RetrogeneDB ID: retro_mmul_1628

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:102673509..102675159(+)
• Located in intron of: ENSMMUG00000030291

Retrocopy information

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

Parental gene information

• Parental gene symbol: ABCE1
• Ensembl ID: ENSMMUG00000004433
• Aliases: None
• Description: ATP-binding cassette sub-family E member 1 [Source:RefSeq peptide;Acc:NP_001253883]

Sequence

>retro_mmul_1628
TCTGAAACTCTTTGTATTGGTTGTGGTATCTGTATTAAGAAATGCCCCTTTGGTGCCTTATCAATTGACAATTTACCAAG
CAACTTGGAAAAAGAAACCACACATCGATATTGTGCCAATGTCTTCAAACTTCACAGGTTGCCTATCCCTCGTCCAGGTG
AAGTTTTGGGATTAGTTGGAACTAATGGTATTGGAAAGTTAACTGCTTTAAAAATTTTTTGCAGGAAAACAAAAGCCAAA
CCTTGAAAAGTATGATGATCCTACTGATTGGCAAGAGATTTTGACTTATTTCCGTGGATCTGAATTACAGAATTACTTTA
CTGAGATTCTAGAAGATGACCTAAAAGCCATCATCAAACCCCAATATGTAGATCAGATTCCTAAGCCTGCAAAGGGGACA
GTGGGATCTATTTTGGACCGAAAAGATGAAACAAAGACACAGGAAATTGTATGTTAGCAGCTTGATTTAACCCACCTAAA
AGAACAAAATGTTGAAGATCTTTCAGGAGGAGAGTTGCAGAGATTTGCCTGTGCTGTCATTTGCATACAGAAAGCTGATA
TTTTCATGTTTGATGAGACTTCTAGTTACCTAGATGTCAAGCAGCATTTAAAGGCTGCTATTACTCTACAATCTCTAATA
AATCCGGATAGATATATCATTGTGGTGGAATATGACCTAAGTGTATTAGACTATCTCTCTGACTTCATCTGCTGTTTATA
TGGTGTACCAAGTGCCTATGGAGTTGTCACTATGCCTTTTAGTGTAAGAAAGGGCATAAACATTTTTTTGGATGGCTATG
TTCCAACAGAAAACTTGAGCTTCAGAGATGCATCACTTGTTTTCAAAGTGGCTGAGACAGCAAATGAAGAAGAAGTCAAA
ATGACGTGTATGTATAAATATCCAAGAATGAAGAAAAAATGGGAGAGTTTGAGCTAGCAATTGTAGCTGGAGAGTTTACA
GATTCTGAAATCATGGTGATGCTGGGGGAAAATGGAATGGGTAAAACAACATTTATCAGAATGCTTGCTGGAAGACTTAA
ACCTCATAAAGGAGGAGAAGTACCAGTTCTAAATGTCAGTTATAAGCCACAGAAAATTAGTCCAAAATCAACTGGAAGTG
TTCACCAGTTACTACATGAAAAGACAAGAGATGCTTATACTCATTCACAATTTGTGACTAATGTAATGAAGCCTCTGCAA
ATTGAAAACATCATCAATCAAGAGGTGCAGATGTTATCGGGTGGTGAACTATAGCGAGTAGTTTTAGCCCTTTGTTTGGG
CAAATCTGCTGATGTCTATTTAATTGATGAACCATCTGCATGTTTGGATTCTGAGCAAAGACTGATGGCAGCTTGAGTTG
CCAAACGTTTCATACTTCATGCAAAAAAGACAGCCTTTGTTGTGGAACATGACTTCATCATGGCCACCTATCTAGCGGAT
CATGTCATCATTTTTGATGGCGTTCCATCTACTAAGAACACAGTTGCAAACAGTCCTCAAACCCTTTTGGCTGGCATGAA
TACATTTTTCTCTCAGCTTGAAACTACATTCAGAAGAGATCCAAGCAACTATAGGCCATGAATAAATAAATTTAATTCAA
TTAAGGATGTAAAACAAAAGAAGAGTGGAAACTACTTTCTCTTGGATGAT

Alignment

ORF - retro_mmul_1628 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.94 %
• Parental protein coverage: 91.65 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SETLCIGCGICIKKCPFGALSIVNLPSNLEKETTHRYCANAFKLHRLPIPRPGEVLGLVGTNGIGKSTAL
          SETLCIGCGICIKKCPFGALSI.NLPSNLEKETTHRYCAN.FKLHRLPIPRPGEVLGLVGTNGIGK.TAL
Retrocopy SETLCIGCGICIKKCPFGALSIDNLPSNLEKETTHRYCANVFKLHRLPIPRPGEVLGLVGTNGIGKLTAL

Parental  KIL-AGKQKPNLGKYDDPPDWQEILTYFRGSELQNYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILD
          KI..AGKQKPNL.KYDDP.DWQEILTYFRGSELQNYFT.ILEDDLKAIIKPQYVDQIPK.AKGTVGSILD
Retrocopy KIF>AGKQKPNLEKYDDPTDWQEILTYFRGSELQNYFTEILEDDLKAIIKPQYVDQIPKPAKGTVGSILD

Parental  RKDETKTQAIVCQQLDLTHLKERNVEDLSGGELQRFACAVVCIQKADIFMFDEPSSYLDVKQRLKAAITI
          RKDETKTQ.IVC.QLDLTHLKE.NVEDLSGGELQRFACAV.CIQKADIFMFDE.SSYLDVKQ.LKAAIT.
Retrocopy RKDETKTQEIVC*QLDLTHLKEQNVEDLSGGELQRFACAVICIQKADIFMFDETSSYLDVKQHLKAAITL

Parental  RSLINPDRYIIVVEHDLSVLDYLSDFICCLYGVPSAYGVVTMPFSVREGINIFLDGYVPTENLRFRDASL
          .SLINPDRYIIVVE.DLSVLDYLSDFICCLYGVPSAYGVVTMPFSVR.GINIFLDGYVPTENL.FRDASL
Retrocopy QSLINPDRYIIVVEYDLSVLDYLSDFICCLYGVPSAYGVVTMPFSVRKGINIFLDGYVPTENLSFRDASL

Parental  VFKVAETANEEEVKKMCMYKYPGMKK-KMGEFELAIVAGEFTDSEIMVMLGENGTGKTTFIRMLAGRLKP
          VFKVAETANEEEVK..CMYKYP.MKK.KMGEFELAIVAGEFTDSEIMVMLGENG.GKTTFIRMLAGRLKP
Retrocopy VFKVAETANEEEVKMTCMYKYPRMKK<KMGEFELAIVAGEFTDSEIMVMLGENGMGKTTFIRMLAGRLKP

Parental  DEGGEVPVLNVSYKPQKISPKSTGSVRQLLHEKIRDAYTHPQFVTDVMKPLQIENIIDQEVQTLSGGELQ
          ..GGEVPVLNVSYKPQKISPKSTGSV.QLLHEK.RDAYTH.QFVT.VMKPLQIENII.QEVQ.LSGGEL.
Retrocopy HKGGEVPVLNVSYKPQKISPKSTGSVHQLLHEKTRDAYTHSQFVTNVMKPLQIENIINQEVQMLSGGEL*

Parental  RVALALCLGKPADVYLIDEPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLADRVIVFDGV
          RV.LALCLGK.ADVYLIDEPSA.LDSEQRLMAA.V.KRFILHAKKTAFVVEHDFIMATYLAD.VI.FDGV
Retrocopy RVVLALCLGKSADVYLIDEPSACLDSEQRLMAA*VAKRFILHAKKTAFVVEHDFIMATYLADHVIIFDGV

Parental  PS-KNTVANSPQTLLAGMNKFLSQLEITFRRDPNNYRPRINKLNSIKDVEQKKSGNYFFLDD
          PS.KNTVANSPQTLLAGMN.F.SQLE.TFRRDP.NYRP.INK.NSIKDV.QKKSGNYF.LDD
Retrocopy PSTKNTVANSPQTLLAGMNTFFSQLETTFRRDPSNYRP*INKFNSIKDVKQKKSGNYFLLDD

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	33.62 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	15.07 RPM
SRP007412_cerebellum	0.06 RPM	28.99 RPM
SRP007412_heart	0.00 RPM	20.73 RPM
SRP007412_kidney	0.00 RPM	24.76 RPM
SRP007412_liver	0.00 RPM	13.93 RPM
SRP007412_testis	0.04 RPM	38.41 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1628 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1628 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1628 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004534	1 retrocopy	retro_chof_1280,
Cavia porcellus	ENSCPOG00000007367	1 retrocopy	retro_cpor_289,
Homo sapiens	ENSG00000164163	1 retrocopy	retro_hsap_3826,
Macaca mulatta	ENSMMUG00000004433	1 retrocopy	retro_mmul_1628 ,
Mus musculus	ENSMUSG00000058355	1 retrocopy	retro_mmus_1503,
Nomascus leucogenys	ENSNLEG00000005460	1 retrocopy	retro_nleu_2125,
Oryctolagus cuniculus	ENSOCUG00000001821	2 retrocopies	retro_ocun_1925, retro_ocun_668,
Procavia capensis	ENSPCAG00000006183	1 retrocopy	retro_pcap_90,
Pongo abelii	ENSPPYG00000015097	1 retrocopy	retro_pabe_3067,
Pan troglodytes	ENSPTRG00000016481	1 retrocopy	retro_ptro_2603,