RetrogeneDB ID: retro_bdis_13

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:14941596..14943435(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G16900
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI2G46477
• Aliases: None
• Description: None

Sequence

>retro_bdis_13
ATGGGGTCCTCCAGCCAGGCCGCCGTCCTGGCCATGTTGCTCCTCATTTCCTCCTCCACAGCCCAGGCCTCCTTCTTCGA
CCCGTTCAACATCTTCCGCGCGGGGGACTTCTTCGGCGACGAGCCCACGCCCCCGACGCGCTCAGAACGCGAAGAAACTG
GCGCGTCGGCGGACACCATGGGCCTCACCAAGGTCCCCCCCACGGGCGACCCCAGCAAGGTCTCCCAGGACACCATCGTG
CTCCCCGTCGACACCGACGACGACAAGCCGGACGGCGCGTGGTCCATCGTGAGCGACAACTCGGGCGTGTCGGCCATGCA
CATGGCCGTCATGCGGCACGGCCGCGCCGTCATGTTCGACACCTCCACCACGGGCCGGTCCCTGATGCGGCTCCGACAGG
ACAACTGCCGCGTCGACCCTCGCGCCAAGAAGCCCGGCACCGCCGACTGCTGGGCGCACGCCGTGGAGTTCGACTACGCC
CGCGGCGCCATCCGGCCGTTGAAGATCCTCACCGACACCTGGTGCTCCTCCGGCGCCTTCGACGCCGACGGCAACCTGGT
CCAGACTGGGGGATACTTCGACGGCGACAAGGCCGTCAGGTACCTCAGCCCGTGCTCGAAATGCGACTGGAAGGAGCACC
CGAGAAGCTTCGCGGACGGGCGGTGGTACGCGACGCAGCAAGTGCTCCCCGACGGGAGGTTCATCGTGTTCGGCGGCCGC
CGGTCCTTCAGCTACGAGTTCGTCCCCAAACCCGGGCTAACCAACCATCAATCCATCCCGCTTCCATTCTTGCGAGAAAC
CACAGACGACGTGGAGAACAATCTTTACCCCTTCGTCAACCTCCTGCCGGACGGGAGCCTCTTCGTGTTCGCCAACGACA
GGGGGATCATCCTCGACCACAGGGCCGAGCTCGTCATCCGCGAGGTCCCGCCGCTTCTCGGCGGTGCCAGGAACTACCCC
GGGTCAGCCATGTCGGCGCTCCTCCCGCTTGACCTCCGCAACAAGCTCCACGGGGCGGACCCGGAGCCCGAGGTGATCAT
CTGCGGGGGCGCGCCGAAGACGGCGTTCAAGGTGGGCGAGAACAACACGTTCCTCCCAGCGCTCAAGGACTGCGCCCGGA
TCAACCTGGCGAACCCGGGCTCCCGGTGGGCCGTGGAGGACATGCCCGTGGGCCGGGTCATGGGCGACATGCTCATCCTC
CCCACGGGGGATCTCCTCATCCTCAGCGGCGCCGCCAGGGGTTGCTCGGGCTGGGGCTTCGCCAGGCAGCCCGTGCTCAC
GCCGCTGCTCTACACCCCTCACGCGCCCATGGGGACCCGGTTCAGGCCCCTCGTGGCGTCCACCATTGCTAGGGTTTACC
ACTCCACGGCGGCGTTGCTCCCGGACGCGACGGTGCTCGTGGCCGGGGGGAACACGAACGCGGCGTACAACTTCAGCGGG
GTCGACTTCCCCACCGAGGTCCGGGTCGAGCGGTTCGCGCCGCCGTACCTGGACCGGGCGCTGGCGGCGAACCGGCCTGT
AATCGACGCGCTGTCGATGCCCGGCGACGGGATGCGGTACGGGGCCCGGTTCGCGTTCCGGTTCACCACGCCGGTGGAGC
CCGTTGTGGAGGCGGATGTCAAGGTCACCATGTACGCGCCGCCGTTCACGACGCACGGGTACTCCATGAACCAGAGGTTG
CTGGTGTTGTCTATGAGCTTGTTCGTGGCGAATGGGTTGGGATACGCTGTGACTGTTGACGCGCCCGGGAAGCCTGAGCT
CGCGCCGCCTGGGTTTTATCTCCTCTTTGTTGTCGCTAAGGACGTGCCCAGCGCCGCCGCCTGGGTCAAGATCCAGTAG

Alignment

ORF - retro_bdis_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.16 %
• Parental protein coverage: 88.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GWWNVLSENAGVSAMHLAVMRHGKAVMFDTTTTGPSLLRLPPGNCRPDPRSIPPGFLDCSAHAVEFDYNT
          G.W...S.N.GVSAMH.AVMRHG.AVMFDT.TTG.SL.RL...NCR.DPR...PG..DC.AHAVEFDY..
Retrocopy GAWSIVSDNSGVSAMHMAVMRHGRAVMFDTSTTGRSLMRLRQDNCRVDPRAKKPGTADCWAHAVEFDYAR

Parental  GRLRPLKILTDTWCSSGAFDGEGMLVQTGGYFEGVKVVRHLSPHDNGDWREFPNTLADGRWYGTTQVLPD
          G..RPLKILTDTWCSSGAFD..G.LVQTGGYF.G.K.VR.LSP....DW.E.P...ADGRWY.T.QVLPD
Retrocopy GAIRPLKILTDTWCSSGAFDADGNLVQTGGYFDGDKAVRYLSPCSKCDWKEHPRSFADGRWYATQQVLPD

Parental  GRFIVIGGRRAFSYEFVPAPGQSNANAIPLPLLRDTTDDVENNLYPFVHLLPDGTIFLFANDRSIVFNPQ
          GRFIV.GGRR.FSYEFVP.PG..N...IPLP.LR.TTDDVENNLYPFV.LLPDG..F.FANDR.I.....
Retrocopy GRFIVFGGRRSFSYEFVPKPGLTNHQSIPLPFLRETTDDVENNLYPFVNLLPDGSLFVFANDRGIILDHR

Parental  NGQILRELPKLPGGARNYPASAMSVLLPLDLR---RGERLNAEVMVCGGAPKDAFKLGEVNKFPNALRDC
          .....RE.P.L.GGARNYP.SAMS.LLPLDLR....G.....EV..CGGAPK.AFK.GE.N.F..AL.DC
Retrocopy AELVIREVPPLLGGARNYPGSAMSALLPLDLRNKLHGADPEPEVIICGGAPKTAFKVGENNTFLPALKDC

Parental  GRINPAKPGARWSMDQMPVGRVMGDMLILPTGDLLLINGAAQGCSGWWFARQPVLSPLLYSTRKPRGARF
          .RIN.A.PG.RW....MPVGRVMGDMLILPTGDLL...GAA.GCSGW.FARQPVL.PLLY....P.G.RF
Retrocopy ARINLANPGSRWAVEDMPVGRVMGDMLILPTGDLLILSGAARGCSGWGFARQPVLTPLLYTPHAPMGTRF

Parental  RALAPSNIPRMYHSSSAVLPDATVLVAGGNTNSAYNFSGVDFPTEVRVERFTPPYLAPELLASRPEIDAA
          R.L..S.I.R.YHS..A.LPDATVLVAGGNTN.AYNFSGVDFPTEVRVERF.PPYL...L.A.RP.IDA.
Retrocopy RPLVASTIARVYHSTAALLPDATVLVAGGNTNAAYNFSGVDFPTEVRVERFAPPYLDRALAANRPVIDAL

Parental  SVPGNGMKYGAKFSFRFSTPGGQPPVLEGDVKVTMYAPPFTTHGYSMNQRLLVLQVTAFKAEGAKHKVTI
          S.PG.GM.YGA.F.FRF.TP....PV.E.DVKVTMYAPPFTTHGYSMNQRLLVL....F.A.G....VT.
Retrocopy SMPGDGMRYGARFAFRFTTP--VEPVVEADVKVTMYAPPFTTHGYSMNQRLLVLSMSLFVANGLGYAVTV

Parental  HAPSKPALAPPGYYMVFVLAKGVPSKAAWVKI
          .AP.KP.LAPPG.Y..FV.AK.VPS.AAWVKI
Retrocopy DAPGKPELAPPGFYLLFVVAKDVPSAAAWVKI

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_13 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004194	1 retrocopy	retro_oind_16,
Brachypodium distachyon	BRADI2G46477	1 retrocopy	retro_bdis_13 ,
Oryza glumaepatula	OGLUM01G30230	1 retrocopy	retro_oglu_1,
Oryza meridionalis	OMERI01G24080	1 retrocopy	retro_omer_13,
Oryza glaberrima	ORGLA01G0215900	1 retrocopy	retro_ogla_7,
Oryza sativa japonica	OS01G0677000	1 retrocopy	retro_osat_22,
Setaria italica	Si004698m.g	1 retrocopy	retro_sita_36,