RetrogeneDB ID: retro_mmus_2443

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:26593489..26594016(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082138
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Prdx3
• Ensembl ID: ENSMUSG00000024997
• Aliases: Prdx3, AW822249, Aop1, D0Tohi1, Ef2l, Mer5, Prx3, SP22, TDXM
• Description: peroxiredoxin 3 [Source:MGI Symbol;Acc:MGI:88034]

Sequence

>retro_mmus_2443
ATAGTCTGTGGAGAGTCCAAAGAGCCATACTTTAATGACTTTTAAGGGGAAACACTTAGTGCTTTTCTTCTCTCCTTTTG
ATTTTGTGTATGTGTGTCCTACAAAAGTTGGTTGTTTTTGTGGTAAAGTCAATGGATTTCACAGTATGAACTGGGAAGTG
GTTGCAGTTGTAGTGAATTCCCATTTTAATTCACCTTACATACCATGGAAGCATGACCATTTGAGTCACAAAAACATTAC
ACTGTTGTGTTAAACTAAGGAAATAGCCTGCAAATACAGGGAGTAATCAGAAGGTGCTGGTGTGACTCTCAGGGACCTCT
TTATAATTGACCTTAATGGTGTCATTAAGCACTTGAGTGTCAGTGACAAAACAGTGAGCTGCTGCATGGAAACAACCTCC
CACTTGGTGAGGGCTCCTTAACTTGGCAAGACCCATGGAGATGTCTGCCTTCCCAAAGGATCCTGGATTCCCCTCTGATA
AACCAAGTCCAATGGCTTCCAAATAGTACCTTGTAAAGGTGTATCAG

Alignment

ORF - retro_mmus_2443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.37 %
• Parental protein coverage: 70.04 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VVNGEFKELSLDDF-KGKYLVLFFYPLDFTFVCPTEIVAFSDKANEFHDVNCEVVAVSVDSHFSHLAWIN
          .V.GE.KE....DF.KGK.LVLFF.P.DF..VCPT....F..K.N.FH..N.EVVAV.V....SH.....
Retrocopy IVCGESKEPYFNDF>KGKHLVLFFSPFDFVYVCPTKVGCFCGKVNGFHSMNWEVVAVVVN---SHFNSPY

Parental  TPRKNGGLGHMNITLLSDITKQISRDYGVLLESAGIALRGLFIIDPNGVVKHLSVNDLPVGRSVEETLRL
          .P.K...L.H.NITLL...TK.I...Y....E.AG..LR.LFIID.NGV.KHLSV.D..V....E.T..L
Retrocopy IPWKHDHLSHKNITLLC*-TKEIACKYRE*SEGAGVTLRDLFIIDLNGVIKHLSVSDKTVSCCMETTSHL

Parental  VKAFQFVETHGEVC-PANWTPESPTI-KPSPTASKEYFEKVHQ
          V.A.....THG.VC.P......SP.I.KPSP.ASK.Y..KV.Q
Retrocopy VRAP*LGKTHGDVC<PSQRILDSPLI<KPSPMASK*YLVKVYQ

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	41.96 RPM
SRP007412_cerebellum	0.00 RPM	33.74 RPM
SRP007412_heart	0.00 RPM	166.83 RPM
SRP007412_kidney	0.00 RPM	131.36 RPM
SRP007412_liver	0.00 RPM	69.64 RPM
SRP007412_testis	0.00 RPM	10.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2443 was not detected

EST

No EST(s) were mapped for retro_mmus_2443 retrocopy.

TSS

No TSS is located nearby retro_mmus_2443 retrocopy 5' end.

Lab

retro_mmus_2443 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2443 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012109	3 retrocopies	retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Ciona savignyi	ENSCSAVG00000001209	1 retrocopy	retro_csav_6,
Erinaceus europaeus	ENSEEUG00000009299	1 retrocopy	retro_eeur_238,
Macropus eugenii	ENSMEUG00000007732	3 retrocopies	retro_meug_1219, retro_meug_1735, retro_meug_62,
Monodelphis domestica	ENSMODG00000009286	1 retrocopy	retro_mdom_1062,
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,
Oryctolagus cuniculus	ENSOCUG00000017334	2 retrocopies	retro_ocun_135, retro_ocun_1434,
Pan troglodytes	ENSPTRG00000002992	1 retrocopy	retro_ptro_29,
Ictidomys tridecemlineatus	ENSSTOG00000002537	2 retrocopies	retro_itri_1098, retro_itri_1753,