RetrogeneDB ID: retro_mmus_931

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:51710408..51710594(-)
• Located in intron of: ENSMUSG00000020955

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lsm2
• Ensembl ID: ENSMUSG00000007050
• Aliases: Lsm2, D17H6S56E-2, D17H6S56E2, Dmapl, Dmpkap, G7b, Sm-X5, SmX5, snRNP
• Description: LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:90676]

Sequence

>retro_mmus_931
ATGCTCTTTCACTCCTTTTTGAAGTCCCCTGTGGTCAAGGGTGTAGTCATGGAACCCAAGAATGACCTGAGCATCTGTGG
AACCCTCCACTCCGTGGAATAGTACCTCAAAATCAAACTAGCCGACATCAGCACCACAGACCCTGAGAAATACCTTCACA
TGTTATCGGTCAAGAACTGCTTCGTC

Alignment

ORF - retro_mmus_931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.42 %
• Parental protein coverage: 65.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLFYSFFKSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVKNCFI
          MLF.SF.KS.V.K.VV.E.KNDLSICGTLHSV..YL.IKL.DIS.TDPEKY.HMLSVKNCF.
Retrocopy MLFHSFLKSPVVKGVVMEPKNDLSICGTLHSVE*YLKIKLADISTTDPEKYLHMLSVKNCFV

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	0.02 RPM	6.59 RPM
SRP007412_cerebellum	0.09 RPM	9.12 RPM
SRP007412_heart	0.00 RPM	6.79 RPM
SRP007412_kidney	0.00 RPM	7.08 RPM
SRP007412_liver	0.00 RPM	9.48 RPM
SRP007412_testis	0.00 RPM	99.35 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_931 was not detected

EST

No EST(s) were mapped for retro_mmus_931 retrocopy.

TSS

No TSS is located nearby retro_mmus_931 retrocopy 5' end.

Lab

retro_mmus_931 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_931 has 0 orthologous retrocopies within eutheria group .

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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,