RetrogeneDB ID: retro_taes_14

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_4DS_scaff_818065:1..646(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Traes_4DS_EBDF63E02
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TRAES3BF044200210CFD_g
• Aliases: None
• Description: None

Sequence

>retro_taes_14
ATGGCTCAAACCATGCTGCTTACTTCGGGAGTTTCTGCGAACCAATTCTTAAGGAACAAGAACCCTCTCGCTCAGCCCAA
AGTTCACCATTTCTTCCTCTCGGGAAACTCTCATGTTGTTCTACCATCTCGAAGACCGTCATTAGTACCTCTTGCCATCT
TCAAACCCAAAACCAAAGCTGCTCCCAAAAAGGTTGAGAAGGTGAAGCCAAAGGTTGAAGACGGTATCTTCGGAACATCT
GGTGGGATAGGTTTCACGAAGCAGAACGAGCTCTTTGTGGGTCGTGTTGCTATGATCGGTTTCGCTGCATCGTTGCTGGG
TGAGGCGTTGACAGGGAAAGGTATATTAGCACAGTTGAATCTGGAGACAGGGATACCGATTTACGAAGCAGAGCCATTAC
TTCTCTTCTTCATATTGTTCACTCTGTTGGGTGCTATCGGAGCTCTTGGGGACAGAGGAAAATTCGTCGACGATCCTCCC
ACCGGACTTGAGAAAGCCGTCATTCCTCCCGGCAAAGGCGTCCGATCTGCCCTCGGTCTTAAAGAACAAGGTCCATTGTT
TGGGTTCACGAAGGCAAACGAGTTGTTCGTAGGAAGATTGGCACAGTTGGGAATAGCATTTTCATTGATAGGAGAGATTA
TAACC

Alignment

ORF - retro_taes_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.3 %
• Parental protein coverage: 63.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVRTMALFGKSKTKAAPAKKVAAPKPKTEDGIFGTSGGIGFTKENELFVGRVAMIGFAASILGEAITGKG
          S....A.F.K.KTKAAP.KKV...KPK.EDGIFGTSGGIGFTK.NELFVGRVAMIGFAAS.LGEA.TGKG
Retrocopy SLVPLAIF-KPKTKAAP-KKVEKVKPKVEDGIFGTSGGIGFTKQNELFVGRVAMIGFAASLLGEALTGKG

Parental  ILSQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGRFVDEQPTTGLDKAVIAPGKGFRSALGLSEG
          IL.QLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRG.FVD..P.TGL.KAVI.PGKG.RSALGL.E.
Retrocopy ILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGKFVDD-PPTGLEKAVIPPGKGVRSALGLKEQ

Parental  GPLFGFTKSNELFVGRLAQLGIAFSIIGEIIT
          GPLFGFTK.NELFVGRLAQLGIAFS.IGEIIT
Retrocopy GPLFGFTKANELFVGRLAQLGIAFSLIGEIIT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Triticum aestivum was not studied using RNA-Seq expression data.

ChIP-Seq

Triticum aestivum was not studied using ChIP-Seq data.

EST

Triticum aestivum was not studied using EST data.

TSS

Triticum aestivum was not studied using FANTOM5 data.

Lab

retro_taes_14 was not experimentally validated.

Homology

Retrocopy orthology:

Triticum aestivum 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004881	1 retrocopy	retro_oind_4,
Oryza longistaminata	KN538837.1_FG036	1 retrocopy	retro_olon_20,
Oryza barthii	OBART01G38720	1 retrocopy	retro_obar_4,
Oryza nivara	ONIVA01G43550	1 retrocopy	retro_oniv_35,
Oryza glaberrima	ORGLA01G0325500	1 retrocopy	retro_ogla_5,
Oryza rufipogon	ORUFI01G42080	1 retrocopy	retro_oruf_10,
Oryza sativa japonica	OS01G0869800	1 retrocopy	retro_osat_18,
Triticum aestivum	TRAES3BF044200210CFD_g	1 retrocopy	retro_taes_14 ,