RetrogeneDB ID: retro_obra_11

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 6:375399..376101(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB06G10670
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB10G26200
• Aliases: None
• Description: None

Sequence

>retro_obra_11
ATGGCGATGGCTCCTTTGGAGGCCGTGCTGTTCGACATCGACGGCACCATGTGCGTCTCCGACCCATTCCACCACAGGGC
CTTCTCCGAGCTGCTCCAGGGCCTCGGCTACAACAACGGCGTCCCCATCACGCCGGAGTTCGGGATGGCGCACATGGCCG
GCCGGAGCAACGACCAGATCGGCCGCTTCCTCTTCCCGGGCTGGGGCCAGGACCAGCTCGACGCCTTCTTCGCCGACAAG
GAGGCCCTCTTCGCGCGCTACGCCGGCGAGGGCCTCCGGGAGGTCGCCGGCCTCAGCGACCTCTGCCGGTGGGCGGCCGA
CCGCGGCCTCAGGCGCGCCGCCGTCACCAACGCGCCGCGCGCCAACGCCGAGCTCATGATCTCCATCCTCGGCCTCTCCG
ACTTCTTCCAGGTCATCGTCGCCGCCGCCGACGACTGCGACCGACCCAAGCCGTCGCCGGACCCCTACCTCCGGGCGCTC
ACCCTGCTCGGCGCGTCTCCCCGTCACACGCTCGTCTTCGAGGACTCGGGGGTCGGGGTGCAGGCCGCCGTCGCCGCCGG
GATGCCGGTGATCGCCGTCGCACAGGAGGCAGGGGAGGCCAAAGTCCTCGCCGCCGGAGCGTCGCTCGTCATCAGGGACT
ACCAAGACGGCAAGCTCTGGGCGGCGCTGGATAAGCTCGACGCCGCAGCTCAAGCCAAGTAG

Alignment

ORF - retro_obra_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.11 %
• Parental protein coverage: 78.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAPLEAILFDIDGTLCDSDPIHFCAFRELLQQVGFNNGVPITEEFYSANISGGHNDDLARALFPDMDHDK
          .APLEA.LFDIDGT.C.SDP.H..AF.ELLQ..G.NNGVPIT.EF..A...G..ND...R.LFP....D.
Retrocopy MAPLEAVLFDIDGTMCVSDPFHHRAFSELLQGLGYNNGVPITPEFGMAHMAGRSNDQIGRFLFPGWGQDQ

Parental  AMKFMDDKEALFRKLAPEQLNAVDGLHELCRWIEHHKLKRAAVTNAPRPNAELMLSLLGLTDFFPVLIIG
          ...F..DKEALF...A.E.L..V.GL..LCRW.....L.RAAVTNAPR.NAELM.S.LGL.DFF.V....
Retrocopy LDAFFADKEALFARYAGEGLREVAGLSDLCRWAADRGLRRAAVTNAPRANAELMISILGLSDFFQVIVAA

Parental  S-ECDRAKPFPDPYLKALELIDASPDHTFIFEDSASGIRAGVAANVPVVGLTTRNPDKVLKDAGASLLIE
          ...CDR.KP.PDPYL.AL.L..ASP.HT..FEDS..G..A.VAA..PV..............AGASL.I.
Retrocopy ADDCDRPKPSPDPYLRALTLLGASPRHTLVFEDSGVGVQAAVAAGMPVIAVAQEAGEAKVLAAGASLVIR

Parental  DFQDPKLLSMLAELE
          D.QD.KL...L..L.
Retrocopy DYQDGKLWAALDKLD

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_11 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
Leersia perrieri	LPERR10G14940	1 retrocopy	retro_lper_23,
Oryza brachyantha	OB10G26200	1 retrocopy	retro_obra_11 ,