RetrogeneDB ID: retro_ocun_985

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 18:7657783..7657972(-)
• Located in intron of: ENSOCUG00000012865

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBP2
• Ensembl ID: ENSOCUG00000008146
• Aliases: None
• Description: retinol binding protein 2, cellular [Source:HGNC Symbol;Acc:9920]

Sequence

>retro_ocun_985
GAGTGTGCTGAGGGCCTGGACAGTTAGTGTGGTAAGATGCTGGTCAGCTGGGGAGGCGATGTCTTGTGTGCATACACAGG
AGGAGGAAGAGAGGAGTGTCCCAGCTAGAGGCAGTGGATCAAGGGGGACAAGCTGCACCTGGAGCTGACCTGAGGCAACC
AGGTGTGCCATCAAGTGTTCACAAAGAAG

Alignment

ORF - retro_ocun_985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.97 %
• Parental protein coverage: 50.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EYTKGLDNRHVKTLVTWEGDCLVCVQKGEKEN-RGWRQWIEDGKLHLELTCGDQVCHQVFKKK
          E...GLD....K.LV.W.GD.L.....G..E.....RQWI...KLHLELT.G.QVCHQVF.KK
Retrocopy ECAEGLDS*CGKMLVSWGGDVLCAYTGGGREECPS*RQWIKGDKLHLELT*GNQVCHQVFTKK

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_985 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_985 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_985 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000001497	1 retrocopy	retro_ocun_1874,
Oryctolagus cuniculus	ENSOCUG00000008146	1 retrocopy	retro_ocun_985 ,