RetrogeneDB ID: retro_mmus_3725

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:162894757..162895154(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081917
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lsm1
• Ensembl ID: ENSMUSG00000037296
• Aliases: Lsm1, 2810025O06Rik, CASM
• Description: LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1914457]

Sequence

>retro_mmus_3725
ATGAACTATATGCCCGGCACCACCAGCTTCATCGAGGACATCGACAAAAAGCACTTGGTCCTACTTCAAGATGGAAAGAC
ACTTATAGGTTTTTTAAAGAAGCATTGATCAATTTGCTAACTTAGTGCTCCATCAGACTGCAGAGTGAATTCATGTGGGC
AAAAAGTACGGTGATATTCCTCGAGGGATTTCCATGTTCAGAGGAGAAAATGTGGTCCTACTAGGAGAAATAGACCTGGA
GAAGGGGAGTGACACGCCCCTTTAGCAAGTGTCTATTGAAGAGATCCTAGAACAGAGGGTGCAACAGCGGACCAGACTGG
AGGCAGAGAAACTGAAGGTCCAGACCCTTAAAGTTCGGGGCCTCTCCATTCCTCGCGGAGATACTCTGGACGAGTAC

Alignment

ORF - retro_mmus_3725 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.06 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNYMPGTASLIEDIDKKHLVLLRDGRTLIGFL-RSIDQFANLVLHQTVERIHVGKKYGDIPRGIFVVRGE
          MNYMPGT.S.IEDIDKKHLVLL.DG.TLIGFL.RSIDQFANLVLHQT.E.IHVGKKYGDIPRGI...RGE
Retrocopy MNYMPGTTSFIEDIDKKHLVLLQDGKTLIGFL>RSIDQFANLVLHQTAE*IHVGKKYGDIPRGISMFRGE

Parental  NVVLLGEIDLEKESDTPLQQVSIEEILEEQRVQQQTRLEAEKLKVQTLKDRGLSIPRADTLDEY
          NVVLLGEIDLEK.SDTPL.QVSIEEIL.EQRVQQ.TRLEAEKLKVQTLK.RGLSIPR.DTLDEY
Retrocopy NVVLLGEIDLEKGSDTPL*QVSIEEIL-EQRVQQRTRLEAEKLKVQTLKVRGLSIPRGDTLDEY

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	11.61 RPM
SRP007412_cerebellum	0.00 RPM	8.55 RPM
SRP007412_heart	0.00 RPM	4.30 RPM
SRP007412_kidney	0.00 RPM	7.06 RPM
SRP007412_liver	0.00 RPM	7.59 RPM
SRP007412_testis	0.00 RPM	7.82 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3725 was not detected

EST

No EST(s) were mapped for retro_mmus_3725 retrocopy.

TSS

No TSS is located nearby retro_mmus_3725 retrocopy 5' end.

Lab

retro_mmus_3725 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3725 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011141	1 retrocopy	retro_amel_263,
Myotis lucifugus	ENSMLUG00000003734	1 retrocopy	retro_mluc_723,
Mustela putorius furo	ENSMPUG00000009883	1 retrocopy	retro_mputfur_490,
Mus musculus	ENSMUSG00000037296	1 retrocopy	retro_mmus_3725 ,
Oryctolagus cuniculus	ENSOCUG00000015399	1 retrocopy	retro_ocun_1276,
Sarcophilus harrisii	ENSSHAG00000017260	1 retrocopy	retro_shar_532,