RetrogeneDB ID: retro_mmul_1542

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 2:167001483..167001915(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMMUG00000021632
• Aliases: None
• Description: None

Sequence

>retro_mmul_1542
TTCAAAGCCAGTTATACCTTCGAAAAGAGTCATGTTTTCATCCAGGGTTTGCCAGAAGGCCTGGGAGTGTCAAGTCTCCA
GCAGATCCTCCAGGTACAAAATCTGTTGGATCGGCTACTTTTCTTGATGTGCTTGGATGAACATGGGCTTGCACAGGGTG
AAGTTGGTGAGGCATGGGTTGGTGAGAGCCTTCAGTGGGATCTGGGTGGTGACCGTGGTCTGAAAGAAGCCTGGGTTGAA
CTAGTACAACTTCAGGACAATGAAGTTGGCTTCTAGATAGGCATTCTCCTTGACCTGCATCTCCACATAGCTCCCCAGGG
TGGCCAGGTTCTCAGAATTATACCTGTGGATATTGTTAAGCAACTTGCCCACATTCACTCTCATCTGCTAAAACATCACT
ATGACTATGGTCACCTTCTACAGCCAGGGCTG

Alignment

ORF - retro_mmul_1542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.09 %
• Parental protein coverage: 95.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FKASYTFQEVHVFIQGLLYPEGLEVAGLQQVPKVQNLSDWPFFLLACLSHTALAPGEICVRQVGEGLQQD
          FKASYTF...HVFIQGL..PEGL.V..LQQ...VQNL.D...FL..CL....LA.GE.....VGE.LQ.D
Retrocopy FKASYTFEKSHVFIQGL--PEGLGVSSLQQILQVQNLLDRLLFLM-CLDEHGLAQGEVGEAWVGESLQWD

Parental  LGGDRGLKEGWVELTARHLQLQDSQVGFQIIGIFLGLRLHIALQGGQVLRITGPVDTLEQLAHVSSHLFK
          LGGDRGLKE.WVEL.....QLQD..VGF..IGI.L.L.LHIA.QGGQVLRI..PVD...QLAH..SHL.K
Retrocopy LGGDRGLKEAWVEL----VQLQDNEVGF-*IGILLDLHLHIAPQGGQVLRII-PVDIVKQLAHIHSHLLK

Parental  HRHDFCRFPQPGL
          H..D.....QPGL
Retrocopy HHYDYGHLLQPGL

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	0.00 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.08 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.04 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1542 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1542 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1542 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2616
Pan troglodytes	retro_ptro_1763
Pongo abelii	retro_pabe_2342
Macaca mulatta	retro_mmul_1478

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000021632	2 retrocopies	retro_mmul_1542 , retro_mmul_2098,
Pongo abelii	ENSPPYG00000009938	2 retrocopies	retro_pabe_136, retro_pabe_2466,