RetrogeneDB ID: retro_obra_26

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 3:24723414..24725028(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB03G40770
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB08G25060
• Aliases: None
• Description: None

Sequence

>retro_obra_26
ATGCCAATGTCCAGTAAAGTGCAGAGATTTTTGTTGCCAGTTTCTGAATGTGAATTTAACATCACATCTGCAATAGAAGA
CCTGAGATCCATGTCTGCTTGCCCACGTGGGCATCGCCCTTTGAGAGCCAGTGGCGCTGCTATTTCCACAGCTGTTGCTC
TTCTAGAAGGTTGTTGTTCACCTAATGCCGGAGGTCGGATTATGGTCTTCACATCTGGTCCCACAACAGTTGGTCCAGGG
CTTGTGGTTGAAACTGATCTTGGGAAAGCAATTCGTTCTCATCGTGACATTTTCAATGGCAATGCTCCTCTCACTGACAA
AGCCCGAGAATTCTATAAGAAAGTTGCAAACAGGCTAACAGCTCACGCACTAGTTCTCGATCTATTTGCTTGCTCTCTAG
ATCAGGTTGGATCTGCAGAGCTGAGGTACCCAATTGAAGTGTCTGGGGGCTTAATGGTGCACTCAGAATCATTTGAGTCC
GAGCAGTTCAAAAGCTGCTTAAGACATGTATTCAAGCGCGAGGGTGTTGATTACCTTAACATGAACTTTAATGCGACAAT
TGAGATAGTAACATCAAGGGAGGTGAAAATTTGTGGTGCCCTTGGTCCCTGCATCTCTCTTCGTAGAAAAAACAGCTCTG
TTAGTGATAAAGAAATTGGAGAGGGTGGGACAAACTATTGGAAAATGAGTACAGTGGACAGCAAAACCTGCATCGTGTTC
ATCTTCCGAGTGGACTGTAGGCATAATACTGAGCCCCCAACTGTCTTCTTTATTCAGTTCATGACGAGGTACCGGCATGG
TGATGGTAGCTACCGTCTAAGGGTTACAACTGTTGCGAGAAGATGGGTTGGACCTCGTTCGCCTGAGATTACAGATGGGT
TTGATCAAGAAGCTGCTGCAGCTGTTATGGCCAGGCTTGCCGTGCACAGGGCAGAGACATACCATGTTAGAGATGTGATA
CGATGGCTTGATAAGATGCTTATTCGCTTTACTGCTAAGTTTGGGAACTATGTCCCTGAAGATCCATCTACATTCCGGCT
GTCAACTAACTTCTCGCTCTATCCTCAATTTATGTACTACCTGCGGAGGTCACAGTTCATTGATGTTTTCAATAGTTCCC
CTGACGAAACTGCTTTCTTTCGGTTGATGTTGAATAGGGAAGGAGTTGTGGGGTCTCTGATCATGATTCAGCCAACTTTA
TTCCAGTACTCATTTGATGGCCCACCTATTCCCGTGTTGCTAGATGTCAGCTCCATCTCTCCCGATGTCATTTTACTATT
TGATTCATACTTCTATATTGTTATTCACTATGGCTCAAAGATTGCTCAATGGAGGAAACTTGGCTATCATAAGGATCCAA
ACCATGAAAATTTGCGGAAGCTGCTTGAAGCCCCAGAAGTTGATGCAGAGGCACTACTGGTAGACCGTTTTCCGGTGCCA
AAACTCATAAAATGTGATCAGCATGGTAGTCAGGCCAGGTTTCTTCTAGCTCGGTTGAATCCATCTGTGACACAGAAAAC
TCAGCTTTCAGATGGCTCGGAAGTCATATTCACCGACGATGTTAGTTTGCAAGTTTTTATTGAACACTTGCAGGAGCTGG
CTGTTCAGGGTTAG

Alignment

ORF - retro_obra_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.87 %
• Parental protein coverage: 66.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RASRCTGTALSVAASLL-GVCVPGSGARIMAFIGGPSTEGPGSIVSKALSEPIRSHKDLDKGSAPLYNKA
          R..R..G.A.S.A..LL.G.C.P..G.RIM.F..GP.T.GPG..V...L...IRSH.D...G.APL..KA
Retrocopy RPLRASGAAISTAVALLEGCCSPNAGGRIMVFTSGPTTVGPGLVVETDLGKAIRSHRDIFNGNAPLTDKA

Parental  VKFYEEISKQLVHQGHVLDLFACALDQVGVAEMKVAVERTGGIVVLAESFGHSVFKESLQRIFQSSDND-
          ..FY......L.....VLDLFAC.LDQVG.AE.....E..GG..V..ESF....FK..L...F.....D.
Retrocopy REFYKKVANRLTAHALVLDLFACSLDQVGSAELRYPIEVSGGLMVHSESFESEQFKSCLRHVFKREGVDY

Parental  LGLSFNGIFEINCSKDVKIQGIIGPCTSLEKKSPLSSDTVVGQGSTSAWKMCGLDRKTSICLVFDIAKKD
          L...FN...EI..S..VKI.G..GPC.SL..K....SD...G.G.T..WKM...D.KT..C.VF.I...D
Retrocopy LNMNFNATIEIVTSREVKICGALGPCISLRRKNSSVSDKEIGEGGTNYWKMSTVDSKT--CIVF-IFRVD

Parental  GPDAINQPTSNQFYFQFLTYYQHHEGQMRLRATTISRRWVAGSGGVQDLIDGFDQEAAAAVMARLVSFKM
          .......PT...F..QF.T.Y.H..G..RLR.TT..RRWV..........DGFDQEAAAAVMARL.....
Retrocopy CRHNTEPPTV--FFIQFMTRYRHGDGSYRLRVTTVARRWVGPRS--PEITDGFDQEAAAAVMARLAVHRA

Parental  EAEADFDPIRWLDRALISLCSKFGDYQKETPSSFSLSPRLSLFPQFMFNLRRSQFVQVFNNSPDETAYFR
          E.....D.IRWLD..LI....KFG.Y..E.PS.F.LS...SL.PQFM..LRRSQF..VFN.SPDETA.FR
Retrocopy ETYHVRDVIRWLDKMLIRFTAKFGNYVPEDPSTFRLSTNFSLYPQFMYYLRRSQFIDVFNSSPDETAFFR

Parental  MMLNREDVTNAVVMIQPSLISYSFQSGPEPVLLDVTAIAADRILLLDSYFTIVIFHGITIAQWRKAGYQD
          .MLNRE.V.....MIQP.L..YSF...P.PVLLDV..I..D.ILL.DSYF.IVI..G..IAQWRK.GY..
Retrocopy LMLNREGVVGSLIMIQPTLFQYSFDGPPIPVLLDVSSISPDVILLFDSYFYIVIHYGSKIAQWRKLGYHK

Parental  HEGHEAFAQLLQAPQEEADSIIKERFPVPRLVVCDQYGSQARFLLAKLNPSVTYNSDNPAPPGGDVIFTD
          ...HE....LL.AP...A......RFPVP.L..CDQ.GSQARFLLA.LNPSVT.........G..VIFTD
Retrocopy DPNHENLRKLLEAPEVDAEALLVDRFPVPKLIKCDQHGSQARFLLARLNPSVTQKTQ--LSDGSEVIFTD

Parental  DVSFQVFMDHLQRLAVQ
          DVS.QVF..HLQ.LAVQ
Retrocopy DVSLQVFIEHLQELAVQ

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_26 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB08G25060	1 retrocopy	retro_obra_26 ,