RetrogeneDB ID: retro_obar_27

Retrocopy location

• Organism: Oryza barthii
• Coordinates: 8:22193790..22194948(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OBART08G23320
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OBART11G08490
• Aliases: None
• Description: None

Sequence

>retro_obar_27
ATGGGTAGAGTAGTGGTCGTCGTGGCGGCGGCGGCGGTAGCCGTGGCCGTCGTCGTGCTGCTGGGCGCGGCGGCGCCGGC
GGCGAGCGCGATGGAGTTCGGCGACAAGGACGTGGCGTCGGAGGAGGCGCTGTGGGAGCTGTACGAGCGGTGGCGCGGGC
AGCACCGGGTGGCGCGGGACCTCGGCGAGAAGGCGCGGCGGTTCAACGTGTTCAAGGACAACGTCCGCCTCATCCACGAG
TTCAACCGCCGCGACGAGCCCTACAAGCTCCGCCTCAACCGCTTCGGCGACATGACCGCCGACGAGTTCCGCCGCGCCTA
CGCCTCCTCCCGCGTCTCCCACCACCGCATGTTCCGCGGCCGCGGCGAGAGGCGGAGCGGCTTCATGTACGCCGGCGCCC
GCGACCTGCCGGCGGCGGTGGACTGGCGCGAGAAGGGCGCCGTCGGGGCGGTCAAGGACCAGGGCCAGTGCGGCAGCTGC
TGGGCGTTCTCGACCATCGCCGCCGTGGAAGGGATCAACGCCATCCGCACCAGCAACCTCACCGCGCTGTCGGAGCAGCA
GCTCGTCGACTGCGACACCAAGACCGGCAACGCGGGCTGCGACGGCGGCCTCATGGACAACGCGTTCCAGTACATCGCCA
AGCACGGCGGCGTCGCCGCCTCCTCCGCCTACCCGTACCGCGCCCGCCAGAGCTCCTGCAAGAGCTCCGCGGCGTCGTCC
CCCACCGTCACCATCGACGGCTACGAGGACGTGCCGGCGAACTCGGAGTCGGCGCTGAAGAAGGCGGTGGCGAACCAGCC
GGTGTCGGTGGCGATCGAGGCGGGGGGCTCGCACTTCCAGTTCTACTCGGAGGGGGTGTTCGCCGGGAAATGCGGGACGG
AGCTCGACCATGGCGTGGCGGCGGTGGGCTACGGCACGACGGTGGATGGCACCAAGTACTGGATCGTCAGGAACTCGTGG
GGCGCAGACTGGGGTGAGAAGGGCTACATCCGGATGAAGCGCGACGTGTCCGCCAAGGAGGGACTCTGCGGCATCGCCAT
GGAAGCATCCTACCCCATCAAGACCTCGCCGAACCCGGCGCCCAAGAAGATCAAGAAGGTCACCGACGACGACGAAGATG
ATGATGACGAGGAGCACCGCCACCACGACGAACTCTAA

Alignment

ORF - retro_obar_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.91 %
• Parental protein coverage: 77.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NARYIHEANRRGGGEGGS-FRYGGEDEDNLPPAVDWRERGAVTGIKDQGQCGSCWAFSAVAAVEGVNKIK
          ..R..H....RG.GE..S.F.Y.G.....LP.AVDWRE.GAV...KDQGQCGSCWAFS..AAVEG.N.I.
Retrocopy SSRVSHHRMFRGRGERRSGFMYAGARD--LPAAVDWREKGAVGAVKDQGQCGSCWAFSTIAAVEGINAIR

Parental  TGRLVTLSEQELVDCDT-SDNQGCDGGLMDYAFQFIKRNGGITTESNYPYRAEQGRCNKAKASSHDVTID
          T..L..LSEQ.LVDCDT...N.GCDGGLMD.AFQ.I...GG....S.YPYRA.Q..C....ASS..VTID
Retrocopy TSNLTALSEQQLVDCDTKTGNAGCDGGLMDNAFQYIAKHGGVAASSAYPYRARQSSCKSSAASSPTVTID

Parental  GYEDVPANDESALQKAVANQPVAVAVEASGQDFQFYSEGVFTGECGTDLDHGVAAVGYDITRDGTKYWIV
          GYEDVPAN.ESAL.KAVANQPV.VA.EA.G..FQFYSEGVF.G.CGT.LDHGVAAVGY..T.DGTKYWIV
Retrocopy GYEDVPANSESALKKAVANQPVSVAIEAGGSHFQFYSEGVFAGKCGTELDHGVAAVGYGTTVDGTKYWIV

Parental  KNSWGEDWGERGYIRMQRGVSSDSNGLCGIAMEASYPVKSGARNAAASNRVVKDE
          .NSWG.DWGE.GYIRM.R.VS....GLCGIAMEASYP.K.....A......V.D.
Retrocopy RNSWGADWGEKGYIRMKRDVSA-KEGLCGIAMEASYPIKTSPNPAPKKIKKVTDD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza barthii was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza barthii was not studied using ChIP-Seq data.

EST

Oryza barthii was not studied using EST data.

TSS

Oryza barthii was not studied using FANTOM5 data.

Lab

retro_obar_27 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza barthii 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G19707	2 retrocopies	retro_bdis_26, retro_bdis_41,
Zea mays	GRMZM2G099765	1 retrocopy	retro_zmay_16,
Hordeum vulgare	MLOC_73076	2 retrocopies	retro_hvul_23, retro_hvul_68,
Oryza barthii	OBART11G08490	1 retrocopy	retro_obar_27 ,
Oryza glumaepatula	OGLUM05G09560	1 retrocopy	retro_oglu_31,
Oryza meridionalis	OMERI11G07520	1 retrocopy	retro_omer_2,
Setaria italica	Si026545m.g	1 retrocopy	retro_sita_27,