RetrogeneDB ID: retro_bdis_14

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:19687618..19688419(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G20670
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI4G11400
• Aliases: None
• Description: None

Sequence

>retro_bdis_14
ATGGCAGCCGCCGCACGCCGGAGCATGCAGGAGCGGTGGAGCCTTGCGGGCGCGACGGCGCTGGTGACCGGCGGCAGCAA
AGGGATCGGGCACGCGATCGTGGAGGAGCTCGCGTCGCTGGGCGCCCGCGTGCACACGTGCTCCCGGAACGCCGCGGAGC
TGGAGGCCTGCCGCCGCCGCTGGGCCGAAACGGGCCTCCAGGTGACCGTCTCCGTCTGCGACGTTTCCTCACGGGCCCAG
AGAGAAAACCTCATGGCCACCGTGGACCAGACCTTCGAGGGGAAGCTCGACATCCTGGTGAACAACGCGGGCCAGTGCGT
GATGAACGCAGCCGCGGGGTACACCGGCGAGGAGTACGCGAAAGTCATGGGCACCAACCTCGAGTCCTCCTTCCACCTGG
CCCAGCTGGCCCACCCGCTGCTCCTCCTCGGCGGCGGAATAACAAGGGCCGTGGTGAACATCTCGTCGATAGCGGGCCAG
GTAGGCCTGCCGAGCCTGGCGGTGTACTCGATGACCAAGGGGGCCATGAACCAGATGACCCGGAGCCTGGCCGTCGAGTG
GGCCGGCGACCGCGTGCGCGTCAACTGCGTGGCGCCTGGTGGGATCAATACGGATATTTCCAGGGACGTGGAGATGGTCA
TGGACCCGGAGGTTGTGGAAAGGATGGCGGCAAGGGTGCCGATGCGGCGGATGGGGGAGACGGAGGAGGTGGCGTCCGTC
GTGGCGTTCCTCTGCATGCCGGCCGCGTCATACATCACCGGGCAGGTCATCTGCGTCGACGGCGGGCACACCATTGGTTA
A

Alignment

ORF - retro_bdis_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.79 %
• Parental protein coverage: 94.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SREQRWSLAGATALVTGGSKGIGHAIVEELAGFGARVHTCSRNEAELEECRLRWEEKGFQVTVSVCDISS
          S...RWSLAGATALVTGGSKGIGHAIVEELA..GARVHTCSRN.AELE.CR.RW.E.G.QVTVSVCD.SS
Retrocopy SMQERWSLAGATALVTGGSKGIGHAIVEELASLGARVHTCSRNAAELEACRRRWAETGLQVTVSVCDVSS

Parental  GADREKLIETVNQTFEGKLDILVNNAAQLLGKAGVEWTSEEYSHIMTTNLESVFHLSQLAHPLLCHASIA
          .A.RE.L..TV.QTFEGKLDILVNNA.Q....A....T.EEY...M.TNLES.FHL.QLAHPLL......
Retrocopy RAQRENLMATVDQTFEGKLDILVNNAGQCVMNAAAGYTGEEYAKVMGTNLESSFHLAQLAHPLL----LL

Parental  GGG---SIINISSITGSLGFPGLALYSMSKGGMNQLTRSFAAEWAQDKIRVNCVAPGVTRTDMASSLE--
          GGG......NISSI.G..G.P.LA.YSM.KG.MNQ.TRS.A.EWA.D..RVNCVAPG...TD.....E..
Retrocopy GGGITRAVVNISSIAGQVGLPSLAVYSMTKGAMNQMTRSLAVEWAGDRVRVNCVAPGGINTDISRDVEMV

Parental  --PELVENELSRTPLGRMGQSVEVASVVAFLCMPAASFVTGQVITVDGGRTI
          ..PE.VE....R.P..RMG...EVASVVAFLCMPAAS..TGQVI.VDGG.TI
Retrocopy MDPEVVERMAARVPMRRMGETEEVASVVAFLCMPAASYITGQVICVDGGHTI

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_14 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	BRADI4G11400	1 retrocopy	retro_bdis_14 ,