RetrogeneDB ID: retro_ocun_1740

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018833:671398..671668(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYRM7
• Ensembl ID: ENSOCUG00000000166
• Aliases: None
• Description: LYR motif containing 7 [Source:HGNC Symbol;Acc:28072]

Sequence

>retro_ocun_1740
CATTGCACCAGACAACAAGTTTTTTAAAATGATGCCAGAGCATTAGAAGCAGCCAGAATAAAGCTAAATGAAGAATTCAA
AAGTCATAAAAGGGAGACCTCTTCCAAGAAAATAGAAGAGCTAAGGAAAATAGGTTCCGATGTGGAACTGTTGCTCAGAA
CATCCGTTATACAAGGTACTCACACAGACCACAATACACTGAAATTGGTCTCTAGGACAGACCTTATTTTAGAAAATGTG
CCATATTGCAATGCACCAACTCAGAAGCAA

Alignment

ORF - retro_ocun_1740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.78 %
• Parental protein coverage: 86.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HRTRQQVFKNDARALEAARIKINEEFKSHKSETSSKKIEELMKIGSDVELLLRTSVIQGIHTDHNTLKLV
          H.TRQQVF.NDARALEAARIK.NEEFKSHK.ETSSKKIEEL.KIGSDVELLLRTSVIQG.HTDHNTLKLV
Retrocopy HCTRQQVF*NDARALEAARIKLNEEFKSHKRETSSKKIEELRKIGSDVELLLRTSVIQGTHTDHNTLKLV

Parental  PRKDLLLENVPYCDAPTQKR
          .R.DL.LENVPYC.APTQK.
Retrocopy SRTDLILENVPYCNAPTQKQ

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	12.80 RPM
SRP017611_kidney	0.00 RPM	13.99 RPM
SRP017611_liver	0.00 RPM	4.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1740 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1740 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1740 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017776	1 retrocopy	retro_amel_1472,
Canis familiaris	ENSCAFG00000000736	1 retrocopy	retro_cfam_1279,
Choloepus hoffmanni	ENSCHOG00000006766	6 retrocopies	retro_chof_1440, retro_chof_2015, retro_chof_2366, retro_chof_2681, retro_chof_488, retro_chof_688,
Echinops telfairi	ENSETEG00000010130	1 retrocopy	retro_etel_1126,
Oryctolagus cuniculus	ENSOCUG00000000166	1 retrocopy	retro_ocun_1740 ,
Ochotona princeps	ENSOPRG00000015568	4 retrocopies	retro_opri_1182, retro_opri_212, retro_opri_361, retro_opri_611,
Rattus norvegicus	ENSRNOG00000045961	1 retrocopy	retro_rnor_552,