RetrogeneDB ID: retro_sscr_779

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 4:55440273..55440659(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000025751
• Aliases: None
• Description: None

Sequence

>retro_sscr_779
TCTGAACCAATCAGAGTCCTTGTGACTGGAGCAACTGGTTAAATTGCATATTCATTGCTGTAGTGTATTGGAAATGGATC
TGTCTTTGGTAAACACCAGCCTATAATTCTTGAGCTGGTGGATTTCATGCCCATGATGGGCATCCTGGATGGTGTCCTAA
TGGAACAGCAAGACTGTACCCACCCCCTCCTGAAAGATATCATCACAACAGATAGAAAAGAGATTGCCTTCAAAAGCCTT
GATGTGATCATTCTTATGAGCTTCATGCCATAAACGTATTGGATGCAAACAAAAGATTACTCAAAGCAAATATGAAAATC
TTCAAGTGCCAGGGTGCAACCTTGGAGAAATATGCGAAGAAGTCAGTTTAAGGTTATTGCGGTGGT

Alignment

ORF - retro_sscr_779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.08 %
• Parental protein coverage: 79.14 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIAT
          SEPIRVLVTGA.G.IAYSLL..IGNGSVFGK.QPIIL.L.D..PMMG.LDGVLME.QDC..PLLKD.I.T
Retrocopy SEPIRVLVTGATG*IAYSLL*CIGNGSVFGKHQPIILELVDFMPMMGILDGVLMEQQDCTHPLLKDIITT

Parental  DKEEIAFKDLDVAILVGSMPRRDGMERKD-LLKANVKIFKCQGAALDKYAKKSVKVYRGG
          D..EIAFK.LDV.IL...MP....M..KD.LLKAN.KIFKCQGA.L.KYAKKSV..Y.GG
Retrocopy DRKEIAFKSLDVIILMSFMP*TYWMQTKD<LLKANMKIFKCQGATLEKYAKKSV*GYCGG

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	13.67 RPM
SRP014902_testis	0.00 RPM	26.31 RPM
SRP018288_heart	0.00 RPM	161.06 RPM
SRP018288_kidney	0.00 RPM	85.90 RPM
SRP018288_liver	0.00 RPM	21.11 RPM
SRP018288_lung	0.00 RPM	9.06 RPM
SRP018856_adipose	0.00 RPM	80.77 RPM
SRP035408_brain	0.00 RPM	71.52 RPM
SRP035408_liver	0.00 RPM	40.22 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_779 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_779 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_779 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019295	1 retrocopy	retro_btau_466,
Choloepus hoffmanni	ENSCHOG00000007281	5 retrocopies	retro_chof_1260, retro_chof_1513, retro_chof_1892, retro_chof_2001, retro_chof_90,
Callithrix jacchus	ENSCJAG00000007018	4 retrocopies	retro_cjac_1848, retro_cjac_2407, retro_cjac_2418, retro_cjac_282,
Dasypus novemcinctus	ENSDNOG00000013329	2 retrocopies	retro_dnov_109, retro_dnov_2562,
Homo sapiens	ENSG00000014641	1 retrocopy	retro_hsap_3426,
Gorilla gorilla	ENSGGOG00000007085	1 retrocopy	retro_ggor_2316,
Loxodonta africana	ENSLAFG00000016504	2 retrocopies	retro_lafr_1134, retro_lafr_972,
Macaca mulatta	ENSMMUG00000006163	2 retrocopies	retro_mmul_1750, retro_mmul_2496,
Nomascus leucogenys	ENSNLEG00000009823	1 retrocopy	retro_nleu_1363,
Otolemur garnettii	ENSOGAG00000014487	1 retrocopy	retro_ogar_741,
Pongo abelii	ENSPPYG00000012373	1 retrocopy	retro_pabe_2839,
Pan troglodytes	ENSPTRG00000011974	1 retrocopy	retro_ptro_2326,
Sorex araneus	ENSSARG00000007690	1 retrocopy	retro_sara_361,
Sus scrofa	ENSSSCG00000025751	1 retrocopy	retro_sscr_779 ,
Tarsius syrichta	ENSTSYG00000001215	2 retrocopies	retro_tsyr_1790, retro_tsyr_190,