RetrogeneDB ID: retro_sscr_792

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 5:19092636..19092891(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000016695
• Aliases: None
• Description: None

Sequence

>retro_sscr_792
GTCGGAACTGCTCGACCTGGGAGCCTAATGGTTATGGTGGGAGGAGTCAAAGACGAATTTGCTGCTGCTCAAGAGGTGCT
GGGGGTGCATGGGCTCCGTTGTGGAGCCCTTAGGGCTGGATAGGCTGCAAGGATCTGCCACAATATGCTGTTAGCTATTC
ATATGATTGGAACTGCTGAAGATGTGAATCTGGGAATCAGGTTAGGGCTTGACCCAAAACTATTGGCTAAAATCCTAACT
ATGAGCTCAATCAGG

Alignment

ORF - retro_sscr_792 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.32 %
• Parental protein coverage: 50.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGAARSGNLTFMVGGVEEEFAAAQELLGCMGSNVVYCGAVGTGQAAKICNNLLLAISMIGTAEAMNLGIR
          VG.AR.G.L..MVGGV..EFAAAQE.LG..G.....CGA...G.AA.IC.N.LLAI.MIGTAE..NLGIR
Retrocopy VGTARPGSLMVMVGGVKDEFAAAQEVLGVHG---LRCGALRAG*AARICHNMLLAIHMIGTAEDVNLGIR

Parental  LGLDPKLLAKILNMSSGR
          LGLDPKLLAKIL.MSS.R
Retrocopy LGLDPKLLAKILTMSSIR

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	13.41 RPM
SRP014902_testis	0.00 RPM	45.97 RPM
SRP018288_heart	0.00 RPM	75.75 RPM
SRP018288_kidney	0.00 RPM	348.32 RPM
SRP018288_liver	0.00 RPM	221.00 RPM
SRP018288_lung	0.00 RPM	21.69 RPM
SRP018856_adipose	0.00 RPM	219.73 RPM
SRP035408_brain	0.00 RPM	11.66 RPM
SRP035408_liver	0.00 RPM	127.08 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_792 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_792 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_792 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005849	1 retrocopy	retro_amel_678,
Choloepus hoffmanni	ENSCHOG00000003153	1 retrocopy	retro_chof_1225,
Dasypus novemcinctus	ENSDNOG00000008640	2 retrocopies	retro_dnov_1465, retro_dnov_1997,
Microcebus murinus	ENSMICG00000000512	1 retrocopy	retro_mmur_1059,
Mus musculus	ENSMUSG00000029776	1 retrocopy	retro_mmus_2360,
Oryctolagus cuniculus	ENSOCUG00000010349	1 retrocopy	retro_ocun_1896,
Sus scrofa	ENSSSCG00000016695	1 retrocopy	retro_sscr_792 ,
Ictidomys tridecemlineatus	ENSSTOG00000004108	1 retrocopy	retro_itri_395,
Tarsius syrichta	ENSTSYG00000014191	1 retrocopy	retro_tsyr_1136,
Tursiops truncatus	ENSTTRG00000015276	4 retrocopies	retro_ttru_124, retro_ttru_150, retro_ttru_589, retro_ttru_807,
Vicugna pacos	ENSVPAG00000012531	1 retrocopy	retro_vpac_571,