RetrogeneDB ID: retro_ocun_754

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:69547721..69548210(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL9
• Ensembl ID: ENSOCUG00000004285
• Aliases: None
• Description: methyltransferase like 9 [Source:HGNC Symbol;Acc:24586]

Sequence

>retro_ocun_754
TGGTTTGTGTGCAACAGAAAGATATTATGTGAATCACTCTAGGCTGTATTTGCTTAGAGTTATCTTGATCAAGGAACAGA
GATATTCTTAAGCAATAGCGTTAGGAGAGTGGTCTGGCTATTTATCTATTTATATCACTCTTTTTTGTCATCTGTTTTTA
GTCTTTTTTTTGTCTAGAACATCTATCAGTGGTTTTCTGGGAAGAGGCTCAATGTTTATGTTATCACAAGAAAAGTTTCA
AAGAGTGCTTAAAATGCATCCAGACTGCAAAACCCATAGACTTCTTAATTAGGTGCTGAAGATTGAGAAGTCACAAAAAT
CATCAGCCCTCATTTTAAAGAAATCTATGCCAATGAGCTTTCTGAAAATATGATATGTCAGCTTCAGAAGAAGAAATATA
GGATGCTCAGCATAAATGAATGACAGAATACGTGTTTCCAGTATGATGTCATCAGCTACTTAAATTTGCTGGACTGCTAC
AACCAACCC

Alignment

ORF - retro_ocun_754 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 51.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WYVCNREKLCESLQAVFVQSYLDQGTQIFLNNSIEKSGWLFIQLYHSFVSSVFSLF-MSRTSINGLLGRG
          W.VCNR..LCESL.AVF..SYLDQGT.IFL.NS.....WLFI.LYHSF.SSVFSLF..SRTSI.G.LGRG
Retrocopy WFVCNRKILCESL*AVFA*SYLDQGTEIFLSNSVRRVVWLFIYLYHSFLSSVFSLF>LSRTSISGFLGRG

Parental  SMFVFSPDQFQRLLKINPDWKTHRLLD-LGAGDGEVTKIMSPHFEEIYATELSETMIWQLQKKKYRVLGI
          SMF..S...FQR.LK..PD.KTHRLL..LGA.D.EVTKI.SPHF.EIYA.ELSE.MI.QLQKKKYR.L.I
Retrocopy SMFMLSQEKFQRVLKMHPDCKTHRLLN<LGAED*EVTKIISPHFKEIYANELSENMICQLQKKKYRMLSI

Parental  NEWQNTGFQYDVISCLNLLDRCDQP
          NE.QNT.FQYDVIS.LNLLD...QP
Retrocopy NE*QNTCFQYDVISYLNLLDCYNQP

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	85.98 RPM
SRP017611_kidney	0.00 RPM	216.19 RPM
SRP017611_liver	0.00 RPM	20.50 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_754 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_754 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_754 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020564	1 retrocopy	retro_cjac_4083,
Mustela putorius furo	ENSMPUG00000016801	2 retrocopies	retro_mputfur_1323, retro_mputfur_1610,
Oryctolagus cuniculus	ENSOCUG00000004285	1 retrocopy	retro_ocun_754 ,
Otolemur garnettii	ENSOGAG00000008169	3 retrocopies	retro_ogar_1745, retro_ogar_307, retro_ogar_588,
Rattus norvegicus	ENSRNOG00000025940	1 retrocopy	retro_rnor_2623,