RetrogeneDB ID: retro_taes_48

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: 4B:306374993..306376439(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Traes_4BL_D9458F705
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_4DL_0D0BF450D
• Aliases: None
• Description: None

Sequence

>retro_taes_48
ATGGCAAACGATTCTTGGCGCGTCCGAGTGATTCGCAGGAGCACCGTCAAGGCCTCCATTACGCGGCCCGGCGCCGTGCT
CCCCGTCTCCAACCTCGATCTGTTGTATTACCCCATGCCGCTCTCGATGGTCTGCGCCTACCGCAGGCCCTCGGCCGGCG
GTGGCTTCGCAGACGTCGTGGCCGCCTTCGACACCAAGCTGCCGTCCCTGCTGGACCACTTCTTTCCGCTCGCCGGCCGC
ATCGTTGCCAACCCGCGCTCGGGGCTCCCGGAGGTGCACTGTGACAACCAGGGCGCGGAGCTCGTCGTCGGCGAGGCCGG
TGTGGCGCTGGCCGGCCTGGACTTCCGCGACCTGGACGCGTCGCTGGCGAGGGTCGGCGTCCCCGTCCAGTACGCCGCGG
ACGTCGCGCTGTCGGTGCAGCTGCTGTCGTTCGCCTGCGGCGGCTTCGTTGTGGCCTGGAGCACCAACCACGGCCTCGCG
GACGGGTGCGCGCTCTGCATGATCGTCGACGCGTGGTCTCAGCTCGCGCGGTCCGGGACGATCGTCGCCGCCCCGAACTA
CGACCGCTCCGTGTTCCGCCCCCGTGCCGCGCCGTCGTACGGCCCTTCGGTGGGCGATCTGTTCATGCCGTTGGCGAGCG
AGCGTCTCGTCAACGCCCTCACGGCCAGGGGCTCCTTGGTCGGCCGCACCTACTACGTCGAGGAGCGGGACCTCACCATG
CTGCGCGCGCAGGCGAGCGCCGACGGGGAGCGCGGCGCGAGCCGCGTCGAGGCGGTGTCTGCGTACCTCTGGAAGGTGTT
CGCCGCCACCGTGGGCTCGTCCGACGACAGTTGCCGCATGGGCTGGTGGGTGAACGGGCGACGGCGTCTCACAGCCGCGC
CGGAGGAAGCCATGCGCAACTACGTCGGCAACGTCACGACGTTCGCGGTGGTGGAGGCGAGCGTGGACGCGATCCAGCGG
CGGCCGCTCCCGGAGATCGCGTCGATGGTGCGCGAGTCGATCAGGTCGACGGCCACGGACGAGCACTTCCAGGAGCTAGT
GGACTGGGTGGAGGAGCACAAGGGCAATGGCAATGGCAATGGCAAGGCTGCGGTCAACAAGTTCGTGGAGACAGCAACCG
TCGGGCTGGGCAGCCCGGCGATGGGCGTGACGTCGTTCACGTCCTTCAGCGTCGACACGGACTTGGGATTCGGGCACGCC
GCCGTAGCGATGCCGACGTGGGCGGACTGCGGTAGGCTGTGCTCCGGCTTCGTGAAGATCATGGCGCGTCCGGAGGGTGA
CGGTGGTGGTGGTGGTTCCTGGATCTTCGGCATGTCCATTTGGCCCAAGCTCGCCGCCGCGCTGGACTCGGACGAGCAGC
GCATCTTCAAGCCTCTCACCGCCGACTATCTCGGCCTCATGCGCTGGACTCGGTCGCATGCAGCATGCATGCATGATGCT
CATTAA

Alignment

ORF - retro_taes_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.72 %
• Parental protein coverage: 99.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANDSSRVRVVRRSTVKASVTRPDTVLPVSNLDLLYYPMPLSMVCAYRRPSAGGGFVDVVAAFEAKLSSL
          MANDS.RVRV.RRSTVKAS.TRP..VLPVSNLDLLYYPMPLSMVCAYRRPSAGGGF.DVVAAF..KL.SL
Retrocopy MANDSWRVRVIRRSTVKASITRPGAVLPVSNLDLLYYPMPLSMVCAYRRPSAGGGFADVVAAFDTKLPSL

Parental  LDHFFPLAGRIVANPRSGLPEVHCDNQGAELVVGEVGLALGSLDFGDLDASLARVGVPVQYGADVALSVQ
          LDHFFPLAGRIVANPRSGLPEVHCDNQGAELVVGE.G.AL..LDF.DLDASLARVGVPVQY.ADVALSVQ
Retrocopy LDHFFPLAGRIVANPRSGLPEVHCDNQGAELVVGEAGVALAGLDFRDLDASLARVGVPVQYAADVALSVQ

Parental  LVSFSCGGFVVVWGTNHGLADGCALYMIVDAWSELARSGTIVAAPNYDRSVFCPRAAPSYGPSVGELFMP
          L.SF.CGGFVV.W.TNHGLADGCAL.MIVDAWS.LARSGTIVAAPNYDRSVF.PRAAPSYGPSVG.LFMP
Retrocopy LLSFACGGFVVAWSTNHGLADGCALCMIVDAWSQLARSGTIVAAPNYDRSVFRPRAAPSYGPSVGDLFMP

Parental  LVSERLVNALTAGGSMLGRTYYVEERDIAMLRAQASGDGERGASRVEAVSAYLWKVLAATVGSSDESCRM
          L.SERLVNALTA.GS..GRTYYVEERD..MLRAQAS.DGERGASRVEAVSAYLWKV.AATVGSSD.SCRM
Retrocopy LASERLVNALTARGSLVGRTYYVEERDLTMLRAQASADGERGASRVEAVSAYLWKVFAATVGSSDDSCRM

Parental  GWWVNGRRCLTTAPEEAMRNYVGNVTTFAVAEASVEAILRRPLPEIASMVRGSIRSTATDEHFQELVDWV
          GWWVNGRR.LT.APEEAMRNYVGNVTTFAV.EASV.AI.RRPLPEIASMVR.SIRSTATDEHFQELVDWV
Retrocopy GWWVNGRRRLTAAPEEAMRNYVGNVTTFAVVEASVDAIQRRPLPEIASMVRESIRSTATDEHFQELVDWV

Parental  EEHKGKGKDNGKAAV-KFVETATVGLGSPAMGVTSFASFSVDTDFGFGHAAVAMPTWVDCGRLCSGFVKI
          EEHKG.G..NGKAAV.KFVETATVGLGSPAMGVTSF.SFSVDTD.GFGHAAVAMPTW.DCGRLCSGFVKI
Retrocopy EEHKGNGNGNGKAAVNKFVETATVGLGSPAMGVTSFTSFSVDTDLGFGHAAVAMPTWADCGRLCSGFVKI

Parental  MARPGGDGGGGGSWIFGMSVWPKLAAALDSDEQRIFKPLTAEYLGLM
          MARP.GDGGGGGSWIFGMS.WPKLAAALDSDEQRIFKPLTA.YLGLM
Retrocopy MARPEGDGGGGGSWIFGMSIWPKLAAALDSDEQRIFKPLTADYLGLM

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_48 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Triticum aestivum	Traes_4DL_0D0BF450D	2 retrocopies	retro_taes_48 , retro_taes_89,