RetrogeneDB ID: retro_bdis_6

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:8762997..8764746(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G10590
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G78220
• Aliases: None
• Description: None

Sequence

>retro_bdis_6
ATGTTGGAGGAGCTGCTCATCTTCACCCGCGGCGGCCTGATCCTGTGGTCGCTGGCCGGCGGCGACGTGCTCAAGGGATC
ACCGATCGATGCCCTCGTGAGGTCCATCCTCCTCGAGGGCCGCTCCGCCGGCGGCGGCGCCGGCTTCTCCCACGGCCAGC
ACAAGCTCCAGTGGGCCTTCCACAACGCGCTCGGCCTCGCCTTCGTCGCGGTCTACCGCCGGGTGCTCCACCTCCTGTAC
GTGGACGACCTCCTGGCCGCCGTCAGCGGCGAGTTCTCGCGGATCTACGACCCGCGCCGCACCTCGTACGACGAGTTCGG
GGAGAGGTTCCGGGAGCTCCATCTCGAGGCCGAGGCGCGCGCTTCCCGTCCACCGCCGGCCGCCCCCGCCCCCAAGAAGC
CTGCTCCAGGTACGCCTGTTGGCTTTCTCCAGGGTGATGATGATGGTGGTGAGAAAACGGGTGATGCTTCTGGAGTGGGT
GACTCCGGTGATGGGCTCAGTTCGGCAGAGGGTAGATTCAGTGGTGTTGAGCAGAATTCTAGTGCCGGCAGTGGCGTTGT
TTTGGAAGAAGAGGAAGTTAAGGGACGACCCAGCAATTGGGCTTTTAATTTAGATGTATTGCGAAATAGGGATAGAAAAC
GGAATAAAAATATAGTCAAGTTTGTTAAACCTGGCCGCAAGGAAAAGGATGACACACCTTCCGTCAAGAAATTGGATTAC
AGTGATCCAGCTGATGGGAGAGAGGTTAGCGTGATGGAACAGGCTGCTGCCAACCAGGGGCCAAGCAAGATGGATAAGCC
TGAAGCTGCAAGCATCAGAAAGAACGGTTGGTTCTCCTCAGTGTTTCAGAGCATTGCTGGTAGCCATGTACTGGAGGATT
CTGATCTGCAACCTGCGCTCAAAGCTCTGAAAGACCAGCTTATGACCAAGAATGTGGCAGAGGAAATTGCAGAGAAGCTC
TGTGAATCAGTTGCAGCTAGCCTCCGAGGCAAGAAGCTCGGATCCTTCACACGGATATCATCTACTGTTCAAGCAGCTAT
GGAGGATGCTCTCGTTCGAATTTTGACCCCGAGGCGATCTATTGACGTGCTGAGAGATGTGCATGCTGCCAAGGAGCGTG
GCAGGCCATATGTCATCGTCTTTGTTGGGGTGAATGGGGTTGGCAAATCCACCAACCTCGCAAAGGTTGCTTATTGGCTT
CTTCAGCATGACCTCACTGTCATGCTGGCAGCATGCGACGCGTTTAGATCTGGTGCTGTTGAGCAGCTGTGCACTCATGC
TTGCAGACTTCAGATTCCCATATTTGAGAAAGGATACGAAAAGGATCCAGCGGTTGTGGCGAAGGGTGCAATTCAGGAAG
CCACTCAGAATAAATCAGATGTCGTCCTTGTTGATACCGCTGGGCGTATGCAGGACAATGAGCCACTCATGAGAGCACTC
TCGAAGCTCATTAATCTCAATAACCCGGATCTGGTTTTATTTGTCGGAGAAGCGCTGGTGGGCAATGATGCTGTTGACCA
ACTCACTAAGTTTGACCAGAAGTTGACAGACCTTTCCACTGCTCCCACTGATAGGTCGATAGATGGCATCCTGCTCACCA
AGTTTGACACCATTGATGACAAGGTTGGAGCAGCGCTTTCCATGGTATATGTATCTGGAGCACCTGTCATGTTTGTTGGC
TGCGGTCAGTCTTACACTGACCTCAAGAAGCTCAACATAAAGTCCATTGTCAATACCCTCCTGGAGTGA

Alignment

ORF - retro_bdis_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.28 %
• Parental protein coverage: 53.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SMMDKDEIVSSDSEDDEEENAEAGQKKKGWFSSMFKSISGNNVLEKADLQPALKALKDRLMTKNVAEEIA
          S.M.........S..D..E.A.....K.GWFSS.F.SI.G..VLE..DLQPALKALKD.LMTKNVAEEIA
Retrocopy SVMEQAAANQGPSKMDKPEAASI--RKNGWFSSVFQSIAGSHVLEDSDLQPALKALKDQLMTKNVAEEIA

Parental  EKLCESVAASLEGKKLGSFTRISSTVQTAMEEALLRILTPRRSIDILRDVHAAKERGKPYVVVFVGVNGV
          EKLCESVAASL.GKKLGSFTRISSTVQ.AME.AL.RILTPRRSID.LRDVHAAKERG.PYV.VFVGVNGV
Retrocopy EKLCESVAASLRGKKLGSFTRISSTVQAAMEDALVRILTPRRSIDVLRDVHAAKERGRPYVIVFVGVNGV

Parental  GKSTNLAKVAYWLLQHNLSVMLAACDTFRSGAVEQLRTHARRLQIPIFEKGYEKDPAVVAKEAIHEATRN
          GKSTNLAKVAYWLLQH.L.VMLAACD.FRSGAVEQL.THA.RLQIPIFEKGYEKDPAVVAK.AI.EAT.N
Retrocopy GKSTNLAKVAYWLLQHDLTVMLAACDAFRSGAVEQLCTHACRLQIPIFEKGYEKDPAVVAKGAIQEATQN

Parental  KSDVVLVDTAGRMQDNEPLMRALSKLINLNSPDLVLFVGEALVGNDAVDQLNKFNQKLADLSTVPTARLI
          KSDVVLVDTAGRMQDNEPLMRALSKLINLN.PDLVLFVGEALVGNDAVDQL.KF.QKL.DLST.PT.R.I
Retrocopy KSDVVLVDTAGRMQDNEPLMRALSKLINLNNPDLVLFVGEALVGNDAVDQLTKFDQKLTDLSTAPTDRSI

Parental  DGILLTKFDTIDDKVGAALSMVYISGSPVMFVGCGQSYTDLKKLNVKSIVKTLLK
          DGILLTKFDTIDDKVGAALSMVY.SG.PVMFVGCGQSYTDLKKLN.KSIV.TLL.
Retrocopy DGILLTKFDTIDDKVGAALSMVYVSGAPVMFVGCGQSYTDLKKLNIKSIVNTLLE

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_6 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G78220	1 retrocopy	retro_bdis_6 ,
Sorghum bicolor	Sb01g050330	1 retrocopy	retro_sbic_43,
Setaria italica	Si034718m.g	1 retrocopy	retro_sita_46,