RetrogeneDB ID: retro_ogar_1596

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873554.1:16329656..16329829(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOGAG00000015671
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGA2
• Ensembl ID: ENSOGAG00000031502
• Aliases: None
• Description: high mobility group AT-hook 2 [Source:HGNC Symbol;Acc:5009]

Sequence

>retro_ogar_1596
GAGAAGCGAGGCCGGGGCAGGCCCCGCGAGCAGCCTCCAAAGGAGCCCGGTGAAGTGCCAACACCGAAGAGACCTCGGGG
CGACCAAAGGGAAGCAAAACCAAGGGTGCTGCCAAGACCTGGGAAACCACCACAACTCCAGGAAGGAAACCAAGGGGCAG
ACCCAAAAACTGG

Alignment

ORF - retro_ogar_1596 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.1 %
• Parental protein coverage: 71.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QKRGRGRPRKQQQEPTGE-PSPKRPR-GRPKGSKNKSPSKAAQKKAEATGEKRPRGRPRKW
          .KRGRGRPR.Q.....GE.P.PKRPR.GRPKGSK.K...K........T....PRGRP..W
Retrocopy EKRGRGRPREQPPKEPGEVPTPKRPR<GRPKGSKTKGAAKTWE--TTTTPGRKPRGRPKNW

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_1596 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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	ENSMUSG00000056758	1 retrocopy	retro_mmus_391,
Otolemur garnettii	ENSOGAG00000031502	1 retrocopy	retro_ogar_1596 ,
Sus scrofa	ENSSSCG00000000471	1 retrocopy	retro_sscr_3,