RetrogeneDB ID: retro_mmus_1595

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:80054025..80054559(+)
• Located in intron of: ENSMUSG00000024095

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_1595
GCTGTGCCTGGTCTGGCAGGCACCATGTGTGCATCCCGCAATGATTGGCGCTGTGCTCGCTCCATGCACGAATTCTCAGC
CAAGGACATCGATGGGCACATGGTCTGCCTGGAAAGTACAGGGGTTTATTTAGTGTGCCTCGTCACCAACGTGGCCTCGC
AATGAGGCAAAACCGATGTAAACTATACTCAGCTAGTCGATCTGCATGCCCGATATGCTGAGAGTGGTTTACGAATCCTG
GCTTTCCCCTGCAACCAGTTCGGGAGGCAGGAGCCAGGAAGTAATCAAGAAATCAAGGAGTTTGCAGCCGGCTACAATGT
TAAGTTTGACATGTACAGCAAGATCTGTGTAAATGGGGACGATGCCCACCCACTGTGGAAATGGATGAAAGTCCAGCCCA
AGGGCAGGGGCATGCTGGGAAATGCCATCAAATGGAACGTTACCAAGTTTCTCATTGGTAAGAACGGCTGCGTGGTGAAG
CGCTACGGTCCCATGGAGGAGCCCCAGCTGATAGAGGACCTGCCGTGCTATCTT

Alignment

ORF - retro_mmus_1595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.06 %
• Parental protein coverage: 90.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAPGLAGTMCASRDDWRCARSMHEFSAKDIDGHMVCLDKYRGF-VCIVTNVASQUGKTDVNYTQLVDLHA
          A.PGLAGTMCASR.DWRCARSMHEFSAKDIDGHMVCL.......VC.VTNVASQ.GKTDVNYTQLVDLHA
Retrocopy AVPGLAGTMCASRNDWRCARSMHEFSAKDIDGHMVCLESTGVYLVCLVTNVASQ*GKTDVNYTQLVDLHA

Parental  RYAECGLRILAFPCNQFGRQEPGSNQEIKEFAAGYNVKFDMYSKICVNGDDAHPLWKWMKVQPKGRGMLG
          RYAE.GLRILAFPCNQFGRQEPGSNQEIKEFAAGYNVKFDMYSKICVNGDDAHPLWKWMKVQPKGRGMLG
Retrocopy RYAESGLRILAFPCNQFGRQEPGSNQEIKEFAAGYNVKFDMYSKICVNGDDAHPLWKWMKVQPKGRGMLG

Parental  NAIKWNFTKFLIDKNGCVVKRYGPMEEPQVIEKDLPCYL
          NAIKWN.TKFLI.KNGCVVKRYGPMEEPQ.IE.DLPCYL
Retrocopy NAIKWNVTKFLIGKNGCVVKRYGPMEEPQLIE-DLPCYL

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	0.16 RPM	64.06 RPM
SRP007412_cerebellum	0.17 RPM	68.04 RPM
SRP007412_heart	0.06 RPM	128.85 RPM
SRP007412_kidney	0.15 RPM	153.07 RPM
SRP007412_liver	0.05 RPM	65.40 RPM
SRP007412_testis	0.14 RPM	387.59 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1595 was not detected

EST

No EST(s) were mapped for retro_mmus_1595 retrocopy.

TSS

No TSS is located nearby retro_mmus_1595 retrocopy 5' end.

Lab

retro_mmus_1595 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1595 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,