RetrogeneDB ID: retro_mmus_560

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:45875290..45875842(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gpx4
• Ensembl ID: ENSMUSG00000075706
• Aliases: Gpx4, GPx-4, GSHPx-4, PHGPx, mtPHGPx, snGPx
• Description: glutathione peroxidase 4 [Source:MGI Symbol;Acc:MGI:104767]

Sequence

>retro_mmus_560
CTGCTGTGCGGGGCTCTGGCTGCGCCTGGTCTGGCAGGCACCATGTGTGCATCCCGCGATGATTGGCGCTGTGCGCGCTC
CATGCACGAATTCTCAGCCAAGGACATCGACGGGCACATGGTCTGCCTGGATAAGTACAGGGGTTTCGTGTGCATCGTCA
CCAATGTGGCCTCGCAATGAGGCAAAACTGACGTAAACTACACTCAGCTAGTCGATCTGCATGCCCGATATGCTGAGTGT
GGTTTACGAATCCTGGCCTTCCCCTGCAACCAGTTTGGGAGGCAGGAGCCAGGAAGTAATCAAGAAATCAAGGAGTTTGC
AGCCGGCTACAACGTCAAGTTTGACATGTACAGCAAGATCTGTGTAAATGGGGACGATGCCCACCCACTGTGGAAATGGA
TGAAAGTCCAGCCCAAGGGCAGGGGCATGCTGGGAAATGCCATCAAATGGAACTTTACCAAGTTTCTCATTGATAAGAAT
GGCTGCGTGGTGAAGCGCTATGGTCCCATGGAGGAGCCCCAGGTGATAGAGAAGGACCTGCCGTGCTATCTC

Alignment

ORF - retro_mmus_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.46 %
• Parental protein coverage: 93.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVCLDKYRGFVCIVTNVASQUGKTDVNYTQL
          LLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVCLDKYRGFVCIVTNVASQ.GKTDVNYTQL
Retrocopy LLCGALAAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVCLDKYRGFVCIVTNVASQ*GKTDVNYTQL

Parental  VDLHARYAECGLRILAFPCNQFGRQEPGSNQEIKEFAAGYNVKFDMYSKICVNGDDAHPLWKWMKVQPKG
          VDLHARYAECGLRILAFPCNQFGRQEPGSNQEIKEFAAGYNVKFDMYSKICVNGDDAHPLWKWMKVQPKG
Retrocopy VDLHARYAECGLRILAFPCNQFGRQEPGSNQEIKEFAAGYNVKFDMYSKICVNGDDAHPLWKWMKVQPKG

Parental  RGMLGNAIKWNFTKFLIDKNGCVVKRYGPMEEPQVIEKDLPCYL
          RGMLGNAIKWNFTKFLIDKNGCVVKRYGPMEEPQVIEKDLPCYL
Retrocopy RGMLGNAIKWNFTKFLIDKNGCVVKRYGPMEEPQVIEKDLPCYL

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	2.38 RPM	64.06 RPM
SRP007412_cerebellum	2.52 RPM	68.04 RPM
SRP007412_heart	7.81 RPM	128.85 RPM
SRP007412_kidney	9.89 RPM	153.07 RPM
SRP007412_liver	3.99 RPM	65.40 RPM
SRP007412_testis	16.28 RPM	387.59 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_560 was not detected

EST

No EST(s) were mapped for retro_mmus_560 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_3535	75 libraries	83 libraries	437 libraries	155 libraries	322 libraries

The graphical summary, for retro_mmus_560 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_560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_560 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022744	1 retrocopy	retro_fcat_1113,
Monodelphis domestica	ENSMODG00000005486	1 retrocopy	retro_mdom_1363,
Mus musculus	ENSMUSG00000075706	2 retrocopies	retro_mmus_1595, retro_mmus_560 ,
Ochotona princeps	ENSOPRG00000008347	4 retrocopies	retro_opri_1144, retro_opri_63, retro_opri_705, retro_opri_929,