RetrogeneDB ID: retro_mmus_1492

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:15736174..15736585(-)
• Located in intron of: ENSMUSG00000022672

Retrocopy information

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

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_1492
ATGGCGGTGGCAGTAAAATGGGTGATATCAAACAGAACTATCTGGAAGCATTTACTTCCAATCCAAAATGGAGCTTTGTC
TAGTGCTTGTCTCGAATCTACATACTCTTCTCTTCCAGATGACTACAATTGCAAGGTGGACCTCACCTTGACAGCCGACA
GCAGGACAATAGTGTGCTACCACCCTTCTGTGGACATCCCCTAGGAACACACCAAACCCATCCCTCAACCAGATCTTCTG
CATAATAATGAGGAAACCCACAAGCAGATCCTGAAAGCCAAGTTAGAAGTTAGAAAGTGAAAGCAGCTGGAGCAAGGGCC
CATGATAGTACAACTGAGCAAGGTGTTTTACACCACGAAGCATCGCTGATACCTGCATGGACAGTATCACAATCGTAAGA
AACTGAATCCC

Alignment

ORF - retro_mmus_1492 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.86 %
• Parental protein coverage: 97.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAVKWAISNRTIWKHLLPIQNGALSSACHKSTYSSLPDDYNCQVDLALTADGRTIVCYHPSVDIPYEH
          MA.AVKW.ISNRTIWKHLLPIQNGALSSAC..STYSSLPDDYNC.VDL.LTAD.RTIVCYHPSVDIP.EH
Retrocopy MAVAVKWVISNRTIWKHLLPIQNGALSSACLESTYSSLPDDYNCKVDLTLTADSRTIVCYHPSVDIP*EH

Parental  TKPIPQPDLLHNNEETHEQILKAKLEVRKSKQLEQGPMIEQLSKVFYTTKHRWYPHGQYHNRRKKLNP
          TKPIPQPDLLHNNEETH.QILKAKLEVRK.KQLEQGPMI.QLSKVFYTTKHR.Y.HGQYHN.RKKLNP
Retrocopy TKPIPQPDLLHNNEETHKQILKAKLEVRK*KQLEQGPMIVQLSKVFYTTKHR*YLHGQYHN-RKKLNP

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	22.50 RPM
SRP007412_cerebellum	0.04 RPM	26.49 RPM
SRP007412_heart	0.37 RPM	174.17 RPM
SRP007412_kidney	0.21 RPM	91.44 RPM
SRP007412_liver	0.03 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_1492 was not detected

EST

No EST(s) were mapped for retro_mmus_1492 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_45052	471 libraries	534 libraries	66 libraries	1 library	0 libraries

The graphical summary, for retro_mmus_1492 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_1492 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1492 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,