RetrogeneDB ID: retro_pabe_2257

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:134542290..134543332(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC2
• Ensembl ID: ENSPPYG00000017883
• Aliases: None
• Description: 26S protease regulatory subunit 7 [Source:RefSeq peptide;Acc:NP_001126144]

Sequence

>retro_pabe_2257
AATTTGGCTGCAGATAAGCAGACACAGCCTTTACAGGTTGCCAGGTGTACAAAGATAATCAAGGCTGATTCAGAGGACCC
AAAATACATTGTCAATGTAAAGCAGTTTGCCAAGTTTGTGATGGACTTTAGTGATCAGGTGGCACCCACTGACATTGAAG
AAGGGATGAGAGTAGGTGTGGACAGAAATAAATATCAAATTCACATCCCATTGCCTCCTAAGACTGACCCAACAGTTACC
ATGATGCAGGTGGAGGAAAAACCTGATGTCACATACAGTGATGTTGGGGAGCAGATTGAGAAATTGCAAGAAGTAGTTGA
AACCCCATTACTTCATCCAGAGAGGTTTGTGAATCTTAGCATTGAGCCTCCCAAGGGCATGCTGCTCTTTAATCCACCCA
GTACAGGAAGACACTCTGTGTGTGGGTAGTTGCTAATCAGACTGATGCATGCTTCATTCGACTTATTGGATCTGAGCTCT
ACAGAAATATGTCAGTGAGAGGGCTCAAATGGTTCATGAGCTCTTTGAAATGGCCAGAACAAAAAAAGCCTGCCTTATCT
TCTTTGATGAAATTGATGCTATTGGAGGGGCTCCGTTTGATGATGGTGCTAGAGGTGACAATGAAGTGCAGAGAACAATG
TTGGAACTGATCAATCAGCTTGACGGTTTTGATCCTCGAGGCAATATTAAAGTGCTGATGGCCACTAACTGACCTGATAA
TTTGGATCCAGCACTGATGAGGCCAGGGAGATTAGATAGAAAAATTGAATTTAGCTTGCCCGATCTAGAGGGTTGGACCC
ACATCTTTAAGATTCACGCTCATTCAATGAGTGTTGAAAGATATATCAGATTTGAATTGTTAGCACGACTGTGTCCAAAT
GGCACTGCTGCTGAGATTAGAAGTGTCTGCACAGAAGCTGGTATGTTTGCCATCAGAGCACAGCGAAAAATTGCTACTGA
GAAGGATTTCTTGGAAGCTGTAAATAAGGTCATTAAGTCTTATGCCAAATTCAGTGCTACTCCTGGCTACATGACATACA
AC

Alignment

ORF - retro_pabe_2257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.52 %
• Parental protein coverage: 81.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLAADKQTLQSEQPLQVARCTKIINADSEDPKYIINVKQFAKFVVDLSDQVAPTDIEEGMRVGVDRNKYQ
          .LAADKQT....QPLQVARCTKII.ADSEDPKYI.NVKQFAKFV.D.SDQVAPTDIEEGMRVGVDRNKYQ
Retrocopy NLAADKQT----QPLQVARCTKIIKADSEDPKYIVNVKQFAKFVMDFSDQVAPTDIEEGMRVGVDRNKYQ

Parental  IHIPLPPKIDPTVTMMQVEEKPDVTYSDVGGCKEQIEKLREVVETPLLHPERFVNLGIEPPKGVLLFGPP
          IHIPLPPK.DPTVTMMQVEEKPDVTYSDVG...EQIEKL.EVVETPLLHPERFVNL.IEPPKG.LLF.PP
Retrocopy IHIPLPPKTDPTVTMMQVEEKPDVTYSDVG---EQIEKLQEVVETPLLHPERFVNLSIEPPKGMLLFNPP

Parental  GTG-KTLCARAVANRTDACFIRVIGSEL-VQKYVGEGARMVRELFEMARTKKACLIFFDEIDAIGGARFD
          .TG.KTLC...VAN.TDACFIR.IGSEL..QKYV.E.A.MV.ELFEMARTKKACLIFFDEIDAIGGA.FD
Retrocopy STG<KTLCVWVVANQTDACFIRLIGSEL<LQKYVSERAQMVHELFEMARTKKACLIFFDEIDAIGGAPFD

Parental  DGAGGDNEVQRTMLELINQLDGFDPRGNIKVLMATNRPDTLDPALMRPGRLDRKIEFSLPDLEGRTHIFK
          DGA.GDNEVQRTMLELINQLDGFDPRGNIKVLMATN.PD.LDPALMRPGRLDRKIEFSLPDLEG.THIFK
Retrocopy DGARGDNEVQRTMLELINQLDGFDPRGNIKVLMATN*PDNLDPALMRPGRLDRKIEFSLPDLEGWTHIFK

Parental  IHARSMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARRKIATEKDFLEAVNKVIKSYAKFSAT
          IHA.SMSVER.IRFELLARLCPN.T.AEIRSVCTEAGMFAIRA.RKIATEKDFLEAVNKVIKSYAKFSAT
Retrocopy IHAHSMSVERYIRFELLARLCPNGTAAEIRSVCTEAGMFAIRAQRKIATEKDFLEAVNKVIKSYAKFSAT

Parental  PRYMTYN
          P.YMTYN
Retrocopy PGYMTYN

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	0.00 RPM	59.77 RPM
SRP007412_cerebellum	0.00 RPM	57.15 RPM
SRP007412_heart	0.00 RPM	39.32 RPM
SRP007412_kidney	0.00 RPM	56.52 RPM
SRP007412_liver	0.00 RPM	53.80 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2257 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2257 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2705
Pan troglodytes	retro_ptro_1826
Gorilla gorilla	retro_ggor_1885

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000005729	1 retrocopy	retro_etel_1316,
Homo sapiens	ENSG00000161057	2 retrocopies	retro_hsap_2705, retro_hsap_3980,
Gorilla gorilla	ENSGGOG00000009167	3 retrocopies	retro_ggor_1885, retro_ggor_2672, retro_ggor_2673,
Myotis lucifugus	ENSMLUG00000008853	1 retrocopy	retro_mluc_1642,
Macaca mulatta	ENSMMUG00000003432	2 retrocopies	retro_mmul_1538, retro_mmul_2299,
Monodelphis domestica	ENSMODG00000017238	1 retrocopy	retro_mdom_868,
Mustela putorius furo	ENSMPUG00000018268	3 retrocopies	retro_mputfur_1025, retro_mputfur_232, retro_mputfur_387,
Nomascus leucogenys	ENSNLEG00000009274	2 retrocopies	retro_nleu_1578, retro_nleu_2042,
Otolemur garnettii	ENSOGAG00000005164	2 retrocopies	retro_ogar_2198, retro_ogar_2309,
Pongo abelii	ENSPPYG00000017883	2 retrocopies	retro_pabe_2257 , retro_pabe_2412,
Pan troglodytes	ENSPTRG00000019553	2 retrocopies	retro_ptro_1826, retro_ptro_2702,
Tarsius syrichta	ENSTSYG00000000666	4 retrocopies	retro_tsyr_1031, retro_tsyr_1272, retro_tsyr_1857, retro_tsyr_2178,
Vicugna pacos	ENSVPAG00000008921	1 retrocopy	retro_vpac_44,