RetrogeneDB ID: retro_mmus_2140

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:18533863..18534286(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000040217
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrpl42
• Ensembl ID: ENSMUSG00000062981
• Aliases: Mrpl42, 2700009F22Rik, 2900055D03Rik, D10Ertd322e, HSPC204, L31mt, MRP-L31, PTD007, Rpml31
• Description: mitochondrial ribosomal protein L42 [Source:MGI Symbol;Acc:MGI:1333774]

Sequence

>retro_mmus_2140
GTGGTGGTGGCAGTAAAATGGGCAATATCAAACAGAACTATCTGGAAGCATTTATTTCCAATCCAAAATGAAGCTTTATC
TAGTGCTTGTCACAAATCTACATATTCTTCTCTTCCAGCTGACTACAATCACAAGGTATACCTCACTTTGACATCTGATG
ACAGGACAGTAGTGTGCTACCACACTTCTGTGGACATTTCCTACAAACATACTAAACCTATCTCTCAACCAGATCATCTG
CATAATAAAGAGAAAACACACAAGCAGGTGCTGAAAACCATATTAGAAGGAAAATTCAATGGGCTTGATCAAGGGCCCAT
TAAAGAACAACTAAGCAAGGTGTTCTTCACTACAAATCATCGCTGGTTCCTGCATGGACAGTTTCACAGACATTCCAAGA
AACTGAATCCTCCCAAAGACAGG

Alignment

ORF - retro_mmus_2140 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAVKWAISNRTIWKHLLPIQNGALSSACHKSTYSSLPDDYNCQVDLALTADGRTIVCYHPSVDIPYEH
          ...AVKWAISNRTIWKHL.PIQN.ALSSACHKSTYSSLP.DYN..V.L.LT.D.RT.VCYH.SVDI.Y.H
Retrocopy VVVAVKWAISNRTIWKHLFPIQNEALSSACHKSTYSSLPADYNHKVYLTLTSDDRTVVCYHTSVDISYKH

Parental  TKPIPQPDLLHNNEETHEQILKAKLEVRKSKQLEQGPMIEQLSKVFYTTKHRWYPHGQYHNRRKKLNPPR
          TKPI.QPD.LHN.E.TH.Q.LK..LE..K...L.QGP..EQLSKVF.TT.HRW..HGQ.H...KKLNPP.
Retrocopy TKPISQPDHLHNKEKTHKQVLKTILE-GKFNGLDQGPIKEQLSKVFFTTNHRWFLHGQFHRHSKKLNPPK

Parental  DR
          DR
Retrocopy DR

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	22.50 RPM
SRP007412_cerebellum	0.00 RPM	26.49 RPM
SRP007412_heart	0.00 RPM	174.17 RPM
SRP007412_kidney	0.00 RPM	91.44 RPM
SRP007412_liver	0.00 RPM	34.38 RPM
SRP007412_testis	0.00 RPM	12.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2140 was not detected

EST

No EST(s) were mapped for retro_mmus_2140 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_93854	543 libraries	142 libraries	354 libraries	30 libraries	3 libraries

The graphical summary, for retro_mmus_2140 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_2140 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2140 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000062981	7 retrocopies	retro_mmus_1432, retro_mmus_1492, retro_mmus_1756, retro_mmus_2140 , retro_mmus_656, retro_mmus_721, retro_mmus_722,
Rattus norvegicus	ENSRNOG00000042740	4 retrocopies	retro_rnor_1383, retro_rnor_633, retro_rnor_729, retro_rnor_920,
Ictidomys tridecemlineatus	ENSSTOG00000026544	12 retrocopies	retro_itri_1020, retro_itri_1132, retro_itri_1266, retro_itri_1285, retro_itri_1353, retro_itri_1695, retro_itri_1793, retro_itri_268, retro_itri_284, retro_itri_393, retro_itri_558, retro_itri_899,