RetrogeneDB ID: retro_ocun_1687

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018765:1294239..1294503(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024475
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TUSC2
• Ensembl ID: ENSOCUG00000005259
• Aliases: None
• Description: tumor suppressor candidate 2 [Source:HGNC Symbol;Acc:17034]

Sequence

>retro_ocun_1687
GTGGCAGCGGCGGGTGCAGAGCAAGCTTTGGTGCGGCCTCGAGGCCGAACCGTGCCGCCCTTCGTATTCACGCGCCGCGG
CTCCATGTTCTACGATGAGGATGGGGACCTGGCTCACGAGTTCTATGAGGAGACAATCGTCACCAAGAATGGACAGAAGC
GGGCCAAGCTGAGGCGGGTACATAAGAATCTGATTCCTCAGGGCCTCGTGAAGCTGGACCCCCCTCGCATCCACGTGGAC
TTCCCCGTGATCCTCTATGAGGTG

Alignment

ORF - retro_ocun_1687 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 84.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAAAGAEQALVRPRGRTVPPFVFTRRGSMFYDEDGDLAHEFYEETIVTKNGQKRAKLRRVHKNLIPQGLV
          VAAAGAEQALVRPRGRTVPPFVFTRRGSMFYDEDGDLAHEFYEETIVTKNGQKRAKLRRVHKNLIPQGLV
Retrocopy VAAAGAEQALVRPRGRTVPPFVFTRRGSMFYDEDGDLAHEFYEETIVTKNGQKRAKLRRVHKNLIPQGLV

Parental  KLDPPRIHVDFPVILYEV
          KLDPPRIHVDFPVILYEV
Retrocopy KLDPPRIHVDFPVILYEV

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	6.35 RPM
SRP017611_kidney	0.10 RPM	2.94 RPM
SRP017611_liver	0.00 RPM	1.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1687 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1687 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000007859	2 retrocopies	retro_dord_20, retro_dord_590,
Mus musculus	ENSMUSG00000010054	2 retrocopies	retro_mmus_2347, retro_mmus_2349,
Oryctolagus cuniculus	ENSOCUG00000005259	1 retrocopy	retro_ocun_1687 ,
Rattus norvegicus	ENSRNOG00000021528	1 retrocopy	retro_rnor_2952,