RetrogeneDB ID: retro_ocun_1512

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:62311610..62312009(-)
• Located in intron of: ENSOCUG00000004848

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEDD
• Ensembl ID: ENSOCUG00000002387
• Aliases: None
• Description: death effector domain containing [Source:HGNC Symbol;Acc:2755]

Sequence

>retro_ocun_1512
GTGATGTGGCTACTGTACATCATCACTCACCATGACTTACTGCCCTGTGTCACCCTTAAGAGGAGATGGTCTGTGTGCTC
TGATCTTGTAGACAAGTATCTGGAAGAGACATCAATTAGCTATGTGATGCCCAGAGCCCTCATTGATCCAAAACTAAGTT
CTCCCTGGCCCCCTTAAACAATACCTTCCCACTGTCCTGTGGTGTGGTGTCCCACCTTGAGTCCTCAGATACATAGCAAA
TGGCCAACCTGAAGGAGAGCCATTCTTGGGAGCCATCACAAACACTATTAGTCAATGACACCAGATCCCAAGGAAAAACA
GACATGTGACATTATACTGCACATTCAGGGTAAATACTGCCAGTGTGAGACTGTTCTGCAGGGCAACATCTTTAACAAT

Alignment

ORF - retro_ocun_1512 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.41 %
• Parental protein coverage: 56.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLQLLRIITRHDLLPYVTLKRRRAVCPDLVDKYLEETSIRYVTPRALSDPEPRPPQPPKTVPPHYPVVCC
          V..LL.IIT.HDLLP.VTLKRR..VC.DLVDKYLEETSI.YV.PRAL.DP....P.PP.T.P.H.PVV.C
Retrocopy VMWLLYIITHHDLLPCVTLKRRWSVCSDLVDKYLEETSISYVMPRALIDPKLSSPWPP*TIPSHCPVVWC

Parental  PTSGPQMCSKRPARGRATLGSQRKRRKSVTPDPKEKQTCDIRLRVRAEYCQHETALQGNVFSN
          PT..PQ..SK.P...RA.LGS..K...S.TPDPKEKQTCDI.L.....YCQ.ET.LQGN.F.N
Retrocopy PTLSPQIHSKWPT*RRAILGSHHKHY*SMTPDPKEKQTCDIILHIQGKYCQCETVLQGNIFNN

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	18.71 RPM
SRP017611_kidney	0.00 RPM	23.92 RPM
SRP017611_liver	0.00 RPM	16.57 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1512 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1512 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1512 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000013973	1 retrocopy	retro_mmus_2223,
Oryctolagus cuniculus	ENSOCUG00000002387	1 retrocopy	retro_ocun_1512 ,
Rattus norvegicus	ENSRNOG00000003779	1 retrocopy	retro_rnor_546,