RetrogeneDB ID: retro_ocun_1780

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018888:435213..435670(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OCIAD2
• Ensembl ID: ENSOCUG00000007907
• Aliases: None
• Description: OCIA domain containing 2 [Source:HGNC Symbol;Acc:28685]

Sequence

>retro_ocun_1780
ATGGCATCCGTGTCGACTCATGAAAGCCGGGAGAAAAGTCCACATTGGCCACCATTAAACAAGAAGAGCCTGCTGTTTTG
TCTGAAATCAGAACCGCAGATCCAAAATGGAGAGGCTGCAAAGATCTGAGAATGTCAAGGACAAAGTCTCTGGAAGACAG
CTCTGACTTCTCTTGTAAGCTCGCTTGTCACCCAGGGACTAGTCCACCAAGGTTACTTAGCAGCTAATCCAAGATCTGGA
TCATTGCCTAAAGTGGCACTTGCTGGTATCTCGGGATTAGGCCTGGGAAAGGCATCCTACATGGAATGTGCCAAAGTAAA
TTCCATTCCTTTGAAAATCAGCTGTGAGGGGCTGGATATAGTCCACATCACAACAGGCTTACATGCCTGCTTAAATGTGA
GAAATGCAAAACAAGGCGTAGATTAAGCCAGAAGGGAACTCACAGCCAGCAGCTTCC

Alignment

ORF - retro_ocun_1780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.52 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASMSTHESQENGPHLPPLNKKSLLFCPKSKLHIHKGEIAKIIRECQEESFWKRALPFSLVSMLVTQGLV
          MAS.STHES.E..PH.PPLNKKSLLFC.KS...I..GE.AKI..ECQ..S.WK.AL..SLVS.LVTQGLV
Retrocopy MASVSTHESREKSPHWPPLNKKSLLFCLKSEPQIQNGEAAKI*-ECQGQSLWKTALT-SLVSSLVTQGLV

Parental  HQGYLAANPRFGSLPKVALAGILGFGLGKASYI-GVCQSKFHSFENQLRGAGFGPHHNR-HCLLTCEECK
          HQGYLAANPR.GSLPKVALAGI.G.GLGKASY..G.CQSKFHSFENQL.GAG..PHHNR..CLL.CE.CK
Retrocopy HQGYLAANPRSGSLPKVALAGISGLGLGKASYM<GMCQSKFHSFENQL*GAGYSPHHNRLTCLLKCEKCK

Parental  TRHGLNQK-GDSQPSAS
          TR..L.QK.G.SQP.AS
Retrocopy TRRRLSQK<GNSQPAAS

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	76.55 RPM
SRP017611_kidney	0.20 RPM	385.56 RPM
SRP017611_liver	0.00 RPM	126.87 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1780 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1780 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018637	1 retrocopy	retro_cjac_1505,
Erinaceus europaeus	ENSEEUG00000006759	1 retrocopy	retro_eeur_504,
Homo sapiens	ENSG00000145247	1 retrocopy	retro_hsap_4082,
Gorilla gorilla	ENSGGOG00000013778	1 retrocopy	retro_ggor_2738,
Microcebus murinus	ENSMICG00000006147	1 retrocopy	retro_mmur_1402,
Macaca mulatta	ENSMMUG00000014869	1 retrocopy	retro_mmul_2353,
Monodelphis domestica	ENSMODG00000025531	1 retrocopy	retro_mdom_1006,
Nomascus leucogenys	ENSNLEG00000017430	1 retrocopy	retro_nleu_2048,
Oryctolagus cuniculus	ENSOCUG00000007907	2 retrocopies	retro_ocun_1734, retro_ocun_1780 ,
Otolemur garnettii	ENSOGAG00000011039	1 retrocopy	retro_ogar_561,
Pongo abelii	ENSPPYG00000014722	1 retrocopy	retro_pabe_3350,
Pan troglodytes	ENSPTRG00000016048	1 retrocopy	retro_ptro_2768,
Vicugna pacos	ENSVPAG00000011765	1 retrocopy	retro_vpac_331,