RetrogeneDB ID: retro_ocun_1850

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019337:33915..34370(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000025342
• Aliases: None
• Description: None

Sequence

>retro_ocun_1850
ATGGCTGACCAGACTTGCATGGATCATTGAGGCCTTGCTGCATAACCACCAGCATCGAACTTGGGGTGCAGACTCCCACC
TGGCCGTGGCACAGGGGAGGAGGAGGGCAGAGCTACTGGCCCTGTGGTTCCTCTGAAGAACAAAATGGGAGATGCTGAAG
CAGGCAAGATCTTTATTCAGAAATGTGCTCAGTGCCATACAGTAGAAAAAGGTGGAAAACACAAGACTGGTCCAAATCTT
TGGAGGTCTCTGGCCAAAAAGCAGGACAAGCAGGAGGATTCTCTTATTCTGATGCAAAAAAAAAAAAAGGTACTATTTGG
GGAGAAGATACTCTGATAGAATATTTGGAGAACCCAAAGAAATATGTCCCTGGAACTAAAATTGTCTTTGCTGATCTTAA
AAAGACTGCTGAGAGAGAAAATCTTATTCAGTATTTGAACCAGGCCACATCTTCA

Alignment

ORF - retro_ocun_1850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADQTCECHRGPAAEPPPSNSGRGLPPGRGTGEEESRATGPVVPLQSKMGDAETGKKIFIQKCAQCHTVE
          MADQTC..H.G.AA.PP.SN.G..LPPGRGTGEEE.RATGPVVPL..KMGDAE.GK.IFIQKCAQCHTVE
Retrocopy MADQTCMDH*GLAA*PPASNLGCRLPPGRGTGEEEGRATGPVVPLKNKMGDAEAGK-IFIQKCAQCHTVE

Parental  KGGKHKTGPNLWG-LFGRKTGQAQGFSYSDANKNKGIVWGEDTLMEYLENPKKYIPGTKMVFAGLKKKTE
          KGGKHKTGPNLW....G.K.GQA.GFSYSDA.K.KG..WGEDTL.EYLENPKKY.PGTK.VFA.LKK..E
Retrocopy KGGKHKTGPNLWR<VSGQKAGQAGGFSYSDAKKKKGTIWGEDTLIEYLENPKKYVPGTKIVFADLKKTAE

Parental  REDLIQYLKQATSS
          RE.LIQYL.QATSS
Retrocopy RENLIQYLNQATSS

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	0.00 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_1850 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1850 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	ENSOCUG00000025342	2 retrocopies	retro_ocun_1345, retro_ocun_1850 ,