RetrogeneDB ID: retro_bdis_49

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 1:64988571..64989129(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI3G32590
• Aliases: None
• Description: None

Sequence

>retro_bdis_49
GGAAAAAGGCCAAGCCTCAGCAGGTCTTCAAGGATACGCAAGCTCTCATTAGCCGCACAAGCTTTGAACTTGGAGATAAT
GCTTCCATCCCTGATCTTCAGCACGGAACTAAACTTCAGCAGGATCCCCTTAACTTTGCTCTAAGTTTTGTCCTCTCCAG
GTACTCATGTCTATTCTGACGCAGCCTGGAAGTTGCCTCGGCGAAGTCCAGGCTCCTCAGAAGCTAAAGCAGGTCTCGGA
GTTTACATCGAACACTTCTCCCAAACAGGAAGATTAAAAGTACAGATCTCGGCAGCTTCTCCTCCCTGTAGCTCTCATTA
CTGGCAGAAGCTTGGGCTCTTCTTCTTGCGGCAGAATGTAGCAGGTGTCTCCAATTTGAAAGAGGCTCTCTTCTCTCAGA
CAACATCACTCTCAGTCAAACTGCTGATCGAAGAAACTTTCAACATTTCCCGAGACACTGGTCTATTAGACATTTGCTTG
CTGAAATATGGAATAAAATTCCACATGCTTTTTCTGTTAAGCATGTCCCTAGAGATTGCAATGGTGTGGCTCTTAATC

Alignment

ORF - retro_bdis_49 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.7 %
• Parental protein coverage: 95.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GARRLLLTLSLPRRTQLDLALLNTIWASKTLIPRVQLFAWRLITRALPTDKRAGTHVYSDAAWKLPQQSS
          G.R..L...S..R...L....LN.......LI....L...R.....L......GTHVYSDAAWKLP..S.
Retrocopy GKRPSLSRSSRIRKLSLAAQALNLEIMLPSLIFSTELNFSRIPLTLL*VLSSPGTHVYSDAAWKLPRRSP

Parental  GSLEAKAGLGVYIEHFSQTEKLKVQVSVASPPSNS-PLLAEAWALLLAADLIRCLQFERGLLLSDNIT-S
          GS.EAKAGLGVYIEHFSQT..LKVQ.S.ASPP..S..LLAEAWALLLAA...RCLQFERG.LLSDNIT.S
Retrocopy GSSEAKAGLGVYIEHFSQTGRLKVQISAASPPCSS<SLLAEAWALLLAAECSRCLQFERGSLLSDNITLS

Parental  QAADQRNLQHSPGHWSIRPLLAEISNKTPPAFSE-SISLETAMQWLMI
          Q.AD.RN.QH.P.HWSIR.LLAEI.NK.P.AFS..S.SLE.AM.WL.I
Retrocopy QTADRRNFQHFPRHWSIRHLLAEIWNKIPHAFSV>SMSLEIAMVWLLI

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_49 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G32590	1 retrocopy	retro_bdis_49 ,