RetrogeneDB ID: retro_taes_36

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: 4A:182762170..182763712(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Traes_4AL_B6154ED13
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_2BS_7DF366FE1
• Aliases: None
• Description: None

Sequence

>retro_taes_36
ATGGCGGCCGGCAGCGTCGGCGTCTCCGAGAGCAATGACGGAGGAGGAGGCGGAAGGGTCACCATGTTCGTGGTGCTGTC
GTGCATCACCGCCGGCATGGGCGGCGCCATCTTCGGCTACGACATCGGGATCGCGGGCGGGGTGTCGTCCATGGAGCCGT
TCCTGCGCAAGTTCTTCCCGGAGGTGTACCGTCGGATGAAGGGCGACTCCCATGTCAGCAACTACTGCAAGTTCGACAGC
CAGATGCTCACCGCCTTCACCTCATCGCTCTACGTCGCCGGCCTGCTCACCACCTTCCTCGCCTCCGGCGTCACGGCCCG
TCTTGGCCGCCGCCCGTCCATGCTCCTTGGCGGTGCCGCTTTCCTCGCCGGCGCGGCTGTCGGAGGCTCGTCGCTGAACG
TCTACATGGCCATCCTGGGGCGCGTGCTCCTCGGCGTCGGGCTGGGCTTCGCCAACCAGGCCGTCCCGCTGTACCTGTCG
GAGATGGCGCCGCCGCGGCACCGCGGCGCGTTCAGCAACGGCTTCCAGTTCAGCGTCGGCGTCGGCGCGCTCGCGGCCAA
CGTCATCAACTTCGGCACGGAGAAGATCAAGGGAGGCTGGGGTTGGCGCGTCTCGCTGTCCCTCGCCGCCGTGCCGGCCG
GGCTCCTGCTCGTCGGCGCGGTCTTCCTCCCGGAGACGCCCAACAGCCTCGTCCAGCAGGGCAAGGACCGCCGGGATGTG
GCGCTCTTGCTGCGTAAGATCCGCGGCATCCATGACGTCGACCACGAGCTTGACGGCATCGTCGCGGCCGCCGACAGCGC
CACGGCGGCCGGCAGCAGCGGCCTGCGGATGCTCCTCACCCAACGGAGGTACCGGCCGCAGCTGGTTATGGCGGTGGCGA
TCCCTTTCTTCCAGCAGGTGACAGGGATCAACGCGATCGCCTTCTACGCGCCCGTGCTGCTGCGCACGATCGGCATGGGC
GAGAGCGCGTCGCTCCTGTCCTCGGTGGTCACGGGGGTCGTCGGCGCGGCCTCCACCCTCCTCTCCATGTTCCTCGTCGA
CCGTTTCGGCCGCCGCACGCTCTTCCTAGCCGGCGGCACGCAGATGCTCGGGTCGCAGCTCCTGATCGGCGCCATCATGG
CGGCAAAGCTGGGCGACGACGGCGGCGTGAGCAAGGGATGGGCAGCGACTCTCATCTTCCTGATCGCGGTGTACGTGGCC
GGGTTCGGGTGGTCGTGGGGGCCGCTGGGGTGGCTGGTGCCGAGCGAGATCTTCCCGCTGGAGGTGCGGTCGTCGGGGCA
GGGCGTGACGGTGGCGACGAGCTTCGTGTTCACGGTGTTCGTGGCGCAGACGTTCCTGGCCATGCTGTGCCGCATGAGGG
CCGGCATATTCTTCTTCTTCGCGGCGTGGCTGGCGGCCATGACGGCGTTCGTGTACCTCCTGCTGCCGGAGACGAGGGGC
GTGCCCATCGAGCAGGTGGACAGGGTGTGGCGCGAGCACTGGTTCTGGAGGAGGGTCCTGGGAATGGGATCCGAGGAGGC
GCCAGCGAGCGGGAAACTCTGA

Alignment

ORF - retro_taes_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.85 %
• Parental protein coverage: 93.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NTGGGKDYPGKLTMFVLFACIVAATGGLIFGYDIGISGGVTSMNPFLMKFFPGVYHKEQEAEWNQSNQYC
          N.GGG....G..TMFV...CI.A..GG.IFGYDIGI.GGV.SM.PFL.KFFP.VY..........SN.YC
Retrocopy NDGGGG---GRVTMFVVLSCITAGMGGAIFGYDIGIAGGVSSMEPFLRKFFPEVYRR-MKGDSHVSN-YC

Parental  KFDSQLLTMFTSSLYLAALVASFFAATVTRVAGRKWSMFAGGVTFLVGAALNGAAKNVLMLILGRVLLGI
          KFDSQ.LT.FTSSLY.A.L...F.A..VT...GR..SM..GG..FL.GAA..G...NV.M.ILGRVLLG.
Retrocopy KFDSQMLTAFTSSLYVAGLLTTFLASGVTARLGRRPSMLLGGAAFLAGAAVGGSSLNVYMAILGRVLLGV

Parental  GVGFANQSVPVYLSEMAPARLRGMLNIGFQLMVTIGILCANLINYGTAKIKGGWGWRVSLALAAVPAGII
          G.GFANQ.VP.YLSEMAP.R.RG....GFQ..V..G.L.AN.IN.GT.KIKGGWGWRVSL.LAAVPAG..
Retrocopy GLGFANQAVPLYLSEMAPPRHRGAFSNGFQFSVGVGALAANVINFGTEKIKGGWGWRVSLSLAAVPAGLL

Parental  AIGALFLPDTPNSLIDRGY-TEDAKKMLRRVRGTDDVEEEYSDLVAASEESKLVSHPWRNIL--QRRYRP
          ..GA.FLP.TPNSL...G....D....LR..RG..DV..E....VAA..............L..QRRYRP
Retrocopy LVGAVFLPETPNSLVQQGKDRRDVALLLRKIRGIHDVDHELDGIVAAADSATAAGSSGLRMLLTQRRYRP

Parental  QLTFAIAIPFFQQLTGINVIMFYAPVLFKTLGFADDASLMSAVITGLVNVFATFVSIVTVDRLGRRKLFL
          QL..A.AIPFFQQ.TGIN.I.FYAPVL..T.G....ASL.S.V.TG.V....T..S...VDR.GRR.LFL
Retrocopy QLVMAVAIPFFQQVTGINAIAFYAPVLLRTIGMGESASLLSSVVTGVVGAASTLLSMFLVDRFGRRTLFL

Parental  QGGTQMLACQIVVGSLIGAKFGFTGVADIPKGYAAFVVFFICAYVAGFAWSWGPLGWLVPSEIFPLEIRS
          .GGTQML..Q...G....AK.G..G.....KG.AA...F.I..YVAGF.WSWGPLGWLVPSEIFPLE.RS
Retrocopy AGGTQMLGSQLLIGAIMAAKLGDDG--GVSKGWAATLIFLIAVYVAGFGWSWGPLGWLVPSEIFPLEVRS

Parental  AGQSITVSMNMLCTFIIAQAFLPMLCRFKFMLFFFFGAWVVVMTLFVAYFLPETKNVPIEEMVLVWKAHW
          .GQ..TV......T...AQ.FL.MLCR.....FFFF.AW...MT.FV...LPET..VPIE....VW..HW
Retrocopy SGQGVTVATSFVFTVFVAQTFLAMLCRMRAGIFFFFAAWLAAMTAFVYLLLPETRGVPIEQVDRVWREHW

Parental  YWGRFI
          .W.R..
Retrocopy FWRRVL

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_36 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G24820	1 retrocopy	retro_bdis_38,
Hordeum vulgare	MLOC_55525	1 retrocopy	retro_hvul_80,
Medicago truncatula	MTR_0009s0370	1 retrocopy	retro_mtru_23,
Oryza glumaepatula	OGLUM07G18360	1 retrocopy	retro_oglu_7,
Oryza meridionalis	OMERI07G15470	2 retrocopies	retro_omer_15, retro_omer_8,
Oryza nivara	ONIVA07G16940	1 retrocopy	retro_oniv_2,
Oryza punctata	OPUNC07G17520	1 retrocopy	retro_opun_36,
Oryza glaberrima	ORGLA07G0149800	1 retrocopy	retro_ogla_30,
Oryza rufipogon	ORUFI07G19310	1 retrocopy	retro_oruf_45,
Oryza sativa japonica	OS07G0559700	1 retrocopy	retro_osat_29,
Triticum aestivum	Traes_2BS_7DF366FE1	1 retrocopy	retro_taes_36 ,