RetrogeneDB ID: retro_taes_18

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_4DS_scaff_1936931:17..455(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Traes_4DS_F5F7EE21A
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_2BL_AFF8E770F
• Aliases: None
• Description: None

Sequence

>retro_taes_18
ATGTGTGCTTCTGTCGGAATCCAAGGCATCGCTTGGGCTTTCGGTGGTATGATCTTCGCTCTCGTCTACTGCACCGCTGG
TATCTCCGGTGGACACATCAACCCAGCAGTCACGTTCGGTCTGTTCTTGGCGCGGAAGCTTTCGCTTACACGAGCTGTGT
ACTACATAGTGATGCAGTGCTTAGGAGCTATCTGTGGAGCTGGTGTGGTCAAGGGGTTCCAACCAAAGCAGTACCAAGCT
CTTGGAGGTGGAGCCAACACTGTAGCTCATGGTTACACCAAAGGAAGTGGTCTCGGAGCTGAGATCATTGGAACCTTTGT
CCTCGTTTACACCGTCTTCTCCGCTACTGATGCTAAGAGAAACGCTCGTGACTCTCATGTTCCGATTCTTGCACCTCTCC
CTATTGGATTCGCTGTGTTCTTGGTCCACTTGGCAACC

Alignment

ORF - retro_taes_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.72 %
• Parental protein coverage: 50.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CATVGIQGIAWSFGGMIFALVYCTAGISGGHINPAVTFGLFLARKLSLTRAVFYIIMQCLGAICGAGVVK
          CA.VGIQGIAW.FGGMIFALVYCTAGISGGHINPAVTFGLFLARKLSLTRAV.YI.MQCLGAICGAGVVK
Retrocopy CASVGIQGIAWAFGGMIFALVYCTAGISGGHINPAVTFGLFLARKLSLTRAVYYIVMQCLGAICGAGVVK

Parental  GFQQGLYMGNGGGANVVAPGYTKGSGLGAEIIGTFVLVYTVFSATDAKRNARDSHVPILAPLPIGFAVFL
          GFQ...Y...GGGAN.VA.GYTKGSGLGAEIIGTFVLVYTVFSATDAKRNARDSHVPILAPLPIGFAVFL
Retrocopy GFQPKQYQALGGGANTVAHGYTKGSGLGAEIIGTFVLVYTVFSATDAKRNARDSHVPILAPLPIGFAVFL

Parental  VHLAT
          VHLAT
Retrocopy VHLAT

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_18 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA04G0185500	1 retrocopy	retro_ogla_3,
Triticum aestivum	Traes_2BL_AFF8E770F	1 retrocopy	retro_taes_18 ,