RetrogeneDB ID: retro_ocun_608

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:39712192..39712851(+)
• Located in intron of: ENSOCUG00000029078

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3H
• Ensembl ID: ENSOCUG00000007534
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit H [Source:HGNC Symbol;Acc:3273]

Sequence

>retro_ocun_608
CTCCTGGATTGTCAGTTCAGTTGCCAGCATGCCACTAAAGAATCTGTTGTTCTCATTTACCATCCCATAAAAACTGCCCA
CGGGTCCCTGTCACCAAAGGCATACAGACTGACTCCTAAGCTGATGGAAGTTTGTAAAGAGATTAATTTTTCCCCTGAAG
CATTGGAAAAGGCAAATATCACCTTTGAGCACATGTTTGAAGAAGTGCCGATTGTAATTAAAAATTCACATCTGATCAGT
GTTCTAATGTGAAAGCTTGAGAAGAAATCGGCTGTAGCAGACAAACATGAACTGCTCAGACTTGCCAGCAGCAATCACTT
GGGGGGAAATCGACAGTTGCTGATGGACAGAGTGGGTGAAATGAGCCAAGATATAGTTAAATATAACAAATACATGAGGA
ATACAAGAAAACAGCAGCTGCAGGAACATTCGTCTCATCAGCGTCGGCAGCAGGAGAAGATGCAGCACCAGAGTCGAGGA
GAACCCCCACGCCCGGAGGAGGACCTGCCAGAGCTCTCCAAACCACCCAGCCACCTGCCAGGATGGGCTCACTGCTCACT
GCAGGCCGAATTAATACTTACTGCCAGAACATCAGGGAATTTACTGCCCAGAACTTGGGCAAACTCTTCATGGCCCAAGT
TCTTCAAGACTACAACAAC

Alignment

ORF - retro_ocun_608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.26 %
• Parental protein coverage: 62.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLDSQFSYQHAIEESVVLIYDPIKTAQGSLSLKAYRLTPKLMEVCKEKDFSPEALKKANITFEHMFEEVP
          LLD.QFS.QHA..ESVVLIY.PIKTA.GSLS.KAYRLTPKLMEVCKE..FSPEAL.KANITFEHMFEEVP
Retrocopy LLDCQFSCQHATKESVVLIYHPIKTAHGSLSPKAYRLTPKLMEVCKEINFSPEALEKANITFEHMFEEVP

Parental  IVIKNSHLINVLMWELEKKSAVADKHELLSLASSNHLGKNLQLLMDRVDEMSQDIVKYNTYMRNTSKQQQ
          IVIKNSHLI.VLM..LEKKSAVADKHELL.LASSNHLG.N.QLLMDRV.EMSQDIVKYN.YMRNT.KQQ.
Retrocopy IVIKNSHLISVLM*KLEKKSAVADKHELLRLASSNHLGGNRQLLMDRVGEMSQDIVKYNKYMRNTRKQQL

Parental  QKHQYQQRRQQENMQRQSRGEPPLPEEDLSKLFKPP-QPPARMDSLLIAGQINTYCQNIKEFTAQNLGKL
          Q.H...QRRQQE.MQ.QSRGEPP.PEEDL..L.KPP.QPPARM.SLL.AG.INTYCQNI.EFTAQNLGKL
Retrocopy QEHSSHQRRQQEKMQHQSRGEPPRPEEDLPELSKPP<QPPARMGSLLTAGRINTYCQNIREFTAQNLGKL

Parental  FMAQALQEYNN
          FMAQ.LQ.YNN
Retrocopy FMAQVLQDYNN

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	65.29 RPM
SRP017611_kidney	0.00 RPM	96.09 RPM
SRP017611_liver	0.00 RPM	36.38 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_608 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_608 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_608 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000816	1 retrocopy	retro_cfam_2073,
Callithrix jacchus	ENSCJAG00000005910	1 retrocopy	retro_cjac_3023,
Echinops telfairi	ENSETEG00000000324	1 retrocopy	retro_etel_24,
Macropus eugenii	ENSMEUG00000015663	4 retrocopies	retro_meug_1223, retro_meug_1244, retro_meug_1790, retro_meug_376,
Monodelphis domestica	ENSMODG00000004154	1 retrocopy	retro_mdom_1243,
Mus musculus	ENSMUSG00000022312	1 retrocopy	retro_mmus_1668,
Oryctolagus cuniculus	ENSOCUG00000007534	1 retrocopy	retro_ocun_608 ,
Otolemur garnettii	ENSOGAG00000008905	1 retrocopy	retro_ogar_2043,
Sorex araneus	ENSSARG00000009067	1 retrocopy	retro_sara_69,
Sarcophilus harrisii	ENSSHAG00000014977	1 retrocopy	retro_shar_561,
Ictidomys tridecemlineatus	ENSSTOG00000001403	1 retrocopy	retro_itri_420,