RetrogeneDB ID: retro_ocun_1488

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:91488253..91489069(+)
• Located in intron of: ENSOCUG00000012433

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3F
• Ensembl ID: ENSOCUG00000004225
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit F [Source:HGNC Symbol;Acc:3275]

Sequence

>retro_ocun_1488
CAGACCTCGGTGCCCTCGCTGCCTAGTCCCATGCTCCTAGGGCCCTTCCCTGGTGGCCGCGTGGTCAGACTGTGTCTGGT
CATTTTGGCCTCCGTCTTGGACAGTTACGAGTGGCACAACGAAGGCGCTGCCCGAGTAATCAGGACCCTACTGGGAACTG
TTGACAAGCACTCAGTGGAGGTCACCAATTGTTTTCCAGTGCTGCATGAGTCAGAAGATGAAGTGGCCGTTGAATGGAAT
TTGCTAAGAACATCTATGAATTGCACAAAAAAATCTGTCCAAATGAACTCATCCTGGGCTGGTACACTACAGGCCATGAC
ATCAAGGAACATTCTGTGCTGATCCGCAAGTGCTACAGCTGGGAGGCCCCCAACCCCGTTCACCTCACTGTGGATGTGAG
TCTTCAGAATGGCCACAGGAGAACCAAGGCCTACGTCAGCACTTCAGTGGGTGTCCATGGGACCATGGAGTGGTGTTCAC
ACCTCTGATGTGAAATATGCCCGTTATGACACTGATCACGTTGGAGTTGACCTGATTATGAAGGCCTGTAGCCCCAACCA
GGTGATTGGACTCTGGAGTGACTTGCAGGAAGTAGGAGGGGCATCCACCCTCATCCAGGATGCCCTGAGCACAATGTTAG
AGTATGCAGAGGATGTGCCGTCTGGAACAATGTTAGCTGACAACACCGTGGGCTGCTTCTTGATGAGCCTGGGTAACCAG
GTACCCAAAGTAGTTCCCGATGACTTCCAGACCATGCTCAACAGCAGCATCAGTGACTTGCTGATGGTGACCTACCTGGC
CATTCTCACACAGTCA

Alignment

ORF - retro_ocun_1488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 86.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QTSAPSLPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVEVTNCFSVPHN
          QTS.PSLP.P.L.GPFPGGRVVRL..VILAS..DSYE..NEGAARVI.TLLGTVDKHSVEVTNCF.V.H.
Retrocopy QTSVPSLPSPMLLGPFPGGRVVRLCLVILASVLDSYEWHNEGAARVIRTLLGTVDKHSVEVTNCFPVLH-

Parental  ESEDEVAVD-MEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSLQNG
          ESEDEVAV..MEFAKN.YELHKK..PNELILGWY.TGHDI.EHSVLI...YS.EAPNP.HLTVD.SLQNG
Retrocopy ESEDEVAVE<MEFAKNIYELHKKICPNELILGWYTTGHDIKEHSVLIRKCYSWEAPNPVHLTVDVSLQNG

Parental  RMSIKAYVSTSMGVPGRTM-GVMFTPLT-VKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQVGGASA
          ....KAYVSTS.GV.G.TM.GV.FTPL..VKYA.YDT...GVDLIMK.C.SPN.VIGL.SDLQ.VGGAS.
Retrocopy HRRTKAYVSTSVGVHG-TM<GVVFTPLM<VKYARYDTDHVGVDLIMKAC-SPNQVIGLWSDLQEVGGAST

Parental  RIQDALSTVLQYAEDVLSGKVSADNTVGRFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLANLTQS
          .IQDALST.L.YAEDV.SG...ADNTVG.FLMSL.NQVPK.VPDDF.TMLNS.I.DLLMVTYLA.LTQS
Retrocopy LIQDALSTMLEYAEDVPSGTMLADNTVGCFLMSLGNQVPKVVPDDFQTMLNSSISDLLMVTYLAILTQS

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	98.62 RPM
SRP017611_kidney	0.00 RPM	118.89 RPM
SRP017611_liver	0.00 RPM	39.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1488 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1488 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004861	1 retrocopy	retro_btau_527,
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Echinops telfairi	ENSETEG00000002717	2 retrocopies	retro_etel_1583, retro_etel_35,
Gorilla gorilla	ENSGGOG00000011702	5 retrocopies	retro_ggor_1566, retro_ggor_1567, retro_ggor_1568, retro_ggor_1589, retro_ggor_1590,
Myotis lucifugus	ENSMLUG00000000825	1 retrocopy	retro_mluc_2356,
Oryctolagus cuniculus	ENSOCUG00000004225	1 retrocopy	retro_ocun_1488 ,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863,
Pongo abelii	ENSPPYG00000003512	1 retrocopy	retro_pabe_175,
Pteropus vampyrus	ENSPVAG00000015764	1 retrocopy	retro_pvam_371,