RetrogeneDB ID: retro_sscr_1202

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:72819116..72819790(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000030981
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UNG
• Ensembl ID: ENSSSCG00000009938
• Aliases: None
• Description: uracil-DNA glycosylase [Source:HGNC Symbol;Acc:12572]

Sequence

>retro_sscr_1202
ATCATTGGCCAGAAGACTCTCTACTCATTCTCTCCAAGCCTACCAGGAAACAACTTCCCCTCATCCCTGGGCTAGCCAAC
CTAGGGTCCAGGGTGGCAATGGTAGTTGAAAGCAGGGATTTATTAGCCAGCCCAGCCAAGAAGTGCTGGGCCAGCAGGAG
GATCCTGGCCCTCTGCCCTTGTCACTGCTGAGCCCAGAGAAATTAGTCCACATCAGAGGGACAANGGCCAGCAAAGCTTC
TCAGACTTACATTGCTCAGTGTGCCCCATGGGTTTGGAGAGAGTGAAAAGAAGCACCTCAGCAGGGAGTTGGGAACCCAT
ATTTTACAGAGTTTATGGGGTTTGTTGCAGAAGAAAGAAAACATTACACCACCCACACTCACACAAAATCTTCACATGGA
TACAAATGTGTACATAACAAATGTGAAAGTTGTCTTTCTGGGACAGGAACTGTATCACAGACCCAATTAAGCTCATGGGC
TCTGATTTAGCATTCAAAGACCTATCCCAACCCAGCCCAGTTTGGAAAACATTTATAAAGAGCTGTCTACAGGCATAGAC
GGTTTTGTTCTTCCTGGTCATGGAGATTTATCTTGATGGGCCAGGCAAGTTGTTCTCCTGTTCAATGCTGTTCTCATGGT
CCAGGCTCATCAGGCCAGTTCTCATAAAGAGAGG

Alignment

ORF - retro_sscr_1202 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.97 %
• Parental protein coverage: 73.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MIGQKTLYSFFSPNASG-KRRACSPEPDDLGTGVAAVVENGDVTASSVKK-IRTGQEEPGTPPSSPLSPE
          .IGQKTLYSF.SP...G.K.....P....LG..VA.VVE..D..AS..KK.....QE.PG..P.S.LSPE
Retrocopy IIGQKTLYSF-SPSLPG<KQLPLIPGLANLGSRVAMVVESRDLLASPAKK<VLGQQEDPGPLPLSLLSPE

Parental  QLARIQRNKA-AALLRLAARNVPVGFGESWKKHLSGEF-GKPY-FIKLMGFVAEERKRYTVYPPAHQVFT
          .L..I....A.A.LLRL....VP.GFGES.KKHLS.E..G.PY.F....G.V...RK.....P..H..FT
Retrocopy KLVHIRGTXA>AKLLRLTLLSVPHGFGESEKKHLSREL<GNPY<FYRVYG-VCCRRKKTLHHPHSHKIFT

Parental  WTQMCD-IRDVKVVILGQDPYHGPNQAHGLCFSVQRPVPPPPSLENIYKELSTDIEGFVHPGHGDLSGWA
          W.QMC..I..VKVV.LGQ..YH.PN.AHGL.FS.QRP.P..PSLENIYKELST.I.GFV.PGHGDLS.WA
Retrocopy WIQMCT<ITNVKVVFLGQELYHRPN*AHGL*FSIQRPIPTQPSLENIYKELSTGIDGFVLPGHGDLS*WA

Parental  KQGVLLLNAVLTVRAHQANSHKER
          .Q.VLL.NAVL.V.AHQA.SHKER
Retrocopy RQVVLLFNAVLMVQAHQASSHKER

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	0.00 RPM	4.91 RPM
SRP014902_testis	0.00 RPM	47.81 RPM
SRP018288_heart	0.00 RPM	6.71 RPM
SRP018288_kidney	0.00 RPM	17.73 RPM
SRP018288_liver	0.00 RPM	11.83 RPM
SRP018288_lung	0.00 RPM	22.91 RPM
SRP018856_adipose	0.00 RPM	14.21 RPM
SRP035408_brain	0.00 RPM	17.31 RPM
SRP035408_liver	0.00 RPM	12.56 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1202 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1202 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1202 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016525	1 retrocopy	retro_amel_153,
Canis familiaris	ENSCAFG00000011144	1 retrocopy	retro_cfam_1567,
Callithrix jacchus	ENSCJAG00000010134	2 retrocopies	retro_cjac_1467, retro_cjac_520,
Cavia porcellus	ENSCPOG00000004634	3 retrocopies	retro_cpor_1339, retro_cpor_6, retro_cpor_863,
Dasypus novemcinctus	ENSDNOG00000005335	2 retrocopies	retro_dnov_1001, retro_dnov_627,
Equus caballus	ENSECAG00000008080	1 retrocopy	retro_ecab_747,
Felis catus	ENSFCAG00000008349	1 retrocopy	retro_fcat_445,
Macropus eugenii	ENSMEUG00000015792	3 retrocopies	retro_meug_1594, retro_meug_1877, retro_meug_2077,
Myotis lucifugus	ENSMLUG00000010755	3 retrocopies	retro_mluc_1305, retro_mluc_2060, retro_mluc_989,
Macaca mulatta	ENSMMUG00000006957	2 retrocopies	retro_mmul_1564, retro_mmul_2115,
Mustela putorius furo	ENSMPUG00000003463	1 retrocopy	retro_mputfur_1592,
Nomascus leucogenys	ENSNLEG00000001442	3 retrocopies	retro_nleu_1325, retro_nleu_1950, retro_nleu_2802,
Oryctolagus cuniculus	ENSOCUG00000003145	1 retrocopy	retro_ocun_1767,
Otolemur garnettii	ENSOGAG00000007441	2 retrocopies	retro_ogar_1593, retro_ogar_2716,
Pongo abelii	ENSPPYG00000004929	3 retrocopies	retro_pabe_1354, retro_pabe_1355, retro_pabe_2792,
Pan troglodytes	ENSPTRG00000005419	1 retrocopy	retro_ptro_1108,
Sus scrofa	ENSSSCG00000009938	1 retrocopy	retro_sscr_1202 ,
Ictidomys tridecemlineatus	ENSSTOG00000006894	1 retrocopy	retro_itri_661,