RetrogeneDB ID: retro_taes_39

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_4DS_scaff_2264118:127..811(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Traes_4DS_F057D6C80
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_3AS_D41508CC4
• Aliases: None
• Description: None

Sequence

>retro_taes_39
ATGTGGTACTTCTTGAACGTGATTTTCAACATCCTTAACAAGAAGATCTACAATTACTTCCCTTACCCCTATTTTGTATC
GGTTATTCACTTGTTCGTTGGAGTTGTCTACTGCTTGGTGAGCTGGTCCGTGGGTCTTCCTAAACGGGCTCCAATTAACT
CGGACATCCTCAAGGTATTGATACCAGTTGCAGTGTGTCATGCCATAGGCCATGTTACTAGCAACGTGTCCTTCGCAGCC
GTCGCTGTGTCCTTCACTCACACCATAAAAGCACTGGAGCCATTCTTCAATGCGTCTGCTTCTCAGTTCCTTCTTGGACA
ACCGATCCCCATAACACTATGGTTGTCTTTAGCTCCTGTTGTACTCGGAGTTGCAATGGCTTCACTCACTGAGTTGTCAT
TCAACTGGCTTGGTTTCATCAGCGCCATGATATCAAACATCTCTTTCACTTACAGAAGCATCTTCTCCAAGAAAGCCATG
ACTGATATGGACAGTACAAATGTCTACGCTTACATCTCCATCATCGCTCTCTTCGTCTGCCTTCCTCCTGCCATCATCGT
CGAAGGGCCTCAACTGTTGAAGCACGGTTTCAATGACGCGATTGCTAAAGTGGGAATGACTAAGTTCATCTCTGATCTCT
TCTGGGTTGGAATGTTTTACCATCTCTACAATCAGTTGGCTACT

Alignment

ORF - retro_taes_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 77.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MWYFLNVIFNILNKKIYNYFPYPYFVSVIHLLVGVVYCLLSWAVGLPKRAPINATLLKLLFPVALCHALG
          MWYFLNVIFNILNKKIYNYFPYPYFVSVIHL.VGVVYCL.SW.VGLPKRAPIN...LK.L.PVA.CHA.G
Retrocopy MWYFLNVIFNILNKKIYNYFPYPYFVSVIHLFVGVVYCLVSWSVGLPKRAPINSDILKVLIPVAVCHAIG

Parental  HVTSNVSFATVAVSFAHTIKALEPFFNAAATQFVLGQTVPLSLWLSLAPVVLGVSMASLTELSFSWKGFI
          HVTSNVSFA.VAVSF.HTIKALEPFFNA.A.QF.LGQ..P..LWLSLAPVVLGV.MASLTELSF.W.GFI
Retrocopy HVTSNVSFAAVAVSFTHTIKALEPFFNASASQFLLGQPIPITLWLSLAPVVLGVAMASLTELSFNWLGFI

Parental  NAMISNISFTYRSIYSKKAMTDMDSTNVYAYISIIALVVCIPPALIIEGPQLMQYGLNDAIAKVGMTKFV
          .AMISNISFTYRSI.SKKAMTDMDSTNVYAYISIIAL.VC.PPA.I.EGPQL...G.NDAIAKVGMTKF.
Retrocopy SAMISNISFTYRSIFSKKAMTDMDSTNVYAYISIIALFVCLPPAIIVEGPQLLKHGFNDAIAKVGMTKFI

Parental  SDLFLVGLFYHLYNQIAT
          SDLF.VG.FYHLYNQ.AT
Retrocopy SDLFWVGMFYHLYNQLAT

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_39 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Triticum aestivum	Traes_3AS_D41508CC4	1 retrocopy	retro_taes_39 ,