RetrogeneDB ID: retro_ocun_219

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018728:802582..803164(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023334
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016961
• Aliases: None
• Description: None

Sequence

>retro_ocun_219
TGTGGCCGCAACCTGCTCCCCGCCCCGCAGCCCGAGGAGGAGGACGAGGAGGAGCCGGCGCTGGAGGAGCTGGAGCAGCG
CGAGGTGCTAGTGCTGGGCCTGGACGGCTCGGGCAAGAGCACGTTTCTGCGCGTGCTGTCGGGGAAGCCACCGCTGGAGG
GCCACATCCCCACCTGGGGCTTCAACTCCGTGCGACTGCCCACCAAGGACTTCGAGGTGGACCTGCTGGAGATCGGCGGC
AACCAGAACCTGCGCTTCTACTGGAAGGAGTTTGTGAACGAGGTGGATGTGCTAGTGTTCATGGTGGACTCGGCTGACCG
GCTGCGGCTGCCCTGGGCCCGCCAGGAGCTGCACAGGCTGCTGGACAAGGACCCCAACCTGCCTGTCGTCGTGGTGGCTA
ACAAGCAGGACCTGAGCGAGGCCTTGAGCGTGGTGGAGCTGCAGCAGGAGCTGGGCCTGCAGGCTGTCGACACCCAGCGG
GAAGTTTTCCTCTTGGCGGCCAGCGTAGCTCCTGCAGGCCCTGGCTTTGAAAATCCCGGCACTGTGCACATCTGGAAACT
GCTCCTGGAGCTTCTCTCCTAG

Alignment

ORF - retro_ocun_219 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.37 %
• Parental protein coverage: 75.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPEEEDEEEPALEELEQREVLVLGLDGSGKSTFLRVLSGKPPLEGHIPTWGFNSVRLPTKDFEVDLLEIG
          .PEEEDEEEPALEELEQREVLVLGLDGSGKSTFLRVLSGKPPLEGHIPTWGFNSVRLPTKDFEVDLLEIG
Retrocopy QPEEEDEEEPALEELEQREVLVLGLDGSGKSTFLRVLSGKPPLEGHIPTWGFNSVRLPTKDFEVDLLEIG

Parental  GNQNLRFYWKEFVNEVDVLVFMVDSADRLRLPWARQELHRLLDKDPDLPVVVVANKQDLSEALSVVELQQ
          GNQNLRFYWKEFVNEVDVLVFMVDSADRLRLPWARQELHRLLDKDP.LPVVVVANKQDLSEALSVVELQQ
Retrocopy GNQNLRFYWKEFVNEVDVLVFMVDSADRLRLPWARQELHRLLDKDPNLPVVVVANKQDLSEALSVVELQQ

Parental  ELGLQAIDTQREVFLLAASVAPAGPGFENPGTVHIWKLLLELLS
          ELGLQA.DTQREVFLLAASVAPAGPGFENPGTVHIWKLLLELLS
Retrocopy ELGLQAVDTQREVFLLAASVAPAGPGFENPGTVHIWKLLLELLS

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	0.00 RPM	5.63 RPM
SRP017611_kidney	0.00 RPM	2.53 RPM
SRP017611_liver	0.00 RPM	1.77 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_219 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_219 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001642	3 retrocopies	retro_cpor_136, retro_cpor_1479, retro_cpor_933,
Dasypus novemcinctus	ENSDNOG00000002678	1 retrocopy	retro_dnov_2004,
Oryctolagus cuniculus	ENSOCUG00000016961	1 retrocopy	retro_ocun_219 ,