RetrogeneDB ID: retro_ocun_1475

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:52734770..52735151(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4H
• Ensembl ID: ENSOCUG00000017685
• Aliases: None
• Description: eukaryotic translation initiation factor 4H [Source:HGNC Symbol;Acc:12741]

Sequence

>retro_ocun_1475
AAGCTGCCCACAGAGCCCCTCTTCCCTTCCCCCACGGCGTACTCTACCTTTTAAAAAGATTCAAGGTGACATAGATTGGT
CTTCAAGGATCTCAGCATAAAAAGTGTACGGCTAGCCAGAGACAAAGACACAGCCAAGTTTAAAGGATTCTGCTGTGTAG
AATGCGATGAGGTGGTGTCCCTTAAGGAAGCTCTGACTTACGATGGTACAGGTGCACTGTTGGGTGATTGGTCACTTTGT
CTGGACATTACCTAAGGCAGAAAACGAGACAGAGGTGGTTTTGGATTCTGGAGAGGCGGACCGGATGACAGAGGCTTCGG
GGATGACTCCTCAGGAGGCCATTGCCCCGGGACCGGCCAACGGGCTCTCCGCTTCAGAGAT

Alignment

ORF - retro_ocun_1475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.08 %
• Parental protein coverage: 51.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELPTEPPYTAYVG-NLPFNTVQGDID-AIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYD
          .LPTEP.........LPF...QGDID...FKDLSI.SVRL.RDKDT.KFKGFC.VE.DEV.SLKEALTYD
Retrocopy KLPTEPLFPSPTA>TLPFKKIQGDID<LVFKDLSIKSVRLARDKDTAKFKGFCCVECDEVVSLKEALTYD

Parental  G--ALLGDRSLRVDIAEGRKQDKGGFGFRRGGPDDRESRGGWDSRADFSSGGPLCLRFRD
          G..ALLGD.SL..DI..GRK.D.GGFGF.RGGPDDR...G...S.......G...LRFRD
Retrocopy GTGALLGDWSLCLDIT*GRKRDRGGFGFWRGGPDDR-GFGDDSSGGHCPGTGQRALRFRD

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	84.16 RPM
SRP017611_kidney	0.00 RPM	56.15 RPM
SRP017611_liver	0.00 RPM	28.59 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1475 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1475 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1475 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002525	2 retrocopies	retro_chof_1279, retro_chof_1903,
Felis catus	ENSFCAG00000029386	1 retrocopy	retro_fcat_580,
Gorilla gorilla	ENSGGOG00000005284	1 retrocopy	retro_ggor_1598,
Macaca mulatta	ENSMMUG00000006205	2 retrocopies	retro_mmul_2634, retro_mmul_619,
Mus musculus	ENSMUSG00000040731	1 retrocopy	retro_mmus_3659,
Oryctolagus cuniculus	ENSOCUG00000017685	1 retrocopy	retro_ocun_1475 ,
Otolemur garnettii	ENSOGAG00000028051	1 retrocopy	retro_ogar_2796,
Pongo abelii	ENSPPYG00000017489	2 retrocopies	retro_pabe_1879, retro_pabe_1988,
Pan troglodytes	ENSPTRG00000019287	1 retrocopy	retro_ptro_1489,
Rattus norvegicus	ENSRNOG00000001454	1 retrocopy	retro_rnor_2924,
Tupaia belangeri	ENSTBEG00000009558	2 retrocopies	retro_tbel_1636, retro_tbel_2470,