RetrogeneDB ID: retro_sscr_706

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:95810912..95811329(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGOH
• Ensembl ID: ENSSSCG00000003849
• Aliases: None
• Description: mago-nashi homolog, proliferation-associated (Drosophila) [Source:HGNC Symbol;Acc:6815]

Sequence

>retro_sscr_706
CTGTGTTACTACCTGGGTTATTAGGGCAAGTTCAACCCTGAATTCCTCAAGTTTGAGTTCTGACCTGACAGGAAACTGAT
ATATGCCAACAACAGTGATTATAAAAATGATGTCATGCTCAGAAAGGAGGCTTATGTACACAAAAATGTGATGGAGGAAC
TGAAAAGAATAACTGATGAAGAAAATGAAATTCCCAAGGATGATGCTTTGTGGCCTCCTCCTGACCCAGGGAGCCAAAAT
AAGCTTGAAATCATCATTGGAGATGAACGTATTTCTTTCACAACATCAAAAATTGGTTCCCTCATTGATATCAATCAACC
CAAGAATCCAGAGAGCTTATGAGTATTATATTATCATGCTCAGGACCTGAAGTGTTTGGTCTTCAGTCTGATTGGAATAG
GCTTCAAGATTAAGCCA

Alignment

ORF - retro_sscr_706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.94 %
• Parental protein coverage: 95.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSEITKEDDAL
          L.YY.G..GKF..EFL.FEF.PD.KL.YANNS.YKNDVM.RKEAYVHK.VMEELKRI.D.......DDAL
Retrocopy LCYYLGY*GKFNPEFLKFEF*PDRKLIYANNSDYKNDVMLRKEAYVHKNVMEELKRITDEENEIPKDDAL

Parental  WPPPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYLVQDLKCLVFSLIGLHFKIKP
          WPPPD......LEI.IGDE.ISFTTSKIGSLID.NQ.K.PE.L.V.YY..QDLKCLVFSLIG..FKIKP
Retrocopy WPPPDPGSQNKLEIIIGDERISFTTSKIGSLIDINQPKNPESL*VLYYHAQDLKCLVFSLIGIGFKIKP

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	13.01 RPM
SRP014902_testis	0.00 RPM	17.82 RPM
SRP018288_heart	0.00 RPM	13.62 RPM
SRP018288_kidney	0.00 RPM	20.98 RPM
SRP018288_liver	0.00 RPM	9.91 RPM
SRP018288_lung	0.00 RPM	42.87 RPM
SRP018856_adipose	0.00 RPM	18.17 RPM
SRP035408_brain	0.00 RPM	28.55 RPM
SRP035408_liver	0.00 RPM	32.09 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_706 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_706 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_706 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009587	1 retrocopy	retro_amel_853,
Erinaceus europaeus	ENSEEUG00000015908	6 retrocopies	retro_eeur_232, retro_eeur_275, retro_eeur_387, retro_eeur_45, retro_eeur_463, retro_eeur_568,
Felis catus	ENSFCAG00000025232	2 retrocopies	retro_fcat_1246, retro_fcat_980,
Rattus norvegicus	ENSRNOG00000012778	1 retrocopy	retro_rnor_1168,
Sorex araneus	ENSSARG00000012081	2 retrocopies	retro_sara_142, retro_sara_150,
Sus scrofa	ENSSSCG00000000635	1 retrocopy	retro_sscr_971,
Sus scrofa	ENSSSCG00000003849	3 retrocopies	retro_sscr_1007, retro_sscr_706 , retro_sscr_977,