RetrogeneDB ID: retro_mmul_668

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1099214194767:357..594(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM6
• Ensembl ID: ENSMMUG00000005524
• Aliases: None
• Description: U6 snRNA-associated Sm-like protein LSm6 [Source:RefSeq peptide;Acc:NP_001253894]

Sequence

>retro_mmul_668
ATGAGTCTTCAGAAGCAAACCTCTGGTGACTCTTAAAGCAAATCATGGGTCAGCCAACTGTGGTAAAATTAAATTCAGAG
TGGATTATCGAGGTGTCCTGGCTTGCCTGGATGGCTACATGAATACAGCCCTGGAGCAGGCAGAAGAGTATATAATGGAC
AACTGAAGAATAAGCATGGGGCTGCAATTAGCCACAGAAACCATGTGTTCTACATTGGTGCACAGAAGAAAAGGATG

Alignment

ORF - retro_mmul_668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSLRKQTPSD-FLKQIIGRPVVVKLNSG-VDYRGVLACLDGYMNIALEQTEEYV-NGQLKNKYGDAFIRG
          MSL.KQT..D..LKQI.G.P.VVKLNS..VDYRGVLACLDGYMN.ALEQ.EEY..NGQLKNK.G.A....
Retrocopy MSLQKQTSGD<LLKQIMGQPTVVKLNSE<VDYRGVLACLDGYMNTALEQAEEYI<NGQLKNKHGAAISHR

Parental  NNVLYISTQKRRM
          N.V.YI..QK.RM
Retrocopy NHVFYIGAQKKRM

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	7.17 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.00 RPM
SRP007412_cerebellum	0.00 RPM	7.62 RPM
SRP007412_heart	0.00 RPM	10.78 RPM
SRP007412_kidney	0.00 RPM	7.51 RPM
SRP007412_liver	0.04 RPM	7.88 RPM
SRP007412_testis	0.00 RPM	10.29 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_668 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_668 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_668 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002482	4 retrocopies	retro_cjac_1173, retro_cjac_1278, retro_cjac_3176, retro_cjac_3248,
Dasypus novemcinctus	ENSDNOG00000009322	5 retrocopies	retro_dnov_1118, retro_dnov_176, retro_dnov_2092, retro_dnov_301, retro_dnov_664,
Microcebus murinus	ENSMICG00000000571	1 retrocopy	retro_mmur_1563,
Macaca mulatta	ENSMMUG00000005524	2 retrocopies	retro_mmul_668 , retro_mmul_991,
Macaca mulatta	ENSMMUG00000009302	4 retrocopies	retro_mmul_1521, retro_mmul_361, retro_mmul_550, retro_mmul_893,
Mus musculus	ENSMUSG00000031683	2 retrocopies	retro_mmus_820, retro_mmus_956,
Otolemur garnettii	ENSOGAG00000026665	1 retrocopy	retro_ogar_233,
Pongo abelii	ENSPPYG00000015105	1 retrocopy	retro_pabe_1994,
Pan troglodytes	ENSPTRG00000016488	1 retrocopy	retro_ptro_1545,
Tarsius syrichta	ENSTSYG00000012759	4 retrocopies	retro_tsyr_1332, retro_tsyr_1727, retro_tsyr_340, retro_tsyr_653,