RetrogeneDB ID: retro_mmul_2585

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:62892945..62894292(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1927
• Ensembl ID: ENSMMUG00000011359
• Aliases: EIF3E, EIF3S6
• Description: eukaryotic translation initiation factor 3, subunit E [Source:RefSeq peptide;Acc:NP_001245017]

Sequence

>retro_mmul_2585
ATGGCAGAGTACAACTTGACTACTCACATTGCCCACTTTTTGGATCGGCATCTAGTCTTACCACTCTTTGAGTTTCTCTC
TGTAAAGGAGATATATAACGAAAAGGAATAAATACAAGGTAAATTGGACCTTCTTAGTAACACTAACATGATAGACTTCG
CTATGGATGTATACAAAAACTTTTATTCTGATGATGTTCCTCAGGCTTTGAGAGAGGAAACAACCACAATTGTTGCACAA
CTAAAACAGCTTCAGGCAGAAACAGAACCAATTGCGAAGCTGTTTGAAGATCCAGAAATTACAAGGTAAATGAAGTCAAC
AAGGGATGGTAGGATGCTCTTTGACTACCTGGTGGACAAGCATGGTTTTAGACAGGAATATTTAGATATGCTCTACACAT
ATGCACAATTTGAAAATGAATGTGGGAGTTACTCAGGAGCAGCAGAATATCTGTGTTTTTTTAGTGTGTTGGTTCCAGCA
ACAGATAGAAATGCTTTAAATTCACTCTGGGGAAAGCTGGCCTCTGAAATCTTAATGTGGAATTGCGATGCAGCCATGGG
AGACCTTACATGGTCAAAAGAGAAGATAGATAATAATTCTGTGAGTTCTCCACTCCAGTCTCTTCAGCAGAAAACATGAC
TCATTAACTGGTCTCTTCTTGTTTTCTTCAATCACCCCAGAATTCTTCACAATATTATTGATCTCTTTCTTACCAGCCAT
GGTATCTTTAAAGCAATTCAGACAATGTGTCCACACAGTTTTTGCTATTTGACTACAGCAGTCATAACAAACAAGGATGT
TTGAAAATGTCGACAGGTGCAAAAAGATCTAGTTAAAGTTACTCAACAGGAGTCTTACACATATAAAAACCCAGTTACAG
AATTTGTTGAATGCTTATATGTTAACTTTGACTTTGATGGAGCTCAGAAAAAGCTGAGGGAATGTGAATGAGTGCTTGTG
AATGATTTCTTCTTGGCGACTTGTCTTGAGGATTTCACTGAAAATGCTCATCTCTTCATATTTGAGACTTTCTGTTGCAT
CCATCAGTTTATCAGCATTAACATGTTGGCAGATAAATTGAACGTGACTCCAGAAGAAGCTGAAAGGTAAATTGTAAATT
TAATTAGAAAATTAATAAGAAATGCAATCTTGGGTGCCAATATTGATTCCAAATTAGGTCATGTGGTTTTGGGTAACAAT
GCAGTCTCACCCTATCAGCAAGTGATTAAAAAGACCAAACACCTTCCTTTTAGAAGCCAGATTTTGGCCATGAATATTAA
GAAGAAATTTAATAAGAATAGCAGGTCAGAGGTTCCTAATTGGGCAACTCAAGATTCTGGCTTCTAC

Alignment

ORF - retro_mmul_2585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.04 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEYDLTTRIAHFLDRHLVFPLLEFLSVKEIYNEKELLQGKLDLLSDTNMVDFAMDVYKNLYSDDIPHAL
          MAEY.LTT.IAHFLDRHLV.PL.EFLSVKEIYNEKE..QGKLDLLS.TNM.DFAMDVYKN.YSDD.P.AL
Retrocopy MAEYNLTTHIAHFLDRHLVLPLFEFLSVKEIYNEKE*IQGKLDLLSNTNMIDFAMDVYKNFYSDDVPQAL

Parental  REKRTTVVAQLKQLQAETEPIVKMFEDPETTRQMQSTRDGRMLFDYLADKHGFRQEYLDTLYRYAKFQYE
          RE..TT.VAQLKQLQAETEPI.K.FEDPE.TR.M.STRDGRMLFDYL.DKHGFRQEYLD.LY.YA.F..E
Retrocopy REETTTIVAQLKQLQAETEPIAKLFEDPEITR*MKSTRDGRMLFDYLVDKHGFRQEYLDMLYTYAQFENE

Parental  CGNYSGAAEYLYFFRVLVPATDRNALSSLWGKLASEILMQNWDAAMEDLTRLKETIDNNSVSSPLQSLQQ
          CG.YSGAAEYL.FF.VLVPATDRNAL.SLWGKLASEILM.N.DAAM.DLT..KE.IDNNSVSSPLQSLQQ
Retrocopy CGSYSGAAEYLCFFSVLVPATDRNALNSLWGKLASEILMWNCDAAMGDLTWSKEKIDNNSVSSPLQSLQQ

Parental  RTWLIHWSLFVFFNHPKGRDNIIDLFL-YQPQYL-NAIQTMCPHILRYLTTAVITNKDVRKRRQVLKDLV
          .T.LI.WSL.VFFNHP....NIIDLFL.YQP.YL..AIQTMCPH...YLTTAVITNKDV.K.RQV.KDLV
Retrocopy KT*LINWSLLVFFNHPRILHNIIDLFL<YQPWYL>KAIQTMCPHSFCYLTTAVITNKDV*KCRQVQKDLV

Parental  KVIQQESYTYKDPITEFVECLYVNFDFDGAQKKLRECESVLVNDFFLVACLEDFIENARLFIFETFCRIH
          KV.QQESYTYK.P.TEFVECLYVNFDFDGAQKKLRECE.VLVNDFFL..CLEDF.ENA.LFIFETFC.IH
Retrocopy KVTQQESYTYKNPVTEFVECLYVNFDFDGAQKKLRECE*VLVNDFFLATCLEDFTENAHLFIFETFCCIH

Parental  QCISINMLADKLNMTPEEAERWIVNLIR----NARLDAKIDSKLGHVVMGNNAVSPYQQVIEKTKSLSFR
          Q.ISINMLADKLN.TPEEAER.IVNLIR....NA.L.A.IDSKLGHVV.GNNAVSPYQQVI.KTK.L.FR
Retrocopy QFISINMLADKLNVTPEEAER*IVNLIRKLIRNAILGANIDSKLGHVVLGNNAVSPYQQVIKKTKHLPFR

Parental  SQMLAMNIEKKLNQNSRSEAPNWATQDSGFY
          SQ.LAMNI.KK.N.NSRSE.PNWATQDSGFY
Retrocopy SQILAMNIKKKFNKNSRSEVPNWATQDSGFY

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	0.00 RPM	52.66 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	28.96 RPM
SRP007412_cerebellum	0.00 RPM	79.10 RPM
SRP007412_heart	0.00 RPM	64.24 RPM
SRP007412_kidney	0.00 RPM	74.41 RPM
SRP007412_liver	0.00 RPM	32.74 RPM
SRP007412_testis	0.00 RPM	97.81 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_2585 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_2585 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_2585 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006702	1 retrocopy	retro_btau_291,
Canis familiaris	ENSCAFG00000000702	1 retrocopy	retro_cfam_1127,
Callithrix jacchus	ENSCJAG00000006458	3 retrocopies	retro_cjac_2333, retro_cjac_2686, retro_cjac_701,
Equus caballus	ENSECAG00000000236	1 retrocopy	retro_ecab_860,
Echinops telfairi	ENSETEG00000013105	1 retrocopy	retro_etel_2048,
Felis catus	ENSFCAG00000003665	1 retrocopy	retro_fcat_231,
Homo sapiens	ENSG00000104408	1 retrocopy	retro_hsap_3489,
Gorilla gorilla	ENSGGOG00000022955	2 retrocopies	retro_ggor_2354, retro_ggor_2355,
Myotis lucifugus	ENSMLUG00000007269	1 retrocopy	retro_mluc_1796,
Macaca mulatta	ENSMMUG00000011359	1 retrocopy	retro_mmul_2585 ,
Mustela putorius furo	ENSMPUG00000005924	2 retrocopies	retro_mputfur_193, retro_mputfur_736,
Mus musculus	ENSMUSG00000022336	2 retrocopies	retro_mmus_1801, retro_mmus_2807,
Nomascus leucogenys	ENSNLEG00000004120	1 retrocopy	retro_nleu_333,
Oryctolagus cuniculus	ENSOCUG00000008050	1 retrocopy	retro_ocun_1399,
Pan troglodytes	ENSPTRG00000020505	1 retrocopy	retro_ptro_2362,
Rattus norvegicus	ENSRNOG00000027690	4 retrocopies	retro_rnor_1133, retro_rnor_2879, retro_rnor_583, retro_rnor_584,
Ictidomys tridecemlineatus	ENSSTOG00000008976	1 retrocopy	retro_itri_545,
Tursiops truncatus	ENSTTRG00000011025	2 retrocopies	retro_ttru_1602, retro_ttru_1794,