RetrogeneDB ID: retro_sscr_337

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:131138752..131139088(+)
• Located in intron of: ENSSSCG00000011776

Retrocopy information

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

Parental gene information

• Parental gene symbol: PA2G4
• Ensembl ID: ENSSSCG00000022666
• Aliases: None
• Description: proliferation-associated 2G4, 38kDa [Source:HGNC Symbol;Acc:8550]

Sequence

>retro_sscr_337
AAAGGTGATGCCATGATGATGGAAGAGATGGGGGTGATTTTTAAGAAAGATAAAGGAATGTAGAAAGGTGTTGCCTTTTC
CACCAGCATTTCGGTAAATAACTGTGTATGTTACTTCTCCTTTTTGAAGAGTGACCAGGACTGTATTGTCAAGGAAGGTG
ACTTGGTAAAAATGGACGTGGGAGTTCATATGGATGGCTGCATTGCTGATGTGGCTCACACTTCCATGGTTGATGTAGCT
CTGGGGACCAAAGTAACCTGGTGGAAAGCAGATGTCATTAAGGCAGCTTACCTTTGTGCTGAAGCTGCCCTATACCCGGT
CAGACCTGGAAACCAG

Alignment

ORF - retro_sscr_337 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.79 %
• Parental protein coverage: 62.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KGDAMIMEETGKIFKKEKEMKKGIAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVHVDGFIAN
          KGDAM.MEE.G.IFKK.K.M.KG.AF.TSISVNNCVC.FS.LKSDQD.I.KEGDLVK.D.GVH.DG.IA.
Retrocopy KGDAMMMEEMGVIFKKDKGM*KGVAFSTSISVNNCVCYFSFLKSDQDCIVKEGDLVKMDVGVHMDGCIAD

Parental  VAHTFVVDVALGTQVTGRKADVIKAAHLCAEAALRLVKPGNQ
          VAHT..VDVALGT.VT..KADVIKAA.LCAEAAL..V.PGNQ
Retrocopy VAHTSMVDVALGTKVTWWKADVIKAAYLCAEAALYPVRPGNQ

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	7.83 RPM
SRP014902_testis	0.14 RPM	13.58 RPM
SRP018288_heart	0.00 RPM	17.10 RPM
SRP018288_kidney	0.00 RPM	21.87 RPM
SRP018288_liver	0.00 RPM	22.07 RPM
SRP018288_lung	0.00 RPM	19.96 RPM
SRP018856_adipose	0.29 RPM	40.86 RPM
SRP035408_brain	0.13 RPM	31.73 RPM
SRP035408_liver	0.00 RPM	24.48 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_337 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_337 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_337 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Callithrix jacchus	ENSCJAG00000011811	2 retrocopies	retro_cjac_4214, retro_cjac_4215,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Macaca mulatta	ENSMMUG00000002164	2 retrocopies	retro_mmul_1168, retro_mmul_2631,
Mus musculus	ENSMUSG00000025364	1 retrocopy	retro_mmus_2803,
Nomascus leucogenys	ENSNLEG00000017544	6 retrocopies	retro_nleu_1212, retro_nleu_1260, retro_nleu_163, retro_nleu_3024, retro_nleu_506, retro_nleu_612,
Oryctolagus cuniculus	ENSOCUG00000017342	1 retrocopy	retro_ocun_1733,
Pongo abelii	ENSPPYG00000025851	7 retrocopies	retro_pabe_1595, retro_pabe_1778, retro_pabe_2375, retro_pabe_2869, retro_pabe_2993, retro_pabe_3430, retro_pabe_3807,
Pan troglodytes	ENSPTRG00000005076	6 retrocopies	retro_ptro_1289, retro_ptro_1389, retro_ptro_1940, retro_ptro_2471, retro_ptro_2846, retro_ptro_3263,
Sus scrofa	ENSSSCG00000000377	1 retrocopy	retro_sscr_338,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337 ,
Tarsius syrichta	ENSTSYG00000006777	1 retrocopy	retro_tsyr_746,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,