RetrogeneDB ID: retro_sscr_452

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:123418018..123418504(-)
• Located in intron of: ENSSSCG00000010586

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM126B
• Ensembl ID: ENSSSCG00000014905
• Aliases: None
• Description: transmembrane protein 126B [Source:HGNC Symbol;Acc:30883]

Sequence

>retro_sscr_452
GAAAAGACTTTAACTATATATGGAACAGTGACCTTTGGAACAACAGCTAGTTTCTCTGGAATGTTGGCAAATTTAATTTT
CAGACATTGCTTCAAGGTTAAACATGATGGTTTGAAGACATGTGCATCATTGACTATGCTTCCATTTTTGCTACAATAGT
TGCTTATAAGCTTCTTGTAACAGATGCTTTGTATTCAGGTAATATAAGCCGGGAAAATTGTGTTCTGAGAAGTTCACTGA
TTGGCATAGCTTGCCGTGTTTTATATCCCACTGCTTTGGCTTCTTCTGAAAATGGACATCTGGCAATCAAGTATCAAACT
GTTCCACTGCCACCCAAAGGAAGGGTTTTACTCCACTGGCTGCTGCTTTGTCACGCAGAGATAAAAGCAATGGTGATTCC
CCTCCTCCTTCAGACAATCTTTGGAGTATTTCATGGTCTATAGCATTATGTGATTTTTGAAAAGTACACTTGAGAAAACT
GTACAT

Alignment

ORF - retro_sscr_452 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.59 %
• Parental protein coverage: 71.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKTLNIYGTVTFGTTAGFSGMLANLIFRHCFKVKHDGLKTYASLTTLPFL-STVVAYKLLVTDALYSGNI
          EKTL.IYGTVTFGTTA.FSGMLANLIFRHCFKVKHDGLKT.ASLT.LPFL..T.VAYKLLVTDALYSGNI
Retrocopy EKTLTIYGTVTFGTTASFSGMLANLIFRHCFKVKHDGLKTCASLTMLPFL<ATIVAYKLLVTDALYSGNI

Parental  SRENCVLRSSLIGIVCGVLYPTALAFSKNGRLAVKYHTVPLPPKGRVLLHWLLLCHTEIKAMVVPFILQT
          SRENCVLRSSLIGI.C.VLYPTALA.S.NG.LA.KY.TVPLPPKGRVLLHWLLLCH.EIKAMV.P..LQT
Retrocopy SRENCVLRSSLIGIACRVLYPTALASSENGHLAIKYQTVPLPPKGRVLLHWLLLCHAEIKAMVIPLLLQT

Parental  IFGVLHGLQHYAIFE-STLEKTVH
          IFGV.HGL.HY.IFE.STLEKTVH
Retrocopy IFGVFHGL*HYVIFE>STLEKTVH

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	4.25 RPM
SRP014902_testis	0.14 RPM	11.03 RPM
SRP018288_heart	0.03 RPM	13.96 RPM
SRP018288_kidney	0.00 RPM	25.61 RPM
SRP018288_liver	0.00 RPM	20.47 RPM
SRP018288_lung	0.31 RPM	5.29 RPM
SRP018856_adipose	0.00 RPM	14.72 RPM
SRP035408_brain	0.06 RPM	4.99 RPM
SRP035408_liver	0.00 RPM	4.78 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_452 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_452 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_452 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020596	1 retrocopy	retro_btau_420,
Echinops telfairi	ENSETEG00000008939	1 retrocopy	retro_etel_200,
Mus musculus	ENSMUSG00000030614	1 retrocopy	retro_mmus_1618,
Oryctolagus cuniculus	ENSOCUG00000016529	3 retrocopies	retro_ocun_1656, retro_ocun_1671, retro_ocun_607,
Sus scrofa	ENSSSCG00000014905	1 retrocopy	retro_sscr_452 ,