RetrogeneDB ID: retro_mmul_1613

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:74262184..74262676(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: mml-mir-762-3
• Ensembl ID: ENSMMUG00000003225
• Aliases: None
• Description: mml-mir-762-1 [Source:miRBase;Acc:MI0012548]

Sequence

>retro_mmul_1613
ATGGCCGGCCGGACCGTACGGGCCGAGACCCAGAGCCGGGCCGAAGATAACATCAAGAAGGTAATGGCGACCATCGAGAA
GGTCCGGAAATGGAAGAAGCAATGAGTGACTGTGGGTGACACTTCCCTTCGTATCTTCAAGTGAGTGCCAGTGGTGGACC
CCCAGGAGGAGGAGCGAAGGCGGGCAGGTGGCAAGGCAAAGAGATCCCGTGGCCGGGAACGTCGGGGCAGGGGCGCCAGT
CCCCGAGGGGGTGGCCCTCTCATCCTGCTGGATCTCAATGATGAGAACAGCAACCAGAGTTTCCATTCGGAAAGTTCCCT
GCAAAAAGGCACAGAGCCCAGTCCTGAGGGCAGCCCCCAGCCCAGCTGCCCTGTGTCACCTGCCGGACCCCCAGAAGGGG
TCCCTAAAGAGGCTCAGCCCCCACGGCTGGGCCAAAAGAAAAATCCCGGGGGCATAACTGCTGGCAGCACTGACGAACCC
CCAATGCTGACC

Alignment

ORF - retro_mmul_1613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.02 %
• Parental protein coverage: 67.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGRTVRAETRSRAKDDIKKVMATIEKVRRWEKRWVTVGDTSLRIFKWVPVVDPQEEERRRAGGGAERSR
          MAGRTVRAET.SRA.D.IKKVMATIEKVR.W.K..VTVGDTSLRIFK.VPVVDPQEEERRRAGG.A.RSR
Retrocopy MAGRTVRAETQSRAEDNIKKVMATIEKVRKWKKQ*VTVGDTSLRIFK*VPVVDPQEEERRRAGGKAKRSR

Parental  GRERRGRGASPRGGGPLILLDLNDENSNQSFHSEGSLQKGTEPSPGGTPQPSRPVSPAGPPEGVPEEAQP
          GRERRGRGASPRGGGPLILLDLNDENSNQSFHSE.SLQKGTEPSP.G.PQPS.PVSPAGPPEGVP.EAQP
Retrocopy GRERRGRGASPRGGGPLILLDLNDENSNQSFHSESSLQKGTEPSPEGSPQPSCPVSPAGPPEGVPKEAQP

Parental  PRLGQERDPGGITAGSTDEPPMLT
          PRLGQ...PGGITAGSTDEPPMLT
Retrocopy PRLGQKKNPGGITAGSTDEPPMLT

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	2.47 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.84 RPM
SRP007412_cerebellum	0.00 RPM	2.26 RPM
SRP007412_heart	0.00 RPM	9.13 RPM
SRP007412_kidney	0.00 RPM	7.28 RPM
SRP007412_liver	0.00 RPM	5.11 RPM
SRP007412_testis	0.00 RPM	30.46 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1613 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1613 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1613 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007604	2 retrocopies	retro_amel_1090, retro_amel_1613,
Bos taurus	ENSBTAG00000008412	1 retrocopy	retro_btau_618,
Canis familiaris	ENSCAFG00000016715	1 retrocopy	retro_cfam_898,
Dipodomys ordii	ENSDORG00000001676	1 retrocopy	retro_dord_517,
Equus caballus	ENSECAG00000000482	1 retrocopy	retro_ecab_704,
Felis catus	ENSFCAG00000029090	1 retrocopy	retro_fcat_1969,
Macaca mulatta	ENSMMUG00000003225	13 retrocopies	retro_mmul_1247, retro_mmul_1613 , retro_mmul_1818, retro_mmul_2108, retro_mmul_2153, retro_mmul_2644, retro_mmul_390, retro_mmul_724, retro_mmul_740, retro_mmul_750, retro_mmul_755, retro_mmul_791, retro_mmul_975,
Mustela putorius furo	ENSMPUG00000011988	1 retrocopy	retro_mputfur_954,