RetrogeneDB ID: retro_mmul_1998

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 6:33604621..33605425(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOMM40
• Ensembl ID: ENSMMUG00000014303
• Aliases: None
• Description: mitochondrial import receptor subunit TOM40 homolog [Source:RefSeq peptide;Acc:NP_001247724]

Sequence

>retro_mmul_1998
ATGGGGAACATGTTGGTAGCCAGCTCGCTGCCTGCAGGGCAGCCGCCACCACCTCTGCCCGCCCTCCTGGGGCTGCGGCC
ACCTCCGTCCTAGCATCCGGGCTTCAGGTTGCAGCCGCTGGGAGGCGGCCTGGGCGCCAGGACCAGTGTGGGTGGAGGTT
CGGAACGGACACCCGGGACTGCAACCGCCAGTGCCTCAGAGGGTGCCGAGGAAGGGGCCTGCGGCTGCCTGCCCAAGCCC
TGCACATTGGAGGAGTGCCACCGGAAGTTCAAGGAGCTGTAGATGGAAGGTGTCAAGTTCACAGTGAACAAAGGGTTGAG
TAAGCATTTTCAGGTGAACCACACAGTAACCCTCAGCACAATCAGGGAGTCCAACTACCACTTTGGTGTCATGTATATGG
GAACAAAGCAGCTGAGTCCCACAGAGGCATTCCCTGTACTGGTGGGTGACATGGACAACAGTGGCGGCCTCAATGCTCAG
GTCATTCACCAGCTGGGCCCCAGCCTCAGGTCCAATATGGCCATCCAGACCTAGCAGTCGAAGTTTGTGAACTGGCAGGT
GGATGGGGAGTACCAGGGCTCTGACTTCATAGTGGATGTCACCCTGGGGAACCCAGACGTCCTGATGGGTTCAGGAATCC
TCATAACCCACTACCTACAGAGCATAACGCCTTGCCTGGCCCTGGGCAGAGAGCGGGTCTACCACCGACGGCCTGGGGAG
GAGGGCACTGTCAAGTCTCTAACTGGGAAATACACATCGAACAACTGGTTGGCAACGGTAACGTTGGGTTGGACATAATA
CCAC

Alignment

ORF - retro_mmul_1998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.34 %
• Parental protein coverage: 75.07 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNVLAASSPPAGPPPPPAPALVGLPPPPPSPPGFTLPPLGGGLGAGTSTSRGSERTPGAATASAAGAAE
          MGN.L.ASS.PAG.PPPP.PAL.GL.PPP...PGF.L.PLGGGLGA.TS...GSERTPG.ATASA...AE
Retrocopy MGNMLVASSLPAGQPPPPLPALLGLRPPPS*HPGFRLQPLGGGLGARTSVGGGSERTPGTATASASEGAE

Parental  DGACGCLPNPGTFEECHRKCKELFPIQMEGVKLTVNKGLSNHFQVNHTVALSTIGESNYHFGVTYVGTKQ
          .GACGCLP.P.T.EECHRK.KE.....MEGVK.TVNKGLS.HFQVNHTV.LSTI.ESNYHFGV.Y.GTKQ
Retrocopy EGACGCLPKPCTLEECHRKFKE---L*MEGVKFTVNKGLSKHFQVNHTVTLSTIRESNYHFGVMYMGTKQ

Parental  LSPTEAFPVLVGDMDNSGSLNAQVIHQLGPGLRSKMAIQTQQSKFVNWQVDGEYRGSDFTAAVTLGNPDV
          LSPTEAFPVLVGDMDNSG.LNAQVIHQLGP.LRS.MAIQT.QSKFVNWQVDGEY.GSDF...VTLGNPDV
Retrocopy LSPTEAFPVLVGDMDNSGGLNAQVIHQLGPSLRSNMAIQT*QSKFVNWQVDGEYQGSDFIVDVTLGNPDV

Parental  LVGSGILVAHYLQSITPCLALGGELVYHRRPGEEGTVMSLAGKYTLNNWLATVTLGQAGMH
          L.GSGIL..HYLQSITPCLALG.E.VYHRRPGEEGTV.SL.GKYT.NNWLATVTLG....H
Retrocopy LMGSGILITHYLQSITPCLALGRERVYHRRPGEEGTVKSLTGKYTSNNWLATVTLGWT*YH

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	18.60 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	45.61 RPM
SRP007412_cerebellum	0.00 RPM	11.56 RPM
SRP007412_heart	0.00 RPM	14.19 RPM
SRP007412_kidney	0.00 RPM	16.43 RPM
SRP007412_liver	0.04 RPM	27.11 RPM
SRP007412_testis	0.45 RPM	11.08 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1998 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1998 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1998 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000014041	1 retrocopy	retro_mmur_420,
Myotis lucifugus	ENSMLUG00000028928	1 retrocopy	retro_mluc_697,
Macaca mulatta	ENSMMUG00000014303	1 retrocopy	retro_mmul_1998 ,
Oryctolagus cuniculus	ENSOCUG00000023582	1 retrocopy	retro_ocun_1143,
Pongo abelii	ENSPPYG00000025858	1 retrocopy	retro_pabe_174,
Pan troglodytes	ENSPTRG00000011126	1 retrocopy	retro_ptro_39,
Ictidomys tridecemlineatus	ENSSTOG00000009019	1 retrocopy	retro_itri_150,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74,