RetrogeneDB ID: retro_ocun_1047

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:73212969..73213230(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDRG1
• Ensembl ID: ENSOCUG00000016709
• Aliases: None
• Description: p53 and DNA-damage regulated 1 [Source:HGNC Symbol;Acc:16119]

Sequence

>retro_ocun_1047
CTGCAGAAGGATCGCAGCCTCTCTGAAGATATGACAGTTTGCTTCGAGAGCATGTTTATCAAGATGCTGCACTCTCACAC
CAAAGGGATGATTGGTAAAGATCAGGATCATCTGGATAAAGAAATAGACAAACTGGGAAAACAATTTAAAGTGGAGATCA
GCCGCCTCTTTGGAGCCAAAAGCAAACCAGAGCTGAAGGGCTGTAACCTGAACCTCCTCAATCAGGATGAGCTTAAGGCT
CTCAAAGTCATCCTGTAAGGT

Alignment

ORF - retro_ocun_1047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.41 %
• Parental protein coverage: 65.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQKELAVSEDVTVCFGSMFIKMPHPQTKEMIEKDQDHLDKEIDKLRKQLKVKVNRLFEAQGKPELKGFNL
          LQK....SED.TVCF.SMFIKM.H..TK.MI.KDQDHLDKEIDKL.KQ.KV...RLF.A..KPELKG.NL
Retrocopy LQKDRSLSEDMTVCFESMFIKMLHSHTKGMIGKDQDHLDKEIDKLGKQFKVEISRLFGAKSKPELKGCNL

Parental  NPLNPAELKALKVILKG
          N.LN..ELKALKVIL.G
Retrocopy NLLNQDELKALKVIL*G

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	17.00 RPM
SRP017611_kidney	0.00 RPM	9.83 RPM
SRP017611_liver	0.00 RPM	3.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1047 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1047 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1047 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020766	1 retrocopy	retro_cjac_3320,
Homo sapiens	ENSG00000088356	1 retrocopy	retro_hsap_1037,
Gorilla gorilla	ENSGGOG00000024924	1 retrocopy	retro_ggor_818,
Macropus eugenii	ENSMEUG00000003915	1 retrocopy	retro_meug_1967,
Myotis lucifugus	ENSMLUG00000007377	1 retrocopy	retro_mluc_348,
Macaca mulatta	ENSMMUG00000000973	1 retrocopy	retro_mmul_824,
Nomascus leucogenys	ENSNLEG00000009712	1 retrocopy	retro_nleu_910,
Oryctolagus cuniculus	ENSOCUG00000016709	1 retrocopy	retro_ocun_1047 ,
Ochotona princeps	ENSOPRG00000006403	1 retrocopy	retro_opri_630,
Pongo abelii	ENSPPYG00000010897	1 retrocopy	retro_pabe_869,
Pan troglodytes	ENSPTRG00000013368	1 retrocopy	retro_ptro_707,