RetrogeneDB ID: retro_ocun_1399

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:20053607..20054401(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3E
• Ensembl ID: ENSOCUG00000008050
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit E [Source:HGNC Symbol;Acc:3277]

Sequence

>retro_ocun_1399
ACTGCAAGGCAAATACAGTCAACCAAGGATAGTTTGATGGCATTTGACAACCTGGCAAACAAATGGTCTTTTAGGCACAA
ATATTCAGATATACTCCATAAGTCTGCAAAGTACCAGTATAAATGTGGGAATTACTTGGAAGCAGAGGAATTCATTTGCT
TTTGTTGAGTGCTGATGCCAGCAATAGATAAAAATGCTTCATGTTCACTCTGGGGAAAACCGCCATCTGAAATTTTACTG
TAAATTGAGATTCAACCAACTAAGATCTTACACACTCCAGAGAGACCATAGGTAACTATTCTGTGAGTTCTCCAATGTCT
TCATCAATGAACTTCGCTCATTCATTCATCTTTCTTTCTTCCAACCTCCCCAAAGTTCCCAATTTTATTGTTCTCTTCCT
TTATCAGTCAAAGTATCTTAATGCAGTTCAGACAATCTGTCTACATGGTCCCTGCTATTCGATTACAGTAGTCATTACAA
ACTAAGATGTTTGAAAACACTGGCAGGTGCCTAGACAAACTAAAGTTATTCAACAGGAGTCTTACACTGATTTACCCAAT
TATAGAATTTGTTGAGTGTATGCTGACTTCAGCTTTGATGGGGCCTTGAAAAAAAAGCTGAGTGAAAGTAATCAGTGCTT
ATGCATGACTTCTTTTTGGTGGCTTGAGGATTTCACTGGAAATGCCTACCTCTTCCTATTTGAGGCTCTTAGTCCTAACT
ACCAGTGTATCAGCATTAAAACATTAGCCAAAACACTAAACATTACTCCCAAACAAGCTGAAAGGCAGATTGTG

Alignment

ORF - retro_ocun_1399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.18 %
• Parental protein coverage: 59.09 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TTRQMQSTRDGRMLFDYLADKHGFRQEYLDTLYRYAKFQYECGNYSGAAEYLYFFRVLVPATDRNALSSL
          T.RQ.QST.D..M.FD.LA.K..FR..Y.D.L...AK.QY.CGNY..A.E...F..VL.PA.D.NA..SL
Retrocopy TARQIQSTKDSLMAFDNLANKWSFRHKYSDILHKSAKYQYKCGNYLEAEEFICFC*VLMPAIDKNASCSL

Parental  WGKLASEILM-QNWDAAMEDLTRLKETIDNNSVSSPLQSLQQRTWLIHWSLFVFFNHPKGRDNIIDLFLY
          WGK..SEIL...N.D....DLT...ETI.N.SVSSP..S........H...F...N.PK...N.I.LFLY
Retrocopy WGKPPSEILL<VN*DSTN*DLTHSRETIGNYSVSSPMSSSMN---FAHSFIFLSSNLPKV-PNFIVLFLY

Parental  QPQYLNAIQTMCPHILRYLTTAVITNKDVRKRRQVLKDLVKVIQQESYTYKDPITEFVECLYVNFDFDGA
          Q..YLNA.QT.C.H...Y..T.VITN.DV.K..QV.....KVIQQES..Y.D.........Y..F.FDGA
Retrocopy QSKYLNAVQTICLHGPCYSITVVITN*DV*KHWQVPRQ-TKVIQQES--YTDLPNYRIC*VYADFSFDGA

Parental  -QKKLRECESVLVNDFFLVACLEDFIENARLFIFETFCRIHQCISINMLADKLNMTPEEAERWIV
          ..KKL.E....L....F....LEDF..NA.LF.FE......QCISI..LA..LN.TP..AER.IV
Retrocopy LKKKLSESNQCLCMTSFW--WLEDFTGNAYLFLFEALSPNYQCISIKTLAKTLNITPKQAERQIV

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	107.73 RPM
SRP017611_kidney	0.00 RPM	180.31 RPM
SRP017611_liver	0.00 RPM	52.41 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1399 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1399 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006702	1 retrocopy	retro_btau_291,
Canis familiaris	ENSCAFG00000000702	1 retrocopy	retro_cfam_1127,
Callithrix jacchus	ENSCJAG00000006458	3 retrocopies	retro_cjac_2333, retro_cjac_2686, retro_cjac_701,
Equus caballus	ENSECAG00000000236	1 retrocopy	retro_ecab_860,
Echinops telfairi	ENSETEG00000013105	1 retrocopy	retro_etel_2048,
Felis catus	ENSFCAG00000003665	1 retrocopy	retro_fcat_231,
Homo sapiens	ENSG00000104408	1 retrocopy	retro_hsap_3489,
Gorilla gorilla	ENSGGOG00000022955	2 retrocopies	retro_ggor_2354, retro_ggor_2355,
Myotis lucifugus	ENSMLUG00000007269	1 retrocopy	retro_mluc_1796,
Macaca mulatta	ENSMMUG00000011359	1 retrocopy	retro_mmul_2585,
Mustela putorius furo	ENSMPUG00000005924	2 retrocopies	retro_mputfur_193, retro_mputfur_736,
Mus musculus	ENSMUSG00000022336	2 retrocopies	retro_mmus_1801, retro_mmus_2807,
Nomascus leucogenys	ENSNLEG00000004120	1 retrocopy	retro_nleu_333,
Oryctolagus cuniculus	ENSOCUG00000008050	1 retrocopy	retro_ocun_1399 ,
Pan troglodytes	ENSPTRG00000020505	1 retrocopy	retro_ptro_2362,
Rattus norvegicus	ENSRNOG00000027690	4 retrocopies	retro_rnor_1133, retro_rnor_2879, retro_rnor_583, retro_rnor_584,
Ictidomys tridecemlineatus	ENSSTOG00000008976	1 retrocopy	retro_itri_545,
Tursiops truncatus	ENSTTRG00000011025	2 retrocopies	retro_ttru_1602, retro_ttru_1794,