RetrogeneDB ID: retro_ocun_282

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:44603993..44604821(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3M
• Ensembl ID: ENSOCUG00000004483
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit M [Source:HGNC Symbol;Acc:24460]

Sequence

>retro_ocun_282
CGCCCATCTCTGAGTCTGCAGCTGCTAAGCAACCTTTTCCATGGAATGGATAAGAATACTCCCGAAAGATAGACGGTGTG
GTGCAGCCTCATTAAAGTGGCAGCGTCTTGTGGGGCCATCCATTACGTTCCAACCGAGCTGGATCAAGTTAGAAAATGGA
TTTCTGACTGGAATCTCACCACTGAGAAGAAACGCACCCTTTTAAGGCTTCTTTATGAGGCACTCGTGGACTGTAAGAAA
AGTGATGCTGCTTCAAAAGTCATGGTGGAATTACTTGGAAGTGACACAGAGGATAATGTTTCCCAGGCTCGAGTTGACGC
CCACAGGTGTATTGTACCAGCACTGAAAGACCCAAATGCATTTCTTTCTGACCATCTTCTTACTTTGAAAGCAGTCAAGT
TATTGGAAGGCAAACTTATTCGTAATCTTTCAACCATTTTTGTGAGTGCTAAATTGGCATCCTATGTCAAGTTCTACCAG
AATAATAAAGACTTCATTGATTTACTTGGGCTATTACAAGAACAGAATATGGCAAAAATGAGAGTACTTACTTTTATGGG
AATGGCAGTAGAAAATAAGGAAATTTCTTTTGATACAATGCAGCAAGAACTCCAGATTGGAGCTGATGATGTTGAAGCAT
TTGTTATTGATGTGGTAAGAACTAAAATGATCTGCAAAATTGATCAAACTCAGAGAAAAGTAGTTGCCAGTCATAGCACA
CATTGAACATTCAGAAAACAGCAGTGGCAACAACTGTATGATACACTTAATGCATGGAAACAAAACTTGAACAAAGTGAA
AAACAGCCTTTTGAGTCTTTCTGATACC

Alignment

ORF - retro_ocun_282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.61 %
• Parental protein coverage: 74.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RPSLRLQLLSNLFHGMDKNTPVRYTVYCSLIKVAASCGAIQYIPTELDQVRKWISDWNLTTEKKHTLLRL
          RPSL.LQLLSNLFHGMDKNTP.R.TV.CSLIKVAASCGAI.Y.PTELDQVRKWISDWNLTTEKK.TLLRL
Retrocopy RPSLSLQLLSNLFHGMDKNTPER*TVWCSLIKVAASCGAIHYVPTELDQVRKWISDWNLTTEKKRTLLRL

Parental  LYEALVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCIVRALKDPNAFLFDHLLTLKPVKFLEGELI
          LYEALVDCKKSDAASKVMVELLGS.TEDN.SQARVDAHRCIV.ALKDPNAFL.DHLLTLK.VK.LEG.LI
Retrocopy LYEALVDCKKSDAASKVMVELLGSDTEDNVSQARVDAHRCIVPALKDPNAFLSDHLLTLKAVKLLEGKLI

Parental  HDLLTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRLLTFMGMAVENKEISFDTMQQELQIGADD
          ..L.TIFVSAKLASYVKFYQNNKDFID.LGLL.EQNMAKMR.LTFMGMAVENKEISFDTMQQELQIGADD
Retrocopy RNLSTIFVSAKLASYVKFYQNNKDFIDLLGLLQEQNMAKMRVLTFMGMAVENKEISFDTMQQELQIGADD

Parental  VEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQLYDTLNAWKQNLNKVKNSLLSLSDT
          VEAFVID.VRTKM..CKIDQTQRKVV.SHSTH.TF.KQQWQQLYDTLNAWKQNLNKVKNSLLSLSDT
Retrocopy VEAFVIDVVRTKMI-CKIDQTQRKVVASHSTH*TFRKQQWQQLYDTLNAWKQNLNKVKNSLLSLSDT

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	45.03 RPM
SRP017611_kidney	0.00 RPM	95.88 RPM
SRP017611_liver	0.00 RPM	25.05 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_282 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_282 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_282 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005338	2 retrocopies	retro_btau_1736, retro_btau_812,
Echinops telfairi	ENSETEG00000013437	1 retrocopy	retro_etel_120,
Myotis lucifugus	ENSMLUG00000014727	2 retrocopies	retro_mluc_1982, retro_mluc_431,
Mus musculus	ENSMUSG00000027170	1 retrocopy	retro_mmus_421,
Oryctolagus cuniculus	ENSOCUG00000004483	1 retrocopy	retro_ocun_282 ,
Otolemur garnettii	ENSOGAG00000015913	1 retrocopy	retro_ogar_1783,
Pteropus vampyrus	ENSPVAG00000015083	1 retrocopy	retro_pvam_1134,
Vicugna pacos	ENSVPAG00000007791	1 retrocopy	retro_vpac_342,