RetrogeneDB ID: retro_mmul_1848

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 4:100043243..100044699(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: R3HDM2
• Ensembl ID: ENSMMUG00000021789
• Aliases: None
• Description: None

Sequence

>retro_mmul_1848
CTTTGTGCTCTCCCACCCACACCTCAGCAATAGCCACCCTTGAATAATAACATGATCTCACAGGCAGATGACCTCAGCAA
CTCCTTTGGACAAATGAGCCCTAGGTGCCAAGGTTCTACTAAAGCAACTGACTCATCGGCACCTCTATTCCAGCTGCCAC
TCATCTCCCAGCACCATCAGTGGGCTAACTTCATCATGGCATCCATGGGTCAGCCCCTCCCCACCTCTAACTGTTCCACC
TCTAGCCAAGCATCAGCTACTCAGCAAGTGCTGCTACCCTGGGGCTACATGCAGCCTTCTCAACAGATCCAGGTTTCTTA
CTAATACCCCTGGACAATATCCTAATTCCAACCAGCAATATTAACATTTCTGTCACCTGGTGGCCTGCAGATCCCGATGT
GGTCAAAAACTTGCTCAGCCATCCCAGCAGCCCGGTTTATAGCCGATGATGCCTAAATGGCAGCAGGTGGCTTACCAAGG
AATGATAGGGGTTCCAGCAGCCACAGAACCAGGGCCTGCTCTGCAGTCAGAGAAGCAGTGTGGGGGGCTAGATGCAAGGC
CTGGTGGTTCAGTACCCTCCACTGCCTTCTTACCAAGTCTCAGTGGGTAATCACTCACAAAATGTGGTCCAGCAGCCTTT
CTAGCAACTCATGCTGGCCCCTGTGAGCCAGTCTGGGTAAGGAGGCCCCCCAAAAGGGGGCATACCAGTGTACTACAGCA
TGATCCCACTGGCTCAGCAGAACCATACAAGCCCTACTGTTGGGTTTCTGCAGCCTCCTGGGTCTCAGCAGTACCAGATG
CTTCAGTTTCCCTCTCCCTGCAGTCTACCACAGATGCCGCAGCAGTAGTCAGGAGTGTCACCTTCTGGACCAGCTGTGGT
GATCATGCAGCTGAATTTCACTAATGGACCCTGAACCTACTCAGAACCCATCCAGGGTCCAGTGGAGTCACTGTAAATAC
TACAACATGGACCACGAGGACCAGAAGCCTGGAGACCTGTACAATCCTGATATCAGCCCCCAGGCCAACACACAAATAAG
CAGCAGCCCTGACACATTTCCTACCCAGGCTTTACCACCCTCTCCTGTCACCAGCTTCAGTGGTGGCTGTCTGCATAGGA
CTCAGTCCCTTGTTTGTCTTCAGATGGTTCCCCTGGCCTGGGGGTCCAGCACAGGGTGATGGGTGTTACTCCCTCTTAGG
CCAGCCTTTAGAGTACAATCTGTCCATCTGCCCTCCCTTGCTCCATGGCCAGTCAACTTACACAGTGCACCAGGGACAGA
GTGGACATGGAAACCAGGGCAACAGACAAGCACTCAAATCTGCCTCCTCTGACATGGAGACAGCAGATGTTGTCTTGGGG
CAGGTGCTGGAGGTGACAGATCTCCCTGAGGGCATCACCTGTACTGAGGCATACAAACTCTTTAAGCAGCTTGCTATGTC
CAATGCCAAGACTCAG

Alignment

ORF - retro_mmul_1848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 55.94 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LPALPPTPQQQPPLNNHMISQADDLSNPFGQMSLSRQGSTEAADPSAALFQTPLISQHPQQTSFIMASTG
          L.ALPPTPQQ.PPLNN.MISQADDLSN.FGQMS...QGST.A.D.SA.LFQ.PLISQH.Q...FIMAS.G
Retrocopy LCALPPTPQQ*PPLNNNMISQADDLSNSFGQMSPRCQGSTKATDSSAPLFQLPLISQHHQWANFIMASMG

Parental  QPLPTSNYSTSSHAPPTQQVLPPQGYMQPPQQIQVSY-YPPGQYPNSNQQYRPLSHPVAYSPQRGQQLPQ
          QPLPTSN.STSS.A..TQQVL.P.GYMQP.QQIQVSY...PGQYPNSNQQY....H.VA.....GQ.L.Q
Retrocopy QPLPTSNCSTSSQASATQQVLLPWGYMQPSQQIQVSY>NTPGQYPNSNQQY*HFCHLVACRSRCGQKLAQ

Parental  PSQQPGLQPMMPNQQQAAYQGMIGV-QQPQNQGLLSSQRSSMGGQMQGLVVQYTPLPSYQVPVGSDSQNV
          PSQQPGL.PMMP..QQ.AYQGMIGV.QQPQNQGLL.SQRSS.GG.MQGLVVQY.PLPSYQV.VG..SQNV
Retrocopy PSQQPGL*PMMPKWQQVAYQGMIGV>QQPQNQGLLCSQRSSVGG*MQGLVVQYPPLPSYQVSVGNHSQNV

Parental  VQPPFQQPMLVPASQSVQGGLPAAGVPVYYSMIPPAQQNGTSPSVGFLQPPGSEQYQMPQSPSPCSPPQM
          VQ.PF.Q.ML.P.SQS..GG.P..G.PVYYSMIP.AQQN.TSP.VGFLQPPGS.QYQM.Q.PSPCS.PQM
Retrocopy VQQPF*QLMLAPVSQSG*GGPPKGGIPVYYSMIPLAQQNHTSPTVGFLQPPGSQQYQMLQFPSPCSLPQM

Parental  PQQYSGVSPSGPGVVVMQLNVPNG-PQPPQNPSMVQWSHCKYYSMDQRGQKPGDLYSPDSSPQANTQMSS
          PQQ.SGVSPSGP.VV.MQLN..NG.P.P.QNPS.VQWSHCKYY.MD...QKPGDLY.PD.SPQANTQ.SS
Retrocopy PQQ*SGVSPSGPAVVIMQLNFTNG>PEPTQNPSRVQWSHCKYYNMDHEDQKPGDLYNPDISPQANTQISS

Parental  SPVTSPTQSPAPSPVTSLSSVCT-GLSPLPVLTQFPRPGGPAQG-DGRYSLLGQPLQYNLSICPPLLHGQ
          SP.T.PTQ...PSPVTS.S..C......L..L...P...G...G.DG.YSLLGQPL.YNLSICPPLLHGQ
Retrocopy SPDTFPTQALPPSPVTSFSGGCLHRTQSLVCLQMVPLAWGSSTG>DGCYSLLGQPLEYNLSICPPLLHGQ

Parental  STYTVHQGQSGLKHGNRGKRQALKSASTDLGTADVVLGRVLEVTDLPEGITRTEADKLFTQLAMSGAKIQ
          STYTVHQGQSG..HGN.G.RQALKSAS.D..TADVVLG.VLEVTDLPEGIT.TEA.KLF.QLAMS.AK.Q
Retrocopy STYTVHQGQSG--HGNQGNRQALKSASSDMETADVVLGQVLEVTDLPEGITCTEAYKLFKQLAMSNAKTQ

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	122.58 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	155.80 RPM
SRP007412_cerebellum	0.00 RPM	77.04 RPM
SRP007412_heart	0.00 RPM	73.43 RPM
SRP007412_kidney	0.00 RPM	80.16 RPM
SRP007412_liver	0.00 RPM	71.05 RPM
SRP007412_testis	0.00 RPM	74.11 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1848 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1848 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1848 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018361	1 retrocopy	retro_btau_637,
Macaca mulatta	ENSMMUG00000021789	1 retrocopy	retro_mmul_1848 ,
Ictidomys tridecemlineatus	ENSSTOG00000020756	1 retrocopy	retro_itri_1550,