RetrogeneDB ID: retro_taes_16

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_4DS_scaff_2265488:0..702(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Traes_4DS_9BC03DB2B
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_4DS_CC9F9317E
• Aliases: None
• Description: None

Sequence

>retro_taes_16
AAGGCCAAGACCGTCTCTGCTGCCAACGACGAGCTCGCCAAGTGGTATGGTCCTGACAGGAGAATCTTCTTGCCGGATGG
TCTTTTGGACAGATCAGAAATCCCAGAGTACTTGAACGGTGAAGTTGCTGGAGACTATGGCTATGACCCATTCGGACTTG
GCAAGAAGCCTGAGAACTTCGCTAAATACCAAGCCTTTGAACTGATTCACGCGAGATGGGCTATGTTGGGAGCAGCTGGT
TGCATCATCCCTGAAGCCTTAAACAAATATGGCGCTAACTGTGGCCCTGAAGCCGTCTGGTTTAAGACTGGTGCTCTTCT
TCTTGATGGAAACACATTGAGCTACTTTGGCAAGAACATCCCAATCAACCTTGTTCTCGCTGTAGTTGCTGAGGTTGTTC
TCCTTGGTGGAGCTGAGTACTACCGAATCACCAACGGCTTGGACTTCGAAGACAAGCTTCACCCAGGAGGCCCATTCGAC
CCTTTGGGACTTGCTAAAGACCCTGAACAAGGAGCTCTTCTCAAGGTTAAAGAGATCAAGAACGGGAGATTGGCCATGTT
TTCCATGTTTGCTTTCTTCATCCAAGCTTATGTTACCGGAGAAGGTCCTGTTGAGAACCTTTCAAAGCATCTAAGTGATC
CTTTCGGAAACAATTTGCTTACCGTCATCGCTGGTACTGCTGAGAGAGCTCCCACTCTCTAA

Alignment

ORF - retro_taes_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88. %
• Parental protein coverage: 78.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDELAKWYGPDRRIYLPNGLLDRSEVPEYLNGEVPGDYGYDPFGLGKKPEDFAKYQAFELIHARWAMLGA
          .DELAKWYGPDRRI.LP.GLLDRSE.PEYLNGEV.GDYGYDPFGLGKKPE.FAKYQAFELIHARWAMLGA
Retrocopy NDELAKWYGPDRRIFLPDGLLDRSEIPEYLNGEVAGDYGYDPFGLGKKPENFAKYQAFELIHARWAMLGA

Parental  AGFIIPEALNKFGANCGPEAVWFKTGALLLDGNTLNYFGNSIPINLILAVVAEVVLVGGAEYYRITNGLE
          AG.IIPEALNK.GANCGPEAVWFKTGALLLDGNTL.YFG..IPINL.LAVVAEVVL.GGAEYYRITNGL.
Retrocopy AGCIIPEALNKYGANCGPEAVWFKTGALLLDGNTLSYFGKNIPINLVLAVVAEVVLLGGAEYYRITNGLD

Parental  FDDKLHPGGPFDPLGLATDPDQAALLKVKEIKNGRLAMFSMLGFFIQAYVTGEGPFENLCAHLSDPFGNN
          F.DKLHPGGPFDPLGLA.DP.Q.ALLKVKEIKNGRLAMFSM..FFIQAYVTGEGP.ENL..HLSDPFGNN
Retrocopy FEDKLHPGGPFDPLGLAKDPEQGALLKVKEIKNGRLAMFSMFAFFIQAYVTGEGPVENLSKHLSDPFGNN

Parental  LLTVISGAAERVPSL
          LLTVI.G.AER.P.L
Retrocopy LLTVIAGTAERAPTL

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_16 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_4DS_CC9F9317E	1 retrocopy	retro_taes_16 ,