RetrogeneDB ID: retro_ocun_1935

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:72166603..72166991(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF6
• Ensembl ID: ENSOCUG00000010588
• Aliases: None
• Description: Eukaryotic translation initiation factor 6 [Source:UniProtKB/TrEMBL;Acc:B7NZI5]

Sequence

>retro_ocun_1935
TTCGAGAGTAACTGTGAAATCAGCTGCTTTGCTAACCTGACCAACACCTACTACCTGATGGCCACTGAAGGATCGGAGAA
CTTTCACAGCAAGTTCAAAGGTGAGCTCATAGATACCATCCCCGTGCTGCAGGCATTCATTGCTGGCTGTCACATCACCG
GGCACCTGTGTGGGGGCGAACAGGCATGGTCTTCTGGTGCTCAACAACACCACTGACCAGGAGCTGGAACACATTTGCAA
TTGCCTCGCAGATTCAATGCAGATTTAGCCAGTAGAGGAGCAACTCTCGGCTCAGAACAATGTTACAACCTGCAATGACT
ACATGGCCTTGGTTCACCCAAACCTGGACAGGGAGACAGAAGAAATCCTGGCTGATGTGTTCCAGGTG

Alignment

ORF - retro_ocun_1935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.85 %
• Parental protein coverage: 50.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FENNCEIGCFAKLTNTYCLVAIGGSENFYSVFEGELSDTIPVVHASIAGCRIIGRMCVG-NRHGLLVPNN
          FE.NCEI.CFA.LTNTY.L.A..GSENF.S.F.GEL.DTIPV..A.IAGC.I.G..C.G.NRHGLLV.NN
Retrocopy FESNCEISCFANLTNTYYLMATEGSENFHSKFKGELIDTIPVLQAFIAGCHITGHLCGG>NRHGLLVLNN

Parental  TTDQELQHIRNCLPDSVQIRRVEERLSALGNVTTCNDYVALVHPDLDRETEEILADVLKV
          TTDQEL.HI.NCL.DS.QI..VEE.LSA..NVTTCNDY.ALVHP.LDRETEEILADV..V
Retrocopy TTDQELEHICNCLADSMQI*PVEEQLSAQNNVTTCNDYMALVHPNLDRETEEILADVFQV

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	27.65 RPM
SRP017611_kidney	0.00 RPM	41.25 RPM
SRP017611_liver	0.00 RPM	17.96 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1935 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1935 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1935 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000007169	1 retrocopy	retro_meug_26,
Monodelphis domestica	ENSMODG00000019689	1 retrocopy	retro_mdom_1926,
Mus musculus	ENSMUSG00000027613	1 retrocopy	retro_mmus_2569,
Oryctolagus cuniculus	ENSOCUG00000010588	1 retrocopy	retro_ocun_1935 ,
Rattus norvegicus	ENSRNOG00000049497	1 retrocopy	retro_rnor_1067,