RetrogeneDB ID: retro_ocun_1723

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018818:789987..791057(+)
• 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_1723
ATGTTTGTGGCGCGCAGCATCGCGGCGGACCACAATGATCTCATCCATGATGTCTCTTTCGACTTCCATGGCCCGCGGAT
GGCGACTTGCTCCAGCGACCAGAGGGTCAAGGTCTGGGATAAAAGTGAAAGTGGGGATTGGCATTGTACTGCTAGTTGGA
AGACACATAGTGGATCTGTATGGCGTGTGACCTGGACCCATCCTGAGTTTGGACAGGTTTTGGCTTCTTGTTCTTTTGAC
CGAACAGCTGCTGTGTGGGAGGAAATAGTAGGAGAGTCAAATGATAAACTGTGAGGACAGAGTCACTGGGTTAAGAGAAC
AACTCTAGTGGATAGCAGAACATCTGTTACTGATGTGAAATTTGCTCCCAAGCATATGGGTCTTATGTTGGCAACTTGTT
CAGCAGATTGTATAGTGAGGATATATGAGGCCCCAGATGTTATGAATCTTAGCCAGTGGTCCCTGCAGCATGAGATCTCA
TGTAAGCTAAGCTGTAGTTGTATTTCTTGGAACCCTTCAAGCTCTCGTGCTCATTCTCCCATGATAGCTGTAGGGAGTGA
TGACAGTAGTCCAAATGCAATGGCCAAAGTTCAGATTTTTGAATATAATGAAAACACCAGGAATACGCAAAAGCTGAAAC
GCTTATGACAGTCACTGATCCTGTTCACGATATTGCATTTGCTCCAAACTTGGGAAGATCTTTCCATATTCTAGCAATAG
CAACCAAAGATGTGAGGATTTTTACACTAAAACCTGTGAGGAAAGAACTTACTTCATCTGGTGGGCCAACAAAATTTGAA
ATCCATATAGTGGCTCAGTTTGATAATCACAGTTCTCAGGTCTGGCGAGTGAGCTGGAATATAACAGGAACAGTGCTAGC
ATCTTCAGGAGATGATGGCTGTGTACGATTGTGGAAAGCTAATTATATGGACAATTGGAAGTGCACTGGTATTTTGAAAG
GTAATGGGAGCCCAGTCAATGGGAGTTCTCAGCAGGGAAATGTAAATCCTTCCCTAGGTTCAAATATTCCAAATCTTTAA
AATTCATTAAATGGAACTTCTGCTGGCAGA

Alignment

ORF - retro_ocun_1723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.93 %
• Parental protein coverage: 85.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFVARSIAADHKDLIHDVSFDFHGRRMATCSSDQSVKVWDKSESGDWHCTASWKTHSGSVWRVTWAHPEF
          MFVARSIAADH.DLIHDVSFDFHG.RMATCSSDQ.VKVWDKSESGDWHCTASWKTHSGSVWRVTW.HPEF
Retrocopy MFVARSIAADHNDLIHDVSFDFHGPRMATCSSDQRVKVWDKSESGDWHCTASWKTHSGSVWRVTWTHPEF

Parental  GQVLASCSFDRTAAVWEEIVGESNDKLRGQSHWVKRTTLVDSRTSVTDVKFAPKHMGLMLATCSADGIVR
          GQVLASCSFDRTAAVWEEIVGESNDKL.GQSHWVKRTTLVDSRTSVTDVKFAPKHMGLMLATCSAD.IVR
Retrocopy GQVLASCSFDRTAAVWEEIVGESNDKL*GQSHWVKRTTLVDSRTSVTDVKFAPKHMGLMLATCSADCIVR

Parental  IYEAPDVMNLSQWSLQHEISCKLSCSCISWNPSSSRAHSPMIAVGSDDSSPNAMAKVQIFEYNENTR-KY
          IYEAPDVMNLSQWSLQHEISCKLSCSCISWNPSSSRAHSPMIAVGSDDSSPNAMAKVQIFEYNENTR..Y
Retrocopy IYEAPDVMNLSQWSLQHEISCKLSCSCISWNPSSSRAHSPMIAVGSDDSSPNAMAKVQIFEYNENTR<EY

Parental  AKAETLMTVTDPVHDIAFAPNLGRSFHILAIATKDVRIFTLKPVRKELTSSGGPTKFEIHIVAQFDNHNS
          AKAETLMTVTDPVHDIAFAPNLGRSFHILAIATKDVRIFTLKPVRKELTSSGGPTKFEIHIVAQFDNH.S
Retrocopy AKAETLMTVTDPVHDIAFAPNLGRSFHILAIATKDVRIFTLKPVRKELTSSGGPTKFEIHIVAQFDNHSS

Parental  QVWRVSWNITGTVLASSGDDGCVRLWKANYMDNWKCTGILKGNGSPVNGSSQQGNVNPSLGSNIPNLQNS
          QVWRVSWNITGTVLASSGDDGCVRLWKANYMDNWKCTGILKGNGSPVNGSSQQGNVNPSLGSNIPNL.NS
Retrocopy QVWRVSWNITGTVLASSGDDGCVRLWKANYMDNWKCTGILKGNGSPVNGSSQQGNVNPSLGSNIPNL*NS

Parental  LNGSSAGR
          LNG.SAGR
Retrocopy LNGTSAGR

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	48.73 RPM
SRP017611_kidney	0.10 RPM	35.88 RPM
SRP017611_liver	0.15 RPM	14.49 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1723 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1723 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,