RetrogeneDB ID: retro_ocun_955

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 17:71588022..71588661(-)
• Located in intron of: ENSOCUG00000029442

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_955
AGTGGCGGCGGCAATGGCAATAAAAGTGGCTACAGCGAGGACACGAGCAGGGTAGTGACCATGAGGGAGGTGATTTCGTT
CTTAGTGAAACTGTTGGGGCCCATCACTGCACTGAAGTTGGTTCTGTACCTGCTCTGAGTGTGCTTAGTGATGGCCTGGA
AATCCAGTGGTGCCAGCCACTTGTAGCTAGTCCACATCTCCACAAAAATGGTATCATAAAGACAGATAAAGTGTTTGAAG
TTATGCTGGCTACAAATCGCTCCCACTAGGCAAAATGTAACCCTTATATGAATTCTCCACAACCCACAGGTTTCCAAGCA
ACAATCATTGCTCCATAAACATATGTATATGCAATAGAACTTCTATTTGATCTATTACATGAAGGAGCTAAAGCTCTTGA
TGTAAGATTGGAAGTGGAACCCTTACTACATGTTTTGCACGTATCGTGGGATGTAGTGGAAAAGTCATAGGAATAGGAAT
TGATCACATTAAAGAGCTAACAGATGACTCAATAAACAGTGTCAGAAAGGATGATGCAACAATTTGTCTTCAGGGAGAGT
GCAACTGGTTGTGGGGGATGGGCAAATGGGCCATGCTGAAGAAGCCTGGGATAATGCTTTTCATGTAGGAGCTGCAGCC

Alignment

ORF - retro_ocun_955 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.35 %
• Parental protein coverage: 73.61 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SGGDGSSSGGDSGDASGAVTVWEVVSLLAKLLGTVAALKVVLYLLRVCLAMAWKSGGASHSELIH-NLRK
          SGG......G.S.D.S..VT..EV.S.L.KLLG...ALK.VLYLL.VCL.MAWKS.GASH..L.H..L.K
Retrocopy SGGGNGNKSGYSEDTSRVVTMREVISFLVKLLGPITALKLVLYLL*VCLVMAWKSSGASHL*LVH<HLHK

Parental  NGIIKTDKVFEVMLATDRSHYAKCNPYMDSPQSIGFQATISAPHMHAYALELLFDQLHEGAKALDV-GSG
          NGIIKTDKVFEVMLAT.RSH.AKCNPYM.SPQ..GFQATI.AP....YA.ELLFD.LHEGAKALDV...G
Retrocopy NGIIKTDKVFEVMLATNRSH*AKCNPYMNSPQPTGFQATIIAP*TYVYAIELLFDLLHEGAKALDV<KIG

Parental  SGILTACFARMVGCSGKV--IGIDHIKELVDDSINNVRKDDPTL-LSSGRVQLVVGDGRMGYAEEAPYDA
          SG.LT.CFAR.VGCSGKV..IGIDHIKEL.DDSIN.VRKDD.T..LSSGRVQLVVGDG.MG.AEEA...A
Retrocopy SGTLTTCFARIVGCSGKVIGIGIDHIKELTDDSINSVRKDDATI<LSSGRVQLVVGDGQMGHAEEAWDNA

Parental  IHVGAAA
          .HVGAAA
Retrocopy FHVGAAA

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	0.11 RPM	174.17 RPM
SRP017611_kidney	0.10 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_955 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_955 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_955 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,