RetrogeneDB ID: retro_sscr_962

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:42848187..42848651(+)
• Located in intron of: ENSSSCG00000008839

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX2
• Ensembl ID: ENSSSCG00000013736
• Aliases: None
• Description: peroxiredoxin 2 [Source:HGNC Symbol;Acc:9353]

Sequence

>retro_sscr_962
TCTGGCAACCAGCACATAGGAAAGCCCACCCTAGAATTCCAGGCCACTGCTGTGGGGAATGGCGCCTTCAAGGAGGAGAA
GCTTTCTGACTCCAAAGGGAGTACTTGGTCCTCTTTTCTTACCCGCTGGATTTCATCTTTGTATGCCCCACACATATCAC
TTTCAGGAATTGAGCTGAGGAGTTCCACAACCTAGGCTGCGAGGTGCTGGGTGTCTCCGTCGACTCTCAGTTTACCCACC
TGCCTTGGATCAACACCCCCCGGAAGGAGGGAGGCTTGGGCCCCCTGAACATCCCCCTGCTGGCTGATGTAACCAGAAAC
TTGTCCCCTGACCATGGAGTGCCAAAGGACGATGAAGATATCGCCTACAGGGGCCTTTTTATCATCCACCGCAAGGGTGT
CCTTTGCCAGATCATGGTCAATGATTTGCCTGTGGGACACTCCGTGGATGAAGCTCTGAAGCTC

Alignment

ORF - retro_sscr_962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.89 %
• Parental protein coverage: 78.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGNAHIGKPAPEFQATAVVNGAFKEVKLSDYKG-KYLVLFFYPLDFTFVCPTEIIAFSDRAEEFHQLGCE
          SGN.HIGKP..EFQATAV.NGAFKE.KLSD.KG..YLVLF.YPLDF.FVCPT.I..F...AEEFH.LGCE
Retrocopy SGNQHIGKPTLEFQATAVGNGAFKEEKLSDSKG<EYLVLFSYPLDFIFVCPTHI-TFRN*AEEFHNLGCE

Parental  VLGVSVDSQFTHLAWINTPRKEGGLGPLKIPLLADVTRNLSLDYGVLKEDEGIAYRGLFIIDGKGVLRQI
          VLGVSVDSQFTHL.WINTPRKEGGLGPL.IPLLADVTRNLS.D.GV.K.DE.IAYRGLFII..KGVL.QI
Retrocopy VLGVSVDSQFTHLPWINTPRKEGGLGPLNIPLLADVTRNLSPDHGVPKDDEDIAYRGLFIIHRKGVLCQI

Parental  TVNDLPVGRSVDEALRL
          .VNDLPVG.SVDEAL.L
Retrocopy MVNDLPVGHSVDEALKL

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
SRP014902_placenta	0.13 RPM	186.22 RPM
SRP014902_testis	0.28 RPM	208.49 RPM
SRP018288_heart	0.03 RPM	133.90 RPM
SRP018288_kidney	0.10 RPM	261.73 RPM
SRP018288_liver	0.00 RPM	74.04 RPM
SRP018288_lung	0.00 RPM	98.98 RPM
SRP018856_adipose	0.34 RPM	203.91 RPM
SRP035408_brain	0.00 RPM	243.70 RPM
SRP035408_liver	0.00 RPM	84.31 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_962 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_962 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_962 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 44 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	ENSSSCG00000003914	1 retrocopy	retro_sscr_719,
Sus scrofa	ENSSSCG00000013736	2 retrocopies	retro_sscr_155, retro_sscr_962 ,
Ictidomys tridecemlineatus	ENSSTOG00000025862	1 retrocopy	retro_itri_842,