RetrogeneDB ID: retro_olon_11

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: AMDW01033043.1:66..429(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMDW01033043.1_FG001
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN540497.1_FG004
• Aliases: None
• Description: None

Sequence

>retro_olon_11
GTGTGGGATTTAGGAGGACAAGAGAGTCTACGGACTTCGTGGGCAACATACTACAGAGGAACCCATGCTGTCATCGTTGT
AATTGACAGCACAGACCGTGCTCGGATCAACATAATCAAGGATGAGCTCTTCCGGCTGCTTCAGCATGGGGACCTCGAGG
GCGCAGTCGTCCTCGTGTTCGCGAACAAGCAGGATCTCAAGGACGCCATGTCGCCAGCTGAGATCACCGACGCCCTGTCC
CTCCACAGCATAAAGAACCACGACTGGCACATACAGGCCTCATGCGCGATCACCGGCGAGGGCCTCTACGACGGGCTCGG
CTGGATAGCTCAGAAAGTCGCCGGCAAGGCCACAACAAGCTGA

Alignment

ORF - retro_olon_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.99 %
• Parental protein coverage: 64.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAM
          VWD.GGQ...R..W..Y...T...I.V.DS.DR.R.....DEL.R.L....L..AV.LVFANKQDL..AM
Retrocopy VWDLGGQESLRTSWATYYRGTHAVIVVIDSTDRARINIIKDELFRLLQHGDLEGAVVLVFANKQDLKDAM

Parental  NAAEITDKLGLHSLRQRHWYIQSTCATTGEGLYEGLDWLSSNIASKA
          ..AEITD.L.LHS.....W.IQ..CA.TGEGLY.GL.W.....A.KA
Retrocopy SPAEITDALSLHSIKNHDWHIQASCAITGEGLYDGLGWIAQKVAGKA

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza longistaminata was not studied using ChIP-Seq data.

EST

Oryza longistaminata was not studied using EST data.

TSS

Oryza longistaminata was not studied using FANTOM5 data.

Lab

retro_olon_11 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza longistaminata 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN540497.1_FG004	1 retrocopy	retro_olon_11 ,
Prunus persica	PRUPE_ppa017304mg	1 retrocopy	retro_pper_38,