RetrogeneDB ID: retro_mmus_2403

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:144791836..144792198(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083998
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Prdx2
• Ensembl ID: ENSMUSG00000005161
• Aliases: None
• Description: peroxiredoxin 2 [Source:MGI Symbol;Acc:MGI:109486]

Sequence

>retro_mmus_2403
ATGGCCTCCAACAACACGCACATCAAAAGCCGGCCCCTGACTTCACTGTCACCGCCGCAGCAGATGGTGTTCTTAAGGAA
ATCAGACTTTCAGACTACAGAGGGAAGTACGTGGTCCTCTTTTTCTACCTACTGGATTTCACTTTTGTTTGCCCCACAGA
GATCATCACTTTTAGCGACCATGACAAGGACTTCCAAAAGCTAGGCTTCGAGGTGCTGGGAGTTTCTATGGACTCTCAGT
TTACCCACCTGGCATTGATCAATACCCCACAGGAGGGAAGTTTGGGAACCCTGAATATCCCTCTGCTTGCTGACGTGACT
AAAAGCTTGTCCCAGAATTACAGCGTGTTGAAAAATGATGAG

Alignment

ORF - retro_mmus_2403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.67 %
• Parental protein coverage: 61.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASGNAQIG-KSAPDFTATAVVDGAFKEIKLSDYRGKYVVLFFYPLDFTFVCPTEIIAFSDHAEDFRKLG
          MAS.N..I..K.APDFT.TA..DG..KEI.LSDYRGKYVVLFFY.LDFTFVCPTEII.FSDH..DF.KLG
Retrocopy MASNNTHIK<KPAPDFTVTAAADGVLKEIRLSDYRGKYVVLFFYLLDFTFVCPTEIITFSDHDKDFQKLG

Parental  CEVLGVSVDSQFTHLAWINTPRKEGGLGPLNIPLLADVTKSLSQNYGVLKNDE
          .EVLGVS.DSQFTHLA.INTP..EG.LG.LNIPLLADVTKSLSQNY.VLKNDE
Retrocopy FEVLGVSMDSQFTHLALINTP-QEGSLGTLNIPLLADVTKSLSQNYSVLKNDE

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	104.81 RPM
SRP007412_cerebellum	0.00 RPM	84.71 RPM
SRP007412_heart	0.00 RPM	172.93 RPM
SRP007412_kidney	0.02 RPM	116.67 RPM
SRP007412_liver	0.00 RPM	57.24 RPM
SRP007412_testis	0.00 RPM	18.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2403 was not detected

EST

No EST(s) were mapped for retro_mmus_2403 retrocopy.

TSS

No TSS is located nearby retro_mmus_2403 retrocopy 5' end.

Lab

retro_mmus_2403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2403 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012307	3 retrocopies	retro_amel_1188, retro_amel_1710, retro_amel_55,
Canis familiaris	ENSCAFG00000017163	3 retrocopies	retro_cfam_1603, retro_cfam_1624, retro_cfam_1739,
Ciona intestinalis	ENSCING00000003002	1 retrocopy	retro_cint_8,
Callithrix jacchus	ENSCJAG00000004882	4 retrocopies	retro_cjac_1269, retro_cjac_1795, retro_cjac_2356, retro_cjac_2392,
Dipodomys ordii	ENSDORG00000009005	1 retrocopy	retro_dord_176,
Felis catus	ENSFCAG00000000473	1 retrocopy	retro_fcat_1755,
Homo sapiens	ENSG00000167815	3 retrocopies	retro_hsap_1184, retro_hsap_3278, retro_hsap_3500,
Gorilla gorilla	ENSGGOG00000025089	3 retrocopies	retro_ggor_2366, retro_ggor_2833, retro_ggor_923,
Macaca mulatta	ENSMMUG00000005689	2 retrocopies	retro_mmul_1780, retro_mmul_2061,
Monodelphis domestica	ENSMODG00000006978	1 retrocopy	retro_mdom_1770,
Mustela putorius furo	ENSMPUG00000004591	2 retrocopies	retro_mputfur_28, retro_mputfur_660,
Mus musculus	ENSMUSG00000005161	2 retrocopies	retro_mmus_2403 , retro_mmus_472,
Mus musculus	ENSMUSG00000024997	1 retrocopy	retro_mmus_2443,
Mus musculus	ENSMUSG00000028691	5 retrocopies	retro_mmus_1466, retro_mmus_1659, retro_mmus_1786, retro_mmus_3129, retro_mmus_3167,
Nomascus leucogenys	ENSNLEG00000012800	2 retrocopies	retro_nleu_2110, retro_nleu_2883,
Otolemur garnettii	ENSOGAG00000024998	2 retrocopies	retro_ogar_1993, retro_ogar_244,
Pongo abelii	ENSPPYG00000009607	3 retrocopies	retro_pabe_2711, retro_pabe_2892, retro_pabe_988,
Pan troglodytes	ENSPTRG00000010541	3 retrocopies	retro_ptro_2217, retro_ptro_2372, retro_ptro_812,
Rattus norvegicus	ENSRNOG00000003520	2 retrocopies	retro_rnor_2288, retro_rnor_497,
Sorex araneus	ENSSARG00000000146	1 retrocopy	retro_sara_96,
Sarcophilus harrisii	ENSSHAG00000015596	1 retrocopy	retro_shar_305,
Sus scrofa	ENSSSCG00000013736	2 retrocopies	retro_sscr_155, retro_sscr_962,
Ictidomys tridecemlineatus	ENSSTOG00000025862	1 retrocopy	retro_itri_842,