RetrogeneDB ID: retro_bdis_35

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:11423330..11424458(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G12730
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI3G28100
• Aliases: None
• Description: None

Sequence

>retro_bdis_35
ATGGCCGCCATTGCCATTGCCTTCCTCCTCGTGCTTGTAGCAGCAGCAGCAGCAGCAGCAGCAATGGCGTCTGCAGCGTC
AATAGGAACAGGTCCTCGTCCCTTCTTCGTGTTCGGCGACTCTCTCGTAGACAGCGGCAACAACAACTACCTGCTCACCA
CGGCCCGCGCCGACTCCCCACCCTACGGCCTGGACTACCCGACCCACCGGGCCACGGGCCGCTTCTCCAACGGCCTCAAC
GTCCCCGACATCATCAGCGAGCACCTGGGCTCCCCGCCGGTCCTCCCTTACCTCAGCCCACACCTCGACGGCCCAACCCT
CCTCACGGGGGCCAACTTCGCCTCCGCCGGCGTCGGCATCCTCAACGACACCGGCATCCAGTTCGCCAACATCATCCGCA
TGCCCAAGCAGCTCCGCTACTTCCAGCAATACCAGACACGCCTCACACGCAGCCTCGCCGGAGACGCCGCCGCCGCTCGC
CGACTTGTCCGATCCGCCCTGGTGCTCATCACGCTCGGCGGCAACGACTTCGTCAACAACTACTACCTGGTGCCATTCTC
TGCCAGGTCACGCCAGTTCTCGCTGCCGGACTACGTCCGCTACCTCATCGCCGAGTACCGCAAGATCCTCCGGCAGCTCT
ACGACCTCGGGGCCCGCCGCGTGCTCGTCACGGGCTCCGGCCCGATCGGCTGCGCGCCGGCCGAGCTCGCCACGAGGAGC
GCCAACGGGGAGTGCGACATCGAGCTGCAGCGGGCCGCGGCGCTGTATAACCCGCAGCTGGTGGCCATGACAAGGGAGCT
CAACGCCGGCTACGGCGCCGACGTGTTCGTGGCAGTCAACGCCTACCGGATGCACATGGACTTCATCTCGGCGCCGGCGG
CCTACGGGTTCCTGACGTCCAAGGTGGCATGCTGTGGCCAGGGACCTTACAATGGCGTCGGCCTCTGCACTGCGCTGTCC
AGCGTCTGCCCGGACAGGTCGCTGTATGCCTTCTGGGACAACTTCCACCCTACTGAGAGGGCCAACAGGATCATCGTTAG
CCAGTTCATGGTTGGCTCGCCGGAGTACATGCACCCGCTCAACCTCTCCACCATCCTCGCCGTTGATGCTGCCGCCGCAA
TGCCGTGA

Alignment

ORF - retro_bdis_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.61 %
• Parental protein coverage: 95.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LWAMSTMLMAVGLLASPVECARAFFVFGDSLVDNGNNNYLMTSARADSPPYGIDFPTHRATGRFSNGLNI
          L.A......A....AS.....R.FFVFGDSLVD.GNNNYL.T.ARADSPPYG.D.PTHRATGRFSNGLN.
Retrocopy LVAAAAAAAAMASAASIGTGPRPFFVFGDSLVDSGNNNYLLTTARADSPPYGLDYPTHRATGRFSNGLNV

Parental  PDIISEHLGAEPTLPYLCPELHGAKLLVGANFASAGVGILNDTGIQFVNIVRMSRQLHYFREYQAKL-RA
          PDIISEHLG..P.LPYL.P.L.G..LL.GANFASAGVGILNDTGIQF.NI.RM..QL.YF..YQ..L.R.
Retrocopy PDIISEHLGSPPVLPYLSPHLDGPTLLTGANFASAGVGILNDTGIQFANIIRMPKQLRYFQQYQTRLTRS

Parental  LVG-AAQATQVVNRALVLITLGGNDFVNNYYLIPFSLRSRQYALPDYVRLLISEYKKILVNLYEMGARRV
          L.G.AA.A...V..ALVLITLGGNDFVNNYYL.PFS.RSRQ..LPDYVR.LI.EY.KIL..LY..GARRV
Retrocopy LAGDAAAARRLVRSALVLITLGGNDFVNNYYLVPFSARSRQFSLPDYVRYLIAEYRKILRQLYDLGARRV

Parental  LVTGTGPLGCAPAELALRSRDGECDKDLMRAAGLFNPQLSDVLGELNGRYGDGTFIAANAMKVHFDFISD
          LVTG.GP.GCAPAELA.RS..GECD..L.RAA.L.NPQL.....ELN..YG...F.A.NA...H.DFIS.
Retrocopy LVTGSGPIGCAPAELATRSANGECDIELQRAAALYNPQLVAMTRELNAGYGADVFVAVNAYRMHMDFISA

Parental  PAAYGFRTAKEACCGQGPHNGLGLCTVASNMCANRDEYVFWDSYHPTERANRIIVSQFMTGSLDYVSPLN
          PAAYGF.T.K.ACCGQGP.NG.GLCT..S..C..R..Y.FWD..HPTERANRIIVSQFM.GS..Y..PLN
Retrocopy PAAYGFLTSKVACCGQGPYNGVGLCTALSSVCPDRSLYAFWDNFHPTERANRIIVSQFMVGSPEYMHPLN

Parental  LSTVLHMDAA
          LST.L..DAA
Retrocopy LSTILAVDAA

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_35 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
Brachypodium distachyon	BRADI2G49781	1 retrocopy	retro_bdis_23,
Brachypodium distachyon	BRADI3G28100	1 retrocopy	retro_bdis_35 ,