RetrogeneDB ID: retro_sscr_686

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:139337463..139337727(-)
• Located in intron of: ENSSSCG00000014269

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM2
• Ensembl ID: ENSSSCG00000004324
• Aliases: None
• Description: LYR motif containing 2 [Source:HGNC Symbol;Acc:25229]

Sequence

>retro_sscr_686
ATGGCCACTTCTCGCTTATCCCCAGCGACGCTAACGCTAAAACAGTTCATGAGAAGGCAGCAAGTTCTCCTCCTCTACAG
AAGGATTTTGCAAGCAATTCGGGAAGTTCCAAATGATTCTGATCGCAGATACCTGAAGGACTGGGCAAGGGAAGAATTCA
AAAGAAACAAAAATGCCACCGAAGAGTATACAATCCGAATGATGATTACTCAAGGCAATATGCAGCTCAAGGAGTTAGAA
AAAACACTTGCCTTAGCCAGATCT

Alignment

ORF - retro_sscr_686 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATSRLPPATLTLKQFMRRQQVLLLYRRILQAIRQVPNDSDRRYLKDWAREEFKRNKNATEEDTIRMMIT
          MATSRL.PATLTLKQFMRRQQVLLLYRRILQAIR.VPNDSDRRYLKDWAREEFKRNKNATEE.TIRMMIT
Retrocopy MATSRLSPATLTLKQFMRRQQVLLLYRRILQAIREVPNDSDRRYLKDWAREEFKRNKNATEEYTIRMMIT

Parental  QGNMQLKELEKTLALARS
          QGNMQLKELEKTLALARS
Retrocopy QGNMQLKELEKTLALARS

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	0.27 RPM	0.80 RPM
SRP014902_testis	0.42 RPM	5.94 RPM
SRP018288_heart	0.10 RPM	10.63 RPM
SRP018288_kidney	0.20 RPM	9.46 RPM
SRP018288_liver	0.00 RPM	5.92 RPM
SRP018288_lung	0.10 RPM	4.28 RPM
SRP018856_adipose	0.02 RPM	4.87 RPM
SRP035408_brain	0.67 RPM	5.75 RPM
SRP035408_liver	0.29 RPM	5.90 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_686 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_686 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_686 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000009916	1 retrocopy	retro_meug_2134,
Microcebus murinus	ENSMICG00000012230	2 retrocopies	retro_mmur_631, retro_mmur_650,
Mus musculus	ENSMUSG00000045854	2 retrocopies	retro_mmus_474, retro_mmus_790,
Otolemur garnettii	ENSOGAG00000034900	1 retrocopy	retro_ogar_508,
Sus scrofa	ENSSSCG00000004324	1 retrocopy	retro_sscr_686 ,
Ictidomys tridecemlineatus	ENSSTOG00000016198	1 retrocopy	retro_itri_1279,
Tursiops truncatus	ENSTTRG00000007420	1 retrocopy	retro_ttru_1516,