RetrogeneDB ID: retro_bdis_27

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 1:13439168..13440314(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI1G16630
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G65520
• Aliases: None
• Description: None

Sequence

>retro_bdis_27
ATGGCTTGCACCGTGGCACCGCCGGGGTCGCCGGTCTTCTCCCCGTCATCCCGGCCCGCCGCCCCTGCACACGTCTCCTT
CAAGCAGCAGCAGCAGCCCGCGCCGCCGGAGGGCTCGCCGCTCCGCCTCATCGCCCTCCGCGCCGCCAAGCTGCGCATCC
GCCCCGCCGACCCGCCTCTCCTCGTCGTCCCAGCCGCTTCGCACGCACCCTCTTCTTCTTCCTCCAACGCCAAGCGCCGC
CGCCCGCCGCCGCTCCTCGTCCCAGCCACGGCCCCGACACCATTAGATGCCGTTGCTGCTGCTCGTGGGATGGAACCGGA
GGTGGCGGAGGACTCAGGGGAGGGCTTCGCGGCCTACTGCAGGCGCGGGAAAGGCCGGAACCGCCTCGAGATGGAGGACC
GCCACGCCGCCACCGTCGCCCTAGGAGGCGACCCCGACGCCGCGCTCTTCGCCGTCTTCGACGGCCACGGCGGGAAGTCC
GCCGCCGAGTTCGCCGCCAACAACATGCCCCGCATCATCGCCAACGAGCTCCTCCACGCAAGCAAAAGCTCGGAGGCCGT
CGAGGCCGCGGTGAGGCGCGCGTACCTCCGCACGGACAAGGAGTTCTCCTCCTCCGCCGCCGCGGCAAACGGAGGCGGCG
CGTGCTGCGTGACGGCGCTGCTGCTCCGCGACCGCCGCCAGCTCGTCGTGTCCGGCGCCGGGGACTGCCGCGCCGTGCTG
GGCCGCGGAAGGTCGCCCGCCCTCGCGCTGACCACGGACCACCGGGCGTCGCGGCGGGAGGAGCGGGAGCGGATCGAGGC
GCTCCCCGGCGGGCTGGTGCTGCGGGACAGCCGCGGGACGTGGCGGGTGCGGGGGTCGCTGGCGGTCACGAGGGGCATCG
GCGACGCGCACCTCAAGCCATGGGTGCTGCCGGACCCGGAGACGACGTCCGTGGACCTTGGAGACGACGACTGCGAGCTG
CTCGTGCTCGCCTCCGACGGGCTCTGGGACAAGGTGGGCAACCAGGAGGCCGTTGATGCTTGCTCCAGTGGCCTGCCGCC
CTCCGTTGCTTGCCGCCGGCTCGTGGACATGGCGGTGGCCAGAGGATCCACGGACGATATCAGCGTCCTCGTCGTCCACC
TCAAACGCCTTCTTCTCCACCCATGA

Alignment

ORF - retro_bdis_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.12 %
• Parental protein coverage: 84.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VFSPSRRSLSCKAASASPETVSISSPAPPAPTAGSPLRPFGLLRAQIR-EEASPSPKTSSAAASAPAGSV
          V..P.....S.....A.P..VS......PAP..GSPLR...L..A..R...A.P......AA..AP..S.
Retrocopy VAPPGSPVFSPSSRPAAPAHVSFKQQQQPAPPEGSPLRLIALRAAKLRIRPADPPLLVVPAASHAPSSSS

Parental  --LKRRRPAPLMVPVDGPAAAAAAAAAVAAVESDPRNEVEEEGDEFAVYCQRGKGRRRVEMEDRHVAKVA
          ...KRRRP.PL.V....PA.A.....AVAA.........E..G..FA.YC.RGKGR.R.EMEDRH.A.VA
Retrocopy SNAKRRRPPPLLV----PATAPTPLDAVAAARGMEPEVAEDSGEGFAAYCRRGKGRNRLEMEDRHAATVA

Parental  LGGDPKVAFFAVFDGHGGNSAAEFAAENMPKFMAEEMKKVGGGDNGEIEGAVKKGYLKTDEQFLK--REE
          LGGDP..A.FAVFDGHGG.SAAEFAA.NMP...A.E............E.AV...YL.TD..F.......
Retrocopy LGGDPDAALFAVFDGHGGKSAAEFAANNMPRIIANELLHASKSSEA-VEAAVRRAYLRTDKEFSSSAAAA

Parental  SGG-ACCVTALL--QKGGLTVSNTGDCRAVLSRA-GKAEALTTDHRASRDDEKERIENL-GGFVV-NYRG
          .GG.ACCVTALL......L.VS..GDCRAVL.R....A.ALTTDHRASR..E.ERIE.L.GG.V....RG
Retrocopy NGGGACCVTALLLRDRRQLVVSGAGDCRAVLGRGRSPALALTTDHRASRREERERIEALPGGLVLRDSRG

Parental  TWRVQGSLAVTRGIGDAHLKQWVVADPDTRTL-LVDQHCEFLILASDGLWDKVENQEAVD
          TWRV.GSLAVTRGIGDAHLK.WV..DP.T....L.D..CE.L.LASDGLWDKV.NQEAVD
Retrocopy TWRVRGSLAVTRGIGDAHLKPWVLPDPETTSVDLGDDDCELLVLASDGLWDKVGNQEAVD

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_27 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00078p00164770	1 retrocopy	retro_atri_15,
Brachypodium distachyon	BRADI1G65520	1 retrocopy	retro_bdis_27 ,