RetrogeneDB ID: retro_ocun_1776

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018886:489991..490365(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB23
• Ensembl ID: ENSOCUG00000004816
• Aliases: None
• Description: RAB23, member RAS oncogene family [Source:HGNC Symbol;Acc:14263]

Sequence

>retro_ocun_1776
GTCAAGATGGTGGTTGTAGGGAATGGAACAGTTGGAAAGTCAAGTATGATTCAGCAATATTGCAAATGCATTTTTATAAA
AGACTACAAGAAAACCTTGGAGTTGATTTTTTGGAGCAACAAATCCAAGTTATTGATGAAGATGTCAGATTGATGTTATG
GGATACTGCTGGTCAAAAGGAATTTGATACAATAATGAATGCCTATTATCCAGGAGCCCAGACTTGTGTGCTTATATTTT
CTACTACAGACAGGGAATCTTTTGAAACAATTTCCAGTTGGAGAGAGAAAGTCGGAGCTGAAGTTGGGGATATATGAACT
GTACTTGTAAAAAATAAGATTGATTTCTTGGATGATTCTTGTACAAAGAATGAG

Alignment

ORF - retro_ocun_1776 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.54 %
• Parental protein coverage: 52.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IKMVVVGNGAVGKSSMIQRYCKGIFTKDYKKTI-GVDFLERQIQVNDEDVRLMLWDTAGQEEFDAITKAY
          .KMVVVGNG.VGKSSMIQ.YCK.IF.KDYKKT..GVDFLE.QIQV.DEDVRLMLWDTAGQ.EFD.I..AY
Retrocopy VKMVVVGNGTVGKSSMIQQYCKCIFIKDYKKTL<GVDFLEQQIQVIDEDVRLMLWDTAGQKEFDTIMNAY

Parental  YRGAQACVLVFSTTDRESFEAISSWREKVVAEVGDIPTVLVQNKIDLLDDSCIKNE
          Y.GAQ.CVL.FSTTDRESFE.ISSWREKV.AEVGDI.TVLV.NKID.LDDSC.KNE
Retrocopy YPGAQTCVLIFSTTDRESFETISSWREKVGAEVGDI*TVLVKNKIDFLDDSCTKNE

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	10.54 RPM
SRP017611_kidney	0.00 RPM	11.96 RPM
SRP017611_liver	0.00 RPM	1.23 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1776 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1776 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1776 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	ENSOCUG00000004816	2 retrocopies	retro_ocun_1752, retro_ocun_1776 ,
Oryctolagus cuniculus	ENSOCUG00000026506	2 retrocopies	retro_ocun_1139, retro_ocun_958,