RetrogeneDB ID: retro_obra_5

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 8:121210..121939(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB08G10170
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB02G32980
• Aliases: None
• Description: None

Sequence

>retro_obra_5
ATGGATCCATCCAAATCCAAGATAGATGATATGAAGGTGAAGGTGAAGGAGGGCGGCGGCGGGGTGGGCGCGTGGACGGT
GGTGGCGCACGTCCTAGCGGTGGCGGCCACGGCGCTGGTGCTGCTCTGGAGCATCCACTTCCGCGGCGGCCTCGCCCTGC
GCTCCCACGACAAGCAGCTCATCTTCAACACGCACCCGGTCCTCATGCTGCTCGGCCTCGTCGTCCTCGCCGCCGAGGCC
ATCCTCTCCTACCGCTCCTTCCCCCACCTTCTTCTCTCCAGGGACGCCCGCAAGAAGACGCACCTGGCGCTGCACGCCGT
CGCCCTCGCCCTCGGCGCCCTCGGCATCTACGCCGTCTTCAAGTACCACGCCGAGGCCGGCATCCCCAACCTCTACTCCC
TCCACTCCTGGATCGGCATCGCCACCATCTCCCTCTACGCCCTCCACTGGCTCGCCGCCTTCCTCACCTTCTTCTTCCCC
GGCGCCCCCCACCCCACCAGGCGCTCCGCCCTCCCATGGCACGCGCTCCTCGGCCTCCTCGTCTTCGCGCTCGCCGTCGG
CAACGCGCAGCTCGGCTTCCTCGAGAAGCTCACCTTCATGCAGGCCCCGCCCCTGCGCCTCTCCAGGTACGGCCCGGAGG
CGCTGCTCGTCAACTTCACGGCGCTCGTCGTCCTCTTCCTCGGCGTCGCCGTCCTCCTCGCCACCGCCAACATCGACACC
ACAAGCTAG

Alignment

ORF - retro_obra_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.71 %
• Parental protein coverage: 91.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GARAAPFTYVAHALAVAAAAMVLVWCIHFRGGLAFEATNKNLIFNVHPVLMLIGYLILGSEAIMVYKVLP
          G......T.VAH.LAVAA.A.VL.W.IHFRGGLA.....K.LIFN.HPVLML.G...L..EAI..Y...P
Retrocopy GGGVGAWTVVAHVLAVAATALVLLWSIHFRGGLALRSHDKQLIFNTHPVLMLLGLVVLAAEAILSYRSFP

Parental  --TWKHDSTKLIHLILHAIALVLGVIGIYCAFKFHNESGIANLYSLHSWLGIGTICLYGIQWIFGFVTFF
          ......D..K..HL.LHA.AL.LG..GIY..FK.H.E.GI.NLYSLHSW.GI.TI.LY...W...F.TFF
Retrocopy HLLLSRDARKKTHLALHAVALALGALGIYAVFKYHAEAGIPNLYSLHSWIGIATISLYALHWLAAFLTFF

Parental  FPRASPNVRKGALPWHILFGLFVYILALATAQLGFLEKLTFLQSS--GLDKYGAEAFLVNFTALAVVLFG
          FP.A....R..ALPWH.L.GL.V..LA...AQLGFLEKLTF.Q.....L..YG.EA.LVNFTAL.V...G
Retrocopy FPGAPHPTRRSALPWHALLGLLVFALAVGNAQLGFLEKLTFMQAPPLRLSRYGPEALLVNFTALVVLFLG

Parental  ASVVVAAVS
          ..V..A...
Retrocopy VAVLLATAN

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_5 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	BGIOSGA005956	1 retrocopy	retro_oind_56,
Oryza brachyantha	OB02G32980	1 retrocopy	retro_obra_5 ,
Oryza barthii	OBART02G25610	1 retrocopy	retro_obar_22,
Oryza glumaepatula	OGLUM02G26140	1 retrocopy	retro_oglu_26,
Oryza nivara	ONIVA02G28050	1 retrocopy	retro_oniv_34,
Oryza punctata	OPUNC02G23460	1 retrocopy	retro_opun_42,
Oryza rufipogon	ORUFI02G27020	1 retrocopy	retro_oruf_43,
Physcomitrella patens	PP1S194_18V6	1 retrocopy	retro_ppat_14,