RetrogeneDB ID: retro_bdis_41

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:6697225..6698368(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G08300
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI4G19707
• Aliases: None
• Description: None

Sequence

>retro_bdis_41
ATGGCGAGAGCGCTGGTGCTCGCGTCCGGGCTGGCCATGGCCGGCGCGCTGGTGCTGCTGCTGCTGGCGACGTCCCCGGC
GCCGGCGAGCGCCATGGACTTCGGCGAGTCGGACCTGGCGTCAGAGGAGTCCCTGTGGGCGCTCTACGAGCGGTGGCGCG
CGCGGCACACGGTGTCCCGCGACCTCGCGGAGAAATCCCGTCGCTTCAACGTGTTCCGCGAGAACGCGCGCCTCGTCCAC
GAGTTCAACCTCCGCCGCGACGCGCCCTACAAGCTCCGCCTCAACCGCTTCGCCGACCTCACCTCCGACGAGTTCCGCCG
CTCCTACGCCTCCTCCCGCGTCTCCCACCACCGCATGTTCAAGCCCCGCGCTGCCAACAACAACGACGACGACGACGACA
AGGGATCGTCGTTCACGCACGGCGGCGCATTGCCGACGTCGGTGGACTGGCGGGAGAAGGGGGCCGTGACGGGGGTCAAG
GACCAAGGGCAGTGCGGCAGCTGCTGGGCATTCTCGACGATCGCCGCCGTGGAAGGCATCAACGCGATCCGGACGAACAA
CCTCACCTCACTCTCAGAACAGCAGCTCGTGGACTGCGACACCAAGACCAACGCCGGCTGCGACGGCGGGCTCATGGACG
ACGCCTTCAGCTACATCGCCAAGCACGGCGGGGTGGCCGCCGAGAAGTCCTACCCGTACAGGGCCCGGCAGAGCAGCAGC
TGCAACAGCAAGAAGGCCGCGGCAGCCGTGGTCAGCATCGACGGGTACGAGGACGTGCCGAGGAACGACGAGACGGCGCT
GAAGAAGGCCGTGGCGGCGCAGCCCGTGGCCGTGGCCATCGAGGCCGGCGGCTCGCACTTCCAGTTCTACTCGGAGGGCG
TGTTCGCGGGTAAGTGCGGGACTGAGCTCGACCATGGCGTGGCGGCCGTCGGGTACGGGGTCACCGTGGACGGGACCAAG
TACTGGATCGTCAAGAACTCGTGGGGCGAGGAATGGGGGGAGAAAGGGTATATCAGGATGAAGCGTGATGTGGCGGACAA
GGAGGGCCTCTGCGGCATCGCCATGGAGGCGTCTTACCCTGTCAAGACCTCGCCCAACCCCAAGCATGCCGCCGCCGAGG
CCGAGCACCATGATGAGCTCTGA

Alignment

ORF - retro_bdis_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.07 %
• Parental protein coverage: 65.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NFTYSDAENLPPAVDWREKGAVTGIKDQGQCGSCWAFSTIAAVESINKIRTGKLVSLSEQELMDCDNVND
          .FT...A..LP..VDWREKGAVTG.KDQGQCGSCWAFSTIAAVE.IN.IRT..L.SLSEQ.L.DCD....
Retrocopy SFTHGGA--LPTSVDWREKGAVTGVKDQGQCGSCWAFSTIAAVEGINAIRTNNLTSLSEQQLVDCDTKTN

Parental  QGCDGGLMDYAFQFIQKNGGVTSEANYPYQGQQNT-CDQAKENTHDVAIDGYEDVPANDESALQKAVAYQ
          .GCDGGLMD.AF..I.K.GGV..E..YPY...Q...C...K.....V.IDGYEDVP.NDE.AL.KAVA.Q
Retrocopy AGCDGGLMDDAFSYIAKHGGVAAEKSYPYRARQSSSCNSKKAAAAVVSIDGYEDVPRNDETALKKAVAAQ

Parental  PVSVAIEASGQDFQFYSEGVFTGQCTTDLDHGVAAVGYGTARDGTKYWIVKNSWGLDWGEKGYIRMQRGV
          PV.VAIEA.G..FQFYSEGVF.G.C.T.LDHGVAAVGYG...DGTKYWIVKNSWG..WGEKGYIRM.R.V
Retrocopy PVAVAIEAGGSHFQFYSEGVFAGKCGTELDHGVAAVGYGVTVDGTKYWIVKNSWGEEWGEKGYIRMKRDV

Parental  SQAEGLCGIAMQASYPIKAAPH----ATTARQADEL
          ...EGLCGIAM.ASYP.K..P.....A..A...DEL
Retrocopy ADKEGLCGIAMEASYPVKTSPNPKHAAAEAEHHDEL

Legend:

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

Expression

RNA-Seq

Brachypodium distachyon was not studied using RNA-Seq expression data.

ChIP-Seq

Brachypodium distachyon was not studied using ChIP-Seq data.

EST

Brachypodium distachyon was not studied using EST data.

TSS

Brachypodium distachyon was not studied using FANTOM5 data.

Lab

retro_bdis_41 was not experimentally validated.

Homology

Retrocopy orthology:

Brachypodium distachyon 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,