RetrogeneDB ID: retro_bdis_36

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:25652029..25653241(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G26880
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G56980
• Aliases: None
• Description: None

Sequence

>retro_bdis_36
ATGATGATGAATCCGGAGCTGATGCGTCTGGCGCAGGAGCAGATGAGCCGCATGTCCCCCTCCGTCCTCGCCAGGATGCA
GCAGCAGATCATGGCCAATCCTGACCTAATCAAGATAGCATCCGAGAACATCAAGAACATGAGAACCGAGGACTTCGAAC
GAGCCGGTCAGCAGCTGAATCAAACAAGCCCAGAGGAAATGCTCGATATGATCGCAAAGATCGCCAGCGCTAAGCCCGAG
GAATTCGCCGCCATGAAGGCCCAGGCCGACGCCCAGATGTCATACGCGGTATCTGGTGCCAAGATGTTAAAGCAGCAGGG
GAACGAGCTCCATGGCCGCGGGCGGTACGCTGATGCTGCAGCCAAGTACAAGCTCGCCAAGGATAACTTGAAGAACATAC
CATTGGCATCGGCGGCTGGGCAGACTCTGCAGTCGCAGTGCGCCGTTAACTTGATGGCTTGTTATCTGAAAACAGGGAAG
TTTGTGGAATGTGTAAATGAAGGTTCAGAGGTTCTGAGTTACGACGCTAGCAATGTCAAAGCGTATTACCGGAGGGGCCA
GGCCTACAAAGAACTAGGAAACCTGGAAGCTGCTGTTTCCGACTTGAGTAAAGCCCAGGGAATTTGTCCAGAGGATAAAA
CAATTGCTGAGGTTCTGAGAGACGCTGAAGAAAAACTTGCAATGGAAGGGGGTGAAGCGAACCTGCCAAGTAAAGGAGTT
GTGATTGAAGAAATTGTAGAAGAAGATGCTTCAGAGCCGTCAAGCACTGATCAACGGAGTTCATCTAGTGGGTACTCTGT
TTCAGACCCACTTGAAGGAGCAGGAAACTCAGCACAATCGGAGTCTTTAGAAGATTTAAGAAATGATCCTGTTACAGTCA
ATCTGCAAGAAGCCATGAGAAAATCTATGAAAGACCCTGCAATGCGGCAGATGATGGCGTCCACGATGAAGAACATGAGT
CCTGATCTGCTGGAGATGATGAGCGAGCAGTTTGGTATGAAGCTGTCGAAGAAGGACGCTGCCAAGGCTCAACAAGCTAT
GTCTTCATTATCTCAGGGCGATTTAGACAGAATGATGAATTTGGTGGATAGAGCACAGCAAGGAGTAGAAATAGCAAAGA
AGACAAAGAACTGGCTGTTTGGCAGGAAAGGATTGGTCCTTCCTATTGCCATGCTCGCCGTGGCCTTCATTCTGCATTGG
CTTGGATTCTAG

Alignment

ORF - retro_bdis_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.79 %
• Parental protein coverage: 51.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMDPEMMRLAQEQMRRMSPDDLARMQQQMMANPDLIKLASESMKNMRTEDFKRAAQQLNQTRPEEMLNMT
          MM.PE.MRLAQEQM.RMSP..LARMQQQ.MANPDLIK.ASE..KNMRTEDF.RA.QQLNQT.PEEML.M.
Retrocopy MMNPELMRLAQEQMSRMSPSVLARMQQQIMANPDLIKIASENIKNMRTEDFERAGQQLNQTSPEEMLDMI

Parental  EKIANAKPEEFAAMKAQADAQMSYAISGAKMLKQQGNELHSRGQYSDAAAKYKLAKDNMKNVP--SAAGQ
          .KIA.AKPEEFAAMKAQADAQMSYA.SGAKMLKQQGNELH.RG.Y.DAAAKYKLAKDN.KN.P..SAAGQ
Retrocopy AKIASAKPEEFAAMKAQADAQMSYAVSGAKMLKQQGNELHGRGRYADAAAKYKLAKDNLKNIPLASAAGQ

Parental  NLQLLCALNLMSCYLKSGKFVECINEGSEVLTYDSNNVKAFYRRGQAYKELGNLEAAVADLSKAHEISPE
          .LQ..CA.NLM.CYLK.GKFVEC.NEGSEVL.YD..NVKA.YRRGQAYKELGNLEAAV.DLSKA..I.PE
Retrocopy TLQSQCAVNLMACYLKTGKFVECVNEGSEVLSYDASNVKAYYRRGQAYKELGNLEAAVSDLSKAQGICPE

Parental  DETIAEVLRDTEEKLATEGGVANLP-KGVVIEEVVEEDASELSCT-QRSLSSGYTVSQPHEGAENPRQSE
          D.TIAEVLRD.EEKLA.EGG.ANLP.KGVVIEE.VEEDASE.S.T.QRS.SSGY.VS.P.EGA.N..QSE
Retrocopy DKTIAEVLRDAEEKLAMEGGEANLPSKGVVIEEIVEEDASEPSSTDQRSSSSGYSVSDPLEGAGNSAQSE

Parental  SSESLRNDPATI
          S.E.LRNDP.T.
Retrocopy SLEDLRNDPVTV

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_36 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G56980	1 retrocopy	retro_bdis_36 ,
Aegilops tauschii	F775_31516	1 retrocopy	retro_atau_10,
Hordeum vulgare	MLOC_56431	1 retrocopy	retro_hvul_94,
Oryza barthii	OBART07G03860	1 retrocopy	retro_obar_28,
Oryza glaberrima	ORGLA07G0032400	1 retrocopy	retro_ogla_27,