RetrogeneDB ID: retro_ocun_1189

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:42949684..42950116(-)
• Located in intron of: ENSOCUG00000010098

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000010245
• Aliases: None
• Description: None

Sequence

>retro_ocun_1189
ATGCAGAAACGACTACAGAAAGAACTGTTGGCTTTGCAAAATGACCCGCCTCCAGGGATGACTTTAAATGAAAAGAGCGT
TCAAAATTCAATTACACAGTGGATTGTAGACATGGAGGGTGCACCAGGTACCTTATATGAAGGGGAAAAATTTCAACTTC
TATTTAAATTTAGTAGTCGATATCCTTTTGACTCTCCTCAGGTCATGTTTACTGGTGAAAATATTCCTGTTCATCCTCAT
GTTTATAGCAATGGTCATATCTGTTTATCCATTCTAACAGAAGACTGGTCCCCAGCGCTCTCAGTCCAGTCAGTTTGTCT
TAGCATTATTAGTATGCTTTCCAGCTGCAAAGAAAAGAGACGACCACCAGATAATTCTTTTTATGTGCGAACATGTAACA
AGAATCCAAAGAAAACAAAATGGTGGTATCAT

Alignment

ORF - retro_ocun_1189 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.31 %
• Parental protein coverage: 97.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQKRLQKELLALQNDPPPGMTLNEKSVQNSITQWIVDMEGAPGTLYEGEKFQLLFKFSSRYPFDSPQVMF
          .QKRLQKELLALQNDPPPGMTLNEKSVQNSITQWIVDMEGAPGTLYEGEKFQLLFKFSSRYPFDSPQVMF
Retrocopy MQKRLQKELLALQNDPPPGMTLNEKSVQNSITQWIVDMEGAPGTLYEGEKFQLLFKFSSRYPFDSPQVMF

Parental  TGENIPVHPHVYSNGHICLSILTEDWSPALSVQSVCLSIISMLSSCKEKRRPPDNSFYVRTCNKNPKKTK
          TGENIPVHPHVYSNGHICLSILTEDWSPALSVQSVCLSIISMLSSCKEKRRPPDNSFYVRTCNKNPKKTK
Retrocopy TGENIPVHPHVYSNGHICLSILTEDWSPALSVQSVCLSIISMLSSCKEKRRPPDNSFYVRTCNKNPKKTK

Parental  WWYH
          WWYH
Retrocopy WWYH

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	4.58 RPM	1.38 RPM
SRP017611_kidney	4.26 RPM	1.32 RPM
SRP017611_liver	1.62 RPM	0.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1189 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1189 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1189 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000025939	1 retrocopy	retro_mmus_3516,
Ornithorhynchus anatinus	ENSOANG00000008597	1 retrocopy	retro_oana_106,
Oryctolagus cuniculus	ENSOCUG00000010245	1 retrocopy	retro_ocun_1189 ,
Oryctolagus cuniculus	ENSOCUG00000012176	3 retrocopies	retro_ocun_1005, retro_ocun_1294, retro_ocun_348,
Otolemur garnettii	ENSOGAG00000027181	2 retrocopies	retro_ogar_460, retro_ogar_766,
Procavia capensis	ENSPCAG00000012043	2 retrocopies	retro_pcap_128, retro_pcap_278,