RetrogeneDB ID: retro_itri_842

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393332.1:8348954..8349549(+)
• Located in intron of: ENSSTOG00000026416

Retrocopy information

• Ensembl ID: ENSSTOG00000023745
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRDX2
• Ensembl ID: ENSSTOG00000025862
• Aliases: None
• Description: Peroxiredoxin 2 [Source:UniProtKB/TrEMBL;Acc:Q3HRI1]

Sequence

>retro_itri_842
ATGGCCTCTGGAAACGCGCACATCGGAAAGCCCGCCCCTGACTTCACAGCCACCGCGGTGGTGGACGGTGCCTTCAAGGA
GGTCAAGCTCTCTGACTCCAGAGGGAAGTACGTGGTCCTCTTTTTCTACCCACTGGACTTCACTTTTGTGTGCCCCATGG
AGATCATGGCTTTCAGCGAACATGCTGAGGACTTCCACAAGCTGGGCTGCGAGGTGCTGGGTGTCTCTGTCGACTCTCAG
TTCACCCACTTGTCTTGGATCAACACCCCGCGGAAGGAGGGAGGCTTGGGCCCCCTGAACATCCCCCTGCTTGCTGACGT
GACCAGAAGCTTGTCCCATAATTATGGCGTGCTGAAACGCGATGAGGGTATTGCCTACAAGGGGCCTCTTCATCATTGAT
GGCAAGGGAGTCCTTCGCCAGATCACTGTTAATGATTTGCCCGTGGGGCGCTCTGTGGATGAGGCTTTGTGGCTGGTCCA
GGCCTTCCAATACACAGATGAGCATGGGGAAGTTTGCCCCGCTGGCTGGAAGCCTGGCAGTGACACAATCAAGCCCAACG
TGGATGACAGCAAGGAGTATTTTTCCAAGCACAAC

Alignment

ORF - retro_itri_842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.98 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASGNAHIGKPAPDFTATAVVDGAFKEVKLSDYRGKYVVLFFYPLDFTFVCPTEIIAFSEHAEDFRKLGC
          MASGNAHIGKPAPDFTATAVVDGAFKEVKLSD.RGKYVVLFFYPLDFTFVCP.EI.AFSEHAEDF.KLGC
Retrocopy MASGNAHIGKPAPDFTATAVVDGAFKEVKLSDSRGKYVVLFFYPLDFTFVCPMEIMAFSEHAEDFHKLGC

Parental  EVLGVSVDSQFTHLAWINTPRKEGGLGPLNIPLLADVTRSLSHNYGVLKSDEGIAY-RGLFIIDGKGVLR
          EVLGVSVDSQFTHL.WINTPRKEGGLGPLNIPLLADVTRSLSHNYGVLK.DEGIAY.RGLFIIDGKGVLR
Retrocopy EVLGVSVDSQFTHLSWINTPRKEGGLGPLNIPLLADVTRSLSHNYGVLKRDEGIAY>RGLFIIDGKGVLR

Parental  QITVNDLPVGRSVDEALRLVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSKHN
          QITVNDLPVGRSVDEAL.LVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSKHN
Retrocopy QITVNDLPVGRSVDEALWLVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSKHN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_842 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_842 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 47 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,
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	ENSSTOG00000002537	2 retrocopies	retro_itri_1098, retro_itri_1753,
Ictidomys tridecemlineatus	ENSSTOG00000023413	2 retrocopies	retro_itri_631, retro_itri_817,
Ictidomys tridecemlineatus	ENSSTOG00000025862	1 retrocopy	retro_itri_842 ,