RetrogeneDB ID: retro_ocun_1647

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018740:1795397..1795686(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HN1
• Ensembl ID: ENSOCUG00000002950
• Aliases: None
• Description: hematological and neurological expressed 1 [Source:HGNC Symbol;Acc:14569]

Sequence

>retro_ocun_1647
TTTGATGAAGTAACAGAACAACCTGTGAGGAAGAACAAAATGGCCTCCACCATCTTTGGGACACTTGAAAAAAAAATCCC
TTTCCTGGGCCAAGTGTGCAGGTACCAAGTCTGATGGTGGCAGGGAAGATTCAAAGTCATCAGGGCTATAGGGAAGGAAC
TCCTTGGAAGCCAGCTTGGGAGACTTCTTTGATCTGAAGGGAGAAGGTGCTATTCATGAAAATGTGGACACGGACTTGCA
AGCCAGCCTGGGGCAGAGGGAAGAGAAGTCTGTACCTGCTGTGCCTGTG

Alignment

ORF - retro_ocun_1647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.29 %
• Parental protein coverage: 62.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FDEPTEQPVRKNKMASSIFGTPEENPP-SWAKSAGAKSGGGREDPEPSGLQRRSSSEASSGDSFDLKGEG
          FDE.TEQPVRKNKMAS.IFGT.E...P.SWAK.AG.KS.GGRED...SGL..R.S.EAS.GD.FDLKGEG
Retrocopy FDEVTEQPVRKNKMASTIFGTLEKKIP>SWAKCAGTKSDGGREDSKSSGL*GRNSLEASLGDFFDLKGEG

Parental  DIHENVDTDLQASLGQSEEKPVPAAPV
          .IHENVDTDLQASLGQ.EEK.VPA.PV
Retrocopy AIHENVDTDLQASLGQREEKSVPAVPV

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	55.19 RPM
SRP017611_kidney	0.00 RPM	9.43 RPM
SRP017611_liver	0.00 RPM	1.46 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1647 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1647 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1647 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014553	1 retrocopy	retro_cjac_2715,
Echinops telfairi	ENSETEG00000013294	1 retrocopy	retro_etel_89,
Homo sapiens	ENSG00000189159	1 retrocopy	retro_hsap_2343,
Gorilla gorilla	ENSGGOG00000013996	1 retrocopy	retro_ggor_1780,
Mustela putorius furo	ENSMPUG00000013971	1 retrocopy	retro_mputfur_1200,
Mus musculus	ENSMUSG00000020737	6 retrocopies	retro_mmus_1096, retro_mmus_2442, retro_mmus_2574, retro_mmus_3706, retro_mmus_864, retro_mmus_934,
Nomascus leucogenys	ENSNLEG00000000610	1 retrocopy	retro_nleu_348,
Oryctolagus cuniculus	ENSOCUG00000002950	2 retrocopies	retro_ocun_1647 , retro_ocun_457,
Ochotona princeps	ENSOPRG00000010887	2 retrocopies	retro_opri_537, retro_opri_88,
Pan troglodytes	ENSPTRG00000024246	1 retrocopy	retro_ptro_1715,
Rattus norvegicus	ENSRNOG00000003661	2 retrocopies	retro_rnor_1794, retro_rnor_454,
Ictidomys tridecemlineatus	ENSSTOG00000015171	1 retrocopy	retro_itri_1449,