RetrogeneDB ID: retro_mmus_472

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:99790431..99791025(-)
• Located in intron of: ENSMUSG00000067028

Retrocopy information

• Ensembl ID: ENSMUSG00000082431
• 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_472
ATGGCCTCTGGCAACGCGCACATAGGAAAGTCGACTCCTGACTTCACGGCCACAGCGGTGGTGGATGGTACCTTCTAGGA
AATCAAGCTTTCGGATTACAGAGGGAAGTATGTAGTCCTCTTTTTCTACCCACTGGACATCACTTTTGTTTGCCCCACGG
AGATCATTGCTTTTAGCGACCATTCTGAGGACTTCTGAAAGCTAGGCTGCGAGGTGCTGGGAGTGTCTGTGGACTCTCAG
TTCACCCACCAGGCATGGATCAATACCCCACGGAAGGAGAGAGGCTTGGGCCCCCTGAATATCCCTCTGCTTGCTGACGT
GACTAAAAGCTTGTCCCAGAATTACGGCGTGTTAAAAAATGATGAGGGCATTGCTTACAGGGGTCTCTTTATCATCGATG
CCAAGGGTGTCCTTCGCCAGATCACAGTCAATGACCTACCTGTGGGACGCTCTGTAGACGAGGCTCTCCGCCTAGTCCAG
GCCTTTCAGTATACAGACGAGCATGGGGAAGTCTCTCCTGCTGTCTGGAAGCCCGGCAGTGACACCATCAAGCCCAATGT
GGATTACAGCAAGTAATACTTCTCCAAACACAAC

Alignment

ORF - retro_mmus_472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.43 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGNAQIGKSAPDFTATAVVDGAFKEIKLSDYRGKYVVLFFYPLDFTFVCPTEIIAFSDHAEDFRKLGC
          MASGNA.IGKS.PDFTATAVVDG.F.EIKLSDYRGKYVVLFFYPLD.TFVCPTEIIAFSDH.EDF.KLGC
Retrocopy MASGNAHIGKSTPDFTATAVVDGTF*EIKLSDYRGKYVVLFFYPLDITFVCPTEIIAFSDHSEDF*KLGC

Parental  EVLGVSVDSQFTHLAWINTPRKEGGLGPLNIPLLADVTKSLSQNYGVLKNDEGIAYRGLFIIDAKGVLRQ
          EVLGVSVDSQFTH.AWINTPRKE.GLGPLNIPLLADVTKSLSQNYGVLKNDEGIAYRGLFIIDAKGVLRQ
Retrocopy EVLGVSVDSQFTHQAWINTPRKERGLGPLNIPLLADVTKSLSQNYGVLKNDEGIAYRGLFIIDAKGVLRQ

Parental  ITVNDLPVGRSVDEALRLVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSKHN
          ITVNDLPVGRSVDEALRLVQAFQYTDEHGEV.PA.WKPGSDTIKPNVD.SK.YFSKHN
Retrocopy ITVNDLPVGRSVDEALRLVQAFQYTDEHGEVSPAVWKPGSDTIKPNVDYSK*YFSKHN

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	0.49 RPM	104.81 RPM
SRP007412_cerebellum	3.39 RPM	84.71 RPM
SRP007412_heart	0.56 RPM	172.93 RPM
SRP007412_kidney	5.10 RPM	116.67 RPM
SRP007412_liver	1.50 RPM	57.24 RPM
SRP007412_testis	1.01 RPM	18.94 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_472 was not detected

EST

No EST(s) were mapped for retro_mmus_472 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_67967	460 libraries	522 libraries	89 libraries	1 library	0 libraries

The graphical summary, for retro_mmus_472 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_472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_472 has 0 orthologous retrocopies within eutheria group .

---

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,