RetrogeneDB ID: retro_mmul_694

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214729053:2466..3784(-)
• 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_694
ATGGCGCCATACAGCCTACTGATGATCTGGCTGCAGAAAGCTCTGGGTGTGCAGCAGTACCATGTGGCCACAGTCCTGTG
CCAACAGGCCAAGGTGGCGACGAGCCACTTTGAGTCCAAGTACGTCCACTATGACCTGCTAGAGAAGAACATTAACATTA
TTCGCAAACGATTGAACCGGCCTCTGACCCTCTCGGAGAAGATTGTGTATGGACACCTGGATGACCCCGCCAGCTAGGAA
ATCGAGTGGGGCAAGATGTACGTGCAGCAGCGGCCAGACAGCGTGGCCATGCAGGATGCGACGGCCCAGATGGCCATGCT
GCAGTTCATCAGCAGCAGGCTCCCAAGGTGACCGTGCTGTCCACCATCCACTGTGACCATCTGATTGAGGCCCAGCTCGG
GAGTGAAAAAGACCTGCGCCGGGCCAAGGACATCAACCACGAAGCTTATAATTTCCTGGCAAATGCAAGTGTCAGATATG
GCGGGGGCTTCTGGAAGCCTGGATCTGGAATCACTCACCAGCTTATTTTGGAAAACTATGAATACCTTGGGGTTCTTCTG
ATTGACACTGACTCCCATACCCCCAGTGGTGGCAGCCTGCGGGGCATCTGCATTGGAGTTGGGGGTGCTGAACTGTGGGT
GTCATGACTGGGATCCCCTGGGAGCTGAAGCGCCCCAAGGTGATTGGCATGAAGCTGATGGGCTCCCTCTCCGGTTGGAT
TTCACCCAAAGGTGTGATTCTGAAGGTGGCAGGCATCCTCACAGTGAAAGGTGGCACAGGTGCAATCGTGGAATACCACG
GGCCTGGTGTAGACTCCATCTCCTGCACTGGCATGGTGATAGTCTGCAACATGGGCACAGAAATTGGGGCCACCACTTCC
GTGTTTCCTTACAACCACAGGATGAAGTAGTACCTGAGCAAGACCTGCCGGGCAGACATTGCCGATCTAGCTGATGAATT
CGAGGATCACTTGGTGCCTGACCCTGGCTGCCATTATGACCAACTAATTGAAGTTAACCTCAGTGAACTGAAGCCGCACA
TCAATGGGCCCTTCACCCCTGACCTGGCTCCCCCCGTGGCAGAAGTGGGCAAGGTGGCAGAGAAGGAAGGATGGCCTCTG
GACATCTGACTGGGTCTGATTGGCAGCTGCACCAATTCAAGCTATGAAGATATGGGGCACTCAGCAGCTGTGGCCAAGCA
GGCACTAGCCCATGGCCTCAAGTGCAAGTCCCAGTTCACGATCACTCCATGCTCTGAGCAGATGTGCACCACCACTGAGT
GGGACGGCTAAGCACAGACCTTGAGGGATGTGGGCGGC

Alignment

ORF - retro_mmul_694 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.97 %
• Parental protein coverage: 56.54 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPYSLLVTRLQKALGVRQYHVASVLCQRAKVAMSHFEPNEYIHYDLLEKNINIVRKRLNRPLTLSEKIV
          MAPYSLL...LQKALGV.QYHVA.VLCQ.AKVA.SHFE...Y.HYDLLEKNINI.RKRLNRPLTLSEKIV
Retrocopy MAPYSLLMIWLQKALGVQQYHVATVLCQQAKVATSHFE-SKYVHYDLLEKNINIIRKRLNRPLTLSEKIV

Parental  YGHLDDPAGQEIERGKSYLRLRPDRVAMQDATAQMAMLQFISSGLP-KVAVPSTIHCDHLIEAQLGGEKD
          YGHLDDPA..EIE.GK.Y...RPD.VAMQDATAQMAMLQFISS.LP.KV.V.STIHCDHLIEAQLG.EKD
Retrocopy YGHLDDPAS*EIEWGKMYVQQRPDSVAMQDATAQMAMLQFISSRLP<KVTVLSTIHCDHLIEAQLGSEKD

Parental  LRRAKDINQEVYNFLATAGAKYGVGFWKPGSGIIHQIILENYAYPGVLLIGTDSHTPNGGGLGGICIGVG
          LRRAKDIN.E.YNFLA.A...YG.GFWKPGSGI.HQ.ILENY.Y.GVLLI.TDSHTP.GG.L.GICIGVG
Retrocopy LRRAKDINHEAYNFLANASVRYGGGFWKPGSGITHQLILENYEYLGVLLIDTDSHTPSGGSLRGICIGVG

Parental  GAD-AVDVMAGIPWELKCPKVIGVKLTGSLSGWTSPKDVILKVAGILTVKGGTGAIVEYHGPGVDSISCT
          GA...V.VM.GIPWELK.PKVIG.KL.GSLSGW.SPK.VILKVAGILTVKGGTGAIVEYHGPGVDSISCT
Retrocopy GAE<TVGVMTGIPWELKRPKVIGMKLMGSLSGWISPKGVILKVAGILTVKGGTGAIVEYHGPGVDSISCT

Parental  GMATICNMGAEIGATTSVFPYNHRMKKYLSKTGRADIANLADEFKDHLVPDPGCHYDQLIEVNLSELKPH
          GM...CNMG.EIGATTSVFPYNHRMK.YLSKT.RADIA.LADEF.DHLVPDPGCHYDQLIEVNLSELKPH
Retrocopy GMVIVCNMGTEIGATTSVFPYNHRMK*YLSKTCRADIADLADEFEDHLVPDPGCHYDQLIEVNLSELKPH

Parental  INGPFTPDLAHPVAEVGKVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFTITP
          INGPFTPDLA.PVAEVGKVAEKEGWPLDI..GLIGSCTNSSYEDMG.SAAVAKQALAHGLKCKSQFTITP
Retrocopy INGPFTPDLAPPVAEVGKVAEKEGWPLDI*LGLIGSCTNSSYEDMGHSAAVAKQALAHGLKCKSQFTITP

Parental  GSEQIRATIERDGYAQILRDLGG
          .SEQ...T.E.DG.AQ.LRD.GG
Retrocopy CSEQMCTTTEWDG*AQTLRDVGG

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	0.00 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_694 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_694 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_694 has 0 orthologous retrocopies within eutheria group .

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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,