RetrogeneDB ID: retro_mmul_1875

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 5:43717402..43717559(+)
• Located in intron of: ENSMMUG00000021719

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM2
• Ensembl ID: ENSMMUG00000006832
• Aliases: None
• Description: U6 snRNA-associated Sm-like protein LSm2 [Source:RefSeq peptide;Acc:NP_001247614]

Sequence

>retro_mmul_1875
CTCTTCTGTTCCTTTTTCAGTCCCTGTGGGCAAGGATGTGGACCTGGAACTCAAGAATGACCTGCATATCTGTGGATCCT
TCCATTCTGCGGATCGGTGTCTCAACATCAAATTAACTCACATCAGTGTTACAGACCCTGAGAAATATCCTCACATC

Alignment

ORF - retro_mmul_1875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.55 %
• Parental protein coverage: 56.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFYSF-FKSL-VGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHM
          LF.SF.F.SL.VGKDV..ELKNDL.ICG..HS.D..LNIKLT.ISVTDPEKYPH.
Retrocopy LFCSF<FQSL<VGKDVDLELKNDLHICGSFHSADRCLNIKLTHISVTDPEKYPHI

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	0.11 RPM	4.48 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.58 RPM
SRP007412_cerebellum	0.13 RPM	6.13 RPM
SRP007412_heart	0.00 RPM	2.89 RPM
SRP007412_kidney	0.00 RPM	6.46 RPM
SRP007412_liver	0.08 RPM	4.24 RPM
SRP007412_testis	0.04 RPM	14.51 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1875 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1875 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1875 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2928
Pan troglodytes	retro_ptro_2063

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002601	2 retrocopies	retro_cjac_1828, retro_cjac_2088,
Felis catus	ENSFCAG00000004511	1 retrocopy	retro_fcat_309,
Macaca mulatta	ENSMMUG00000006832	3 retrocopies	retro_mmul_1389, retro_mmul_1875 , retro_mmul_2099,
Mus musculus	ENSMUSG00000007050	1 retrocopy	retro_mmus_931,
Nomascus leucogenys	ENSNLEG00000006371	1 retrocopy	retro_nleu_960,
Ochotona princeps	ENSOPRG00000003668	2 retrocopies	retro_opri_250, retro_opri_917,
Pongo abelii	ENSPPYG00000016461	1 retrocopy	retro_pabe_2765,
Pan troglodytes	ENSPTRG00000017986	3 retrocopies	retro_ptro_1349, retro_ptro_2063, retro_ptro_2284,
Rattus norvegicus	ENSRNOG00000048725	1 retrocopy	retro_rnor_1463,
Ictidomys tridecemlineatus	ENSSTOG00000013144	1 retrocopy	retro_itri_189,