RetrogeneDB ID: retro_obra_21

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 7:8212310..8213492(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB07G19000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB01G50760
• Aliases: None
• Description: None

Sequence

>retro_obra_21
ATGGGTTCGACGACCAAACCGCGCGGCGTCGCGCTCGCGGCGACGCTCATCTTCTTCGCCCTCCTGTTCGTCGCCGGCGC
TTCCGTTAAGCTGCATCGCTCTGAGCGCCGTACGTCGGCCGCTGCCGGCGACGAGATCGGATGTCTTCTCGCGCGCAAGA
TGCTGCGCGTCAAGGCGCGGACGGGGGAGGCTAGCGTGACCATGGCGCGGCAAGATGATGATCAGCGTCGGAGCAGCCGC
ACGGCCGACGCCGTGGCGCCGACGACGTCCAGCGGGGGTCCTCTTCCGGCCGGCATTGTGCATGGCACGTCCAACCTCGA
GATGGAGCCGATGGTCGGCGACGTCCCCGAGAAGCGCGGCGGTGGGGCGAGGGCGAGCAAGAAGAGCCTCCTGGCCGTCC
CCGTTGGGATCAAGAACAAGGCCCCCGTGGACAAGCTGGTGTCCAAGTTCCCCGCCGAGGAGTTCGCCGTGATGCTGTTC
CACTACGACGGCGCCGTGGAGCAGTGGAGCGACGTGGAGTGGCACGGCCGCGCGGTGCACGTGGCGGCGCCCGGCCAGAC
CAAGTGGTGGTTCGCCAAGCGGTTCCTGCACCCGGACGTGGTGGCTGAGTACGACTACGTCTTCCTCTGGGACGAGGACG
TCGAGGTGGACGCCTTCGACCCGCTCCGCTACCTCGCCGTCGTCAGGCGGGAAGGCCTCGAGGTCTCGCAGCCGGCGCTG
GGGCGCGGCTCGGAGATCCACCACGGCATCACCGTCCGGTCGGCGGCCGGCGGCGGCGTGCACCGGCGGTTCTACAGGCC
GTCCGGGCCGCGGTGCGACGGCGAGAGCACGGCGCCGCCGTGCACCGGGTGGGTGGAGATGATGGTGCCCGTGTTCTCCC
GCGCGGCGTGGCGGTGCGCGTGGGGCATGGTGCAGAACGACCTCGTCCACGCGTGGGGCCTCGACTACAAGCTCGGCTAC
TGGCCCGGCGGAGACCGGACGCTCAAGGTCGGCGTCGTCGACAGCGAGTACGTCTTCCACCGTGGCGTCCCCACCCTCGG
CGGCGGCGGTGGCTCCGCCGCCCCCGCCTTCCGGGCGGCGGTGAGGCGGCGCTCGTACGCCGAGATGCAGATATTCAACC
GGAGGTGGAAGCAGGCCGTCGCCGAGGACGCCTCGTGGACCGACCCTTACCCCGAGCATTGA

Alignment

ORF - retro_obra_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.83 %
• Parental protein coverage: 72.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGSEPLPKGIVQDKSNFEMESLGGN-PERRSVAGRPAK-SLLAIPVGIKQKAVVDKLVSKFPGDRFTVML
          S...PLP.GIV...SN.EME...G..PE.R....R..K.SLLA.PVGIK.KA.VDKLVSKFP...F.VML
Retrocopy SSGGPLPAGIVHGTSNLEMEPMVGDVPEKRGGGARASKKSLLAVPVGIKNKAPVDKLVSKFPAEEFAVML

Parental  FHYDGAVDGWRDLRWSDRAIHVAAIDQTKWWFGKRFLHPDMVADYDYIFLWDEDIEVDGFDPIRYLKVVK
          FHYDGAV..W.D..W..RA.HVAA..QTKWWF.KRFLHPD.VA.YDY.FLWDED.EVD.FDP.RYL.VV.
Retrocopy FHYDGAVEQWSDVEWHGRAVHVAAPGQTKWWFAKRFLHPDVVAEYDYVFLWDEDVEVDAFDPLRYLAVVR

Parental  REGLEISQPALDRRSQIHHRLTLRSRKGQ-VHRRFYKTRGGGRCDGNSTGPPCTGWVEMMVPVFSRAAWR
          REGLE.SQPAL.R.S.IHH..T.RS..G..VHRRFY....G.RCDG.ST.PPCTGWVEMMVPVFSRAAWR
Retrocopy REGLEVSQPALGRGSEIHHGITVRSAAGGGVHRRFYRP-SGPRCDGESTAPPCTGWVEMMVPVFSRAAWR

Parental  CAWHMIQNDLIYAWGLDFKLGYCARGDRRLNVGIVDSEYVLHRGIPTLGDGGGKAAPSTKAATDRLAVRQ
          CAW.M.QNDL..AWGLD.KLGY...GDR.L.VG.VDSEYV.HRG.PTLG.GGG..A....A...R.AVR.
Retrocopy CAWGMVQNDLVHAWGLDYKLGYWPGGDRTLKVGVVDSEYVFHRGVPTLG-GGGGSA----APAFRAAVRR

Parental  RSYTELQIFNRRWKAAAAEDVCWTDPYP
          RSY.E.QIFNRRWK.A.AED..WTDPYP
Retrocopy RSYAEMQIFNRRWKQAVAEDASWTDPYP

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_21 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB01G50760	1 retrocopy	retro_obra_21 ,
Oryza punctata	OPUNC01G40860	1 retrocopy	retro_opun_24,