RetrogeneDB ID: retro_bdis_19

Retrocopy location

• Organism: Purple false brome (Brachypodium distachyon)
• Coordinates: 2:48717569..48718382(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BRADI2G48420
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BRADI2G42720
• Aliases: None
• Description: None

Sequence

>retro_bdis_19
ATGGCCGGCGTCGTGGTGGTGTTCGACTTCGACAAGACGATCATCGACGTGGACAGCGACAACTGGGTCGTCGACAGCCT
CGGCGCCACGGAGCTGTTCGACCGGCTCCTCCCCACCATGCCGTGGAACGCCCTCATCGACACGATGATGGGGGAGCTCC
ACGCGCGTGGCAAGACCGTCCACGACGTGGCCGAGGTGCTCAGGTCGGCCCCGATCGACCCGCGCGTCGGGGCCGCCATC
AAGGCCGCCTACGGCCTCGGCTGCGACCTCCGGGTCCTCAGCGACGCCAACGGCTTCTTCATCGAGACCATCCTCGACCA
CCACGGCCTCCGCGGCTGCTTCTCCGAGATCAACACCAACCCGAGCCTCGTGGACGCCGACGGCCGCCTCCGGATCGGCC
CGTACCACGCGACGCCCCACGGGTGCGGCGTCGGCACGTGCCCGCCCAACATGTGCAAGGGCCAGGTGCTCGACCGCATC
CGCGCCTCGTCTGTCGGCAAGCGGGTCATCTACCTGGGCGACGGGCGCGGGGACTACTGCCCGTCGCTGCGGCTCGGGAG
GGACGACTTCGTGATGCCGCGCAGGGGGTTCCCCGTGTGGGACCTCATCTGCGAGAACCCGGGCCTGCTGCAGGCGGAGG
TGCACCCATGGAGCGACGGCGGGGACATGGAGGAGACGCTGCTGCGGCTCGTCAGGAAGGTGCTCGTCGAGGAGAGCAGG
CTGTTGCCGCTCGACTGCTGCAAGCTCGAGTCGCTGCCGGTCGCCGCCGTCCAGGACGGCATGCCCATGCCGCTCGGCGT
CAAGAACGTCTGA

Alignment

ORF - retro_bdis_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.43 %
• Parental protein coverage: 90.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AALVVVFDFDKTIIEWDSDNWVVTKLGATDAFNRLRPTMSWTPLMDRMMGELHEQGKSAEDIRQCLRSAP
          A..VVVFDFDKTII..DSDNWVV..LGAT..F.RL.PTM.W..L.D.MMGELH..GK...D....LRSAP
Retrocopy AGVVVVFDFDKTIIDVDSDNWVVDSLGATELFDRLLPTMPWNALIDTMMGELHARGKTVHDVAEVLRSAP

Parental  LDAHVISAIRTASALGCDLKVVSDANAFFIETVLEHHGILGCFSEINTNPARVDSDGRLRISPFHDPASS
          .D..V..AI..A..LGCDL.V.SDAN.FFIET.L.HHG..GCFSEINTNP..VD.DGRLRI.P.H.....
Retrocopy IDPRVGAAIKAAYGLGCDLRVLSDANGFFIETILDHHGLRGCFSEINTNPSLVDADGRLRIGPYH---AT

Parental  PHGCSL--CPENMCKGKIIERIQATDSAKNKHFIYIGDGKGDYCPSLKLREGDYVMPKENYPLWNLITSN
          PHGC....CP.NMCKG....RI.A..S...K..IY.GDG.GDYCPSL.L...D.VMP....P.W.LI..N
Retrocopy PHGCGVGTCPPNMCKGQVLDRIRA--SSVGKRVIYLGDGRGDYCPSLRLGRDDFVMPRRGFPVWDLICEN

Parental  KQLLKAEVHAWNTGEGLERILLQLVNKLITPPAQVTQVD
          ..LL.AEVH.W..G...E..LL.LV.K...........D
Retrocopy PGLLQAEVHPWSDGGDMEETLLRLVRKVLVEESRLLPLD

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_19 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA001283	1 retrocopy	retro_oind_8,
Brachypodium distachyon	BRADI2G42720	1 retrocopy	retro_bdis_19 ,
Zea mays	GRMZM2G035134	1 retrocopy	retro_zmay_14,
Hordeum vulgare	MLOC_52823	1 retrocopy	retro_hvul_27,
Oryza brachyantha	OB01G31280	1 retrocopy	retro_obra_4,
Oryza glumaepatula	OGLUM01G25430	1 retrocopy	retro_oglu_22,
Oryza meridionalis	OMERI01G19970	1 retrocopy	retro_omer_22,
Oryza nivara	ONIVA01G24910	1 retrocopy	retro_oniv_37,
Oryza punctata	OPUNC01G21870	1 retrocopy	retro_opun_7,
Oryza rufipogon	ORUFI01G24440	1 retrocopy	retro_oruf_27,