RetrogeneDB ID: retro_ocun_569

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:84404795..84405047(-)
• Located in intron of: ENSOCUG00000013852

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOL7
• Ensembl ID: ENSOCUG00000007251
• Aliases: None
• Description: nucleolar protein 7, 27kDa [Source:HGNC Symbol;Acc:21040]

Sequence

>retro_ocun_569
GCCCTGAGGCTCAAAGACCAAGAACTGAGAGATTTGAGGCAGCAAGCGGCCAGGGCCTTCATACACGAATCTTTATATGG
CCCAGGAACCAACAGAACTAGTGTAAACAAGTTCCTGTCTCTCGACAACAAGCGCTTACCAGTGAAGAAGGCTGCAGCCC
AGTTTTTGAACAGTGCTTGGGGAACCCAGAAAAAACAGAATGCCAAGAGATATAAAAGACGATGGATGATCAGAAAGATG
AAAACTCCTAAG

Alignment

ORF - retro_ocun_569 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.81 %
• Parental protein coverage: 50.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALRLKDQELRDSRQQAARAFIHESLYGPGTNRTSVNKFLSLDNKRLPVKKAAAQFLNSAWGTQKKQNAKR
          ALRLKDQELRD.RQQAARAFIHESLYGPGTNRTSVNKFLSLDNKRLPVKKAAAQFLNSAWGTQKKQNAKR
Retrocopy ALRLKDQELRDLRQQAARAFIHESLYGPGTNRTSVNKFLSLDNKRLPVKKAAAQFLNSAWGTQKKQNAKR

Parental  YKRRWMIRKMKTPK
          YKRRWMIRKMKTPK
Retrocopy YKRRWMIRKMKTPK

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
SRP017611_brain	0.22 RPM	26.38 RPM
SRP017611_kidney	0.71 RPM	28.18 RPM
SRP017611_liver	0.23 RPM	19.65 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_569 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_569 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_569 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000007251	3 retrocopies	retro_ocun_1079, retro_ocun_1096, retro_ocun_569 ,
Tarsius syrichta	ENSTSYG00000008153	1 retrocopy	retro_tsyr_536,