RetrogeneDB ID: retro_taes_172

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_2AS_scaff_5261595:2764..3582(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_7DS_5458757D9
• Aliases: None
• Description: None

Sequence

>retro_taes_172
CTAAGGATGTTCCCGTAGGCGACGGACCTATGCGCGATGAGGGGCTACTGCCACCACTGTGAGTTTAAAACCCACGACAC
TTCCACTACTAGATCAACGATCGGGTACCGTGAGCCAAGACCGATGCTACAGATCTTCTTGCCGAGTCTATCGACCTTCA
AAGCATACCCCGTTAGCGTCTACGGAATCGTTGCTGTCCGGGATGCCCTGGAGCCGCGGCGGAATCTCGTGTTTAATCGT
CCCGGCAGAGTTAATGATGCTCTCACGGTTGATCGGGAATCCTTTACCTTGCCTCTTTTGTAGTCCTTGTCGAGGAATGT
ACATGATAAGGGAGAGGGCATTGCTAGAAGTTGATCTTTGGGTGAAGGAGGAAGGGGATGGGTTATCCGACAAACGGCTA
CTTTCTGTGTATGCCGAGATCGATGGGGGGTATGACTTGGATGAACTGTTGGATGAAGAGGTTTCTAGTGACCTTGGCAG
CTTGGTCGTCGACTATCTGTTACTTGATGAGAGTGTTGAGGTTGTAATACAAGTCTCTGCAAAGATTGACCGCCCTCACA
TGTGAGATTCACCCGTTCACTAGTGGCTTTGATCGGGAGATTGTGTTGTCTGATGATAAGTTCTCTGGGAATGGAAAATT
GTTCCGGCATGTCGTCGCCGTGAAGGCCGAGGGGAAATTGGATGTTTGCTTAAAATTGGAGGAATCATTGTTTTGGTGGA
CTTTAGAGGAAGGAGTTGTTGGAGCTGTTAGGTCCCTTGATGACCGAGTGTTAGACTATGCGCAGTTTGATGTAAGGGTG
CTTTTTGCTCCTAAGAAC

Alignment

ORF - retro_taes_172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.32 %
• Parental protein coverage: 60.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MKVFPQAIGACVLRGYCHHRIYKTHDTSTTKSTLGYREPNRMLQVFSLRLSSSPSYPVSVYGIIAVRDSL
          ...FP.A...C..RGYCHH...KTHDTSTT.ST.GYREP..MLQ.F...LS....YPVSVYGI.AVRD.L
Retrocopy LRMFP*ATDLCAMRGYCHHCEFKTHDTSTTRSTIGYREPRPMLQIFLPSLSTFKAYPVSVYGIVAVRDAL

Parental  EPLRNYVFSRPCR-DDAVTIDQDSFILPL-CSPCRGMY-LRQDALLEVDLWVKEEGDGSADKQILSAYAE
          EP.RN.VF.RP.R..DA.T.D..SF.LPL.CSPCRGMY..R..ALLEVDLWVKEEGDG..DK..LS.YAE
Retrocopy EPRRNLVFNRPGRVNDALTVDRESFTLPL>CSPCRGMYMIRERALLEVDLWVKEEGDGLSDKRLLSVYAE

Parental  IESCPAYDEMLYGQIRSGLFSLDIGYISFTRSIEAVIEVFAKVDGPH-HVRF-GAFSSGFDHEIVLFDDT
          I......DE.L.....S.L.SL...Y.....S.E.VI.V.AK.D.PH.HVRF...F.SGFD.EIVL.DD.
Retrocopy IDGGYDLDELLDEEVSSDLGSLVVDYLLLDESVEVVIQVSAKIDRPH<HVRF<HPFTSGFDREIVLSDDK

Parental  FSGTKMQFQHVVVVKAEEKLDVCLKLGESLFWWTFQDGHVGPVRIPDDSMSKYGQFDVRVFFAPKN
          FSG....F.HVV.VKAE.KLDVCLKL.ESLFWWT...G.VG.VR..DD....Y.QFDVRV.FAPKN
Retrocopy FSGNGKLFRHVVAVKAEGKLDVCLKLEESLFWWTLEEGVVGAVRSLDDRVLDYAQFDVRVLFAPKN

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_172 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Triticum aestivum	Traes_7DS_5458757D9	1 retrocopy	retro_taes_172 ,