RetrogeneDB ID: retro_taes_27

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_4DS_scaff_2266576:1..544(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Traes_4DS_D277993E3
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_5AL_31CDB68F2
• Aliases: None
• Description: None

Sequence

>retro_taes_27
AAAGCTGGAACTTATGATCCTAAGAAACTCCTTGGAGTTACTACACTTGATGTTGCTCGTGCCAACACATTTGTGGCTGA
AGTTCTTGGCCTTGATCCAAGAGAAGTCGATGTACCAGTGGTTGGAGGACATGCTGGAGTCACAATATTGCCACTGTTGT
CACAGGTTAAACCTCCAAGCAGCTTCACACCTTCAGAGATTGAGTACCTCACAAACAGGATTCAAAACGGTGGAACTGAA
GTTGTGGAGGCAAAAGCTGGAGCTGGATCTGCAACACTTTCAATGGCATATGCTGCAGCCAAGTTTGCAGATGCTTGCCT
TCGCGGGTTAAGAGGAGATGCGAATGTCATTGAATGCTCTTTTGTTGCTTCACAGGTGACAGAGTTAGCATTCTTTGCAA
CCAAAGTGCGTCTTGGACGTACAGGAGCAGAGGAAGTGTTCCAGCTTGGGCCCTTGAACGAATATGAAAGGGTTGGTCTG
GAGAAAGCAAAAGAAGAACTAGCTGGAAGTATTCAGAAAGGTGTCGACTTCATCAGGAAATGA

Alignment

ORF - retro_taes_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.78 %
• Parental protein coverage: 66.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RAGTYCPKRLLGVTTLDVARANTFVAEVLGVDPREVNVPVVGGHAGVTILPLLSQVSPPCSFTPDEISYL
          .AGTY.PK.LLGVTTLDVARANTFVAEVLG.DPREV.VPVVGGHAGVTILPLLSQV.PP.SFTP.EI.YL
Retrocopy KAGTYDPKKLLGVTTLDVARANTFVAEVLGLDPREVDVPVVGGHAGVTILPLLSQVKPPSSFTPSEIEYL

Parental  TNRIQNGGTEVVEAKAGAGSATLSMAFAAAKFADACLRGMRGDAGIVECSYVASEVTELPFFASKVRLGR
          TNRIQNGGTEVVEAKAGAGSATLSMA.AAAKFADACLRG.RGDA...ECS.VAS.VTEL.FFA.KVRLGR
Retrocopy TNRIQNGGTEVVEAKAGAGSATLSMAYAAAKFADACLRGLRGDANVIECSFVASQVTELAFFATKVRLGR

Parental  GGAEEILPLGPLNDFERAGLEKAKKELSESIQKGVSFMNK
          .GAEE...LGPLN..ER.GLEKAK.EL..SIQKGV.F..K
Retrocopy TGAEEVFQLGPLNEYERVGLEKAKEELAGSIQKGVDFIRK

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_27 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT5G09660	1 retrocopy	retro_atha_10,
Brassica rapa	Bra009397	1 retrocopy	retro_brap_19,
Prunus persica	PRUPE_ppa007722mg	1 retrocopy	retro_pper_5,
Triticum aestivum	Traes_5AL_31CDB68F2	1 retrocopy	retro_taes_27 ,