RetrogeneDB ID: retro_olon_19

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN539121.1:37813..39325(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN539121.1_FG003
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN539908.1_FG004
• Aliases: None
• Description: None

Sequence

>retro_olon_19
ATGGGGAGGACGGGGAGACGTGTGAGGGCCTTGGCGGTCGCGGCATTGGCCGCGGTGCTTGTTCTGGTGGCGTCCACTGA
GGCACGGCTCCTTGAGAAGGAGACGTTGGGTGGCGGAGGAGGCATCGGTGGTGGCGGTGGCTTTGGTGGTGGTGGTGGTC
TTGGAGGAGGTGGTGGTGCAGGTGGTGGTTTCAGTGGAGGGCTTGGTCATGGTGGAGGTCTTGGCGGTGGGTTTGGAGGG
GGTAAAGGTGGCGGCCTAGGCGGAGGCGGTGGTCTTGGTGGCGGAGGCGGCGCAGGTGGTGGTTTCGGTGGAGGGCTTGG
TCATGGTGGTGGCCTTGGCGGTGGGTTCGGTGGTGGGAAGGGCAGTGGTCTTGGCGGAGGCGGCGGTCTTGGTGGTGGAG
CCGGTGGAGGTGGAGGGCTTGGTGGTGGCAGTGGGCTAGGTGGCGGAGCTGGTGGTGGCCTTGGTGGTGGTGCAGGTGGA
GGCGGCGGACTTGGTGGTGGTGCTGGAGGAGGACTTGGTGGCGGAGCCGGTGGTGGTGGTGGTGCCGGAGGTGGGCTTGG
TGGCGGTGCTGGCGGAGGCGGTGGACTTGGTGGTGGTGCAGGAGGCGGCCTTGGTGGGGGTGCCGGTGGAGGCGGTGGGC
TTGGTGGTGGTGCAGGGGGAGGAATAGGTGGCGGTGCTGGTGCCGGTGGAGGTGGTGGACTCGGCGCCGGAGGTGGTGCA
GGAGAAGGAGGAGGGCTAGGTGGCGGTGCTGGTGCCGGTGGAGGTGGTGGACTCGGTGGTGGTGCTGGAGGAGGTGGCGG
ACTAGGCGGTGGTGCCGGAGGCGGCCTTGGTGGTGGTGCAGGAGTGGGCGGTGGGTTTGGTGGCGGTGGCGCCGGAGGAG
GTGGCGGACTAGGTGGTGGTGCTGGAGGCGGTGCAGGAGCAGGTGGCGGGTTTGGTGGAGGTGCCGGTGCTGGTGCTGGT
GCTGGTGGAGGTAGCGGACTTGGTGGTGGCGCCGGAGGAGGTGGCGGACTAGGTGGTGGTGCTGGAGGCGGTGCAGGAGC
AGGTGGCGGGTTTGGTGGAGGTGCCGGTGCTGGTGCTGGTGCTGGTGGAGGTAGCGGACTTGGTGGTGGCGCCGGAGGAG
GTGGCGGACTAGGTGGTGGTGCTGGAGGCGGTGCAGGAGCAGGTGGCGGGTTTGGTGGAGGTGCCGGTGCTGGTGCAGGT
GGAGGTGGTGGACTCGGCGGTGGAGGTGGAGGAGGTGGCGGACTTGGCGGTGGCGCCAGAGGCGGCCTTGGTGGTGGTGC
AGGAGCAGGCGGTGGCTTTGGGGGTGGCAAAGGTGGTGGCTTCGGCGGGGGGCTCGGTGGCGGTGGCGGTAGTGGTTTTG
GTGGTGGGTTTGGTGCTGGTGGTGGAGCCGGAGGCGGTGCTGGTGCAGGCTTCGGTGGGGGCGCCGGTGCGGGTGGTGGT
GGAGGGCTAGGTGCCGGAGCCGGAGGTGGTGGAGGTTTTGGCGGCGGTGGCGGCGTTGGCGGAAAGCTGTGA

Alignment

ORF - retro_olon_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.39 %
• Parental protein coverage: 86.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKGLGAGLGGGYGKGGGLGGGGGGGLGGGGGFGKGGGLGSGFGKGGGFGKGGGLGGGFGKGGGIGGGIGH
          G.G.G.GLGGG.G.GGG.GGG.GGG.GGGGG.G.G.G.G.G.G.GGG.G.GGGLGGG.G.GGG.GGG.G.
Retrocopy GAGGGGGLGGGSGLGGGAGGGLGGGAGGGGGLGGGAGGGLGGGAGGGGGAGGGLGGGAGGGGGLGGGAGG

Parental  GAGGGFGKGGGIGGGIGPGIGGGPG-GYGKGFGLGGGIGKGGGLGGGFGKGGGLGGGGGLGDGGGLGGGV
          G.GGG.G.GGG.GGG.G.GIGGG.G.G.G.G.G.GGG.G.GGGLGGG.G.GGG.G.GGG.G.GGGLGGG.
Retrocopy GLGGGAGGGGGLGGGAGGGIGGGAGAGGGGGLGAGGGAGEGGGLGGGAGAGGGGGLGGGAGGGGGLGGGA

Parental  GKGGGLGGGIGKGGGLGGGFGKGGGLGGGGSLGGGIGKGGGGGLGGGGGLGGGEGGGLGGGIGKGGGIGG
          G..GGLGGG.G.GGG.GGG.G.GGG.G.GG..GGG.G.GGG.G.G.G.G.G.G.G.GLGGG.G.GGG.GG
Retrocopy G--GGLGGGAGVGGGFGGG-GAGGGGGLGGGAGGGAGAGGGFGGGAGAGAGAGGGSGLGGGAGGGGGLGG

Parental  GFGKGGGLGGG--GGLGGGGGLGGGSGLGGGIGKGGGLGGGFGKGGGLGGGF--GKGGGIGGGFGKGGGL
          G.G.G.G.GGG..GG.G.G.G.GGGSGLGGG.G.GGGLGGG.G.G.G.GGGF..G.G.G.GGG.G.GGG.
Retrocopy GAGGGAGAGGGFGGGAGAGAGAGGGSGLGGGAGGGGGLGGGAGGGAGAGGGFGGGAGAGAGGGGGLGGGG

Parental  GGGGGLGGGGGGGLGG--GGGGGFGGGGGSGIGGGFGKGGGFGFGGG-GGGFGGGGGGGGGGGGGIGA
          GGGGGLGGG..GGLGG..G.GGGFGGG.G.G.GGG.G.GGG.GFGGG.G.G.G.GGG.G.G.GGG.GA
Retrocopy GGGGGLGGGARGGLGGGAGAGGGFGGGKGGGFGGGLGGGGGSGFGGGFGAGGGAGGGAGAGFGGGAGA

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_19 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza longistaminata	KN539908.1_FG004	1 retrocopy	retro_olon_19 ,