RetrogeneDB ID: retro_taes_196

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_4AL_scaff_7160848:2648..3934(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_2BS_4304B3EDD
• Aliases: None
• Description: None

Sequence

>retro_taes_196
ATTTTGTACAGCAATCCGGACAAATCCAAACACTTGGAAACTGCTAAGACGTACATGTTCGACAGAGAAATTGATTTTGT
TAACTTGAGGTCCGAAAAATATGCAGAAAGCACCCGCATTCCTACTGTGGAGCAGGACGCCACTCCTGAAGAAGATGCCC
ACCGCAGGGACCTAACAATTAATAGTTTATTCTTCAACATCAACGACAACATTGTGGAAGATTTTACTAAAAGAGGTATC
GACGACCTCATCAAGGGTCTTATTGATACTCCTTTACATGCCGAAGCTACCTTCTTGGATGACCCACTTAGAGTTCTTCG
GGCAATTCGATTTGCCGCTAGATTCAACTTTACATTATCCGATAGGTTGAAAGAAGCTGCTTCGGACGAAAAGGTGAAGT
TGGAACTTGGTTGCAAGATTAGCAAAGAACGTGTTGGGAAGGAGATTGATCTTATGATGTCAGGCGAACACCCAGCCGAG
GCAATGTCTTACATTCGTGATCTGGGGCTATTTCATATTGCACTTGCTTTCCCCAAAAATTGCAGCCCTCCAGTTTTTGA
CAATTGTGATCGCTGTTGTGTTTCACACTTGAATCAGCTTGGAACTTTGCAATTTCTGTGCGCAGCAGTGTTTCTCATCC
CATGCTGCCGGGTGAACAGGAAAAGCTTTACCTCTATAGTGCATTCTTTTTTCCCCTCCGAAAGATGTTCTACTTGAATA
AAAAATCTAAGAAGATTGTTGTCACTAGCTATATTATTCAGGAATCATTAAAGCTGCCAGCATGTGTTGCTAAATCGGTT
CTCGACGTGCATGTTGCCAGCGGAAAATTTGCTGATCTAGTGCTCCTCTTTGAATCGAATGTCGCTTCGCGAGCTGTCAG
GGAGGAGGTGGAAGATGTATATCATGATATACCAATGGACACATGGAAGCGTGTTTATGCAGGAGTCGTACTTAGTGAAA
TAAAGGACTTATGGCGGGTGGCACTTGCTATATCCATTATCTTTCATCCAGAAGCTGAAAATGCGGGCGGCACACTCAGC
CAGCAGCGGGATGAGCTGCATCGGAGGAAAGAGCAGTACATGAGAGTTGAGCGTTCCATAACTGATCTAGGTCTCATTGA
GGTGTGGAAGTTGGAGCCATTGGTCAATGGCAACATCATAATGCGAATTATGCAAAAGTCAGAAAGTCCACTGATCGGAG
AATGGAAAAAACGTGTGTTCAAGTGGCAGCTTGCGCATCCTGAAGGAAGCAGGGGTGATTGCGTCGATTGGTTGACGGGA
TCGCGA

Alignment

ORF - retro_taes_196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.81 %
• Parental protein coverage: 93.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IIPCNPGQSKHLETARICLSDISKISIDFVNLRTEKYAENSRIPTVE-DGTPEEDAFRRDLTINSLFYNI
          I...NP..SKHLETA.....D.....IDFVNLR.EKYAE..RIPTVE.D.TPEEDA.RRDLTINSLF.NI
Retrocopy ILYSNPDKSKHLETAKTYMFDRE---IDFVNLRSEKYAESTRIPTVEQDATPEEDAHRRDLTINSLFFNI

Parental  NTKSVEDLTRRGLEDLKAGLIVTPLPAKVTFLDGPLRVLRAIRFAARFSFTLAENLREAASDEKVKLNLG
          N...VED.T.RG..DL..GLI.TPL.A..TFLD.PLRVLRAIRFAARF.FTL...L.EAASDEKVKL.LG
Retrocopy NDNIVEDFTKRGIDDLIKGLIDTPLHAEATFLDDPLRVLRAIRFAARFNFTLSDRLKEAASDEKVKLELG

Parental  SKISRERIGQEVEHMMSDKYPVDAMCHIRDLGLFYVVFAFPEKTVPPVLNKHDWLCVSH-IEAAWNLAQS
          .KIS.ER.G.E...MMS...P..AM..IRDLGLF....AFP....PPV....D..CVSH..E.AWN.A.S
Retrocopy CKISKERVGKEIDLMMSGEHPAEAMSYIRDLGLFHIALAFPKNCSPPVFDNCDRCCVSH<LESAWNFAIS

Parental  IGCSVFRGGSGSMSQDEQRRLCMYSALFTPVRNMVYTKKKE----VVRYIIGNSLKLNGSDAEAIVRIHA
          ...SV....S..M...EQ..L..YSA.F.P.R.M.Y..KK.....V..YII..SLKL....A......H.
Retrocopy VRSSV----SHPMLPGEQEKLYLYSAFFFPLRKMFYLNKKSKKIVVTSYIIQESLKLPACVAKSVLDVHV

Parental  ASDKFADLIIFLESNGNLETVKENPNDKYLEIPTDMVARVLAGLTLLGIKDLWRLALLISTLSYPEVLSA
          AS.KFADL....ESN.....V.E...D.Y..IP.D...RV.AG..L..IKDLWR.AL.IS....PE...A
Retrocopy ASGKFADLVLLFESNVASRAVREEVEDVYHDIPMDTWKRVYAGVVLSEIKDLWRVALAISIIFHPEAENA

Parental  NGSLSQQ-DKLNRRKEIYIRVERLITDLDLEGVWKIGIKPLLDGNDIMGVLDIGEGPLVKEWKERLVKWQ
          .G.LSQQ.D.L.RRKE.Y.RVER.ITDL.L..VWK....PL..GN.IM......E.PL..EWK.R..KWQ
Retrocopy GGTLSQQRDELHRRKEQYMRVERSITDLGLIEVWK--LEPLVNGNIIMRIMQKSESPLIGEWKKRVFKWQ

Parental  LAHPKGTAEECHEWMKQSK
          LAHP.G....C..W...S.
Retrocopy LAHPEGSRGDCVDWLTGSR

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_196 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 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Triticum aestivum	Traes_2BS_4304B3EDD	2 retrocopies	retro_taes_193, retro_taes_196 ,
Triticum aestivum	Traes_5BL_DA5693099	4 retrocopies	retro_taes_167, retro_taes_194, retro_taes_195, retro_taes_197,