RetrogeneDB ID: retro_sscr_961

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:32792503..32792837(+)
• Located in intron of: ENSSSCG00000023112

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2E2
• Ensembl ID: ENSSSCG00000011209
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 2 [Source:HGNC Symbol;Acc:12478]

Sequence

>retro_sscr_961
ACTATACCTGGTCTAACAGGTTCTTATATATGAAGGTGGTCTTTTTTTTCCTGGATTTCACATTTTCATCCAATTATCCA
TTTAAACTCCCAAAGGTTACTTTCGGCACCAGAATCTATCACTGCAGCATCAACAGTCAGAGAGTCATCTGCCTGGACAT
CCTTAGAGACAACTGGAGTCCTGCTTTGACTTTCCAAAGGTTCTGCTGTTGACCTGTTCTCTTTTGACATACTGTAACCC
TGTATATCCTCTGGCTGGAAGCAGAGCCACTCAGTGTTTGACCAACAGTACAGAATATGACAGGATAGCCAGACAGTGGA
CCAAGAGATATGCA

Alignment

ORF - retro_sscr_961 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.05 %
• Parental protein coverage: 88.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TILGPPGS-VYEGGVFF-LDITFSPDYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSPALTIS-KV
          TI.G..GS..YEGG....LD.TFS..YPFK.PKVTF.TRIYHC.INSQ.VICLDIL.DNWSPALT...KV
Retrocopy TIPGLTGS>IYEGGXXX>LDFTFSSNYPFKLPKVTFGTRIYHCSINSQRVICLDILRDNWSPALTFQ<KV

Parental  LLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYA
          LL..CSLLT.CNP..PL.GS.ATQ..TN..E.DR.ARQWTKRYA
Retrocopy LLLTCSLLTYCNPVYPLAGSRATQCLTNSTEYDRIARQWTKRYA

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	16.46 RPM
SRP014902_testis	0.00 RPM	16.55 RPM
SRP018288_heart	0.00 RPM	17.05 RPM
SRP018288_kidney	0.00 RPM	8.96 RPM
SRP018288_liver	0.00 RPM	9.43 RPM
SRP018288_lung	0.20 RPM	17.51 RPM
SRP018856_adipose	0.00 RPM	6.88 RPM
SRP035408_brain	0.00 RPM	22.93 RPM
SRP035408_liver	0.00 RPM	5.72 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_961 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_961 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_961 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Sus scrofa	ENSSSCG00000011209	2 retrocopies	retro_sscr_759, retro_sscr_961 ,
Sus scrofa	ENSSSCG00000016722	2 retrocopies	retro_sscr_671, retro_sscr_79,
Sus scrofa	ENSSSCG00000024306	1 retrocopy	retro_sscr_783,
Sus scrofa	ENSSSCG00000029822	4 retrocopies	retro_sscr_1016, retro_sscr_672, retro_sscr_673, retro_sscr_918,