RetrogeneDB ID: retro_mmul_1987

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:157592340..157594438(-)
• Located in intron of: ENSMMUG00000023400

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2327
• Ensembl ID: ENSMMUG00000004380
• Aliases: None
• Description: trifunctional enzyme subunit alpha, mitochondrial [Source:RefSeq peptide;Acc:NP_001252819]

Sequence

>retro_mmul_1987
ATAAACAAAGAGCTGCATTCAGAGTTCACAGAAGTTATGGATGAAATCTGGGCTAGTGATCAAATCAGAAGTGTCATCCT
TATCTCATCAAAGCCAGGCTGCTTTACTGTAGGTGCTGATATCAACATGTTAGCCACTTGCAAGACCCCTCAAGAAGTAA
CACAGATGTCACAAGAAGCACCGAGAACATTTGAGAAATTGAAAAGTCCACAAAGCCTGTTGTGACTGCCATCAGTGGAT
CCTGCCTGGGAGGAGGACTTGAGTTTGCCATTTTATGCCAATACAGAATAGCAACAAAAGACAGAAAAACAGTATTAGGT
GCTCCTGAAGTCTCGCTGGGGATCTTACCAGGCGCAGGAGGTGCACAAAGGCTGCCCAAAATGGTGGGTGTGCCTGCTGC
TTTTGACATGATGCTGACTGGTAGAAACATTCATGCAGACAGGGCAAAGAAAATGGGACTTGTTGACCAATTGGTGGAAT
CCCTGGGACCAGGACTAAAACTTCCAGAGGAACAGAAAATCAAATACCTAGAAGAAGTCACAATTACTTTTGCCAAAGGA
CTAGCTGATAAGATCTCTCCAAAGAGAGACAAGGGATTGGTAGAAAAATTGACAGTGTATGCCATAACTATTCCATTTGT
CAGGCAGCAAATTTACAAAACAAGTGGAAGAAAATGTGTGAAAGCAGACTAAAGGGCTTTATCCTGCACCTCTGAAAATA
ATTGATATGGTAAAGACTAGAATTGAGCAAGGAAGTGATGCTGGTTATCTCTCTGAATCTCAGAAATTTGGAGAGCTTGT
AATGACCAAAGAATCAAAGGCCTTGATGGGACTCTACCATGGTCAGGTCTTGTGCAAGAAGAATACATCTGGAGCTCCAC
AGAGGGAAGTTAAGCATCTGGCTATTCTTGGTGCAGGGATGATGGAAGCAGGCATCACCCAAGTCTCCATGGATAAGGGG
CTAAAGACTATACTTAAAGATGCCACACTCACTGAGCTAGGCCGAGGACAGCAACAAGTGTTCAAAGGACTGACTGACAA
AGTGAAGAAGAAAGCTCTAACATCATTTGAAAGGGATTCCATCGTCAGCAACTTGACTGGGCAGTTTGATTACCATGGAT
TTTAAAAAGACCAACATGTTGATGGACACTGTGTTTGAGGACCTTAGTTTTAAGCACAGAGTGCTAAAGGAAGTAGAAGC
GGTGACTCTAGATCACTGTGTCTTTGCCAGTAACACATCTGCTCTCCCAATCAGTGAAATTACCGCTATCAGCAAAAGAC
CTGAGAAGGTGATTGGCAAGCACTACTTCTCTCCTGCGGACAAGAGGCAGCTGCTGGAGATGATCACAACCGGGAAGACT
TCCAAAGACACCAGTGCCTCAGCTGTAGCAGTCCGTCTCAAGCAGGGGAAGGTCATCATTGTGGTTAAGGATGGACCTGG
CTTCTATACCACCAGGTGTCTTGCACCCATGATGTCTGAAGTCATCCGAATCCTCCAGGAAGGAGTTGACCCGAAGAAGC
TGGATTCCCTGACCACAAGCCTTGGCTTTCCTATGGTTGCTGCCACACTGGTGGATGAAGTTGGTGTGGATGTAGCGAAA
CATGTGGCGAAAGATCTGGGCAAAGCTTTTGGGGAGCAGTCTGGAGGTGGAAACCCAGAACTGCTGACACAGATGGTGTC
CAAGGGCTTTCTAGGTCACAAGTCTGGGTAGGGCTTTTCCATCTGTCAGGAGGGTGTGAAGAGTAAGAATTTGAATTCTG
ACATGGACAGTATTTTAGCAAGTCTGAAGATGCCTCCTAAGTCTGAAGTCTCCTCAGATGAAGACATCCAGTTCTGCCTA
GTGACAAGATTAGTGAGTAAGGCAGTCATGTGCCTGCAAGAGGGGACCTTGGTCACACCTGCAGAGGGAGACACTGGAGC
CATCTTTGGGCTCAGCTTCCCACCTTGTCTTGGAGGGCCTTTCCGCTTTGTGCATCTGTATGGCACCCAGAAGATAGTGG
ACGGGCTCAAGAGGTATGAAGCTGCCTATGGAAAAGAGTTCACCCCATGCCAGCTGCTAGTTGACCACACTAACAGCCCT
AACAAGAAGTGTTACCAG

Alignment

ORF - retro_mmul_1987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 91.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LSKELHSEFTEVMNEIWASDQIRSAVLISSKPGCFIAGADINMLSACKTLQEVTQLSQEAQRILEKL-EK
          ..KELHSEFTEVM.EIWASDQIRS..LISSKPGCF..GADINML..CKT.QEVTQ.SQEA.R..EKL.EK
Retrocopy INKELHSEFTEVMDEIWASDQIRSVILISSKPGCFTVGADINMLATCKTPQEVTQMSQEAPRTFEKL<EK

Parental  SPKPVVAAINGSCLGGGLELAISCQYRIATKDRKTVLGVPEVLLGALPGAGGTQRLPKMVGVPAALDMML
          S.KPVV.AI.GSCLGGGLE.AI.CQYRIATKDRKTVLG.PEV.LG.LPGAGG.QRLPKMVGVPAA.DMML
Retrocopy STKPVVTAISGSCLGGGLEFAILCQYRIATKDRKTVLGAPEVSLGILPGAGGAQRLPKMVGVPAAFDMML

Parental  TGRNIRADRAKKMGLVDQLVEPLGPGLKPPEERTMEYLEEVAITFAKGLADKKISPKRNKGLVEKLTAYA
          TGRNI.ADRAKKMGLVDQLVE.LGPGLK.PEE....YLEEV.ITFAKGLADK.ISPKR.KGLVEKLT.YA
Retrocopy TGRNIHADRAKKMGLVDQLVESLGPGLKLPEEQKIKYLEEVTITFAKGLADK-ISPKRDKGLVEKLTVYA

Parental  MTIPFVRQQVYK-KVEEKVRKQTKGLYPAPLKIIDVVKTGIEQGSDAGYLSESQKFGELVMTKESKALMG
          .TIPFVRQQ.YK..VEE.V.KQTKGLYPAPLKIID.VKT.IEQGSDAGYLSESQKFGELVMTKESKALMG
Retrocopy ITIPFVRQQIYK>QVEENV*KQTKGLYPAPLKIIDMVKTRIEQGSDAGYLSESQKFGELVMTKESKALMG

Parental  LYHGQVLCKKNKFGAPQKDVKHLAILGAGLMGAGIAQVSVDKGLKTILKDATLTGLDRGQQQVFKGLNDK
          LYHGQVLCKKN..GAPQ..VKHLAILGAG.M.AGI.QVS.DKGLKTILKDATLT.L.RGQQQVFKGL.DK
Retrocopy LYHGQVLCKKNTSGAPQREVKHLAILGAGMMEAGITQVSMDKGLKTILKDATLTELGRGQQQVFKGLTDK

Parental  VKKKALTSFERDSIFSNLTGQLDYQGF-EKADMVIEAVFEDLSLKHRVLKEVEAVIPDHCIFASNTSALP
          VKKKALTSFERDSI.SNLTGQ.DY.GF..K..M....VFEDLS.KHRVLKEVEAV..DHC.FASNTSALP
Retrocopy VKKKALTSFERDSIVSNLTGQFDYHGF>KKTNMLMDTVFEDLSFKHRVLKEVEAVTLDHCVFASNTSALP

Parental  ISEIAAVSKRPEKVIGMHYFSPVDKMQLLEIITTEKTSRDTSASAVAVGLKQGKVIIVVKDGPGFYTTRC
          ISEI.A.SKRPEKVIG.HYFSP.DK.QLLE.ITT.KTS.DTSASAVAV.LKQGKVIIVVKDGPGFYTTRC
Retrocopy ISEITAISKRPEKVIGKHYFSPADKRQLLEMITTGKTSKDTSASAVAVRLKQGKVIIVVKDGPGFYTTRC

Parental  LAPMMSEVIRILQEGVDPKKLDSLTTSFGFPVGAATLVDEVGVDVAKHVAEDLGKVFGERFGGGNPELLT
          LAPMMSEVIRILQEGVDPKKLDSLTTS.GFP..AATLVDEVGVDVAKHVA.DLGK.FGE..GGGNPELLT
Retrocopy LAPMMSEVIRILQEGVDPKKLDSLTTSLGFPMVAATLVDEVGVDVAKHVAKDLGKAFGEQSGGGNPELLT

Parental  QMVSKGFLGRKSGKGFYIYQEGVKRKDLNSDMDSILASLKLPPKSEVSSDEDIQFRLVTRFVNEAVMCLQ
          QMVSKGFLG.KSG.GF.I.QEGVK.K.LNSDMDSILASLK.PPKSEVSSDEDIQF.LVTR.V..AVMCLQ
Retrocopy QMVSKGFLGHKSG*GFSICQEGVKSKNLNSDMDSILASLKMPPKSEVSSDEDIQFCLVTRLVSKAVMCLQ

Parental  EGILATPAEGDIGAVFGLGFPPCLGGPFRFVDLYGAQTIVDRLKKYEAAYGKQFTPCQLLADHANSPNKK
          EG.L.TPAEGD.GA.FGL.FPPCLGGPFRFV.LYG.Q.IVD.LK.YEAAYGK.FTPCQLL.DH.NSPNKK
Retrocopy EGTLVTPAEGDTGAIFGLSFPPCLGGPFRFVHLYGTQKIVDGLKRYEAAYGKEFTPCQLLVDHTNSPNKK

Parental  FYQ
          .YQ
Retrocopy CYQ

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	0.45 RPM	55.02 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	55.85 RPM
SRP007412_cerebellum	1.61 RPM	61.67 RPM
SRP007412_heart	0.24 RPM	306.62 RPM
SRP007412_kidney	0.00 RPM	191.31 RPM
SRP007412_liver	0.00 RPM	102.13 RPM
SRP007412_testis	0.11 RPM	178.21 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1987 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1987 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2109
Pongo abelii	retro_pabe_2576

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006972	1 retrocopy	retro_dnov_1863,
Homo sapiens	ENSG00000084754	1 retrocopy	retro_hsap_958,
Gorilla gorilla	ENSGGOG00000004918	1 retrocopy	retro_ggor_772,
Macaca mulatta	ENSMMUG00000004380	2 retrocopies	retro_mmul_1987 , retro_mmul_787,
Macaca mulatta	ENSMMUG00000023254	1 retrocopy	retro_mmul_2217,
Mustela putorius furo	ENSMPUG00000008546	1 retrocopy	retro_mputfur_705,
Nomascus leucogenys	ENSNLEG00000001616	2 retrocopies	retro_nleu_1588, retro_nleu_772,
Pongo abelii	ENSPPYG00000012583	2 retrocopies	retro_pabe_2576, retro_pabe_817,
Pan troglodytes	ENSPTRG00000011732	2 retrocopies	retro_ptro_2109, retro_ptro_664,
Ictidomys tridecemlineatus	ENSSTOG00000001593	1 retrocopy	retro_itri_681,