RetrogeneDB ID: retro_mmul_647

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:78509328..78510548(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2851
• Ensembl ID: ENSMMUG00000001454
• Aliases: None
• Description: aconitate hydratase, mitochondrial [Source:RefSeq peptide;Acc:NP_001248093]

Sequence

>retro_mmul_647
CTGGCAAATGCAAGTGTCAGATATGGCGGGGGCTTCTGGAAGCCTGGATCTGGAATCACTCACCAGCTTATTTTGGAAAA
CTATGAATACCTTGGGGTTCTTCTGATTGACACTGACTCCCATACCCCCAGTGGTGGCAGCCTGGGGGGCATCTGCATTG
GAGTTGGGGGTGCTGAACTGTGGGTGTCATGACTGGGATCCCCTGGGAGCTGAAGCCCCCCAAGGTGATTGGCATGAAGC
TGATGGGCTCCCTCTCCGGTTGGATTTCACCCAAAGGTGTGATTCTGAAGGTGGCAGGCATCCTCACAGTGAAAGGTGGC
ACAGGTGCAATCGTGGAATACCACGGGCCTGGTGTAGACTCCATCTCCTGCACTGGCATGGTGATAGTCTGCAACATGGG
CACAGAAATTGGGGCCACCACTTCCGTGTTTCCTTACAACCACACGATGAAGTAGTACCTGAGCAAGACCTGCCGGGCAG
ACATTGCCAATCTAGCTGATGAATTCGAGGATCACTTGGTGCCTGACCCTGGCTGCCATTATGACCAACTAATTGAAGTT
AACCTCAGTGAACTGAAGCCGCACATCAATGGGCCCTTCACCCCTGACCTGGCTCCCCCCGTGGCAGAAGTGGGCAAGGT
GGCAGAGAAGGAAGGATGGCCTCTGGACATCTGACTGGGTCTGATTGGCAGCTGCACCAATTCAAGCTATGAAGATATGG
GGCACTCAGCAGCTGTGGCCAAGCAGGCACTAGCCCATGGCCTCAAGTGCAAGTCCCAGTTCACGATCACTCCATGCTCT
GAGCAGATGTGCACCACCACTGAGCGGGACGGCTAAGCACAGACCTTGAGGGATGTGGGCGGCATCGTCCTGGCCAATGC
TTGTGGCCCCTGCAATGGCCAGTGGGACAGGAAGGACATCAAGAAGCAGGAGAAGAACATAACTGTCACCTCCTACAACA
GGAACTTCACGGGCTGCAATGACACAAACCCTGAGACCCACGCCTTCGTCACATCCCCAGAGACTGTCACAGCCCTGGCC
ATTGTGGGAACCCTCAAGTTCAACCCAGAGACCAACTACCTGACAGGCAAGGATGGCAAGAAGTTCAAGTTGGAGGGTCC
TGATGCAGATGGGCTTCCTCAAGCAGAGCTGGACCCAGGATAGGACACCTACCAGCACTCCTGCAAGGGCTACCACTGAT
CACATCTCGGCTGCTGGCCC

Alignment

ORF - retro_mmul_647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.09 %
• Parental protein coverage: 52.18 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LATAGAKYGVGFWKPGSGIIHQIILENYAYPGVLLIGTDSHTPNGGGLGGICIGVGGAD-AVDVMAGIPW
          LA.A...YG.GFWKPGSGI.HQ.ILENY.Y.GVLLI.TDSHTP.GG.LGGICIGVGGA...V.VM.GIPW
Retrocopy LANASVRYGGGFWKPGSGITHQLILENYEYLGVLLIDTDSHTPSGGSLGGICIGVGGAE<TVGVMTGIPW

Parental  ELKCPKVIGVKLTGSLSGWTSPKDVILKVAGILTVKGGTGAIVEYHGPGVDSISCTGMATICNMGAEIGA
          ELK.PKVIG.KL.GSLSGW.SPK.VILKVAGILTVKGGTGAIVEYHGPGVDSISCTGM...CNMG.EIGA
Retrocopy ELKPPKVIGMKLMGSLSGWISPKGVILKVAGILTVKGGTGAIVEYHGPGVDSISCTGMVIVCNMGTEIGA

Parental  TTSVFPYNHRMKKYLSKTGRADIANLADEFKDHLVPDPGCHYDQLIEVNLSELKPHINGPFTPDLAHPVA
          TTSVFPYNH.MK.YLSKT.RADIANLADEF.DHLVPDPGCHYDQLIEVNLSELKPHINGPFTPDLA.PVA
Retrocopy TTSVFPYNHTMK*YLSKTCRADIANLADEFEDHLVPDPGCHYDQLIEVNLSELKPHINGPFTPDLAPPVA

Parental  EVGKVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFTITPGSEQIRATIERDGY
          EVGKVAEKEGWPLDI..GLIGSCTNSSYEDMG.SAAVAKQALAHGLKCKSQFTITP.SEQ...T.ERDG.
Retrocopy EVGKVAEKEGWPLDI*LGLIGSCTNSSYEDMGHSAAVAKQALAHGLKCKSQFTITPCSEQMCTTTERDG*

Parental  AQILRDLGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDANPETHAFVTSPEIVTALAIA
          AQ.LRD.GGIVLANACGPC.GQWDRKDIKK.EKN..VTSYNRNFTG.ND.NPETHAFVTSPE.VTALAI.
Retrocopy AQTLRDVGGIVLANACGPCNGQWDRKDIKKQEKNITVTSYNRNFTGCNDTNPETHAFVTSPETVTALAIV

Parental  GTLKFNPETDYLTGTDGKKFKLEAPDADELPKGEFDPGQDTYQHPPKDSSGQHVDVSP
          GTLKFNPET.YLTG.DGKKFKLE.PDAD.LP..E.DPG.DTYQH..K.....H....P
Retrocopy GTLKFNPETNYLTGKDGKKFKLEGPDADGLPQAELDPG*DTYQHSCKGYH*SHLGCWP

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	198.67 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	426.95 RPM
SRP007412_cerebellum	0.00 RPM	138.38 RPM
SRP007412_heart	0.00 RPM	599.63 RPM
SRP007412_kidney	0.00 RPM	412.43 RPM
SRP007412_liver	0.04 RPM	124.33 RPM
SRP007412_testis	0.00 RPM	98.68 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_647 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_647 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_647 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2583

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100412	2 retrocopies	retro_hsap_2583, retro_hsap_324,
Myotis lucifugus	ENSMLUG00000002472	1 retrocopy	retro_mluc_2566,
Macaca mulatta	ENSMMUG00000001454	2 retrocopies	retro_mmul_647 , retro_mmul_694,
Mus musculus	ENSMUSG00000022477	1 retrocopy	retro_mmus_535,
Nomascus leucogenys	ENSNLEG00000015482	2 retrocopies	retro_nleu_1519, retro_nleu_1767,
Pongo abelii	ENSPPYG00000011871	1 retrocopy	retro_pabe_1903,
Pan troglodytes	ENSPTRG00000014428	1 retrocopy	retro_ptro_260,
Drosophila melanogaster	FBgn0010100	1 retrocopy	retro_dmel_56,