RetrogeneDB ID: retro_obra_23

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 5:19924204..19925590(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB05G35520
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB01G29280
• Aliases: None
• Description: None

Sequence

>retro_obra_23
ATGGGGCGCTGCGTCGTGGTGCTGCTGCTGCTCGGCCTCGGGGGCGCAGTGTGCGGGCGGTGGCAGGAGGAGTTCCTGCG
GCTGGGGTCGGAGGGAGGCGGGACGAGGTGGGGCGTGCTGGTGGCGGGGTCGAAGGGGTTCTACAACTACCGGCACCAGG
CGGACGTGTGCCACGCGTACCAGATCATGAGGAAAGGAGGCCTCAACGACGACAACATCGTGGTGATGATGTACGACGAC
ATCGCCAGCCACCCCGACAACCCCAGGCCCGGGACCATCATCAACCACCCTTCCGGCCCCGACGTCTACGCCGGAGTCCC
CAAGGATTACACTCGCAAGGACGTCACCGTCAACAACTTCCTGGCCGTGCTGCTGGGCAACAGGTCGGCCCTCACCGGCG
CCGGCAGCGGCAAGGTCGTCAGCAGCGGCCCCAACGACCACGTGTTCGTCTACTACGCCGACCACGGCGGCCCCGGCGTG
CTGAGCATGCCAGGACCGGCGGAGGGCGAGTACCTGTACGCCAACGACCTGGTGCAGGCGCTGAAGAAGAAGCACGCCGC
CGGCGCCTACAAGAGCCTCGTCATGTACGTGGAGGCGTGCGAGTCCGGCAGCATCTTCGAGGGCCTCCTCCCCACCGACA
TCGCCGTCTACGCCACCACGGCCTCCAACGCCGACGAGAGCAGCTGGGGCACCTACTGCCCCGGCGACGACCATGGCGCC
CCGCCGCCGGAGTTCGACACCTGCCTCGGCGACCTCTACAGCGTGGCCTGGATGGAGGACGCCGACGCGCACCAGGACGG
CCGCCGGGGCGAGACGCTGCAGCAGCAGTACAGGTCGGTCAAGAACCGCACGTCGGACGCGGGCACCTACTTCCTCGGCT
CCCACGTCATGCAGTACGGCGACATGAGCCTCAGCCCGCAGAGCCTCCACCTCTACTACATGGACACACCTGCTGCAGCC
AGCCGTGCTGACGACGCCGCCGCCGCCATACCTGCGAGTGTGAGCGTGAACCAGCGTGACGCCGATCTCCTCTACCTGTG
GCGCAAGTACATGAGAGCGGCGCCCGAGAAGAAGGTGGAGGCTCGGGAGCGGCTTCTGCAAGAGATGGGGCGGCGATCCC
GCGTGGACAGCAGCGTGGAGCTGGTCGAGGGCCTCATCTTCAGCTCCGGCAAGGAGAAGGAGGAGAAGAAGGCGAAGGCG
GGGCAGGCGGTGGTGGAGGACTGGGAGTGCCTCAAGTCGATGGTGCGGACGTTCGAGGCGCGGTGTGGGTCGCTGGGGCA
GTACGGCATGAAGCACATGCGCTCCTTCGCCAACATCTGCAACGCCGGCGTCTCTCACCACGCCATGGCAACTGCCGCCT
CCCTCGCATGTCCTCCTCACTTGTAA

Alignment

ORF - retro_obra_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.19 %
• Parental protein coverage: 81.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTRWAVLIAGSNGYYNYRHQADVCHAYQIMKKGGLKDENIIVFMYDDIAHNSENPRPGVIINHPQGGDVY
          GTRW.VL.AGS.G.YNYRHQADVCHAYQIM.KGGL.D.NI.V.MYDDIA....NPRPG.IINHP.G.DVY
Retrocopy GTRWGVLVAGSKGFYNYRHQADVCHAYQIMRKGGLNDDNIVVMMYDDIASHPDNPRPGTIINHPSGPDVY

Parental  AGVPKDYTGKDVNVKNLFAVLLGDKTAVSG-GSGKVLDSGPNDHIFIFYSDHGGPGVL---GMPTYPYLY
          AGVPKDYT.KDV.V.N..AVLLG...A..G.GSGKV..SGPNDH.F..Y.DHGGPGVL...G.....YLY
Retrocopy AGVPKDYTRKDVTVNNFLAVLLGNRSALTGAGSGKVVSSGPNDHVFVYYADHGGPGVLSMPGPAEGEYLY

Parental  GDDLVDVLKKKHAAGTYKSLVFYLEACESGSIFEGLLPDDINVYATTASNADESSWGTYCPG-EYPSPPP
          ..DLV..LKKKHAAG.YKSLV.Y.EACESGSIFEGLLP.DI.VYATTASNADESSWGTYCPG.....PPP
Retrocopy ANDLVQALKKKHAAGAYKSLVMYVEACESGSIFEGLLPTDIAVYATTASNADESSWGTYCPGDDHGAPPP

Parental  EYDTCLGDLYSVAWMEDCDVH--NLRTESLRQQYNLVKERTSVQHTYDSGSHVMQYGSIELNAHHLFLYM
          E.DTCLGDLYSVAWMED.D.H....R.E.L.QQY..VK.RTS...TY..GSHVMQYG...L....L.LY.
Retrocopy EFDTCLGDLYSVAWMEDADAHQDGRRGETLQQQYRSVKNRTSDAGTYFLGSHVMQYGDMSLSPQSLHLYY

Parental  GSNPANDNSTFVEDNSLPSFSRAVNQRDADLVYFWQKYRKLAEGSPEKN-EARKQLLEMMAHRSHVDNSV
          ...PA............P..S..VNQRDADL.Y.W.KY...A...PEK..EAR..LL..M..RS.VD.SV
Retrocopy MDTPAAASRADDAAAAIPA-SVSVNQRDADLLYLWRKYMRAA---PEKKVEARERLLQEMGRRSRVDSSV

Parental  ELIGNLLFGSEEGPRVLKAVRATGEPLIDDWSCLKSMVRAFEAQCGSLAQYGMKHMRSFANICIAGISAE
          EL...L.F.S.......KA....G.....DW.CLKSMVR.FEA.CGSL.QYGMKHMRSFANIC.AG.S..
Retrocopy ELVEGLIFSSGKEKEEKKA--KAGQAVVEDWECLKSMVRTFEARCGSLGQYGMKHMRSFANICNAGVSHH

Parental  EMAKVAAQAC
          .MA..A..AC
Retrocopy AMATAASLAC

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_23 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G093032	1 retrocopy	retro_zmay_6,
Oryza longistaminata	KN538817.1_FG009	1 retrocopy	retro_olon_1,
Oryza brachyantha	OB01G29280	1 retrocopy	retro_obra_23 ,
Oryza barthii	OBART01G19640	1 retrocopy	retro_obar_1,
Oryza glumaepatula	OGLUM01G23260	1 retrocopy	retro_oglu_32,
Oryza meridionalis	OMERI01G18100	1 retrocopy	retro_omer_24,
Oryza punctata	OPUNC01G20010	1 retrocopy	retro_opun_12,
Oryza glaberrima	ORGLA01G0161200	1 retrocopy	retro_ogla_9,
Oryza sativa japonica	OS01G0559600	1 retrocopy	retro_osat_9,