RetrogeneDB ID: retro_mmul_1391

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 19:20503278..20503594(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2072
• Ensembl ID: ENSMMUG00000011089
• Aliases: None
• Description: cytochrome c oxidase assembly protein COX16 homolog, mitochondrial [Source:RefSeq peptide;Acc:NP_001181826]

Sequence

>retro_mmul_1391
ATGTTTGCACCTGCAGTGATGCGTGCTTTGTGCAAGAACAAGACTCTCTGCTACGAAGTCCCCATGTTGTTGCTAATTGT
TGGAGTTTCTTTTGGTCTTTGTGAGTTTTCACAAATCTGACATGATGCTGTGAAGATTAAAATGGATCCTGAGTTGGAAA
AAAAATACTGAAAGCAAATAGTATTATTAGGTCAGAATATGAGAAAATAAAAGACTCTACTTTTGATGACTGGAAGAATA
TTCAAGGACCCAAGCCTTGGAAAGACCTGACCTCCTCCAAGAAAGAAATCCAGAAATCCTTAAGACTAAGACAACT

Alignment

ORF - retro_mmul_1391 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MFAPAVMRAFRKNKTLRYGVPMLLLIVGGSFGLREFSQIRYDAVKIKMDPELEKKLKENKISL-ESEYEK
          MFAPAVMRA..KNKTL.Y.VPMLLLIVG.SFGL.EFSQI..DAVKIKMDPEL..........L..SEYEK
Retrocopy MFAPAVMRALCKNKTLCYEVPMLLLIVGVSFGLCEFSQI*HDAVKIKMDPELXXXY*KQIVLL<RSEYEK

Parental  IKDCKFDDWKNIRGPRPWED-PDVLQGRNPESLKTKTT
          IKD..FDDWKNI.GP.PW.D.PD.LQ.RNPE.LKTKTT
Retrocopy IKDSTFDDWKNIQGPKPWKD<PDLLQERNPEILKTKTT

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	0.22 RPM	7.06 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.98 RPM
SRP007412_cerebellum	0.00 RPM	9.30 RPM
SRP007412_heart	0.12 RPM	19.61 RPM
SRP007412_kidney	0.00 RPM	20.30 RPM
SRP007412_liver	0.00 RPM	11.04 RPM
SRP007412_testis	0.00 RPM	10.03 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1391 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1391 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1391 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000133983	1 retrocopy	retro_hsap_2038,
Macaca mulatta	ENSMMUG00000011089	2 retrocopies	retro_mmul_1368, retro_mmul_1391 ,
Nomascus leucogenys	ENSNLEG00000001776	1 retrocopy	retro_nleu_2908,
Otolemur garnettii	ENSOGAG00000028663	1 retrocopy	retro_ogar_3045,
Pongo abelii	ENSPPYG00000005951	2 retrocopies	retro_pabe_1663, retro_pabe_1664,
Pan troglodytes	ENSPTRG00000006494	1 retrocopy	retro_ptro_1355,
Rattus norvegicus	ENSRNOG00000047115	1 retrocopy	retro_rnor_1546,
Tarsius syrichta	ENSTSYG00000013313	1 retrocopy	retro_tsyr_1700,
Tursiops truncatus	ENSTTRG00000014791	1 retrocopy	retro_ttru_1513,