RetrogeneDB ID: retro_pabe_3172

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:109190952..109192556(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MIPEP
• Ensembl ID: ENSPPYG00000005207
• Aliases: None
• Description: mitochondrial intermediate peptidase precursor [Source:RefSeq peptide;Acc:NP_001124737]

Sequence

>retro_pabe_3172
AAAACTAGGCAAGTGGCCTAACTGTTTATGTTTGATTTTGAAATTAGTGGAATCCATCTAGACAAAGAAAAGTGTAAAAG
AGCAGTGGACCTCAATGTTAAAATCTTGGATTTGAGTAGTACATGTCTTATGGCAAACAACTTTCCCAACAAGATTGAGA
AGCATCTCTTACTAGAACACATTCACAATAACTTTTATCTGATGGGGATCGTATCATAATTGGTGGTCTCCATGCAGCAG
CACCAGGCGACTTGGTGTGAGAAGCTGCTTACAAAATTTTTCTTTATCCCTATACTGGTCAATTAAAATGTTTAGAAGAA
TTGCTCAGCAACAGAGATCCTCTGCAAAAGTTGGTAGGGTATTCTGTGTTTTCCAACAGGGCTCTCCAAGGAAAAATAGT
TAAAAATTCAGAGACTGTCATCCAGTTTCTTGAGAAACTCTCTGACAAACTTTCTGAAAGAACTCGAAAAGATTTTGAGA
TGATACGAGGGATGAAAATGAAACAGAATTCTCAAAATTCCAAAGTAATGCCTTGGGAGCCCCGCTACCACAGTGGTGTG
AATCATGCACAAAGGTATAATATTGAGCCTGGCTTATATTGCCTGTTTTTCTCCCTTGGAGCATGCATGGAAGGCCTGAA
TATTTGGCTTAACAAACTGTTGGGGATTTCCTTATATGCAGAGTAGCCTGCAAAAGGAGAGGTATGGTGTGAAGATGTCC
GAAAACTGACTGTCATTCATGAATCTGAAGGACTGTTGGGGTGCATTTACTTTGATTTTTTTCAGCAAGGAGACAAACCA
TATCAGGATTGCCATTTTACAATCCACGGAGGCAGATTAAAGGAAGACAGAGACTACCAACTCCCAGTCATAGTTCTTAT
GCTGAATCTTTCCCATTCCTCAAGGAGTTCACCAACTTTGCTAACTCCTGGAATGATGGAAAATCTTGACCATGAAATGG
GACATGCTATGCATTCAATGCTAGGACATACTTGTTACCAACACGTCACTGGAACCAGGTACCCCACTGATTTTGCAGGG
GTTCCTTCTATTCTAATAGAGTACTTTGCAAATGATTATCGAGTAACCAGTTTGCCAGACAAAATTAGAATGGGCAGCCA
CTGCCAAAAAAATATGGTGTCTCAGCTTTGTGAATCTAAAAAGGTTTGTGCTTCAGCTGATATGAAACTTCAGGTCTTTT
ATGCCACTCTGGATCAAATCTACCATAGGAAGCATCCCCTGAGGAATTCAACCATAGGCATTCTCAAGGAAACACAAGAG
ACATTCTGTGGCTTACCATATGTTCCAAATACTGCCTGGAAGCTGCAGATCACCTACCTTGTGGGCTATAGTGCCAAATA
TTACTCTTACCTCATGTCTAGGGCAGTCACTTCCATGGTTTGGAAGGAATGTTTTCTACAAAATCCTTTTAACAGGGCCA
CCATGGAGTGCTATTGCAGGGAGATGCTGGCCCACAGTGGAGGCAAGAAGCCCATGCTCATGGTTGAAGGTGTGCTTCAA
AAGTGCCCTTCTATTGATTACTTTGTAAGTGCCCTTGTTTCTGACTTGGATCTCGACTTTGAAACTTTTGTCATGGATTC
TGAA

Alignment

ORF - retro_pabe_3172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.58 %
• Parental protein coverage: 75.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETRRVAELFMFDFEISGIHLDKEKRKRAVDLNVKILDLSSTFLMGTNFPNKIEKHLLPEHIRRNF-TSAG
          .TR.VA.LFMFDFEISGIHLDKEK.KRAVDLNVKILDLSST.LM..NFPNKIEKHLL.EHI..NF..S.G
Retrocopy KTRQVA*LFMFDFEISGIHLDKEKCKRAVDLNVKILDLSSTCLMANNFPNKIEKHLLLEHIHNNF<LSDG

Parental  DHIIIDGLHAESPDDLGREAAYKIFLYPNAGQLKCLEELLSSRDLLAKLVGYSTFSHRALQGTIAKNPET
          D.III.GLHA..P.DL..EAAYKIFLYP..GQLKCLEELLS.RD.L.KLVGYS.FS.RALQG.I.KN.ET
Retrocopy DRIIIGGLHAAAPGDLV*EAAYKIFLYPYTGQLKCLEELLSNRDPLQKLVGYSVFSNRALQGKIVKNSET

Parental  VMQFLEKLSDKLSERTLKDFEMIRGMKMKLNPQNSEVMPWDPPYYSGVIRAERYNIEPSLYCPFFSLGAC
          V.QFLEKLSDKLSERT.KDFEMIRGMKMK.N.QNS.VMPW.P.Y.SGV..A.RYNIEP.LYC.FFSLGAC
Retrocopy VIQFLEKLSDKLSERTRKDFEMIRGMKMKQNSQNSKVMPWEPRYHSGVNHAQRYNIEPGLYCLFFSLGAC

Parental  MEGLNILLNRLLGISLYAEQPAKGEVWSEDVRKLSCRHDLKD-VGYIYCDFF-SADKPHQDCHFTIRGGR
          MEGLNI.LN.LLGISLYAE.PAKGEVW.EDVRKL...H......G.IY.DFF...DKP.QDCHFTI.GGR
Retrocopy MEGLNIWLNKLLGISLYAE*PAKGEVWCEDVRKLTVIHESEGLLGCIYFDFFQQGDKPYQDCHFTIHGGR

Parental  LKEDGDYQLPVVVLMLNLPRSSRSSPTLLTPGMMENLFHEMGHAMHSMLGRTRYQHVTGTRCPTDFAEVP
          LKED.DYQLPV.VLMLNL..SSRSSPTLLTPGMMENL.HEMGHAMHSMLG.T.YQHVTGTR.PTDFA.VP
Retrocopy LKEDRDYQLPVIVLMLNLSHSSRSSPTLLTPGMMENLDHEMGHAMHSMLGHTCYQHVTGTRYPTDFAGVP

Parental  SILMEYFANDYRVVNQFARHYQTGQPLPKNMVSRLCESKKVCAAADMQLQVFYATLDQIYHGKHPLRNST
          SIL.EYFANDYRV..........G....KNMVS.LCESKKVCA.ADM.LQVFYATLDQIYH.KHPLRNST
Retrocopy SILIEYFANDYRVTS-LPDKIRMGSHCQKNMVSQLCESKKVCASADMKLQVFYATLDQIYHRKHPLRNST

Parental  TDILKETQEKFYGLPYVPDTAWQLRFSHLVGYGAKYYSYLMSRAVASMVWKECFLQDPFNRAAGERYRRE
          ..ILKETQE.F.GLPYVP.TAW.L....LVGY.AKYYSYLMSRAV.SMVWKECFLQ.PFNRA..E.Y.RE
Retrocopy IGILKETQETFCGLPYVPNTAWKLQITYLVGYSAKYYSYLMSRAVTSMVWKECFLQNPFNRATMECYCRE

Parental  MLAHGGGREPMLMVEGMLQKCPSVDDFVSALVSDLDLDFETFLMDSE
          MLAH.GG..PMLMVEG.LQKCPS.D.FVSALVSDLDLDFETF.MDSE
Retrocopy MLAHSGGKKPMLMVEGVLQKCPSIDYFVSALVSDLDLDFETFVMDSE

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	8.63 RPM
SRP007412_cerebellum	0.12 RPM	10.94 RPM
SRP007412_heart	0.00 RPM	27.33 RPM
SRP007412_kidney	0.00 RPM	24.00 RPM
SRP007412_liver	0.00 RPM	10.92 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3172 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3172 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3891
Gorilla gorilla	retro_ggor_2619
Macaca mulatta	retro_mmul_1732

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000027001	1 retrocopy	retro_hsap_3891,
Gorilla gorilla	ENSGGOG00000009424	1 retrocopy	retro_ggor_2619,
Macaca mulatta	ENSMMUG00000006942	1 retrocopy	retro_mmul_1732,
Nomascus leucogenys	ENSNLEG00000013401	1 retrocopy	retro_nleu_1131,
Pongo abelii	ENSPPYG00000005207	1 retrocopy	retro_pabe_3172 ,
Sus scrofa	ENSSSCG00000009290	1 retrocopy	retro_sscr_415,
Sus scrofa	ENSSSCG00000025544	1 retrocopy	retro_sscr_414,