RetrogeneDB ID: retro_ocun_871

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:42408471..42409089(+)
• Located in intron of: ENSOCUG00000015999

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCMT1
• Ensembl ID: ENSOCUG00000000499
• Aliases: None
• Description: protein-L-isoaspartate (D-aspartate) O-methyltransferase [Source:HGNC Symbol;Acc:8728]

Sequence

>retro_ocun_871
GAAAATGTTATCATAAAGACAGATAAAGTGTTTGAAGTTATGCTGGCTACGGATCGTTCCCACTATACCAAATGTTATGC
TTATATGGATTCTGCACAATCAATAGGTTTCCAAGCAACAACCAGTGCTCCACACATGCATGCATATGCACTATAACTTC
TATTTGATCAATTACATGAAGGAGCTAAAGCTCTTGATGTAGGAGCTGAAAGTGGAATTCTTACTGCATGTATTGCACGT
ACAGTGGGATGTACTGGAAAAGTCATAGGAATTGATCTCATTAAAGAGCTAGTAGACGACTCAATAAACAATGTCAGAAA
GGATGACCCAACACTTTTGTCTTCAGGAAGAGTACACCTGGTTGTGGGGGATGGGCAAATGGACTATGCTGAAGAAGCCC
CATAGGATACTATTCATGTTGGATCCGCAGCCCCAGTCGTGCGCTAGGCACTAATAGACCAGTTAAAGGCTGGTGGAAGA
TTGATATTCCCAGTTGGTTCTGCAGGTGGAAACCAAATGCTGGAGCACTACAAGAAGCTACAAGATGGCAGCGTCAAAAT
GAAGCCTTTGATGGGGGTGATCTATGTGCCTTTAACAGATAAAGAAAAGCAATGGTCT

Alignment

ORF - retro_ocun_871 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.89 %
• Parental protein coverage: 71.53 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNGIIKTDKVFEVMLATDRSHYAKCNPYMDSPQSIGFQATISAPHMHAYALELLFDQLHEGAKALDVGSG
          .N.IIKTDKVFEVMLATDRSHY.KC..YMDS.QSIGFQAT.SAPHMHAYAL.LLFDQLHEGAKALDVG..
Retrocopy ENVIIKTDKVFEVMLATDRSHYTKCYAYMDSAQSIGFQATTSAPHMHAYAL*LLFDQLHEGAKALDVGAE

Parental  SGILTACFARMVGCSGKVIGIDHIKELVDDSINNVRKDDPTLLSSGRVQLVVGDGRMGYAEEAPYDAIHV
          SGILTAC.AR.VGC.GKVIGID.IKELVDDSINNVRKDDPTLLSSGRV.LVVGDG.M.YAEEAP.D.IHV
Retrocopy SGILTACIARTVGCTGKVIGIDLIKELVDDSINNVRKDDPTLLSSGRVHLVVGDGQMDYAEEAP*DTIHV

Parental  GAAAPVVPQALIDQLKPGGRLILPVGPAGGNQMLEQYDKLQDGSVKMKPLMGVIYVPLTDKEKQWS
          G.AAPVV..ALIDQLK.GGRLI.PVG.AGGNQMLE.Y.KLQDGSVKMKPLMGVIYVPLTDKEKQWS
Retrocopy GSAAPVVR*ALIDQLKAGGRLIFPVGSAGGNQMLEHYKKLQDGSVKMKPLMGVIYVPLTDKEKQWS

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	0.61 RPM	174.17 RPM
SRP017611_kidney	0.00 RPM	39.22 RPM
SRP017611_liver	0.00 RPM	19.58 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_871 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_871 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_871 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009230	1 retrocopy	retro_cjac_75,
Macaca mulatta	ENSMMUG00000029462	1 retrocopy	retro_mmul_134,
Oryctolagus cuniculus	ENSOCUG00000000499	2 retrocopies	retro_ocun_871 , retro_ocun_955,
Ochotona princeps	ENSOPRG00000002833	2 retrocopies	retro_opri_171, retro_opri_434,
Tupaia belangeri	ENSTBEG00000000451	1 retrocopy	retro_tbel_883,