RetrogeneDB ID: retro_mmus_160

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:78393319..78393631(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000064317
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Lsm7
• Ensembl ID: ENSMUSG00000035215
• Aliases: Lsm7, 0910001B06Rik, 1110033F18Rik
• Description: LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913344]

Sequence

>retro_mmus_160
ATGGCGGACAAAGAGAAAAAGAAGAAAGAAAGCATCTTGGACCTCTCCAAGTACATCGATAAGACCATTCGGGTGAAGTT
CCAGGGTGGCCGGGAAGCCAGCGGTATCCTGAAGGGCTTTGACCCACTGCTCAACCTGGTGCTGGATGGGACCATGGAGT
ACATGAGAGACCCTGATGACCAGTACAAGCTGACGGAGGACACTCGGCAGCTGGGGCTTGTCGTATGTCGTGGCACCTCG
GTGGTGCTCATCTGCCCACAGGACGGCATGGAGGCCATCCCCAACCCCTTCGTGCAGCAGCAGGACACTTAG

Alignment

ORF - retro_mmus_160 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MADKEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTMEYMRDPDDQYKLTEDTRQ
          MADKEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTMEYMRDPDDQYKLTEDTRQ
Retrocopy MADKEKKKKESILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTMEYMRDPDDQYKLTEDTRQ

Parental  LGLVVCRGTSVVLICPQDGMEAIPNPFVQQQDT
          LGLVVCRGTSVVLICPQDGMEAIPNPFVQQQDT
Retrocopy LGLVVCRGTSVVLICPQDGMEAIPNPFVQQQDT

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	0.09 RPM	6.19 RPM
SRP007412_cerebellum	0.00 RPM	5.73 RPM
SRP007412_heart	0.00 RPM	8.47 RPM
SRP007412_kidney	0.04 RPM	6.03 RPM
SRP007412_liver	0.03 RPM	3.77 RPM
SRP007412_testis	0.05 RPM	4.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_160 was not detected

EST

1 EST(s) were mapped to retro_mmus_160 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
W13130	78393343	78393502	100	159	0	159

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_5638	92 libraries	156 libraries	661 libraries	146 libraries	17 libraries

The graphical summary, for retro_mmus_160 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_160 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_160 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000013097	1 retrocopy	retro_mluc_331,
Mus musculus	ENSMUSG00000035215	1 retrocopy	retro_mmus_160 ,
Otolemur garnettii	ENSOGAG00000000144	3 retrocopies	retro_ogar_107, retro_ogar_2736, retro_ogar_2867,
Rattus norvegicus	ENSRNOG00000019552	1 retrocopy	retro_rnor_1403,