RetrogeneDB ID: retro_bdis_39

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:15787663..15788680(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G17730
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI4G36290
• Aliases: None
• Description: None

Sequence

>retro_bdis_39
ATGTACTGCTCGGCGGCGGACGAGCGGGTGTACTGCACGGACTGCCACCGCGCGACGGAGGTGGTGCTCGACCACGGCAC
CGGCGACACCATCTGCACCGACTGCGGCATGGTCCTGGACGAGCACTACATCGACGAGGGACAGGAGTGGCGCGTCTTCG
GCGACGACAGCGCTGGCGGCGAGGACCGCGACCCCTGCCGCGTCGGCTCGGCCGGCGACCCCTTCCTCCGCGGCGACGGC
CTGCTCTCCACTTGCATCGTCCACTCGGCCAAGTCCAAGTCAAGGTCCAGGTCCGGGTCCGACCCAGCCGCCGCCCTGCA
CCTGCCCAGGATGATGCTCGACGTCGGCGGCCCGGCCCCCGACACGGCGCTCGTCGACGCGTTCCGCGGCATCGCCGACA
TGGCGGACCGGCTGGGGCTCGTGGCCACCATCCGGGACTCGGCCAAGCAGACGTTCAAGCGGCTCGAAGAGGCCAAGGGG
TGCCCGCGCGGCGCCCGGAGCCGCGACGCCGTCTACGCCGCCTGCCTCTACGTCGCCTGCCGCAAGGAAGGCATGCCTCG
GACGTACAAGGAGCTGGCCTCCGTCACGGCGCAGGGGGCGGCGGCGCGCAAGGACATTGGCAAGATGACGACACACATCA
AGAAGCTGCTCGGGGAGGAGGACGGCCAGGTGCTCGACATCGGCGTCGTGCGCGCCACCAGCTACCTGCGCCGCTTCTGC
TCCATCCTCGGCCTCGGCAACCAGCAGATGCTCGCCGCCCAGGAGGCCGTGAGCAGGCTCGAGATGGAGCTCGACGTGCG
CCGCAACCCCGAGTCCATCGCCGCCGCCATCATCTACATGGTCGTGCAGCGCGCCGGCGCCCGCAGGTCCGTCAAGGACG
TGTCCGCCGCCACCGGCGTCGCCGAGGGCACCATCAAGGAGGCGCACAAGGACCTCGTCCCGCACACGGAGTTGCTTTTC
GCTGAGCGCCCGCCGCGCGGTTCTTCCGCGCGCCCTGCTCCTGCTGCAGGCCATTAA

Alignment

ORF - retro_bdis_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.71 %
• Parental protein coverage: 63.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSNPDRSLILAFRTIANMADRLGLVATIKDRANEIYKKVEDLKSI-RG-RNQDAILAACLYIACRQEDRP
          G..PD..L..AFR.IA.MADRLGLVATI.D.A....K..E..K...RG.R..DA..AACLY.ACR.E..P
Retrocopy GPAPDTALVDAFRGIADMADRLGLVATIRDSAKQTFKRLEEAKGCPRGARSRDAVYAACLYVACRKEGMP

Parental  RTVKEICSVA--NGATKKEIGRAKEFIVKQLEVEMGQSMEMGTIHAGDFLRRFCSTLGMNNTAVKAAQEA
          RT.KE..SV.....A..K.IG.....I.K.L..E.GQ....G...A...LRRFCS.LG..N....AAQEA
Retrocopy RTYKELASVTAQGAAARKDIGKMTTHIKKLLGEEDGQVLDIGVVRATSYLRRFCSILGLGNQQMLAAQEA

Parental  VQRSE-ELDIRRSPISIAAAVIYMITQLSEDKKPLKDISLATGVAEGTIRNSYKDLYPYASRL
          V.R.E.ELD.RR.P.SIAAA.IYM..Q........KD.S.ATGVAEGTI....KDL.P....L
Retrocopy VSRLEMELDVRRNPESIAAAIIYMVVQRAGARRSVKDVSAATGVAEGTIKEAHKDLVPHTELL

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_39 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G36290	1 retrocopy	retro_bdis_39 ,
Aegilops tauschii	F775_29675	1 retrocopy	retro_atau_5,
Hordeum vulgare	MLOC_10647	1 retrocopy	retro_hvul_45,
Medicago truncatula	MTR_7g091230	2 retrocopies	retro_mtru_26, retro_mtru_3,
Sorghum bicolor	Sb02g031020	1 retrocopy	retro_sbic_35,