RetrogeneDB ID: retro_obra_12

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 4:9730214..9731252(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB04G19840
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB01G28610
• Aliases: None
• Description: None

Sequence

>retro_obra_12
ATGGCGGCGACAATGCGTTGGGGCCGCGGCGCGCTCGTGGTGGCGGCGTTCGCGGCGGTGGTCGCGGTGTCCGGGCTCGG
CGTGGCGGCGAACTACGGCGCCCCCGGCGGCGGCGGGTTCTTGTTCCCGCAGTTCTACCAGCACACGTGCCCGCAGATGG
AGGCGGTGGTGGGCGCCATCGTGGCGAAGGCGCACGCCGAGGACCCGCGCATGGCGGCGTCGCTGCTGCGGATGCACTTC
CACGACTGCTTCGTGCAGGGCTGCGACGCGTCGGTGCTGCTCGACGCCGACGGCAGCGGGCGGGTCGCCACCGAGAAGCG
GTCCAACCCCAACCGCGACTCGCTCCGCGGGTACGAGGTGATCGACGAGATCAAGGCGGCGCTGGAGCACGCCTGCCCGC
GCACCGTCTCCTGCGCCGACATCGTCGCCGTCGCCGCCAGGGACTCCACCGTCCTCACCGGCGGGCCAGGCTGGGAGGTG
CCGCTCGGGAGGAGGGACTCGCTGACGGCCAGCCTCAGCGGCTCCAACAACCTCATCCCGGCTCCGAACGACACCCTCGC
CACCATCGTCGGCAAGTTCCGCAACCAGGGCCTCGACCTCGTGGACCTCGTCGCGCTCTCCGGCAGCCACACCATCGGCA
ACTCCAGGTGCGTCAGCTTCCGCCAGAGGCTGTACAGCCAGAACAACGACGGGAAGCCCGACTTCACGCTGAACCCGGCG
TACGCGGCGGAGCTCCGGGGCCGGTGCCCGCGCTCCGGCGGCGACCAGAACCTGTTCGCGCTGGACCCCGTCAGCCAGTT
CCGGTTCGACAACCAGTACTACCGCAACATCCTCGCCATGAGCGGCCTGCTCAACTCCGACGAGGTGCTGCTGACGCAGA
GCCACGAGACGATGGAGCTCGTCCACCGCTACGCCGCCAGCAACGAGCTCTTCTTCCAGCAGTTCGCCAAGTCCATGGTG
AAGATGGGCAACATCTCCCCGCTCACCGGCCACAACGGCGAGATCAGGATGAACTGCAGGAGGGTCAACCACTTCTAG

Alignment

ORF - retro_obra_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.15 %
• Parental protein coverage: 92.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LDPHFYDRSCPQAQQIVASIVGKVHYQDPRMAASLLRLHFHDCFVKGCDASILLDS--SATIVSEKRSNP
          L.P.FY...CPQ....V..IV.K.H..DPRMAASLLR.HFHDCFV.GCDAS.LLD...S.....EKRSNP
Retrocopy LFPQFYQHTCPQMEAVVGAIVAKAHAEDPRMAASLLRMHFHDCFVQGCDASVLLDADGSGRVATEKRSNP

Parental  NRDSARGFEVIDEIKAALEAACPHTVSCADILALAARDSTVMTGGPGWIVPLGRRDSRGASVQGSNNDIP
          NRDS.RG.EVIDEIKAALE.ACP.TVSCADI.A.AARDSTV.TGGPGW.VPLGRRDS..AS..GSNN.IP
Retrocopy NRDSLRGYEVIDEIKAALEHACPRTVSCADIVAVAARDSTVLTGGPGWEVPLGRRDSLTASLSGSNNLIP

Parental  APNNTLPTIITKFKLQGLDILDLVALLGSHTIGDSRCTSFRQRLYNRTGTGLPDLTLDASYAAALRPRCP
          APN.TL.TI..KF..QGLD..DLVAL.GSHTIG.SRC.SFRQRLY.....G.PD.TL...YAA.LR.RCP
Retrocopy APNDTLATIVGKFRNQGLDLVDLVALSGSHTIGNSRCVSFRQRLYSQNNDGKPDFTLNPAYAAELRGRCP

Parental  RSGGDQNLFFLDPVTPFKFDNQYYKNLLAYRGLLSSDEVLLTASPATAELVKLYAADQDVFFQHFARSMV
          RSGGDQNLF.LDPV..F.FDNQYY.N.LA..GLL.SDEVLLT.S..T.ELV..YAA....FFQ.FA.SMV
Retrocopy RSGGDQNLFALDPVSQFRFDNQYYRNILAMSGLLNSDEVLLTQSHETMELVHRYAASNELFFQQFAKSMV

Parental  KMGNISPLTGGNGEIRANCRKVNRY
          KMGNISPLTG.NGEIR.NCR.VN..
Retrocopy KMGNISPLTGHNGEIRMNCRRVNHF

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_12 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA003712	1 retrocopy	retro_oind_39,
Oryza brachyantha	OB01G28610	1 retrocopy	retro_obra_12 ,
Oryza sativa japonica	OS01G0543100	1 retrocopy	retro_osat_3,