RetrogeneDB ID: retro_obra_13

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 1:33796206..33797322(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB01G54990
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB05G11140
• Aliases: None
• Description: None

Sequence

>retro_obra_13
ATGGTGCAGCGCAGCGCTTCATCCGCCGCGGAGGCCATGAGCATGGATCTCAGCCCCAAGCGCCCCGCCAAGGCCTACTC
CGCCGACGGCGGCGCCTACTACGACTGGTCCCCCTCCGACCTCCCCATGCTCGCCGCCGCCTCCATCGGCGCCGCCAAGC
TCTCCCTCGCCGCCGGCGGCCTCGCCCTCCCCTCCTACTCCGACTCCGCCAAGGTCGCCTACGTCCTCCAGGGCAAGGGC
ACCTGCGGCCTCCTCCTCCCGGAGGCCACCGCCGAGAAGATCATCCCCGTCAAGGAGGGCGACGCGCTCGCGCTCCCCTT
CGGCGTCGTCACCTGGTGGCACAACCTCCACGCCGCCGCCACCGACCTCCTCGTCCTCTTCCTCGGGGACACCGCCAAGG
CCCACACCCCCGGCCGCTTCACCAACATGCAGCTCACCGGCTCCAACGGCATCTTCACCGGCTTCTCCACCGAGTTTGTC
GCCCGCGCCTGGGACCTCCCGCAGGACGCCGCCGCCGCGCTGGTGTCCAGCCAGGCCGGGGCTGGCATCGTCAAGGTCAA
GGACGGGCAGAGGATGCCCGAGGCGTCCGACAAGGAGCGGGAGGGCGTGGTGCTCAACTGCCTGGAGGCGCCGCTGGACG
TGGACATCAAGAACGGCGGGCGCGTGGTGGTGCTGAACACGCAGAACCTGCCGCTGGTGAAGGAGGTGGGGCTGGGCGCG
GACCTGGTGAGGATCGACGGGCACTCCATGTGCTCGCCGGGGTTCTCGTGCGACTCGGCGTACCAGGTGACGTACATCGT
GCGCGGCGGCGGGCGCGTGCAGGTGGTGGGCATCGACGGGACGCGCGTGCTGGAGACCCGCGCCGAGGCCGGCTGCCTGT
TCATCGTGCCCAGGTTCTTCGTGGTGTCGAAGATCGCCGACGAGAGCGGCATGTCCTGGTTCTCCATCATCACCACGCCC
AACCCCATCTTCTCCCACCTGGCCGGGAGGACCTCCGTCTGGAAGGCCATTTCGCCCGCGGTGCTCGAGGCCTCCTTCAA
CGCCACCCCCGACATGGAGAAGCTCTTCCGCTCCAAGAGGCTCGACTCCGAGATCTTCTTCGCACCCACTCACTAG

Alignment

ORF - retro_obra_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.41 %
• Parental protein coverage: 98.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDLTPRPPRKAYGGEGGAYYEWSPADLPMLGLASIGGAKLCLAAGGLSLPSYSDSAKVAYVLQGKGTCGI
          .DL.P..P.KAY...GGAYY.WSP.DLPML..ASIG.AKL.LAAGGL.LPSYSDSAKVAYVLQGKGTCG.
Retrocopy MDLSPKRPAKAYSADGGAYYDWSPSDLPMLAAASIGAAKLSLAAGGLALPSYSDSAKVAYVLQGKGTCGL

Parental  VLPEATKEKVVAVKEGDALALPFGVVTWWHNLPESATELVVLFLGDTSKGHKSGQFTNFQLTGATGIFTG
          .LPEAT.EK...VKEGDALALPFGVVTWWHNL...AT.L.VLFLGDT.K.H..G.FTN.QLTG..GIFTG
Retrocopy LLPEATAEKIIPVKEGDALALPFGVVTWWHNLHAAATDLLVLFLGDTAKAHTPGRFTNMQLTGSNGIFTG

Parental  FSTEFVGRAFDLPESDASKLVSSQAASGIVKLKAGQKLPEPSAADREGMALNCLEAPLDVDIKNGGRVVV
          FSTEFV.RA.DLP...A..LVSSQA..GIVK.K.GQ..PE.S...REG..LNCLEAPLDVDIKNGGRVVV
Retrocopy FSTEFVARAWDLPQDAAAALVSSQAGAGIVKVKDGQRMPEASDKEREGVVLNCLEAPLDVDIKNGGRVVV

Parental  LNTQNLPLVKEVGLGADLVRIDAHSMCSPGFSCDSAYQVTYIVRGSGRVQVVGTDGKRVLETRVEGGNLF
          LNTQNLPLVKEVGLGADLVRID.HSMCSPGFSCDSAYQVTYIVRG.GRVQVVG.DG.RVLETR.E.G.LF
Retrocopy LNTQNLPLVKEVGLGADLVRIDGHSMCSPGFSCDSAYQVTYIVRGGGRVQVVGIDGTRVLETRAEAGCLF

Parental  IVPRFFVVSKIADASGMEWFSIITTPNPIFSHLAGRTSVWKAISPEVLEASFDASPEMEKLFRSKRLDSE
          IVPRFFVVSKIAD.SGM.WFSIITTPNPIFSHLAGRTSVWKAISP.VLEASF.A.P.MEKLFRSKRLDSE
Retrocopy IVPRFFVVSKIADESGMSWFSIITTPNPIFSHLAGRTSVWKAISPAVLEASFNATPDMEKLFRSKRLDSE

Parental  IFFAP
          IFFAP
Retrocopy IFFAP

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_13 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA018931	1 retrocopy	retro_oind_1,
Oryza brachyantha	OB05G11140	1 retrocopy	retro_obra_13 ,
Oryza glumaepatula	OGLUM05G01170	1 retrocopy	retro_oglu_9,
Oryza nivara	ONIVA05G01190	1 retrocopy	retro_oniv_21,
Oryza punctata	OPUNC05G01050	1 retrocopy	retro_opun_21,
Oryza glaberrima	ORGLA05G0012000	1 retrocopy	retro_ogla_28,
Oryza rufipogon	ORUFI05G01180	1 retrocopy	retro_oruf_6,
Oryza sativa japonica	OS05G0116000	1 retrocopy	retro_osat_27,