RetrogeneDB ID: retro_sscr_53

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:99927388..99927736(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000003703
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000024080
• Aliases: None
• Description: None

Sequence

>retro_sscr_53
ATGCACGCCCTTCCTGCTTTTGAGTCATTCTTACTTTTCAAAGACGAAAAGATCACCATCCACAAGGACACCAAGGCACC
CAATGCCTGTTTGTTCACCATCGACAAGGAAGACCACACGCTAGGAAATGTTATTAAATCGCAGCTGTTGAAGGACCCCC
AGGTGCTTTTTGCTGGCTGCCAAGTCCCCCACCCCTGGGAGCACAAGATCATTGTCCCAGTGCAGACCACACCGGACTAC
ACCCCCCAGGAGGCCCTCCTCAATGTCATCACAGACCTCATCAGCAAGCTCTCCCTGCTGGAAGAGCGATTGCGGGTGGC
CATCAAAGACAAGCAAGAAGGAATCGAG

Alignment

ORF - retro_sscr_53 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.88 %
• Parental protein coverage: 96.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PFLSLFLQFSGSRXITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIR
          P....FL.F.....ITI.KDTK.PNACLFTI.KEDHTLGN.IKSQLLKDPQVLFAG..VPHP.EHKII..
Retrocopy PAFESFLLFKDEK-ITIHKDTKAPNACLFTIDKEDHTLGNVIKSQLLKDPQVLFAGCQVPHPWEHKIIVP

Parental  VQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE
          VQTTPDY.PQEA..N.ITDLIS.LSLLEER.RVAIKDKQEGIE
Retrocopy VQTTPDYTPQEALLNVITDLISKLSLLEERLRVAIKDKQEGIE

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	0.13 RPM
SRP014902_testis	0.00 RPM	0.42 RPM
SRP018288_heart	0.00 RPM	0.03 RPM
SRP018288_kidney	0.00 RPM	0.10 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.00 RPM	0.20 RPM
SRP018856_adipose	0.00 RPM	0.02 RPM
SRP035408_brain	0.00 RPM	0.00 RPM
SRP035408_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_53 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_53 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_53 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000021507	1 retrocopy	retro_lafr_361,
Myotis lucifugus	ENSMLUG00000010467	2 retrocopies	retro_mluc_2479, retro_mluc_2499,
Monodelphis domestica	ENSMODG00000013617	2 retrocopies	retro_mdom_1699, retro_mdom_1927,
Sus scrofa	ENSSSCG00000024080	1 retrocopy	retro_sscr_53 ,
Ictidomys tridecemlineatus	ENSSTOG00000006377	1 retrocopy	retro_itri_519,