RetrogeneDB ID: retro_ocun_1142

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 20:10163905..10164244(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD3
• Ensembl ID: ENSOCUG00000010259
• Aliases: None
• Description: COMM domain containing 3 [Source:HGNC Symbol;Acc:23332]

Sequence

>retro_ocun_1142
CAGAAAGGCTCCCAGACACTGGTGGATCCCCGTTCCTTGGACTCCAATGCTTTCACACTTCTCCTCCGGGCGGAAGTCCA
GAGCCTGCTGGATGCCCAGGTGGATGAGGCCCTGCCAGATCACCCAGGTCTGAAACATATTGACCCAGTGGTCTTAAAAC
ATTGTCCTGGAGCAGCTGCAACTTACACATTGGAGGCAAGAAAGTACAGAGCTGCCAAGTGGACTCTGAGCTCTTATCTA
GAAGGCTGTAAATCTGACAGGGAGCAAATAGAACTGTTTTGTATGCAATATCAAAATGCCAACAATTCCTTAGCAATCTT
ACTGGGAAGTATAGGTAGA

Alignment

ORF - retro_ocun_1142 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.34 %
• Parental protein coverage: 57.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKGFQMLADPGSFDSNAFTLLLRAAFQSLLDAQADEAVLDHPDLKHIDPVVLKHCHAAAATYILEAGKHR
          QKG.Q.L.DP.S.DSNAFTLLLRA..QSLLDAQ.DEA..DHP.LKHIDPVVLKHC..AAATY.LEA.K.R
Retrocopy QKGSQTLVDPRSLDSNAFTLLLRAEVQSLLDAQVDEALPDHPGLKHIDPVVLKHCPGAAATYTLEARKYR

Parental  VDKSTLSSYLEDCKFDRERIDLFCTEYQNNKNSLEILLGSISR
          ..K.TLSSYLE.CK.DRE.I.LFC..YQN..NSL.ILLGSI.R
Retrocopy AAKWTLSSYLEGCKSDREQIELFCMQYQNANNSLAILLGSIGR

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	32.12 RPM
SRP017611_kidney	0.00 RPM	30.20 RPM
SRP017611_liver	0.00 RPM	11.48 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1142 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1142 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1142 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000010259	1 retrocopy	retro_ocun_1142 ,