RetrogeneDB ID: retro_bdis_4

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:25409645..25412789(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G26670
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G61220
• Aliases: None
• Description: None

Sequence

>retro_bdis_4
ATGGCGAGCGAGGCCCAGCTCAAGACGCGGGTCTCCGATCGGCTGATGGCGCTGCTGGGCTGCTCAACGGGCACGGCGGT
GCAGGTCGTGATCCGCCTCGCACGGGAAAGCGCCTCGGCGACCGTCCTCGCGTCGCGGCTCGTCGATCTCGTCGGGTTCC
CCTCCTCCGCCGACACCGTCGCGTTCGCGGAGGACGTGTGCGGAATGATTCCGCGCAACGCCGCCGCCGGAGGAGTCGGG
GCCAGCGAATACCAGAAGCAGATTCAGGAGGCGACGGCGCTGGCCAAAAACCAGAGCACCTTCAAGCTGCCCGACGACGA
CGACGACGACCATGAAGATGCAATCGTCACCGCGCCGTCCTCTAACACCGGAAAAAAACGTTTCAGGAGGAAGGCCGGGA
ACCAAGGGGGTGAGGAGGATGACGAGACAACGCACGATTTGGGGCGGAAAGTGCGAGCGCGGCCTGATCCGGAGGAATGT
GGTGGTGGTGGTTCTGATGGGGAAGAGGAGATGGTTCGGGATCAGATCGAGAGGGCTAATCTCGAACGGCACATCCGGGA
ACGCGACGCAGCGAGCACTAGGAAATTGATGGATCGGAAGCCAACCAAAGGGGAACAGGACGAACTCGCCCGCCGATCCG
AAGCAATGGCAAGGGACGACACCTCGGAGCTCAGGAGGTTCTCGCGGCACGCGTACCTGCAGAAGCGTAAGGAGAAGAAG
CTCGACGAGGCACTGGACGAGATCATCGACCACGAGTACATCTTCCAGGGCGTCAAGCTGACGGACTCCGAGGAGAGAGA
TTTCAGGCGGAAGAAGGAAATTTACAAGCTCGTCACCGATCGCGTCGGGAAGGACGAGGATGCCGGCGACTGCTACAGGA
TGCCCGAGGCCTACGACGCTGTCGCAAATGTCGATCAGGAGAAGCGGTGGGCCGCGGCGAGGCGGCGGTACGAAGACCCT
GCAGAGGCGAGAGAGGGCAAGAGGAGCAGCTTGTCAGAGCAGGAGGCCTGGGAAGAGCAGCAGATCAGGAAATCCCGGCT
ACAGTTCGGATCAAGCGATCATGGACAGCGGGACGACGGCTACGAGCTCGTCCTGGACGACAGGGTTGACTTCGTCAAAT
CGACGGCGCTGTCGCCGGACGACGAGATGGAAGAATTGGCCGAGGCCATTGATGCAAAGGTGACATTGCAGAGGGAGCTC
CAAGACGAGAGGAAGAATTTGCCCGTGTACAAGCTCAAGGATGATCTTCTCAAAGCCATCGAAGAGCACCAGGTGCTGAT
CATAGTCGGAGAGACCGGGTCCGGCAAGACCACGCAGATTCCTCAGTACCTCCACGAGGCCGGGTACACGGCGCAGGGGA
AGAAGATCGCGTGCACGCAGCCGCGGCGCGTGGCGGCCATGAGCGTGGCGGCGAGGGTGGCGCAGGAGATGGGCGTGAAG
CTCGGGCACGAGGTCGGCTACTCCATCAGGTTCGAGGACTGCACCTCGGACAAGACGGTGGTCAAGTACATGACCGACGG
GATGCTCCTGCGGGAGTTCCTCGGCGAGCCGGACCTGGCGAGCTACAGCGTGGTGATCGTGGACGAGGCGCACGAGCGCA
CGCTGTCCACGGACATCCTCTTCGGCCTCGTCAAGGACATCGCGCGCTTCCGGCCGGACATGAAGCTGCTCATCTCCAGC
GCCACGCTCAACGCCAGCAAGTTCAGCGACTTCTTCGACCTGGCCCCGATCTTCAAGATCCCCGGGAGGCGGTACAAAGT
AGACGTCCACTACACAAAGGCGCCGGAGGCGGACTACGTGGACGCGGCCGTCGTCACGGTCCTGCAGCTGCACGTCAGGC
AGCCCGCCGGCGACATCCTGCTGTTCCTCACGGGGCAGGAGGAGATAGAGACGGTGGAAGAGATCCTGAAACAGAGGATG
AAGGCTCTTGGCAGTAAAATGGCGGAACTGGTGATATGCCCGATCTACGCGAACCTGCCGACGGAGCTCCAGGCCAAGAT
TTTCCTGCCGGCGCCGGCGGGCGCGCGCAAGGTGGTCCTGGCCACCAACATCGCCGAGACGTCGCTGACCATCGATGGGA
TCAAGTACGTGGTCGACCCTGGGTTCTGCAAGGTCAAGTCGTACAACCCGCGCACGGGCATGGAGTCGCTGCTGGTGGCG
CCCATCTCCAAGGCGTCGGCGGACCAGCGCGCCGGCCGTTCGGGCCGCACCGGCCCGGGCAAGTGCTTCCGCCTCTTCAC
GGAGTACAACTTCAGGAACGACCTGGAGGACGACACAGTCCCGGAGATCCAGAGGAGCAACCTGGCAAACGTCGTGCTCA
GGCTCAAGGCGCTGGGCATCAACGACCTGGTGAGCTTCGACTTCATGGACCCTCCAGCGTCGGAGTCGCTGCTCAAGGCC
CTGGAGGAGCTCTACGCGCTCGGCGCGCTCAACGGCCGCGGCGAGCTCACCAAGACCGGGAGGAGGATGGCGGAATTCCC
CTTGGACCCCATGCTCTCTAAGGCCATCGTCGCGTCGGAGAAGTACAGGTGCTCCGAGGAGGTGATCACCATTGCGGCCA
TGCTATCGGCCGGGCCCGGGAGCGCTGTCTTCTACCGGCCCAAGGACAAGCAGGTGCACGCCGACGCCGCGCGGCAGGCA
TTCCACGCCGGCGACGTTGGCGACCACGTGGCGCTGCTCAACGTGTACAACGCGTGGAAGGAGTCGGGATACTCGCCGCA
GTGGTGCCGCGAGAGCTTCGTGCAGTCGCGCACCATGAAGCGCGCGCGGGACGTGCGAGACCAGCTGGAGGCGCTGCTCG
AGCGGGTGGAGATCGAGCCCTGCTCCGGCGCCGGCGACCCCAACGCGATCAGGAAGGCGATTACGGCGGGGTACTTCCGC
AACGCGGCGCGGCTGCAAAAGGACGGGTCTTATCGTGCCGTTAAGAGCCGGCAGACGGTGTTCGTGCACCCCAGCTCCGG
GATGGAGCAGGTACTCCCGCGGTGGATTGTGTACCACGAACTGGTGCAAACCTCGAAGGAATACATGCGGCAGGTGACGG
AGCTCAAGCCGGAGTGGCTGCTGGAGATCGCGCCGCACTACTACCAGTGCAAGGACATCGACGAACACGAGCAGAAGAAG
AAATTAGCCAAGGGAACCACGTAG

Alignment

ORF - retro_bdis_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.34 %
• Parental protein coverage: 88.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DNHTSSLASTPSKS--RKHFRRRAEDQEDLKDDDETITHDSERSVRRRIEEADDEDGDETFDEEREIIRD
          D.H.......PS.....K.FRR.A..Q.....DDET.THD..R.VR.R......E.G....D.E.E..RD
Retrocopy DDHEDAIVTAPSSNTGKKRFRRKAGNQGG-EEDDET-THDLGRKVRARPDP--EECGGGGSDGEEEMVRD

Parental  QQERAQLEKNMRERDAVNTRKLMERQLSKEEQEDLTRRSQAMDKNDTSDLRNFSRQAYLQKRRDKKIDEI
          Q.ERA.LE...RERDA..TRKLM.R...K.EQ..L.RRS.AM...DTS.LR.FSR.AYLQKR..KK.DE.
Retrocopy QIERANLERHIRERDAASTRKLMDRKPTKGEQDELARRSEAMARDDTSELRRFSRHAYLQKRKEKKLDEA

Parental  RDEILDHEYIFQDVKLTEAEEKDFRYKKKIYDHIKERVESADDIAE-YKMPEAYD-MGEGNQEKRFSVAM
          .DEI.DHEYIFQ.VKLT..EE.DFR.KK.IY.....RV....D....Y.MPEAYD......QEKR...A.
Retrocopy LDEIIDHEYIFQGVKLTDSEERDFRRKKEIYKLVTDRVGKDEDAGDCYRMPEAYDAVANVDQEKRWAAAR

Parental  QRYKDP-EAKD-KMNPFAEQEAWEEHQIGKSKLQFGSKDRKRSSDEYQYVFDDQIDFVKSSVIEGTQFED
          .RY.DP.EA...K.....EQEAWEE.QI.KS.LQFGS.D.....D.Y..V.DD..DFVKS........E.
Retrocopy RRYEDPAEAREGKRSSLSEQEAWEEQQIRKSRLQFGSSDHGQRDDGYELVLDDRVDFVKSTALSPDD-EM

Parental  DSDQETIDAKDILKRELQDERKTLPIYKFRDELLKAVDEYQVIVIVGETGSGKTTQIPQYLHEAGYTARG
          ....E.IDAK..L.RELQDERK.LP.YK..D.LLKA..E.QV..IVGETGSGKTTQIPQYLHEAGYTA.G
Retrocopy EELAEAIDAKVTLQRELQDERKNLPVYKLKDDLLKAIEEHQVLIIVGETGSGKTTQIPQYLHEAGYTAQG

Parental  K-VACTQPRRVAAMSVAARVSQEMGVKLGHEVGYSIRFEDCTSEKTMIKYMTDGMLLREFLGEPDLAGYS
          K..ACTQPRRVAAMSVAARV.QEMGVKLGHEVGYSIRFEDCTS.KT..KYMTDGMLLREFLGEPDLA.YS
Retrocopy KKIACTQPRRVAAMSVAARVAQEMGVKLGHEVGYSIRFEDCTSDKTVVKYMTDGMLLREFLGEPDLASYS

Parental  VVMVDEAHERTLSTDILFGLVKDIARFRPDLKLLISSATLDAEKFSDYFDSAPIFKIPGRRYPVEVHYTK
          VV.VDEAHERTLSTDILFGLVKDIARFRPD.KLLISSATL.A.KFSD.FD.APIFKIPGRRY.V.VHYTK
Retrocopy VVIVDEAHERTLSTDILFGLVKDIARFRPDMKLLISSATLNASKFSDFFDLAPIFKIPGRRYKVDVHYTK

Parental  APEADYIDAAIVTVLQIHVTQPPGDILVFLTGQEEIETVDEILKQRTRGLGTKIAELNICPIYANLPTEL
          APEADY.DAA.VTVLQ.HV.QP.GDIL.FLTGQEEIETV.EILKQR...LG.K.AEL.ICPIYANLPTEL
Retrocopy APEADYVDAAVVTVLQLHVRQPAGDILLFLTGQEEIETVEEILKQRMKALGSKMAELVICPIYANLPTEL

Parental  QAKIFEQTPEGSRKVVLATNIAETSLTIDGIKYVIDPGFCKIKSYNPRTGMESLLINPISKASANQRAGR
          QAKIF...P.G.RKVVLATNIAETSLTIDGIKYV.DPGFCK.KSYNPRTGMESLL..PISKASA.QRAGR
Retrocopy QAKIFLPAPAGARKVVLATNIAETSLTIDGIKYVVDPGFCKVKSYNPRTGMESLLVAPISKASADQRAGR

Parental  SGRTGPGKCFRLYTSYNYMHDLEDNTVPEIQRTNLANVVLTLKSLGIHDLVNFDFMDPPPSEALLKALEQ
          SGRTGPGKCFRL.T.YN...DLED.TVPEIQR.NLANVVL.LK.LGI.DLV.FDFMDPP.SE.LLKALE.
Retrocopy SGRTGPGKCFRLFTEYNFRNDLEDDTVPEIQRSNLANVVLRLKALGINDLVSFDFMDPPASESLLKALEE

Parental  LFALSALNSRGELTKTGRRMAEFPLDPMLSKMIVASEKYKCSDEVISIASMLSI--GNSIFYRPKDKQVH
          L.AL.ALN.RGELTKTGRRMAEFPLDPMLSK.IVASEKY.CS.EVI.IA.MLS...G...FYRPKDKQVH
Retrocopy LYALGALNGRGELTKTGRRMAEFPLDPMLSKAIVASEKYRCSEEVITIAAMLSAGPGSAVFYRPKDKQVH

Parental  ADNARLNFHTGNVGDHIALLNVYNSWKETDFSTQWCYENYIQVRSMKRARDIRDQLEGLLERVEIEVCSN
          AD.AR..FH.G.VGDH.ALLNVYN.WKE...S.QWC.E...Q.R.MKRARD.RDQLE.LLERVEIE.CS.
Retrocopy ADAARQAFHAGDVGDHVALLNVYNAWKESGYSPQWCRESFVQSRTMKRARDVRDQLEALLERVEIEPCSG

Parental  ASDLDAIKKAITSGFFHHSARLQKNGSYRTVKNPQTVFVHPSSGLAQLLPRWVIYHELVLTTKEYMRQVT
          A.D..AI.KAIT.G.F...ARLQK.GSYR.VK..QTVFVHPSSG..Q.LPRW..YHELV.T.KEYMRQVT
Retrocopy AGDPNAIRKAITAGYFRNAARLQKDGSYRAVKSRQTVFVHPSSGMEQVLPRWIVYHELVQTSKEYMRQVT

Parental  ELKPEWLVEIAPHYYQLKDVDD-SGSKKLPKG
          ELKPEWL.EIAPHYYQ.KD.D.....KKL.KG
Retrocopy ELKPEWLLEIAPHYYQCKDIDEHEQKKKLAKG

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_4 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 16 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027162	1 retrocopy	retro_oind_65,
Brassica oleracea	Bo5g087070	1 retrocopy	retro_bole_7,
Brassica rapa	Bra010168	1 retrocopy	retro_brap_26,
Brachypodium distachyon	BRADI1G61220	1 retrocopy	retro_bdis_4 ,
Glycine max	GLYMA06G21821	1 retrocopy	retro_gmax_7,
Leersia perrieri	LPERR08G09260	1 retrocopy	retro_lper_14,
Hordeum vulgare	MLOC_5589	1 retrocopy	retro_hvul_14,
Oryza meridionalis	OMERI08G09070	1 retrocopy	retro_omer_5,
Oryza nivara	ONIVA08G11780	1 retrocopy	retro_oniv_26,
Oryza punctata	OPUNC08G10350	1 retrocopy	retro_opun_23,
Oryza glaberrima	ORGLA08G0098600	1 retrocopy	retro_ogla_26,
Oryza rufipogon	ORUFI08G12410	1 retrocopy	retro_oruf_44,
Solanum tuberosum	PGSC0003DMG402024649	1 retrocopy	retro_stub_33,
Prunus persica	PRUPE_ppa000714mg	1 retrocopy	retro_pper_32,
Sorghum bicolor	Sb04g022460	1 retrocopy	retro_sbic_37,
Setaria italica	Si021302m.g	1 retrocopy	retro_sita_41,