RetrogeneDB ID: retro_bdis_46

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:8021251..8022580(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G09777
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI3G59430
• Aliases: None
• Description: None

Sequence

>retro_bdis_46
ATGGCGACGATGGTCGCCGCTTGCCACTCCCCAGCTCGCCTCTCAGTCTCCTGCTCTTCCTCCTCGTCGGCTCGCCCGCT
GCGCGTGGCCGTGGTGGGCGGCGGGCCTGCCGGCGCGTCGGCGGCCGAGGCGCTGGCCTCCGCGGGCGCCCAGGCGTTCC
TCCTGGAGCGCAGCCCGGCGGGGGCCAAGCCCTGCGGCGGCGCCATCCCGCTCTGCATGCTGGACGAGTTCTCCATCCCT
CTGGAGCTTGTCGACCGCCGCGTCACCCGCATGCGCGTCCTCTCCCCCTCCAACCTCGCCGCCGACTTCTCCAAGACGCT
CCCCCCGGGCGCGCACATCCCCATGCTCCGCCGCGAGGTGCTCGACTCCTTCCTCCGCCGCCGCGCCGCCGACGCTGGCG
CCACCCTCGTCCCGGGCCTCGTCACCTCCCTCTCCCTCCCCGCGGGGCCCTCCGACCCCTACCTCGTCCACTACATCTCC
TCCGCCGCCGCCGACGGCCGGAGCGTGCTGGAGGTGGACGCCGTGGTGGGCGCGGACGGCGCCAACAGCCGGGTCGCACG
CGAGGTCGGCGCCGGCGGGTACTCGACGGCCATCGCCTTCCAGGAGCGCATCCGGCTCCCCGACGCGGCCATGGGGTACT
ACGACGACCTGGCCGAGATGTACGTGGGCGGGGACGTGTCCCCGGACTTCTACGGCTGGGTGTTCCCCAAGTGCGACCAC
GTGGCCGTCGGCACGGGCACCGTGGCCGCCAAGCCAGACATCAAGAAATTCCAGGCCGGCATCCGCGCGCGGGCCGGGCC
GAAGATCGCGGGGGGGAAGGTGATCAAGGTGGAGGCCCACCCGATCCCGGAGCACCCGCGCCCGCGCCGCGTGGTCGGCC
GCGTGGCGCTCGTGGGCGACGCGGCGGGGTACGTCACCCGGTGCTCCGGGGAAGGCATCTACTTCGCGGCCAAGTCCGGG
AGGCTCTGCGGGCAGGCCATGGCGGATGAGTGGCGGGTGACCGGGAAGGTGACCGAGGGCGGGATCAGGCAAGGGTACCT
CCGGGCTTGGGACGACGAGTTCCTGCTGACGTTCCGGTTCCTGGACCTGCTGCAGCGGGTGTTCTACGGGGGCAACGCGG
GGCGGGAGGCGCTGGTGGAGATGTGCGCCGACGAGCACGTGCAGCGGCGGACGTTCGACTGCTACCTCAACAAGCGGATG
GCGCCGGGGGAGCCGTGGGCCGACCTCCAGCTGCTCTGGCGCACGGCCGGCAGCATGGTGCGCTGCAGCGTACTCGGCAA
GGAGGTCCAGCGCCTCCGCCGGCTCGAGATGCTGCAGCAGGCTACCTGA

Alignment

ORF - retro_bdis_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.15 %
• Parental protein coverage: 91.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RAAATSPKLPAGRRLRVAVVGGGPAGGAAAEALAKGGVETVLIERKMDNCKPCGGAIPLCMVSEFDLPLD
          R...........R.LRVAVVGGGPAG..AAEALA..G....L.ER.....KPCGGAIPLCM..EF..PL.
Retrocopy RLSVSCSSSSSARPLRVAVVGGGPAGASAAEALASAGAQAFLLERSPAGAKPCGGAIPLCMLDEFSIPLE

Parental  LVDRKVTKMKMISPSNVAVDIGRTLAPHEYIGMVRREVLDDFLRTRAQKAGAEVLNGLFLRYEAPKEANG
          LVDR.VT.M...SPSN.A.D...TL.P...I.M.RREVLD.FLR.RA..AGA....GL......P.....
Retrocopy LVDRRVTRMRVLSPSNLAADFSKTLPPGAHIPMLRREVLDSFLRRRAADAGATLVPGLVTSLSLPAGPSD

Parental  TYTVHYNHYDSSSGKVGGEKRSFEVDAIVGADGANSRVAKDMGAGDYEYAIAFQERVKIPDDKMRYYEER
          .Y.V...HY.SS....G......EVDA.VGADGANSRVA...GAG.Y..AIAFQER...PD..M.YY...
Retrocopy PYLV---HYISSAAADG--RSVLEVDAVVGADGANSRVAREVGAGGYSTAIAFQERIRLPDAAMGYYDDL

Parental  AEMYVGDDVSPDFYGWVFPKCDHVAVGTGTVTHKADIKKFQAATRLRAKDKIDGGRIIRVEAHPIPEHPR
          AEMYVG.DVSPDFYGWVFPKCDHVAVGTGTV..K.DIKKFQA..R.RA..KI.GG..I.VEAHPIPEHPR
Retrocopy AEMYVGGDVSPDFYGWVFPKCDHVAVGTGTVAAKPDIKKFQAGIRARAGPKIAGGKVIKVEAHPIPEHPR

Parental  PKRVSGRVTLVGDAAGYVTKCSGEGIYFAAKSGRMCAEAIVAGSANGTRLVEEGDLRK-YLAEFDRLYWP
          P.RV.GRV.LVGDAAGYVT.CSGEGIYFAAKSGR.C..A..A.....T..V.EG..R..YL...D.....
Retrocopy PRRVVGRVALVGDAAGYVTRCSGEGIYFAAKSGRLCGQA-MADEWRVTGKVTEGGIRQGYLRAWDDEFLL

Parental  TYKVLDILQKVFYRSNAAREAFVEMCADDYVQRMTFDSYLYKRVVPGNPLEDIKLAVNTIGSLVRATALR
          T...LD.LQ.VFY..NA.REA.VEMCAD..VQR.TFD.YL.KR..PG.P..D..L...T.GS.VR...L.
Retrocopy TFRFLDLLQRVFYGGNAGREALVEMCADEHVQRRTFDCYLNKRMAPGEPWADLQLLWRTAGSMVRCSVLG

Parental  REMSKL
          .E...L
Retrocopy KEVQRL

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_46 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G59430	1 retrocopy	retro_bdis_46 ,
Zea mays	GRMZM2G105644	1 retrocopy	retro_zmay_29,
Oryza meridionalis	OMERI02G30980	1 retrocopy	retro_omer_17,
Oryza nivara	ONIVA06G04710	1 retrocopy	retro_oniv_24,
Oryza punctata	OPUNC02G29860	1 retrocopy	retro_opun_22,
Oryza rufipogon	ORUFI02G34000	1 retrocopy	retro_oruf_42,
Oryza sativa japonica	OS02G0744900	1 retrocopy	retro_osat_44,
Sorghum bicolor	Sb04g028050	1 retrocopy	retro_sbic_27,
Triticum aestivum	Traes_6DL_0FF72D765	1 retrocopy	retro_taes_28,