RetrogeneDB ID: retro_bdis_38

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:13798304..13799846(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G15510
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G24820
• Aliases: None
• Description: None

Sequence

>retro_bdis_38
ATGGCGGGCGGCGTGGTGGTGAGCGCGGCGGGGGGCAAGGTCTACCCAGGCCGGATGACATTCTTCGTCTTCTTCACCTG
CCTCGTGGCCAGCTCCGGCGGGCTCATCTTCGGCTACGACATCGGCATCTCCGGCGGGGTCACCTCCATGGACTCCTTCC
TGAGCGAGTTCTTCCCCTCCGTCTACGCGCAATCCAAAGCCAACAAGGACACGAACCAATACTGCAAGTTCAACAGCCAG
CTGCTGACCCTCTTCACCTCCTCCCTCTACCTCGCCGCCCTGGCGACCTCCTTCGTCGCCGCGTCCGTGACCCGGGTCTA
CGGCCGGAAATGGTCCATGTTCTGCGGCGGGCTGACCTTCCTCGCCGGGTCCGCCCTCAACGGCGCCGCCACGGGCGTCT
CCATGCTCATCGCCGGCCGCATCCTCCTCGGCATCGGCGTCGGGTTCGCCAACCAGTCCGTCCCGCTCTACCTCTCCGAG
ATGGCGCCGGCGAACCTCCGCGGGATGCTCAACATCGGGTTCCAGCTCATGACCACCATCGGGATCCTGGCGGCGAATCT
CATCAACTACGCCACCGTCAGCATCCCCGGCGGCTGGGGATGGCGGGTCGGGCTCGGGCTCGCCGGCGTCCCCGCCCTCG
TGATAACCCTAGGAGCCCTCTCCCTCCCCGACACCCCAAATTCCCTAATCGCCAGAGGCTACACGGCGGAGGCCAAGAAA
GTCCTCGTCAAGATCCGGGGAACCTCCGACGTCCACGAGGAGTACGACGACATGGTCGCCGCCAGCGAAGAAGCCAAATC
CATCAAGCATCCATGGCGGAACATTCTGGAACCCAAATACCGGCCGCAGCTGACAATCGCGATCCTGATCCCCTTCTTCC
AGCAGCTCACCGGCATCAACGTGATCATGTTCTACGCGCCGGTGCTCTTCCTGACGATAGGCTTCGGCGGCGACGCCTCC
TTAATGTCCGCCGTGATCACGGGGCTTGTCAACATGTTCGCCACCATCATCTCCATCATCTGCGTCGACAGGCTCGGCCG
GCGAGCGCTCTTCCTGCAGGGCGGCACGCAGATGTTCGTGTCGCAGATCGTCGTCGGCACGCTCATCGCCATGCAGTTCG
GCACCGCCGGCGTCGGGGAGATGGCGCGCTCGTACGCGCTGCTGCTCGTGCTCTTCATCTGCCTCTATGTCGCGGGGTTC
GCTTGGTCCTGGGGCCCGCTGGGGTGGCTGGTGCCCAGCGAGGTGTTCGCGCTCGAGATCCGGTCGGCGGGCCAGAGCAT
CGCCGTCTGCGTCAACATGACGCTCACCTTCATCATCGGCCAGGCGTTCCTGACGATGCTGTGCCATCTCAAGTTTGGGC
TTTTTTATTTCTTCGCGGCGTGGATGGTGGTCATGACGACGTTCATCGCGTTGTTTCTGCCGGAGACGAAAGGGGTGGCC
ATTGATGAGATGAGTTTGGTGTGGAGCAGACACTGGTTCTGGAGCAAGTACGTTCCCCCTGCCGGTGAAGGAGGAAGCAG
CCGCAGAGCGCACGGCGTCTAG

Alignment

ORF - retro_bdis_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.0 %
• Parental protein coverage: 94.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGGAVVNTGGGKDYPGKLTMFVLFACIVAATGGLIFGYDIGISGGVTSMNPFLMKFFPAVYRQEQEAER
          MAGG.VV...GGK.YPG..T.FV.F.C.VA..GGLIFGYDIGISGGVTSM..FL..FFP.VY.Q......
Retrocopy MAGGVVVSAAGGKVYPGRMTFFVFFTCLVASSGGLIFGYDIGISGGVTSMDSFLSEFFPSVYAQSKA--N

Parental  NQSNQYCKFDSQLLTMFTSSLYLAALVASFFAATVTRVAGRKWSMFAGGVTFLAGAALNGAAKDVLMLIL
          ...NQYCKF.SQLLT.FTSSLYLAAL..SF.AA.VTRV.GRKWSMF.GG.TFLAG.ALNGAA..V.MLI.
Retrocopy KDTNQYCKFNSQLLTLFTSSLYLAALATSFVAASVTRVYGRKWSMFCGGLTFLAGSALNGAATGVSMLIA

Parental  GRVLLGIGVGFANQSVPVYLSEMAPARLRGMLNIGFQQMITIGILCANLINYGTAKIKGGWGWRVSLALA
          GR.LLGIGVGFANQSVP.YLSEMAPA.LRGMLNIGFQ.M.TIGIL.ANLINY.T..I.GGWGWRV.L.LA
Retrocopy GRILLGIGVGFANQSVPLYLSEMAPANLRGMLNIGFQLMTTIGILAANLINYATVSIPGGWGWRVGLGLA

Parental  AVPAAIIAVGALFLPDTPNSLIDRGYTDDAKRMLRRVRGTDDVDEEYRDLVAASEESKLVSHPWRNILQR
          .VPA..I..GAL.LPDTPNSLI.RGYT..AK..L...RGT.DV.EEY.D.VAASEE.K...HPWRNIL..
Retrocopy GVPALVITLGALSLPDTPNSLIARGYTAEAKKVLVKIRGTSDVHEEYDDMVAASEEAKSIKHPWRNILEP

Parental  RYRPQLTFAIAIPFFQQLTGINVIMFYAPVLFKTLGFADDASLMSAVITGLVNVFATSVSIVTVDRLGRR
          .YRPQLT.AI.IPFFQQLTGINVIMFYAPVLF.T.GF..DASLMSAVITGLVN.FAT..SI..VDRLGRR
Retrocopy KYRPQLTIAILIPFFQQLTGINVIMFYAPVLFLTIGFGGDASLMSAVITGLVNMFATIISIICVDRLGRR

Parental  KLFLQGGVQMLVCQIVVGGLIGAKFGFSGVAVIPKEYAAFVVLFICAYVAGFAWSWGPLGWLVPSEIFPL
          .LFLQGG.QM.V.QIVVG.LI...FG..GV......YA...VLFIC.YVAGFAWSWGPLGWLVPSE.F.L
Retrocopy ALFLQGGTQMFVSQIVVGTLIAMQFGTAGVGEMARSYALLLVLFICLYVAGFAWSWGPLGWLVPSEVFAL

Parental  EIRSAGQSITVSVNMFCTFVIAQAFLPMLCRFKFMLFFFFGAWVVLMTLFVAFFLPETKNVPIEEMVLVW
          EIRSAGQSI.V.VNM..TF.I.QAFL.MLC..KF.LF.FF.AW.V.MT.F.A.FLPETK.V.I.EM.LVW
Retrocopy EIRSAGQSIAVCVNMTLTFIIGQAFLTMLCHLKFGLFYFFAAWMVVMTTFIALFLPETKGVAIDEMSLVW

Parental  KAHWYWGRFI
          ..HW.W....
Retrocopy SRHWFWSKYV

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_38 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G24820	1 retrocopy	retro_bdis_38 ,
Brachypodium distachyon	BRADI1G78400	1 retrocopy	retro_bdis_18,
Hordeum vulgare	MLOC_55525	1 retrocopy	retro_hvul_80,
Medicago truncatula	MTR_0009s0370	1 retrocopy	retro_mtru_23,
Oryza glumaepatula	OGLUM07G18360	1 retrocopy	retro_oglu_7,
Oryza meridionalis	OMERI07G15470	2 retrocopies	retro_omer_15, retro_omer_8,
Oryza nivara	ONIVA07G16940	1 retrocopy	retro_oniv_2,
Oryza punctata	OPUNC07G17520	1 retrocopy	retro_opun_36,
Oryza glaberrima	ORGLA07G0149800	1 retrocopy	retro_ogla_30,
Oryza rufipogon	ORUFI07G19310	1 retrocopy	retro_oruf_45,
Oryza sativa japonica	OS07G0559700	1 retrocopy	retro_osat_29,
Triticum aestivum	Traes_2BS_7DF366FE1	1 retrocopy	retro_taes_36,