RetrogeneDB ID: retro_mmus_1940

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:82507312..82507741(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000080979
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrpl18
• Ensembl ID: ENSMUSG00000057388
• Aliases: None
• Description: mitochondrial ribosomal protein L18 [Source:MGI Symbol;Acc:MGI:1914931]

Sequence

>retro_mmus_1940
ACTAAGGATAAGGAAGTGGTGGCCCCTGAGTTCACCAACCGGAACCCTCGGAATCTGGAGCTCTTAGGGGTAGCTCAGAA
AGAACGGGGCTTGGCTACTGTGTGGCCTAACCGGGAGTTCTGGCACAGGTTGCGAGTTGTAAGGACTCAGCATCACGTAG
AAGCATTTGTTGAGCATCTTAATGGCCAGGTTGTTGTTTCAGCATCCACTGGAGAATGGGCTATTAAAAAACACCTTTAT
AGTACCAGAAACGTGGTGGCTTGTGAGAGCATTGGGCGAGTGCTGGCACAGCGGTGCTTAGAAGCAGGAGTCAACTTCAT
GTTCTACCATCCCACCCCGTGGGAGGCGTCCTCAGACTCGATAAAACGTTTACAAAATGCCATGACAGAAAGTGGCGTGA
TGTTTCGGGAGCCTCGAAAAATCTATGAA

Alignment

ORF - retro_mmus_1940 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 79.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKENEAVAPEFTNRNPRNLELLGVARKERGWATVWPNREFWHRLRVVKTQHHVEAFVEHLNGQVVVSAST
          .K..E.VAPEFTNRNPRNLELLGVA.KERG.ATVWPNREFWHRLRVV.TQHHVEAFVEHLNGQVVVSAST
Retrocopy TKDKEVVAPEFTNRNPRNLELLGVAQKERGLATVWPNREFWHRLRVVRTQHHVEAFVEHLNGQVVVSAST

Parental  REWAIKKHLYSTRNVVACESIGRVLAQRCLEAGINFMVYQPTPWEASSDSIKRLQNAMTESGVMLREPRR
          .EWAIKKHLYSTRNVVACESIGRVLAQRCLEAG.NFM.Y.PTPWEASSDSIKRLQNAMTESGVM.REPR.
Retrocopy GEWAIKKHLYSTRNVVACESIGRVLAQRCLEAGVNFMFYHPTPWEASSDSIKRLQNAMTESGVMFREPRK

Parental  IYE
          IYE
Retrocopy IYE

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	16.42 RPM
SRP007412_cerebellum	0.00 RPM	14.55 RPM
SRP007412_heart	0.03 RPM	41.06 RPM
SRP007412_kidney	0.02 RPM	26.99 RPM
SRP007412_liver	0.00 RPM	22.56 RPM
SRP007412_testis	0.00 RPM	16.51 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1940 was not detected

EST

No EST(s) were mapped for retro_mmus_1940 retrocopy.

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_89464	324 libraries	240 libraries	449 libraries	54 libraries	5 libraries

The graphical summary, for retro_mmus_1940 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_1940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1940 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015398	1 retrocopy	retro_amel_1445,
Dipodomys ordii	ENSDORG00000011514	1 retrocopy	retro_dord_741,
Echinops telfairi	ENSETEG00000007591	1 retrocopy	retro_etel_438,
Homo sapiens	ENSG00000112110	1 retrocopy	retro_hsap_1664,
Gorilla gorilla	ENSGGOG00000014075	1 retrocopy	retro_ggor_1255,
Macaca mulatta	ENSMMUG00000017037	1 retrocopy	retro_mmul_61,
Mus musculus	ENSMUSG00000057388	1 retrocopy	retro_mmus_1940 ,
Otolemur garnettii	ENSOGAG00000007327	1 retrocopy	retro_ogar_1660,
Pongo abelii	ENSPPYG00000017147	3 retrocopies	retro_pabe_1416, retro_pabe_1418, retro_pabe_1421,
Pan troglodytes	ENSPTRG00000018761	1 retrocopy	retro_ptro_1128,
Pteropus vampyrus	ENSPVAG00000005322	2 retrocopies	retro_pvam_1480, retro_pvam_252,
Tarsius syrichta	ENSTSYG00000005598	1 retrocopy	retro_tsyr_1847,