RetrogeneDB ID: retro_sscr_873

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:73916537..73916845(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000030273
• Aliases: None
• Description: None

Sequence

>retro_sscr_873
TCTGGCTCTGTGGACATTACTGTAACGACATGCCCTATTGGATAAGGATGGTCTCCAAGAAGAGAAACTGGTACCTTTAC
CCAGCTTGCTTCTGGGAGATGAGTCATGTTTGTGGACTGGGGACAGGCCAAGCTGTACTACATGCTCAGGACAGGAGACG
CTTCACCAAGGCATTACCCGGAATGGGGTGTGTGTGGTGTGGATGGTGGAAGGTGCCAAGTGTCTGGGTGAACCTAGGGG
GTTTTCTTGCTTTGGATTATCTTCTGAAACATATACCTCAAACTTTTGTTCATCCTTCAGAACAAGAT

Alignment

ORF - retro_sscr_873 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.35 %
• Parental protein coverage: 62.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGSVDIIVT-DMPFGKRMGSKKRNWDLYPACLREMSRVCRPGTGRAVLLTQDKKCFTKALSAMGHVW---
          .GSVDI.VT.DMP...RM.SKKRNW.LYPAC..EMS.VC..GTG.AVL..QD...FTKAL..MG.VW...
Retrocopy SGSVDITVT<DMPYWIRMVSKKRNWYLYPACFWEMSHVCGLGTGQAVLHAQDRRRFTKALPGMGCVWCGW

Parental  RKVHTVWVNIGGLHAAVYLLKRTPQTFVHPSEQD
          .KV..VWVN.GG..A..YLLK..PQTFVHPSEQD
Retrocopy WKVPSVWVNLGGFLALDYLLKHIPQTFVHPSEQD

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	15.93 RPM
SRP014902_testis	0.00 RPM	26.87 RPM
SRP018288_heart	0.00 RPM	12.31 RPM
SRP018288_kidney	0.00 RPM	19.70 RPM
SRP018288_liver	0.00 RPM	13.59 RPM
SRP018288_lung	0.00 RPM	17.62 RPM
SRP018856_adipose	0.00 RPM	8.15 RPM
SRP035408_brain	0.00 RPM	19.44 RPM
SRP035408_liver	0.00 RPM	13.03 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_873 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_873 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_873 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000008538	1 retrocopy	retro_mluc_1991,
Macaca mulatta	ENSMMUG00000017307	1 retrocopy	retro_mmul_1600,
Otolemur garnettii	ENSOGAG00000017111	1 retrocopy	retro_ogar_3452,
Sus scrofa	ENSSSCG00000030273	1 retrocopy	retro_sscr_873 ,
Tupaia belangeri	ENSTBEG00000003450	7 retrocopies	retro_tbel_2328, retro_tbel_2589, retro_tbel_3717, retro_tbel_4362, retro_tbel_4489, retro_tbel_4567, retro_tbel_969,