RetrogeneDB ID: retro_bdis_8

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:7201704..7202709(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G09100
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G38297
• Aliases: None
• Description: None

Sequence

>retro_bdis_8
ATGGCCGCCTTCGTCATTTCTTCGGCGAGGATCTCCACGCTCGCGGTTGCTCTCCTCGTCGCCACCACGATCTCCTGCCG
AGGCGCCGGAGTCGCGGCGGCCACACTGTCGAACAAGTACTACGACAAGACGTGCCCGGGGCTGCAGCCCATCGTGCGGT
CGGCGATGGCGCAGGCGGTGGCCGCGGATCCCCGCACGGGCGCCTCCGTGCTCCGGCTCTTCTTCCACGACTGCTTCGTC
AACGGCTGCGACGGCTCCGTGCTCCTGGACGACGCGCCGCCGGGGTTCACGGGCGAGAAGGGCGCCGGGCCGAACCTGGG
CTCCGCGCGGGGCTTCGAGGCCGTGGACGCGGCCAAGGCGCAGGCCGAGGCGGCCTGCAACGCCACCGTGTCCTGCGCGG
ACGTGCTCGCGCTGGCAGCCCGCGACGCCGTGGGCCTGCTCGGCGGGCCGGCGTGGGCCGTCAAGCTGGGCCGGAAGGAC
TCGCGCACCGCGAGCCAGGCCGCGGCCAACGCCAACCTTCCCGGGCCTGGGTCCGGCCTATCCTCGCTGCTGGCCTCGTT
CGCGGCCAAGGGGCTGTCGGCGCGGGACATGACGGCGCTGTCCGGCGCGCACACGGTGGGGCGCGCGCGGTGCCTGACGT
TCCGGGCCCGCGTCAACGGCGGGGACGCCGGCGTCAATGCCACCTTCGCGGCGCGGATCCGGCAGGGATGCCCGGCGACC
AACGGCGTTGGGGACAGCAGCCTGGCGCCGCTGGACGGGGAGACGCCGGACGCGTTCGACAACGGGTACTTCCGGGGTCT
CCTGCAGCAGCGCGGGCTGCTGCACTCGGACCAGGAGCTCTTCAGCGGCGGCGGCGGGTCGCAGGACTCGCTGGTGCGCA
AGTACGCCGGCAACGCGGGCATGTTCGCGAGCGACTTCGCCAGGGCGATGGTTAAGATGGGCGGCCTTGAGCCCGCGGCC
GGGACGCCGCTGGAAGTCAGGATCAACTGTCGGAAGCCCAACTAG

Alignment

ORF - retro_bdis_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 91.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKFTSKFYGKTCPNLGAIVRSVMAPAVAKEPRMGASIIRLFFHDCFVNGCDGSILLDDTPT-FTGEKNAG
          A....K.Y.KTCP.L..IVRS.MA.AVA..PR.GAS..RLFFHDCFVNGCDGS.LLDD.P..FTGEK.AG
Retrocopy ATLSNKYYDKTCPGLQPIVRSAMAQAVAADPRTGASVLRLFFHDCFVNGCDGSVLLDDAPPGFTGEKGAG

Parental  ANVNSVRGYEVIDAIKTQVETACKATVSCADIIALASRDAVNLVGGPTWNVQLGRKDSRTASQSAANANL
          .N..S.RG.E..DA.K.Q.E.AC.ATVSCAD..ALA.RDAV.L.GGP.W.V.LGRKDSRTASQ.AANANL
Retrocopy PNLGSARGFEAVDAAKAQAEAACNATVSCADVLALAARDAVGLLGGPAWAVKLGRKDSRTASQAAANANL

Parental  PGPGSSAASLVSAFAAKGLSAREMTALSGAHTVGRARCVLFRGRIY-SDPNINATFAAARQQTCPQAG--
          PGPGS...SL...FAAKGLSAR.MTALSGAHTVGRARC..FR.R....D...NATFAA...Q.CP.....
Retrocopy PGPGSGLSSLLASFAAKGLSARDMTALSGAHTVGRARCLTFRARVNGGDAGVNATFAARIRQGCPATNGV

Parental  GDGNLAPFDDQTPDAFDNAYYKNLMAQRGLLHSDQELFN--GGPQDALVRKYSGNAGIFAGDFAKAMVKM
          GD..LAP.D..TPDAFDN.Y...L..QRGLLHSDQELF...GG.QD.LVRKY.GNAG.FA.DFA.AMVKM
Retrocopy GDSSLAPLDGETPDAFDNGYFRGLLQQRGLLHSDQELFSGGGGSQDSLVRKYAGNAGMFASDFARAMVKM

Parental  GGLMPVAGTPTEVRLNCRK
          GGL.P.AGTP.EVR.NCRK
Retrocopy GGLEPAAGTPLEVRINCRK

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_8 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA021077	1 retrocopy	retro_oind_30,
Brachypodium distachyon	BRADI1G38297	1 retrocopy	retro_bdis_8 ,