RetrogeneDB ID: retro_ocun_524

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:100155406..100156210(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000009673
• Aliases: None
• Description: None

Sequence

>retro_ocun_524
ATGGCTAAGAACCTGCTAGCAGCGACCACCTGTCCAATTTGCCTGGGATATTTCTCATGTCCCGTCTCTCTCTCCTGTGG
ACATGTCTTCTGCTTAGATTGCCTTCGAGTCTGGGTGTCAGGAAGAGAGGATTTTGTGCTGGTTTGCCCCACATGTCGCT
CAGTCAGCGAGAGAGTACCTATGGAAGAGTGGCAAATCAGAAACCTGACCTTGCTAACCAGGCATCATGCTGGTCTCCTG
GAGCAGAGTCTGCTCCTTAGTGAGGAGGTTCTGAGGTTCCAGGAGGACGAGGTCCTGGACACAGCTACCGCACACTCCCT
CCTTGAGCTCTCCAGCGACCTGAGGAGCGTTGAATGTGGGAAGACCTGCCACAACCTGCTGGAAGACCCCAGTAGTTTCC
CTCACCTGGTCTGCATCCAGGGAAACACCTGCTTCTCCTGGGGCCGCCATTACTGGGAGGTTGAAGTAGGAGAAGCCAAG
GAGTGGTCCCTGGGTGTCTGGCAAGTGTCAGCTGACACAAAGAGAAATGGTGATTTAACCTCCGACCACGGTTTCTGGAT
CATCTTTGTAGAGGGAGGACTCATTCACCCCAGCACCAACACAGAAGTAATCGTTCCTGCAAGCCCTAGTCTTCACCGCG
TAGGAGTTTTCCTGGATGTGGATTTGGGAGAGATCAAGTTTTTTGATGTTGGAAATAAAGCTCTCATCTACATGCACAGG
TTCCTCTCCACCGTGGAGCCTTTTCATCCGTTCTTCTGTTTTGTACCTTTTTAATGTGCCACTGGTGCCCCCCTGAGCAT
CTGC

Alignment

ORF - retro_ocun_524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.44 %
• Parental protein coverage: 99.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKNLLTATTCPICLGYFSCPVSLSCGHVFCLDCLHVWGLGREDFVLVCPTCRSVSERAPVEEWHIGKLT
          MAKNLL.ATTCPICLGYFSCPVSLSCGHVFCLDCL.VW..GREDFVLVCPTCRSVSER.P.EEW.I....
Retrocopy MAKNLLAATTCPICLGYFSCPVSLSCGHVFCLDCLRVWVSGREDFVLVCPTCRSVSERVPMEEWQIXXXX

Parental  HLTRHHGGLLEQSLLLTEEVLRFQEDEVLDTATALSLIELSSNQRSVECGKTCHNPLEDPIRLSSLVCVL
          ............SLLL.EEVLRFQEDEVLDTATA.SL.ELSS..RSVECGKTCHN.LEDP.....LVC..
Retrocopy XXXXXXXXXXXXSLLLSEEVLRFQEDEVLDTATAHSLLELSSDLRSVECGKTCHNLLEDPSSFPHLVCIQ

Parental  GNTCFSWGRHYWEVEVGEAKEWTLGVWQESDNTKRNGDLTSDQGFWIICVEAGLIHPSTNIEVMVPASPS
          GNTCFSWGRHYWEVEVGEAKEW.LGVWQ.S..TKRNGDLTSD.GFWII.VE.GLIHPSTN.EV.VPASPS
Retrocopy GNTCFSWGRHYWEVEVGEAKEWSLGVWQVSADTKRNGDLTSDHGFWIIFVEGGLIHPSTNTEVIVPASPS

Parental  LHRVGVFLDVDLGEIKFFDVGNKALIYMHRFLSTVEPFRPFYCFEIKHCHVTGNVVAVC
          LHRVGVFLDVDLGEIKFFDVGNKALIYMHRFLSTVEPF.PF.CF....C..TG.....C
Retrocopy LHRVGVFLDVDLGEIKFFDVGNKALIYMHRFLSTVEPFHPFFCFVPF*C-ATGAPLSIC

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	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_524 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_524 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_524 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000009673	2 retrocopies	retro_ocun_524 , retro_ocun_525,