RetrogeneDB ID: retro_ocun_1422

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:80809954..80810787(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LPCAT4
• Ensembl ID: ENSOCUG00000006180
• Aliases: None
• Description: lysophosphatidylcholine acyltransferase 4 [Source:HGNC Symbol;Acc:30059]

Sequence

>retro_ocun_1422
GGCCCTGGCGTACTCAAAGTCCTCTGGCTCACAGCCTCTCAGCCCTGCAGCATCGTGGATGTGGAGTTCCTCCCTGTGTA
TCACCCCAGCCCGGAGGAGAGCAGGGACCCCACCCTCTATGCTAACAATGTCCAGAGGGTCATGACAAAGGCCCTGGGCA
TTCCTGCCACCGAGTGTGAGTTTGTAGGGAGCTTGCCTGTGATTGTGGTGGGCCTGCTGAAGGTGGTGTTGGAGCCGCAG
CTCTGGAACTGGGAAAGGTGCTTCAGAGCTGGCTGTCCCCAGCTGTGTGGACGCTGGGGCAGAGCCAGGCCCGGAGTCGA
ATGATCAGCCAGGAAGAGTTTGCCAGGCAGCTGCGGCTCTCTGGTCCTCAGACAGTGGCTGGTGGCTTTAGCTACTTCCA
GCAGGATGCCCAGGGTTTGGTGGATTTCCGCGATGTGGCACTCTCACTAGCAGCTCTAGATGGGGGCAGGAGCCTGGAGG
AGCTGACCCGCCTGACCTTTGAGCACTTCACTGAGGAGCAGGCAGAGGGGTCTGGCCACGTACTGTACAAAGACGGATTT
AGCACCATCCTGCACCTGCTGCTGGGTTCACCCCACCTTGCTGCCATGACTTAGCATGCTGAGCTGTGCCAGGCAGGACC
CAGCCAAGGCCTCTCCCTCTGTCAATTCTAAAACTTCTCCCTCCATGACCCACTCTATGGGAAGCTGTTCAGCACCTACC
TGCGCCCCCCACACACCCCTCCAGGCACCTCCCAGATGCAACATGCCTCGTCCCCAGGCAGCCCCACTGCTCGGGCCAAT
GGCACTGTATAGGTGCCCAAGCAGAAGGGTGAC

Alignment

ORF - retro_ocun_1422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.3 %
• Parental protein coverage: 53.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GPGVLKVLWLTASQPCSVVDVEFLPVYHPSPEESRDPTLYANNVQRVMAQALGIPATECEFVGSLPVIVV
          GPGVLKVLWLTASQPCS.VDVEFLPVYHPSPEESRDPTLYANNVQRVM..ALGIPATECEFVGSLPVIVV
Retrocopy GPGVLKVLWLTASQPCSIVDVEFLPVYHPSPEESRDPTLYANNVQRVMTKALGIPATECEFVGSLPVIVV

Parental  GRLKVALEPQLW-ELGKVLRKAGLSPGR-VDAGAEPG-RSRMISQEEFARQLQLSDPQTVAGAFSYFQQD
          G.LKV.LEPQLW.ELGKVL....LSP...VDAGAEPG.RSRMISQEEFARQL.LS.PQTVAG.FSYFQQD
Retrocopy GLLKVVLEPQLW<ELGKVL-QSWLSPAV<VDAGAEPG>RSRMISQEEFARQLRLSGPQTVAGGFSYFQQD

Parental  AQGLVDFRDVALALAALDGGRSLEELTRLAFELFAEEQAEGPGRLLYKDGFSTILHLLLGSPHPAATTLH
          AQGLVDFRDVAL.LAALDGGRSLEELTRL.FE.F.EEQAEG.G..LYKDGFSTILHLLLGSPH.AA.T.H
Retrocopy AQGLVDFRDVALSLAALDGGRSLEELTRLTFEHFTEEQAEGSGHVLYKDGFSTILHLLLGSPHLAAMT*H

Parental  AELCQAGPSQGLSLCQFQNFSLHDPLYGKLFSTYLRPPHTPRGTSQMQRASSPGSPTALANGTVQAPKQK
          AELCQAGPSQGLSLCQF.NFSLHDPLYGKLFSTYLRPPHTP.GTSQMQ.ASSPGSPTA.ANGTV..PKQK
Retrocopy AELCQAGPSQGLSLCQF*NFSLHDPLYGKLFSTYLRPPHTPPGTSQMQHASSPGSPTARANGTV*VPKQK

Parental  GD
          GD
Retrocopy GD

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	156.46 RPM
SRP017611_kidney	0.00 RPM	13.58 RPM
SRP017611_liver	0.00 RPM	4.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1422 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1422 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1422 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000023492	1 retrocopy	retro_cpor_247,
Oryctolagus cuniculus	ENSOCUG00000006180	1 retrocopy	retro_ocun_1422 ,