RetrogeneDB ID: retro_taes_170

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_2AL_scaff_6420033:5927..6725(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: TRAES3BF058700080CFD_g
• Aliases: None
• Description: None

Sequence

>retro_taes_170
GAATCAAAAGTGGCTCTAGTTTACGGCCAGATGAATGAACCGCCTGGAGCTCGTATGAGAGTTGGTTTGACTGCCCTAAC
TATGGCGGAATATTTCCGAGATGTTAATGAACAAGACGTACTTCTATTTATCGACAATATCTTCCGTTTCGTCCAAGCAG
GATCCGAAGTATCGGCCTTATTGGGTAGAATGCCTTCTGCTGTCGGTTATCAACCTACCCTGAGTACCGAAATGGGTACT
TTACAAGAAAGAATTACTTCTACCAAAGAAGGGTCCATAACTTCTATTCAAGCAGTTTATGTACCTGCAGACGATTTGAC
CGACCCTGCTCCTGCTACGACATTTGCACATTTAGATGCTACTACCGTACTATCAAGAGGATTAGCTGCCAAGGGGATCT
ATCCAGCAGTAGATCCTTTAGATTCAACGTCAACCATGCTTCAACCTCGGATCGTTGGTGAGGAACATTACGAAACTGCG
CAAAGAGTTAAGCAAACTTTACAACGTTACAAAGAGCTTCAGGACATTATAGCTATCCTTGGGTTGGACGAATTATCCGA
AGAGGATCGTTTAACCGTAGCAAGAGCGCGAAAAATTGAACGTTTCTTATCACAACCTTTTTTTGTAGCAGAAGTATTTA
CCGGTTCTCCAGGTAAATATGTTGGTCTAGCAGAAACCATTAGAGGGTTTCAATTGATCCTTTCCGGAGAATTAGATGGT
CTTCCTGAACAGGCCTTTTATTTGGTAGGTAATATCGATGAAGCTACCGCGAAGGCTATGAACTTAGAAATGGAGAGC

Alignment

ORF - retro_taes_170 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.68 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESKCALVYGQMNEPPGARARVGLTGLTVAEHFRDAEGQDVLLFIDNIFRFTQANSEVSALLGRIPSAVGY
          ESK.ALVYGQMNEPPGAR.RVGLT.LT.AE.FRD...QDVLLFIDNIFRF.QA.SEVSALLGR.PSAVGY
Retrocopy ESKVALVYGQMNEPPGARMRVGLTALTMAEYFRDVNEQDVLLFIDNIFRFVQAGSEVSALLGRMPSAVGY

Parental  QPTLATDLGGLQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRQISELGIYPAVDPL
          QPTL.T..G.LQERIT.TK.GSITS.QA.YVPADDLTDPAPATTFAHLDATTVLSR.....GIYPAVDPL
Retrocopy QPTLSTEMGTLQERITSTKEGSITSIQAVYVPADDLTDPAPATTFAHLDATTVLSRGLAAKGIYPAVDPL

Parental  DSTSRMLSPHVLGEAHYNTARGVQKVLQNYKNLQDIIAILGMDELSEDDKLTVARARKIQRFLSQPFHVA
          DSTS.ML.P...GE.HY.TA..V...LQ.YK.LQDIIAILG.DELSE.D.LTVARARKI.RFLSQ...VA
Retrocopy DSTSTMLQPRIVGEEHYETAQRVKQTLQRYKELQDIIAILGLDELSEEDRLTVARARKIERFLSQXXXVA

Parental  EVFTGAPGKYVELKEGVQSFQGVLDGKYDDLSEQAFYMVGGIEEVIAKAEKIAKEN
          EVFTG.PGKYV.L.E....FQ..L.G..D.L.EQAFY.VG.I.E..AKA.....E.
Retrocopy EVFTGSPGKYVGLAETIRGFQLILSGELDGLPEQAFYLVGNIDEATAKAMNLEMES

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_170 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00006p00059970	1 retrocopy	retro_atri_7,
Oryza sativa indica	BGIOSGA017602	2 retrocopies	retro_oind_104, retro_oind_87,
Chlamydomonas reinhardtii	CHLREDRAFT_78348	1 retrocopy	retro_crei_1,
Aegilops tauschii	F775_32946	1 retrocopy	retro_atau_18,
Hordeum vulgare	MLOC_70791	1 retrocopy	retro_hvul_13,
Oryza glaberrima	ORGLA01G0220100	1 retrocopy	retro_ogla_47,
Triticum aestivum	TRAES3BF058700080CFD_g	2 retrocopies	retro_taes_170 , retro_taes_31,