RetrogeneDB ID: retro_obra_18

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 6:14344682..14345315(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB06G26150
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB05G16630
• Aliases: None
• Description: None

Sequence

>retro_obra_18
ATGGAGGCGCACGTGGAGCGGGCGCTGCGGGAGGGCCTGACGGAGGAGGAGAGGGCGGCGCTGGAGCCGGCGGTGCTGGC
GCACCACACGTTCCCCGGCAGGGCAGCGGCGCCGGCGGAGGGGGCCGCGGCCGCCACCGCCACCGCCACGTCGCTGGTGA
CGCAACACGTGGCGGCGCCGCTGCGCGCGGTGTGGCCCATCGTCCGCAGCTTCGGCAACCCGCAGCGGTACAAGCACTTC
GTCCGCACCTGCGCGCTCGCCGAGGGCGACGGCGCCAGCGTCGGCAGCGTCCGGGAGGTCGCCGTCGTGTCGGGCCTCCC
GGCGTCCACCAGCACCGAGCGCCTCGAGATCCTCGACGACGACCGCCACATCATCAGCTTCCGCGTCCTCGGCGGCCAGC
ACCGCCTCCGGAACTACCGCTCCGTCACCTCCGTCACCGAGTTCCAGCCGCAGCCGGGTGCGCCCTCGCCCTACTGCGTC
GTCGTCGAGTCCTACGTCGTCGACGTCCCCGACGGGAACACCGAGGACGACACCAGGATGTTCACCGACACCGTCGTCAA
GCTCAACCTCCAGAAGCTCGCCGCCGTCGCCGAGGAATCCGCTGCCTCCTCTGCTTCGCGGCGGCGCGACTAG

Alignment

ORF - retro_obra_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.9 %
• Parental protein coverage: 87.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSALVKHIKAPVHLVWSLVRSFDQPQRYKPFVSRCVVRGGD-LEIGSVREVNVKTGLPATTSTERLELLD
          .S....H..AP...VW..VRSF..PQRYK.FV..C....GD....GSVREV.V..GLPA.TSTERLE.LD
Retrocopy TSLVTQHVAAPLRAVWPIVRSFGNPQRYKHFVRTCALAEGDGASVGSVREVAVVSGLPASTSTERLEILD

Parental  DDEHILSVKFVGGDHRLRNYSSIITV---HPESIDGRPGTLVIESFVVDVPDGNTKDETCYFVEAVIKCN
          DD.HI.S....GG.HRLRNY.S...V....P......P...V.ES.VVDVPDGNT.D.T..F...V.K.N
Retrocopy DDRHIISFRVLGGQHRLRNYRSVTSVTEFQPQPGAPSPYCVVVESYVVDVPDGNTEDDTRMFTDTVVKLN

Parental  LTSLAEVSERLAVQS
          L..LA.V.E..A..S
Retrocopy LQKLAAVAEESAASS

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza brachyantha was not studied using ChIP-Seq data.

EST

Oryza brachyantha was not studied using EST data.

TSS

Oryza brachyantha was not studied using FANTOM5 data.

Lab

retro_obra_18 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza brachyantha 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00107p00103680	1 retrocopy	retro_atri_5,
Oryza brachyantha	OB05G16630	1 retrocopy	retro_obra_18 ,
Oryza barthii	OBART05G07210	1 retrocopy	retro_obar_15,
Prunus persica	PRUPE_ppa012114mg	1 retrocopy	retro_pper_8,