RetrogeneDB ID: retro_bdis_12

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 3:38493854..38495384(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI3G36210
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI1G44430
• Aliases: None
• Description: None

Sequence

>retro_bdis_12
ATGATCGCATCCCTCACGGTGCTCACGCTCTTGTTGCTCCCATTCATGGCGGCGGCGGCGGCTGAGCTGGACTATAAGAA
GGCGCTCCACAGCAGCCTGCTCTACTTCGAGGCGCAGCGGTCGGGCCACCTGCCGTACAACCAGCGCGTGCACTGGCGCG
GCCACTCGGGCCTGGCCGACGGGCTTCAGCAAGGCGTGGACCTTGTGGGCGGCTACTACGACGCCGGCGACAACGTCAAG
TTCGGGCTCCCCATGGCGTTTACGGTGACCATGCTGTCCTGGAGCGCCATGGAGTTCGCGGACGACATCGCGAGCGCCGG
GGCCGACGGCGAGGAGTGGCGGCACGTCCTGGAGGCCATCAAGTGGGGCACGGACTACTTCATCAAGGCCCACACGGCCC
CTGACGAGCTGTGGGCCGAGGTGGGCGACGGCGACACGGACCACTACTGCTGGCAGCGGCCCGAGGACATGACCACGTCC
CGGCAGGCCTACAAGGTGGACCGCGACAACCCCGGGTCGGACCTCGTGGGCGAGACCGCCGCCGCGCTCGCCGCGGCGTC
CATGGTGTTCCGCCGCACGAACCGGCACTACGCGCAGGTGCTCCTCCACCACGCCCGGCAGCTGTTCGAGTTCGGGGACA
CGCACAGGGGCAAGTACGACAGCAGCATCGCCGAGGTGGAGAGCTACTACGCGTCCGTGAGCGGGTACGGGGACGAGATG
CTGTGGGCCGCGCTCTGGCTGCACCGGGCCACGGGCCAGGCCCGGTACCTGGACTACGCCGTGGAGAAGGCGGAGGAGTT
CGGGGGCACCACGTGGGCCATCGACGAGTTCAGCTGGGACGTCAAGTACGCCGGCCTCCAGATCCTAGCCGCCAAGGTGC
TCATGGAAGGGAACCACCGGCCCGAGCAGAAGGCCACGCTGGAGACGTATAAATCCAAGGCGGAGCACTATCTCTGTGCC
TGCCTGGGCAAGAATGGAGAAGCCGGCAATGTCAACCGCACGGCAGGGGGAATGCTCTTCGTCAGGCAGTGGAACAACAT
GCAGTATGTGACCAACGCGGCATTCCTCAGCACCGTCTACTCCCGGTACCTCACGGCAGACCAGAACCAGAACCAGAACC
AGATGATGCGGTGCCCGGATGGGCCGGCGCGGGCCGAGGAGCTGCGGGGCCTTGCCAAGGCCCAGACGGACTACGTCCTG
GGCGACAACCCGGCCGGGGTCAGCTACATGGTCGGGTACGGGCGGCGGTTCCCGCGGCGGGTGCACCACCGGGGCGCGTC
CATCGTGTCCCACCGCGGCGACGCGCGGTTCATCGGGTGCGTCCAAGGGTACGACGGCTGGTTCAGGCGCAAGGGCGCGA
ACCCGAACGTGGTCGTGGGCGCCATTGTCGGCGGGCCGGACGGCCGGGACCGGTTCAGGGACAGCCGCGACAACTACATG
CAGACGGAGGCGTGCACGTACAACACCGCGCCCATGGTCGGCCTCTTCGCGCACCTGCACAGCCAGACGGCGGGCTCCAG
GAGGAAATAA

Alignment

ORF - retro_bdis_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.36 %
• Parental protein coverage: 63.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADAAHDYEEALRKSLVYFEAQRSGRLPHGQRVAWRDHSGLTDGLEQGVDLVGGYYDAGDHVKFGLPMAFT
          A.A..DY..AL..SL.YFEAQRSG.LP..QRV.WR.HSGL.DGL.QGVDLVGGYYDAGD.VKFGLPMAFT
Retrocopy AAAELDYKKALHSSLLYFEAQRSGHLPYNQRVHWRGHSGLADGLQQGVDLVGGYYDAGDNVKFGLPMAFT

Parental  VTMLSWSLLEYGADVAAAG----ELAHALESIKWGTDYFIKAHTQPDELWAEVGDGDTDHYCWQRPEDMT
          VTMLSWS..E...D.A.AG....E..H.LE.IKWGTDYFIKAHT.PDELWAEVGDGDTDHYCWQRPEDMT
Retrocopy VTMLSWSAMEFADDIASAGADGEEWRHVLEAIKWGTDYFIKAHTAPDELWAEVGDGDTDHYCWQRPEDMT

Parental  TSRQAYKVDRDRPGSDVAGETAAALAAASMAFRDTNPHYAHLLLHHAQQLFEFADKYRGKYDSSIAEVKS
          TSRQAYKVDRD.PGSD..GETAAALAAASM.FR.TN.HYA..LLHHA.QLFEF.D..RGKYDSSIAEV.S
Retrocopy TSRQAYKVDRDNPGSDLVGETAAALAAASMVFRRTNRHYAQVLLHHARQLFEFGDTHRGKYDSSIAEVES

Parental  YYASVSGYHDELLWAALWLHRATGRASYLDYVVDNADAFGGTGWAITEFSWDVKYAGVQILATRLLLLQG
          YYASVSGY.DE.LWAALWLHRATG.A.YLDY.V..A..FGGT.WAI.EFSWDVKYAG.QILA....L..G
Retrocopy YYASVSGYGDEMLWAALWLHRATGQARYLDYAVEKAEEFGGTTWAIDEFSWDVKYAGLQILAAK-VLMEG

Parental  EHTERQRETLEGYRAKAEHYVCACMGKNNNENNNVERSPGGMLYVRQWNNMQYVTSAAFLLSVYSGYLT
          .H...Q..TLE.Y..KAEHY.CAC.GK.N.E..NV.R..GGML.VRQWNNMQYVT.AAFL..VYS.YLT
Retrocopy NHRPEQKATLETYKSKAEHYLCACLGK-NGEAGNVNRTAGGMLFVRQWNNMQYVTNAAFLSTVYSRYLT

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_12 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G44430	1 retrocopy	retro_bdis_12 ,