RetrogeneDB ID: retro_omer_32

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 4:28964331..28965228(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI04G24530
• Aliases: None
• Description: None

Sequence

>retro_omer_32
ATCGGCGAGCACGAGCGCCGGTTCCGCGTGTTCTGGGACAACCTCAAGTTCGTCGACGCCCACAACGCCCGCGCCGACGA
GCGCGGCGGGTTCCGCCTCGGGATGAACCGCTTCGCCGACCTAACCAACGGCGAGTTCCGCGCCGCCTACCTCGGCACCA
CGCCCGCCGGCAGGGGGCGCCGCGTCGGGGAGGCGTACCGCCACGACGGCGTCGAGGCGCTGCCGGACTCCGTGGACTGG
AGGGACGAGGGCGCCGTCGTCGCCCCCGTCAAGAACCAGGGCCAGTGCGGCAGCTGCTGGGCGTTCTCGGCGGTCGCCGC
CGTGGAGGGCATCAACAAGATCGTCACCGGCGAGCTGGTGTCGCTGTCGGAGCAGGAGCTCGTGGAGTGCGCGAGGAACG
GGCAGAACAGCGGGTGCAACGGCGGGATCATGGACGACGCGTTCGCCTTCATCGCCCGGAACGGCGGCCTCGACACGGAG
GAGGACTACCCGTACACGGCCATGGACGGCAAGTGCAACCTCGCCAAGAGGAGCCGCAAGGTGGTGTCCATCGACGGCTT
CGAGGACGTGCCCGAGAACGACGAGCTGTCGCTCCAGAAGGCCGTGGCGCACCAGCCCGTCAGCGTCGCCATCGACGCCG
GCGGCCGCGAGTTCCAGCTCTACGACTCCGGCGTGTTCACCGGCCGGTGCGGCACCAACCTGGATCACGGCGTGGTGGCG
GTGGGGTACGGCACGGACGCCGCCACCGGCGCCGCCTACTGGACGGTGCGCAACTCGTGGGACCCCGACTGGGGCGAGAA
CGGCTACATCCGCATGGAGCGCAACGTCACCGCGCGCACCGGCAAGTGCGGCATCGCCATGATGGCGTCGTACCCGATCA
AGAAGGGGCCCAACCCG

Alignment

ORF - retro_omer_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.59 %
• Parental protein coverage: 63.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGEHERRFRIFWDNLRFVDAHNARADERGGFRLGMNRFADLTNEEFRATFLGAKVAERSRAAGERYRHDG
          .GEHERRFR.FWDNL.FVDAHNARADERGGFRLGMNRFADLTN.EFRA..LG...A.R.R..GE.YRHDG
Retrocopy IGEHERRFRVFWDNLKFVDAHNARADERGGFRLGMNRFADLTNGEFRAAYLGTTPAGRGRRVGEAYRHDG

Parental  VEELPESVDWREKGA-VAPVKNQGQCGSCWAFSAVSTVESINQLVTGEMITLSEQELVECSTNGQNSGCN
          VE.LP.SVDWR..GA.VAPVKNQGQCGSCWAFSAV..VE.IN..VTGE...LSEQELVEC..NGQNSGCN
Retrocopy VEALPDSVDWRDEGAVVAPVKNQGQCGSCWAFSAVAAVEGINKIVTGELVSLSEQELVECARNGQNSGCN

Parental  GGLMDDAFDFIIKNGGIDTEDDYPYKAVDGKCDINRENAKVVSIDGFEDVPQNDEKSLQKAVAHQPVSVA
          GG.MDDAF.FI..NGG.DTE.DYPY.A.DGKC.......KVVSIDGFEDVP.NDE.SLQKAVAHQPVSVA
Retrocopy GGIMDDAFAFIARNGGLDTEEDYPYTAMDGKCNLAKRSRKVVSIDGFEDVPENDELSLQKAVAHQPVSVA

Parental  IEAGGREFQLYHSGVFSGRCGTSLDHGVVAVGYGTD--NGKDYWIVRNSWGPKWGESGYVRMERNINVTT
          I.AGGREFQLY.SGVF.GRCGT.LDHGVVAVGYGTD...G..YW.VRNSW.P.WGE.GY.RMERN....T
Retrocopy IDAGGREFQLYDSGVFTGRCGTNLDHGVVAVGYGTDAATGAAYWTVRNSWDPDWGENGYIRMERNVTART

Parental  GKCGIAMMASYPTKSGANP
          GKCGIAMMASYP.K.G.NP
Retrocopy GKCGIAMMASYPIKKGPNP

Legend:

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

Expression

RNA-Seq

Oryza meridionalis was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza meridionalis was not studied using ChIP-Seq data.

EST

Oryza meridionalis was not studied using EST data.

TSS

Oryza meridionalis was not studied using FANTOM5 data.

Lab

retro_omer_32 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza meridionalis 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
Oryza meridionalis	OMERI04G24530	1 retrocopy	retro_omer_32 ,
Oryza meridionalis	OMERI11G07520	1 retrocopy	retro_omer_2,
Oryza punctata	OPUNC04G26560	1 retrocopy	retro_opun_41,