla gorilla	ENSGGOG00000016025	4 retrocopies	retro_ggor_2078, retro_ggor_2093, retro_ggor_2188, retro_ggor_935,
Macaca mulatta	ENSMMUG00000012473	4 retrocopies	retro_mmul_1229, retro_mmul_1919, retro_mmul_1940, retro_mmul_2281,
Mus musculus	ENSMUSG00000079197	1 retrocopy	retro_mmus_145,
Nomascus leucogenys	ENSNLEG00000015260	4 retrocopies	retro_nleu_2086, retro_nleu_2726, retro_nleu_3086, retro_nleu_844,
Otolemur garnettii	ENSOGAG00000016584	1 retrocopy	retro_ogar_61,
Pongo abelii	ENSPPYG00000005684	4 retrocopies	retro_pabe_1000, retro_pabe_2486, retro_pabe_2512 , retro_pabe_2669,
Pongo abelii	ENSPPYG00000008372	1 retrocopy	retro_pabe_413,
Pan troglodytes	ENSPTRG00000006196	4 retrocopies	retro_ptro_2028, retro_ptro_2046, retro_ptro_2172, retro_ptro_820,