RetrogeneDB ID: retro_taes_215

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_5BL_scaff_10824101:12680..14084(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_5DL_BB10A3B4B
• Aliases: None
• Description: None

Sequence

>retro_taes_215
ATCCAGCCGCTCGAGGTGTCTCTCGAGGCCGGCAACCTCGCCGACCCCGCCGCGGTCGCGCTCGATGACGACGGCCGCCC
GCGCCGCACCGGCACCGTCCTCACCACAAGCGCGCACATCGTCACCGCCGTCGTCGGCTCCGGCGTCCTCTCGCTCGCCT
GGGCCACCGCGCAGCTCGGTTGGGTCGCGGGTCCCACCACCATGGCGCTCTTCGGCGGCATCGTCTACTACAGCTCCACG
CTTCTCGCCGACTGCTACCGCACCGGCGACCCGGCCGCCGGCACCCGGAACTACTCCTACGTGGAGGCCGTCCGAACCAT
CCTCGGCGGCGCCAAAGTGAAGTTCTGCGGCGTCATACAGTACGCCAACCTCGTCGGCATCGCCATTGGCTACACCATCG
CCGCCTCCATCAGCTTTCATGCCATCACGAGGGCCAACTGCTTCCACAGCAAGGGGCACGACAACGCGTGCCACACCTCC
AGCACGCCCTACATGATCGGCTTCGGCGCCGCGCAGATCGTCTTCTCTCAGATACCCAACTTCGATCAGATACGGTGGCT
CTCCGTCGTCGCCTCCGCCATGTCCTTCGCCTACTCCGGCATCGGGCTCGGGCTCGGAATCGCCCAGACCGTGGCCAACG
GCGGCTTCGGAGGCACCCTCACCGGCGTCGCCATCGGCACGGCGGGCGTCACCGTGATGCAGAAGCTGTGGCGCGTCCTG
CAGGCGCTGGGCAACATCGCCTTCGCCTACTCCTTCTCCAACGTGCTCATCGAGATCCAGGACACCATCAAGGCGCCACC
GCCGTCGGAGGCAGCCGTGATGAAGAAGGCCACGGCGCTGAGCGTGGCCACCACGACGGCGTTCTACGTCATGTGCGGGT
GCATGGGCTACGCGGCCTTCGGCAACGACGCGCCGGACAATCTCCTCACCGGGTTCGGCTTCTACGAGCCCTTCTGGCCG
GTGGACGTCGCCAACGCCGCCATCGTCGTGCACCTCGTCGGCGCCTACCAGGTCTTCTGCCAGCCCATCTTCGCCTTCGT
CCAGCGCTGGGCCGCCGCCAGATGGCCAGAGAGCGACTTCGTCACGAGGGTGGGGCCGTTCGCGCTGAGCGCGCTCCGGC
TTGTGTGGCGCTCGGCGTTCGTGTGCCTGACCACCCTGGTCGCCATGGCGATGCCATCCTTCGGCGCCATCGTGGGGCTC
ATGGGCGCGCTCTCGTTCTGGCCGCTCACCGTCTACTTCCCCGTGGAGATGTACATGAAGCAGCGCGCCGTGGCGCGCGG
GAGCGCGAGGTGGCTCTGCCTCAAGGCGCTCACCGTCGGCTGCCTCGTCGTGTCGGTGGCCGCCACCGTGGGATCAATCG
CCGGCATGGTCGGCGCGTTCAAGGTGTTCCGCCCTTTCAGTGGC

Alignment

ORF - retro_taes_215 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.91 %
• Parental protein coverage: 97.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAPMEVSVEAGNAGD--AAWMDDDGRPRRSGTFWTASAHIITAVIGSGVLSLAWAIAQLGWVAGPAVMLL
          ..P.EVS.EAGN..D..A...DDDGRPRR.GT..T.SAHI.TAV.GSGVLSLAWA.AQLGWVAGP..M.L
Retrocopy IQPLEVSLEAGNLADPAAVALDDDGRPRRTGTVLTTSAHIVTAVVGSGVLSLAWATAQLGWVAGPTTMAL

Parental  FAAVIYYTSTLLAECYRTGDPATGKRNYTYMDAVRSNLGGPKVIFCGVIQYANLVGVAIGYTIASSISMR
          F....YY.STLLA.CYRTGDPA.G.RNY.Y..AVR..LGG.KV.FCGVIQYANLVG.AIGYTIA.SIS..
Retrocopy FGGIVYYSSTLLADCYRTGDPAAGTRNYSYVEAVRTILGGAKVKFCGVIQYANLVGIAIGYTIAASISFH

Parental  AIRRADCFHANGHADPCKSSSNPYMILFGLVQIVFSQIPDFDQIWWLSIVAAVMSFTYSGIGLSLGITQT
          AI.RA.CFH..GH...C..SS.PYMI.FG..QIVFSQIP.FDQI.WLS.VA..MSF.YSGIGL.LGI.QT
Retrocopy AITRANCFHSKGHDNACHTSSTPYMIGFGAAQIVFSQIPNFDQIRWLSVVASAMSFAYSGIGLGLGIAQT

Parental  ISNGGIKGSLTGISIG-VGITATQKVWRSLQAFGDIAFAYSFSNILIEIQDTIRAPPPSEAKVMKQATRL
          ..NGG..G.LTG..IG..G.T..QK.WR.LQA.G.IAFAYSFSN.LIEIQDTI.APPPSEA.VMK.AT.L
Retrocopy VANGGFGGTLTGVAIGTAGVTVMQKLWRVLQALGNIAFAYSFSNVLIEIQDTIKAPPPSEAAVMKKATAL

Parental  SVATTTVFYMLCGCMGYAAFGDAAPDNLLTGFGFYEPFWLLDIANVAIVVHLVGAYQVFCQPIFAFVERW
          SVATTT.FY..CGCMGYAAFG..APDNLLTGFGFYEPFW..D.AN.AIVVHLVGAYQVFCQPIFAFV.RW
Retrocopy SVATTTAFYVMCGCMGYAAFGNDAPDNLLTGFGFYEPFWPVDVANAAIVVHLVGAYQVFCQPIFAFVQRW

Parental  AASTWPDSVFISREFRVGPFALSVFRLTWRSAFVCLTTVFAMLLPFFGNVVGLLGAVSFWPLTVYFPVEM
          AA..WP.S.F..R...VGPFALS..RL.WRSAFVCLTT..AM..P.FG..VGL.GA.SFWPLTVYFPVEM
Retrocopy AAARWPESDFVTR---VGPFALSALRLVWRSAFVCLTTLVAMAMPSFGAIVGLMGALSFWPLTVYFPVEM

Parental  YIRQRGVPGRSMQGICLRMLSVGCLIVSIAAAAGSIANVIEALKVYKPFSG
          Y..QR.V...S....CL..L.VGCL.VS.AA..GSIA....A.KV..PFSG
Retrocopy YMKQRAVARGSARWLCLKALTVGCLVVSVAATVGSIAGMVGAFKVFRPFSG

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_215 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA037101	1 retrocopy	retro_oind_7,
Oryza brachyantha	OB12G14670	1 retrocopy	retro_obra_17,
Oryza glumaepatula	OGLUM12G05640	1 retrocopy	retro_oglu_3,
Oryza nivara	ONIVA12G04480	1 retrocopy	retro_oniv_32,
Oryza punctata	OPUNC12G04770	1 retrocopy	retro_opun_43,
Triticum aestivum	Traes_5DL_BB10A3B4B	2 retrocopies	retro_taes_215 , retro_taes_217,