RetrogeneDB ID: retro_ocun_1635

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018733:1304976..1305246(+)
• Located in intron of: ENSOCUG00000005131

Retrocopy information

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

Parental gene information

• Parental gene symbol: RP9
• Ensembl ID: ENSOCUG00000029333
• Aliases: None
• Description: retinitis pigmentosa 9 (autosomal dominant) [Source:HGNC Symbol;Acc:10288]

Sequence

>retro_ocun_1635
CGGTTGGGCAGTTGTCGGTATTTGTTGGCTGATTATGAAAAACCTTCTCTTGGACTTATCAAAGAAGATAAGATGAAGCC
AGAAGACTGTATACCGGATGTACCAGGCAATGAACATGCCCAGGAATTTCTGGCTCATGCGCCAACTAAAGGACTTTGGA
TGCCCCCGGGGAAGGAAGTCAAAGTGACGCAACGTTGATGTTGCAAATGTTATGATCACCAAACGGGCGACACAGAATGT
CCTTTCTTTATCAAAGGCAACCAAAAGTTA

Alignment

ORF - retro_ocun_1635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.44 %
• Parental protein coverage: 60.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLQQLKHLESFYEKPPPGLIKEDETKPEDCIPDVPGNEHAREFLAHAPTKGLWMPLGKEVKVMQCWRCKR
          .L.....L...YEKP..GLIKED..KPEDCIPDVPGNEHA.EFLAHAPTKGLWMP.GKEVKV.Q...CK.
Retrocopy RLGSCRYLLADYEKPSLGLIKEDKMKPEDCIPDVPGNEHAQEFLAHAPTKGLWMPPGKEVKVTQR*CCKC

Parental  YGHRTGDKECPFFIKGNQKL
          Y.H.TGD.ECPFFIKGNQKL
Retrocopy YDHQTGDTECPFFIKGNQKL

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	0.06 RPM	2.65 RPM
SRP017611_kidney	0.10 RPM	2.53 RPM
SRP017611_liver	0.00 RPM	1.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1635 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1635 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1635 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025514	17 retrocopies	retro_mdom_1205, retro_mdom_1515, retro_mdom_1553, retro_mdom_1622, retro_mdom_1759, retro_mdom_1840, retro_mdom_1905, retro_mdom_1912, retro_mdom_265, retro_mdom_317, retro_mdom_386, retro_mdom_560, retro_mdom_623, retro_mdom_687, retro_mdom_761, retro_mdom_818, retro_mdom_896,
Oryctolagus cuniculus	ENSOCUG00000029333	1 retrocopy	retro_ocun_1635 ,