RetrogeneDB ID: retro_ocun_457

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:73004380..73004799(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025764
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_457
ACCACCACCACCACCACAAGGGTGTCAGCCCCAGCAGCAAGAACAGAGGGGTTTACGTCCTCCAGCTGCTGGATCCAACT
TTTCATTGAGTTTCGATGAACCAACAGAACAACCTGTGAGGAAGAACAAAATGGCCTCTACCATCTTTGGGACCCCTGAA
GAAAATCCCCCTTCCCGGGCCAAGTCTGCAGCTGCAAGTCTGGTGTTGGCAGGGAGGATCCGGAGTCATCCGGCTAGGGA
GAAGGAACGCCTCGGAAGCCAGCTCGGGAGACTTCTTTGATCTGAAGGAAGAAGGTGATATTCATGAAAATGCAGACACA
GACTTGCAAGCCAGCCTGGGGCAGAGTGAAGAGAAGTCTGTACCCGCCATGCCTGTGCCCCAACTCCACGGCCCTGGTCC
TGTCCAGGAGAAACGCTCC

Alignment

ORF - retro_ocun_457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.22 %
• Parental protein coverage: 91.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TTTTF-KGVDPNSRNSFRVLRPPGGGSNFSLGFDEPTEQPVRKNKMASSIFGTPEENPPSWAKSAGA-KS
          TTTT...G..P......R.LRPP..GSNFSL.FDEPTEQPVRKNKMAS.IFGTPEENPPS.AKSA.A.KS
Retrocopy TTTTT>QGCQPQQQEQ-RGLRPPAAGSNFSLSFDEPTEQPVRKNKMASTIFGTPEENPPSRAKSAAA<KS

Parental  GGGREDPEPSG-LQRRSSSEASSGDSFDLKGEGDIHENVDTDLQASLGQSEEKPVPAAPVPSPVAPAPAP
          G.GREDPE.SG.L.RR..SEASSGD.FDLK.EGDIHEN.DTDLQASLGQSEEK.VPA.PVP....P.P..
Retrocopy GVGREDPESSG<LGRRNASEASSGDFFDLKEEGDIHENADTDLQASLGQSEEKSVPAMPVPQLHGPGPVQ

Parental  SRRN
          ..R.
Retrocopy EKRS

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_457 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_457 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_457 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,