RetrogeneDB ID: retro_taes_227

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_7DS_scaff_3965846:1580..2508(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_5BL_8D494D60C
• Aliases: None
• Description: None

Sequence

>retro_taes_227
GTCAGCGAGGAGGACGGATACGCCGTGAATGATGTGCTCGCACAAAGCAGACACCGTGATGGTTCTATATACAGGGGTGT
GGATTCACTTTGGTGGAAGAGAGAGTATCGTATTGCGGACCGTACAGAGACGCGGCTCGAGGCAATGACACTGTCAAATC
CCACAAATTGCATAATCCACGATGGAACTTGCATAACTCATGATGCTTTTAGCATGCTGCAATTTTACTCGGTGGAGTTG
GCTGAAGTTCCCGTGGATGGTGGTTTAGTAGAGCTGTACGGATACATAGCGGTGCGGGATGATATTGATCCATTGCTTAA
TTATGTCGTCAATATGCAGGGATGATCCCATCGTTGTGGAGGAGGGTTCTCTCATCCACATGACTGGCCCTAAGCGAGGG
ATAGATATCGCGGATAGTGTTCTAATTGAATATGACATGAGGATCAAGGCTGGTGAAGAAGAAAAGGATGACATACAATT
GATTGATGGTGCATCAATCATAGGCCACGAAGGCAAATGGGATCAGCCATTCACATTTCGCATTCCTGGTGATGGTGGTG
CGGTTGACATAATTTTATCATGTCTTTTATATGCAGTTGAGGCGACTGTAGAGGTTCTTATATCGGAAGTTCAAAGCAGT
TTTAATTTGTCTATCGAATGTTTAAGTAGTGGGTTTGGTGAGGAAATCCGGCTCTTCGATGGTGCGGTTGCTGAATCACG
TGGCTTAAAGAGGTCTGTGGTTGCTGTATTGAAAAATTCTTCGATAGATTTGGAGTTCAAGGTTGCTGCACTGTCATCCC
GTTCCGACCACCAACATTGTTGTTCTTTCAAGGCTAAAACGCATGGGCATGATAATCAAGAAATAAAGAATGATTTTGCG
GTAATCTCGGTGAAGGTGACTTGGTCGACGTTGCCTGCTAGCTTATCT

Alignment

ORF - retro_taes_227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.51 %
• Parental protein coverage: 64.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSDDEGYSVNGILAKSRHRDGSIYRDMDLYDWKKHYRIADRIETRLEAMTLSDPAANCNVHDGICTRHFA
          .S...GY.VN..LA.SRHRDGSIYR..D...WK..YRIADR.ETRLEAMTLS.P..NC..HDG.C..H.A
Retrocopy VSEEDGYAVNDVLAQSRHRDGSIYRGVDSLWWKREYRIADRTETRLEAMTLSNP-TNCIIHDGTCITHDA

Parental  RSMLQIYSLELAKIPVD-GLVELYGYVAVRDDLDPLLNYVVNIS-RDDPVIVEQGSLINMIGPKRGIDMA
          .SMLQ.YS.ELA..PVD.GLVELYGY.AVRDD.DPLLNYVVN....D..V..E.GSLI.M.GPKRGID.A
Retrocopy FSMLQFYSVELAEVPVDGGLVELYGYIAVRDDIDPLLNYVVNMQ>DDPIVVEE-GSLIHMTGPKRGIDIA

Parental  DHALLEYDMKIKSGEQEKNDLQLIDGASFIGPLGSWDQPCTFHIAGDCGSVDITLSRLLKAVEATVEVLI
          D..L.EYDM.IK.GE.EK.D.QLIDGAS.IG..G.WDQP.TF.I.GD.G.VDI.LS.LL.AVEATVEVLI
Retrocopy DSVLIEYDMRIKAGEEEKDDIQLIDGASIIGHEGKWDQPFTFRIPGDGGAVDIILSCLLYAVEATVEVLI

Parental  LEVKSSFSLSVGCLASGFNEEIQLFDGTIADSQGLKRSVVAVMKNSSIDLKFKVGALSSSSD-QHCCSFK
          .EV.SSF.LS..CL.SGF.EEI.LFDG..A.S.GLKRSVVAV.KNSSIDL.FKV.ALSS.SD.QHCCSFK
Retrocopy SEVQSSFNLSIECLSSGFGEEIRLFDGAVAESRGLKRSVVAVLKNSSIDLEFKVAALSSRSDHQHCCSFK

Parental  AKMHGHDIEEIKTDFALILVKVIWSTLPRGFS
          AK.HGHD..EIK.DFA.I.VKV.WSTLP...S
Retrocopy AKTHGHDNQEIKNDFAVISVKVTWSTLPASLS

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_227 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Triticum aestivum	TRAES3BF098800030CFD_g	1 retrocopy	retro_taes_134,
Triticum aestivum	Traes_5BL_8D494D60C	3 retrocopies	retro_taes_154, retro_taes_158, retro_taes_227 ,