RetrogeneDB ID: retro_atau_18

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Pt:52317..53817(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: EPlATAG00000010080
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_32946
• Aliases: None
• Description: None

Sequence

>retro_atau_18
ATGAGAACCAATCCTACTACTTCTCCTCCCGGGGTTTCCACAATTGAAGAAAAAAGTACAGGTCGTATCGATCAAATTAT
TGGACCCGTGCTGGATGTCACTTTTCCCCCAGGCAAGTTACCTTATATTTATAACGCTTTGGTAGTCCAGAGTAGAGACA
CTGCCGATAAGCAAATTAATGTGACTTGTGAGGTACAACAATTATTAGGAAATAATCGAGTTAGAGCTGTAGCTATGAGT
GCTACGGACGGGTTGATGAGAGGAATGGAAGTGATTGACACGGGAGCTCCTCTCAGTGTTCCGGTCGGTGGAGCTACTCT
CGGACGAATTTTCAACGTTCTTGGGGAGCCTGTTGACAATTTGGGTCCTGTAGATAGTAGTGCAACGTTCCCTATTCATA
GATCTGCGCCTGCCTTTATCGAGTTAGATACGAAATTATCCATCTTTGAAACAGGTATTAAGGTCGTCGATCTTTTAGCT
CCTTATCGACGTGGAGGAAAAATAGGACTATTTGGGGGGGGGGCTGGAGTAGGTAAAACAGTACTGATCATGGAATTAAT
CAATAACATTGCTAAAGCTCATGGGGGCGTATCCGTATTCGGTGGAGTAGGGGAACGGACTCGTGAAGGAAATGATCTTT
ATATGGAAATGAAGGAATCCGGAGTAATTAATGAAAAAAATATTGAGGAATCAAAGGTAGCTCTAGTCTATGGCCAAATG
AATGAACCACCGGGAGCTCGTATGAGAGTTGGTTTAACTGCCCTAACTATGGCGGAATATTTCCGAGATGTTAATAAGCA
AGACGTGCTTTTATTTATCGATAATATCTTTCGTTTTGTTCAAGCAGGATCAGAGGTATCCGCTTTATTAGGGAGAATGC
CCTCCGCAGTGGGTTATCAACCTACTCTTAGTACAGAAATGGGTTCTTTGCAAGAAAGAATTGCTTCTACTAAAAAGGGA
TCTATAACTTCGATTCAAGCAGTTTATGTACCTGCAGACGATTTGACCGACCCTGCCCCTGCCACAACATTTGCACATTT
GGATGCTACTACCGTACTTTCCAGAGGATTAGCTTCCAAGGGTATTTATCCAGCAGTAGATCCTTTAGATTCAACCTCGA
CTATGTTACAGCCTCGGATCGTTGGCAACGAACATTATGAAACTGCGCAAAGAGTTAAGGAAACTTTACAACGTTACAAA
GAACTTCAGGACATTATCGCAATTCTTGGCTTGGATGAATTATCGGAAGAGGATCGTTTAACTGTAGCAAGAGCAAGAAA
AATTGAGCGTTTCTTATCACAACCGTTCTTTGTGGCAGAAGTTTTTACTGGTTCTCCAGGAAAGTATGTTGCTCTTGCGG
AAACTATTAGGGGATTTCAACTAATCCTTTCCGGAGAATTAGACGGCCTACCTGAACAGGCTTTTTATTTGGTGGGTAAC
ATCGATGAAGCTAGCACGAAAGCTATAACCTTAGAAGAGGAGAACAAATCGAAGAAATGA

Alignment

ORF - retro_atau_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.49 %
• Parental protein coverage: 81.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILTALEVLDNSIRLVLEVAQHLGENVVRTIAMDGTEGLVRGQRVLNTGSPITVPVGRATLGRIINVIGEP
          ........D..I....EV.Q.LG.N.VR..AM..T.GL.RG..V..TG.P..VPVG.ATLGRI.NV.GEP
Retrocopy VVQSRDTADKQINVTCEVQQLLGNNRVRAVAMSATDGLMRGMEVIDTGAPLSVPVGGATLGRIFNVLGEP

Parental  IDHKGDIKTNSYLPIHREAPAFVEQATEQQILVTGIKVVDLLAPYQRGGKIGLFGG-AGVGKTVLIMELI
          .D..G........PIHR.APAF.E..T...I..TGIKVVDLLAPY.RGGKIGLFGG.AGVGKTVLIMELI
Retrocopy VDNLGPVDSSATFPIHRSAPAFIELDTKLSIFETGIKVVDLLAPYRRGGKIGLFGGGAGVGKTVLIMELI

Parental  NNVAKAHGGFSVFAGVGERTREGNDLYREMIESGVIKLDDKQSESKCALVYGQMNEPPGARARVGLTGLT
          NN.AKAHGG.SVF.GVGERTREGNDLY.EM.ESGVI.......ESK.ALVYGQMNEPPGAR.RVGLT.LT
Retrocopy NNIAKAHGGVSVFGGVGERTREGNDLYMEMKESGVIN-EKNIEESKVALVYGQMNEPPGARMRVGLTALT

Parental  VAEHFRDAEGQDVLLFIDNIFRFTQANSEVSALLGRIPSAVGYQPTLATDLGGLQERITTTKKGSITSVQ
          .AE.FRD...QDVLLFIDNIFRF.QA.SEVSALLGR.PSAVGYQPTL.T..G.LQERI..TKKGSITS.Q
Retrocopy MAEYFRDVNKQDVLLFIDNIFRFVQAGSEVSALLGRMPSAVGYQPTLSTEMGSLQERIASTKKGSITSIQ

Parental  AIYVPADDLTDPAPATTFAHLDATTVLSRQISELGIYPAVDPLDSTSRMLSPHVLGEAHYNTARGVQKVL
          A.YVPADDLTDPAPATTFAHLDATTVLSR.....GIYPAVDPLDSTS.ML.P...G..HY.TA..V...L
Retrocopy AVYVPADDLTDPAPATTFAHLDATTVLSRGLASKGIYPAVDPLDSTSTMLQPRIVGNEHYETAQRVKETL

Parental  QNYKNLQDIIAILGMDELSEDDKLTVARARKIQRFLSQPFHVAEVFTGAPGKYVELKEGVQSFQGVLDGK
          Q.YK.LQDIIAILG.DELSE.D.LTVARARKI.RFLSQPF.VAEVFTG.PGKYV.L.E....FQ..L.G.
Retrocopy QRYKELQDIIAILGLDELSEEDRLTVARARKIERFLSQPFFVAEVFTGSPGKYVALAETIRGFQLILSGE

Parental  YDDLSEQAFYMVGGIEEVIAKAEKIAKEN
          .D.L.EQAFY.VG.I.E...KA.....EN
Retrocopy LDGLPEQAFYLVGNIDEASTKAITLEEEN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Aegilops tauschii was not studied using RNA-Seq expression data.

ChIP-Seq

Aegilops tauschii was not studied using ChIP-Seq data.

EST

Aegilops tauschii was not studied using EST data.

TSS

Aegilops tauschii was not studied using FANTOM5 data.

Lab

retro_atau_18 was not experimentally validated.

Homology

Retrocopy orthology:

Aegilops tauschii 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00006p00059970	1 retrocopy	retro_atri_7,
Arabidopsis thaliana	AT5G08670	1 retrocopy	retro_atha_12,
Oryza sativa indica	BGIOSGA017602	2 retrocopies	retro_oind_104, retro_oind_87,
Brassica rapa	Bra006013	2 retrocopies	retro_brap_51, retro_brap_57,
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,