RetrogeneDB ID: retro_bdis_26

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:56139091..56140225(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G58120
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_bdis_26
ATGGGGCTGCTTAGCAAGAAGCTTCTGGTGGCTTGCTTGGCCCTGCTGGCCGTGGTTTCCTTGTGCAGCGCGATCCCGTT
CGACGCCAAGGACCTGGAGTCAGAGGAAGCGCTGTGGGAGCTCTACACGCGGTGGCAGAGCGCGCACCGGCTGCCCCCGC
AGCACCACGCCGAGAAGCACCGCCGCTTCGGCACCTTCAAGTCCAACGTCCTCTTCATCCACGCCCACAACACCCGCCTC
AACGACACAAGCACCAACAATAACGGCCCATCCTACCGCCTCCGCCTCAACCGCTTCGGCGACATGGACCAGGCCGAGTT
CCGCTCCACCTTCGCCGGCCCACTCCACCGCCATACCAGGCCGGCCCAGTCCATCCCGGGCTTCATCTACGACACCGTCA
AGGACATTCCCCAGGCCGTGGACTGGCGCCAGAAGGGCGCCGTGACGGGCGTCAAGGACCAGGGGAAATGCGGCAGCTGC
TGGGCCTTCTCCGCCGTGGCGTCCGTGGAAGGCCTCAACGCGATCCGGACGGGCAGCCTCGTGTCCCTCTCCGAGCAAGA
GCTCATCGACTGCGACACGGGCGGCGACGACAACGGGTGCCAGGGCGGGCTCATGGAGAGCGCCTTCGAGTTCATCGCCC
ACAGCGCCGGCGGCCTCGCCACGGAAGCCGCCTACCCGTACCACGCATCCAACGGCACCTGCAACGCCAACCGTGGATCC
TCCGTGTCCGTCCGGATCGACGGCCACCAGAGCGTGCCGGCCGGGAACGAGGAAGCTCTAGCCAAGGCCGTGGCCCACCA
GCCCGTGTCCGTGGCCATTGATGCCGGCGGCCAGGCGTTCCAGTTTTACTCCGAGGGGGTTTTCACTGGGGATTGTGGCA
GTGAGTTGGACCATGGGGTTGCTGTTGTTGGGTACGGGGTTGCGGAGGAGGACGGGAAGGAGTACTGGATCGTGAAGAAC
TCTTGGGGCCCTGGGTGGGGCGAGCATGGGTATGTGAGGATGCAGAGGGACTCCGGGGTTGATGGCGGGCTTTGTGGGAT
CGCCATGGAAGCCTCGTACCCTGTCAAGAACGAGCAGACGAAGAAGAAGCCCCGGCGCGCGCTCGGGGAGAAGAAGGCGT
ACTACTCCCAGTGA

Alignment

ORF - retro_bdis_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.32 %
• Parental protein coverage: 61.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTYSDAENLPPAVDWREKGAVTGIKDQGQCGSCWAFSTIAAVESINKIRTGKLVSLSEQELMDCDNV-ND
          F.Y......P.AVDWR.KGAVTG.KDQG.CGSCWAFS..A.VE..N.IRTG.LVSLSEQEL.DCD....D
Retrocopy FIYDTVKDIPQAVDWRQKGAVTGVKDQGKCGSCWAFSAVASVEGLNAIRTGSLVSLSEQELIDCDTGGDD

Parental  QGCDGGLMDYAFQFIQKN-GGVTSEANYPYQGQQNTCDQAKENTHDVAIDGYEDVPANDESALQKAVAYQ
          .GC.GGLM..AF.FI....GG...EA.YPY.....TC.........V.IDG...VPA..E.AL.KAVA.Q
Retrocopy NGCQGGLMESAFEFIAHSAGGLATEAAYPYHASNGTCNANRGSSVSVRIDGHQSVPAGNEEALAKAVAHQ

Parental  PVSVAIEASGQDFQFYSEGVFTGQCTTDLDHGVAAVGYGTA-RDGTKYWIVKNSWGLDWGEKGYIRMQRG
          PVSVAI.A.GQ.FQFYSEGVFTG.C...LDHGVA.VGYG.A..DG..YWIVKNSWG..WGE.GY.RMQR.
Retrocopy PVSVAIDAGGQAFQFYSEGVFTGDCGSELDHGVAVVGYGVAEEDGKEYWIVKNSWGPGWGEHGYVRMQRD

Parental  VSQAEGLCGIAMQASYPIK
          .....GLCGIAM.ASYP.K
Retrocopy SGVDGGLCGIAMEASYPVK

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_26 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,