RetrogeneDB ID: retro_ocun_1801

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018921:328216..329238(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000006858
• Aliases: None
• Description: None

Sequence

>retro_ocun_1801
ATGTCTTTCAACTTCCATGGCCGGCAGATGGCGATTTGCTCCAGCGACCAGGACGTCAAGGTCTGCGATAAAAGTGAAAG
TGGGGATTGTACTGCTAGTCGGAAGACACGTAGTGGATCTGAATGGCGTGTGACCTGGGCCCATCCTGAGTTTGGACAGG
TTTTGGCTTCCTGTTCTTTTGACCGAAAAGCTGCTGCGTGGGAGTAAATAGTAGGAGAGTCAAAGGATAAACTGCGAGGA
CAGAGTCCCTGGGTTAAGAGAACAACTCTAGTGCATAGCAGAACATCCGTTACTGATGTGAAAGTTGCTCTGAAGCATAT
GGGTCTTGTGTCGGCTACTTGCTCAGCAGATGGTATAGTGAGGATATATGAGGCCCCAGATGCTATGAATCTTAGTCAGG
GGTCCCTGCAGCATGAGATCTCGTGTCAGCTAAGCTGTAGTTGTATTTCTTGGAACCTTCAAGCTCTCGTGTTCATTCTC
CCAGGAGAGCTGTAGGGAGTGATGACAATAGTCCAAATGCAATGGCCAAAGTTCAGATTTTTGAATATAATGAAAACACC
AGGAAATATGCAAAAGCTGAAACTCTTATGACAATCACTGATCCTGTTCATGATACTGCATTTGCTCCAAACTTGGGAAG
ATCTTTCCATATTCTAGCAATAGCAACCAAAGATGTGAGGATTTTTACACTAAAACCTGTGAGGAAAGAACTTACTTCAT
CTGGTGGACCAACAAAATTTGAAATCCATATAGCGGCTCAGTTTGATAATCACAATTCTCAGGTCTGGAGAGTGAGCTGG
AATATAATAGGAACAGTGCTAGCATCTTCAGGAGATGATGGCAGTGTACGATTGTGGATAGTTAATTATATAGACAATTG
GAAGTGCACTGGTATTTTGAAAGGTAATGGGAGCCCAGTCAATGGGAGTTCTCAGCAGGGAAATGTAAATCCTTCCCTAG
GTTCAAATATTACAAATCTTCAAAATTCATAAAATGGATTTTCTGCTGCCAGAAAGCACAGC

Alignment

ORF - retro_ocun_1801 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.83 %
• Parental protein coverage: 95.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSFDFHGRRMATCSSDQSVKVWDKSESGDWHCTASWKTHSGSVWRVTWAHPEFGQVLASCSFDRTAAVWE
          .SF.FHGR.MA.CSSDQ.VKV.DKSESGD..CTAS.KT.SGS.WRVTWAHPEFGQVLASCSFDR.AA.WE
Retrocopy MSFNFHGRQMAICSSDQDVKVCDKSESGD--CTASRKTRSGSEWRVTWAHPEFGQVLASCSFDRKAAAWE

Parental  EIVGESNDKLRGQSHWVKRTTLVDSRTSVTDVKFAPKHMGLMLATCSADGIVRIYEAPDVMNLSQWSLQH
          .IVGES.DKLRGQS.WVKRTTLV.SRTSVTDVK.A.KHMGL..ATCSADGIVRIYEAPD.MNLSQ.SLQH
Retrocopy *IVGESKDKLRGQSPWVKRTTLVHSRTSVTDVKVALKHMGLVSATCSADGIVRIYEAPDAMNLSQGSLQH

Parental  EISCKLSCSCISWN-PSSSRAHSPMIAVGSDDSSPNAMAKVQIFEYNENTSRKYAKAETLMTVTDPVHDI
          EISC.LSCSCISWN.PSSSR.HSP..AVGSDD.SPNAMAKVQIFEYNENT.RKYAKAETLMT.TDPVHD.
Retrocopy EISCQLSCSCISWN<PSSSRVHSPRRAVGSDDNSPNAMAKVQIFEYNENT-RKYAKAETLMTITDPVHDT

Parental  AFAPNLGRSFHILAIATKDVRIFTLKPVRKELTSSGGPTKFEIHIVAQFDNHNSQVWRVSWNITGTVLAS
          AFAPNLGRSFHILAIATKDVRIFTLKPVRKELTSSGGPTKFEIHI.AQFDNHNSQVWRVSWNI.GTVLAS
Retrocopy AFAPNLGRSFHILAIATKDVRIFTLKPVRKELTSSGGPTKFEIHIAAQFDNHNSQVWRVSWNIIGTVLAS

Parental  SGDDGCVRLWKANYMDNWKCTGILKGNGSPVNGSSQQGNVNPSLGSNIPNLQNSLNGSSAGRKHS
          SGDDG.VRLW..NY.DNWKCTGILKGNGSPVNGSSQQGNVNPSLGSNI.NLQNS.NG.SA.RKHS
Retrocopy SGDDGSVRLWIVNYIDNWKCTGILKGNGSPVNGSSQQGNVNPSLGSNITNLQNS*NGFSAARKHS

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	0.06 RPM	48.73 RPM
SRP017611_kidney	0.00 RPM	35.88 RPM
SRP017611_liver	0.00 RPM	14.49 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1801 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1801 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1801 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000545	2 retrocopies	retro_chof_165, retro_chof_2594,
Oryctolagus cuniculus	ENSOCUG00000006858	2 retrocopies	retro_ocun_1723, retro_ocun_1801 ,
Sus scrofa	ENSSSCG00000030252	2 retrocopies	retro_sscr_178, retro_sscr_186,