RetrogeneDB ID: retro_oruf_30

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 3:152940..153762(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI03G00260
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI10G19380
• Aliases: None
• Description: None

Sequence

>retro_oruf_30
ATGGTTAGCGGTGATGTAGTGTACTACCTGCTGCTAGTATTAGTGGTGGTGCAGGGGTGCAAAGGCAGCAGCGCGGTGCA
GGGTGAAGGTCGGTGGTACAACGAGAGCGAGGCCATCGGTGGTGCGGCGGCGTGGGGGAACGCGAAGGCGACGTGGTACG
GGCAGCCGAACGGCGCCGGGGCGGCGGACAACGGCGGGGCGTGCGGGTTCAAGAAGGTGAACCAGTACCCGTTCATGGGG
ATGACGTCGTGCGGGAACCAGCCGCTGTACAAGGGCGGCAAGGGCTGCGGCTCCTGCTACCGCGTCAGGTGCAATCGAAA
CCCCGCCTGCTCCGGCAACGCCCAGACCGTCGCCATCACCGACATGAACTACTTCCCCCTCTCCCAGTACCACTTCGACC
TCAGCGGCATCGCCTTCGGCCGCCTCGCCAAGCCCGGCCGCGCCGACGACCTCCGCCGCGCGGGGATCATCGACGTGCAG
TTCGCGCGCGTGCCGTGCGAGTTCCCGGGCCTCAAGGTGGGATTCCACGTGGAGGAAGGGTCCAGCCCCGTGTACCTGGC
GGTGCTGGTGGAGTACGAGAACGGCGACGGAGACGTGGCGCAGGTGGACCTCAAGGAGGCCGGCGCCGGAGGAGGAAGGT
GGACGCCGATGCGGGAGTCGTGGGGGTCGGTGTGGAGGCTGGACTCCAACCACCGCCTGCGGGCGCCATTCTCCATCCGC
ATCCGGAGCGACTCCGGCAAGACGTTGGTGGCACCCGACGTCATCCCCCTCAACTGGACGCCCAACACCTTCTACCGTTC
CTTCGTCCAGTACTCCTCCTAG

Alignment

ORF - retro_oruf_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.49 %
• Parental protein coverage: 87.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNGVDFNSSDAAVYWGPWTKARATWYGQPNGAGPDDNGGACGFKHTNQYPFMSMTSCGNQPLFKDGKGCG
          G.G...N.S.A......W..A.ATWYGQPNGAG..DNGGACGFK..NQYPFM.MTSCGNQPL.K.GKGCG
Retrocopy GEGRWYNESEAIGGAAAWGNAKATWYGQPNGAGAADNGGACGFKKVNQYPFMGMTSCGNQPLYKGGKGCG

Parental  SCYKIRCTKDQSCSGRSETVIITDMNYYPVAPFHFDLSGTAFGRLAKPGLNDKLRHSGIIDIEFTRVPCE
          SCY..RC.....CSG...TV.ITDMNY.P....HFDLSG.AFGRLAKPG..D.LR..GIID..F.RVPCE
Retrocopy SCYRVRCNRNPACSGNAQTVAITDMNYFPLSQYHFDLSGIAFGRLAKPGRADDLRRAGIIDVQFARVPCE

Parental  FPGLKIGFHVEEYSNPVYFAVLVEYEDGDGDVVQVDLMESKTAHGPPTGRWTPMRESWGSIWRLDTNHRL
          FPGLK.GFHVEE.S.PVY.AVLVEYE.GDGDV.QVDL.E.....G...GRWTPMRESWGS.WRLD.NHRL
Retrocopy FPGLKVGFHVEEGSSPVYLAVLVEYENGDGDVAQVDLKEA----GAGGGRWTPMRESWGSVWRLDSNHRL

Parental  QAPFSIRIRNESGKTLVANNVIPANWRPNTFYRSFVQYS
          .APFSIRIR..SGKTLVA..VIP.NW.PNTFYRSFVQYS
Retrocopy RAPFSIRIRSDSGKTLVAPDVIPLNWTPNTFYRSFVQYS

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza rufipogon was not studied using ChIP-Seq data.

EST

Oryza rufipogon was not studied using EST data.

TSS

Oryza rufipogon was not studied using FANTOM5 data.

Lab

retro_oruf_30 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza rufipogon 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 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA033426	1 retrocopy	retro_oind_67,
Zea mays	GRMZM2G013002	1 retrocopy	retro_zmay_9,
Oryza longistaminata	KN539761.1_FG003	1 retrocopy	retro_olon_5,
Leersia perrieri	LPERR10G14060	1 retrocopy	retro_lper_25,
Oryza barthii	OBART10G18180	1 retrocopy	retro_obar_7,
Oryza glumaepatula	OGLUM10G18290	1 retrocopy	retro_oglu_25,
Oryza nivara	ONIVA10G20720	1 retrocopy	retro_oniv_16,
Oryza glaberrima	ORGLA10G0133100	1 retrocopy	retro_ogla_8,
Oryza rufipogon	ORUFI10G18850	1 retrocopy	retro_oruf_14,
Oryza rufipogon	ORUFI10G19380	1 retrocopy	retro_oruf_30 ,
Oryza sativa japonica	OS10G0556100	1 retrocopy	retro_osat_34,
Physcomitrella patens	PP1S100_99V6	1 retrocopy	retro_ppat_8,