RetrogeneDB ID: retro_rnor_2288

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:50394982..50395399(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Prdx2
• Ensembl ID: ENSRNOG00000003520
• Aliases: Prdx2, Tdpx1
• Description: Peroxiredoxin-2 [Source:UniProtKB/Swiss-Prot;Acc:P35704]

Sequence

>retro_rnor_2288
ATCATTGCTTTCAGTAACAGGGCAAGAGAAATTAAGAAACTCAATGTCCCAGTGATTGGTGCTTCTGTGGAGTCTCACTT
CTGTCATCTGGTGTGGATCAATATAGCCAAGAAATAAGGGGCCCTTGGGCAATCCTTTGGTATCAGGTCCCAAGCATACC
ATTGTCATGGTTACGGAGTTTTAATGGCAGGTGAAGGTTTTCATTTCAGGGGTTGCTTTATGATTGATGTTAAAGATGTC
CTTCCTTAGATCACTAAAAGTGTCCTTCCTGTTGGCTACCTTGTACACCAGATGCTGAGATTACTTTAAGCCTTCCAAAT
CCCTGACACACATGACGTAGTGTGCCAAGCTGGCTGGAAACCCAGCAGTGATAACATCAAGCCTGATGTCAGGAAAAGTA
AAGAATATTTTTCTAAG

Alignment

ORF - retro_rnor_2288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.08 %
• Parental protein coverage: 71.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IIAFSDHAEDFRKLGCEVLGVSVDSQFTHLAWINT-PRKEGGLGPLNIPLLADVTKSL-SQNYGVLKNDE
          IIAFS..A....KL...V.G.SV.S.F.HL.WIN..PR.....GPL..PL............YGVL...E
Retrocopy IIAFSNRAREIKKLNVPVIGASVESHFCHLVWINI>PRNK---GPLGNPLVSGPKHTI<CHGYGVLMAGE

Parental  GIAYRGLFIIDAKGVLRQITVNDLPVGRSVDEALRLVQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKE
          G...RG.F.ID.K.VL..IT...LPVG..V...LRL..AFQ..D.H..VC.AGWKP.SD.IKP.V..SKE
Retrocopy GFHFRGCFMIDVKDVLP*ITKSVLPVGYLVHQMLRLL*AFQIPDTHDVVCQAGWKPSSDNIKPDVRKSKE

Parental  YFSK
          YFSK
Retrocopy YFSK

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
SRP017611_brain	0.00 RPM	130.92 RPM
SRP017611_kidney	0.00 RPM	105.44 RPM
SRP017611_liver	0.00 RPM	35.30 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2288 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2288 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 51 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,
Rattus norvegicus	ENSRNOG00000017194	8 retrocopies	retro_rnor_1401, retro_rnor_1488, retro_rnor_1574, retro_rnor_1656, retro_rnor_1736, retro_rnor_2063, retro_rnor_2292, retro_rnor_2401,
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,