RetrogeneDB ID: retro_ocun_869

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:42250145..42251123(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: L2HGDH
• Ensembl ID: ENSOCUG00000011422
• Aliases: None
• Description: L-2-hydroxyglutarate dehydrogenase [Source:HGNC Symbol;Acc:20499]

Sequence

>retro_ocun_869
CTTATAGTAGCCATTAAACAAGAAATTCCCAGACTTCAGGCCCTGTATGAGAGAGGCCTGCAGAATGGTGTCCAGGGCCT
GAGGCTGATCCAGCAGTAAGATATAAAGAAGAAGGAGCCATATTGCAGGGGTCTAGTGGCTGTAGATTGTCCATACACTG
GCATTGTGGACTAACGGCAGGTTGCTTTGTCCTTTGCCCAGGATTTCCAACAAGCGGGTGGTTCTATCTTAACCAATTTT
AAAGTAAATGATATTGAAATGGCTAAAGAAAGCCCTTCGAGAAGTAAAGATGGGATGAAATATCCAATTGTTATAAAGAA
TACAAAGGGAGAGGAAGTTCGGAGTCAGTATGTTGTGACGTATGCGGGGCTTTACTCAGACCGCATTTCCAAGTTGAGTG
GCTGCAATCCTGATCCTCGAATTGTACCATTCCGGGGAGATTATCTGCTGCTGAAGCCAGAAAAATGCTATCTTGTAAAA
GGGAACATTTATCCGATGCCAGATAGCCGGTTTCCTTTCCTAGGAGTCCACTTCACACCAAGGATGGACGGCAGCATTTG
GCTAGGACCTAATGCAATTCTTGCCTTTAAATGGGAAGGTTATAGACCCTTTGATTTCAATGCCAGAAATGTTATGGATA
TAATTATCAATAGTGGCTTGTTTAAACTGGTGTTCCAGAATTTTTCCTACGGAGTTAGTGAAATGTATAAAGCCTGTTTT
CCTGGTGAAACAGTGAAGCACCTTCAGAAGTTCATCCCTGAAATTACCATCGGTGACATCCTCAGAGGTCCTGCTGGAGT
ACGCGCCCAGGCCCTGGACAGAGACGGAAATCCGGTAGAAGATTTTGTATTTGATGGAGGAGTTGGGGGTATTGGAAATC
GCATTCTTCATGTGAGAAATGCACTTTCCCCTGCTGCCACTTCTTCTCTTGCAATTTCTGAAATGATTGCAGATGAAGTG
CAGCAAAGATTTGAATTA

Alignment

ORF - retro_ocun_869 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.8 %
• Parental protein coverage: 70.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIVAVEQEEIPRLQALYERGLQNGVQGLRLIQQEDIKKKEPYCRGLMAVDCPYTGIVDYRQVALSFAQDF
          LIVA..QE.IPRLQALYERGLQNGVQGLRLIQQ.DIKKKEPYCRGL.AVDCPYTGIVD.RQVALSFAQDF
Retrocopy LIVAIKQE-IPRLQALYERGLQNGVQGLRLIQQ*DIKKKEPYCRGLVAVDCPYTGIVD*RQVALSFAQDF

Parental  QQAGGSILTNFEVNDIEMAKESPSRSKDGMKYPIVIKNTKGEEVRSQYVVTCAGLYSDRISELSGCNPDP
          QQAGGSILTNF.VNDIEMAKESPSRSKDGMKYPIVIKNTKGEEVRSQYVVT.AGLYSDRIS.LSGCNPDP
Retrocopy QQAGGSILTNFKVNDIEMAKESPSRSKDGMKYPIVIKNTKGEEVRSQYVVTYAGLYSDRISKLSGCNPDP

Parental  RIVPFRGDYLLLKPEKCYLVKGNIYPVPDSRFPFLGVHFTPRMDGSIWLGPNAILAFKREGYRPFDFNAR
          RIVPFRGDYLLLKPEKCYLVKGNIYP.PDSRFPFLGVHFTPRMDGSIWLGPNAILAFK.EGYRPFDFNAR
Retrocopy RIVPFRGDYLLLKPEKCYLVKGNIYPMPDSRFPFLGVHFTPRMDGSIWLGPNAILAFKWEGYRPFDFNAR

Parental  DVMDIIINSGLFKLVFQNFSYGVSEMYKACFLGETVKHLQKFIPEITIGDILRGPAGVRAQALDRDGNLV
          .VMDIIINSGLFKLVFQNFSYGVSEMYKACF.GETVKHLQKFIPEITIGDILRGPAGVRAQALDRDGN.V
Retrocopy NVMDIIINSGLFKLVFQNFSYGVSEMYKACFPGETVKHLQKFIPEITIGDILRGPAGVRAQALDRDGNPV

Parental  EDFVFDGGVGDIGSRILHVRNAPSPAATSSLAISEMIADEVQQRFEL
          EDFVFDGGVG.IG.RILHVRNA.SPAATSSLAISEMIADEVQQRFEL
Retrocopy EDFVFDGGVGGIGNRILHVRNALSPAATSSLAISEMIADEVQQRFEL

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	0.17 RPM	14.62 RPM
SRP017611_kidney	0.20 RPM	43.89 RPM
SRP017611_liver	0.00 RPM	7.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_869 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_869 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_869 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
Mus musculus	ENSMUSG00000020988	1 retrocopy	retro_mmus_659,
Oryctolagus cuniculus	ENSOCUG00000011422	1 retrocopy	retro_ocun_869 ,