RetrogeneDB ID: retro_taes_140

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: 5B:242641839..242642782(+)
• 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_DEAE3B117
• Aliases: None
• Description: None

Sequence

>retro_taes_140
GGAGGATCTGTCCCCGACTTAGTGAGCAACAACGACGAGAAAGCTGATAAAGGACATACAATTGACTCTTCCTCAACAAT
GGCAGGCAGGCCAGTTTTAATCCTAAAGAGCATTCTTATGAATTTGCTTATTCTCACTGGAAGAAGTCCTTTCTTTGTAA
AGCTTTTCACTAATGGCATGAAGGAATCTGATGAGACGCATCCAAGAATTAGGATTGTTGATTCAGAGGAAAATGCTCTT
ACGGAGCTTCTAAGATTCATGTATAGTGGGAAGTTGACAACAATTGAGCCCACTCTTCTGCTCGACATATTGATGGCTGT
TGATAAATTTGAGGTTCTTGCTTGCATGAGGCACAATCAGTTGCTCACAAGCCTGCCTATGACCACATAATTTGCATTTC
TATACCTAGACCATCCATGACCCTCTTTAATGGTTGCTGAAGTTTAAAGTGTAGTACGTGTAGCCAAGGAATTCCTTGCT
GACAAATACAAGGATTTTCGTAAGTTCCCAGCTGAAGTGATGAACATCGCTCTTGTTGGGATCGAGGCCATTTTTTGAGT
ACTAACCTGATACTACTATCTGAAGATGAGGCATATTACTTCTTTCTCAAGTGGGCCAGTCTCCGATACCTAGAATATGA
GGAAAGACCGAAGATCTAGAGTTGTCGTTTACTTCCATTGGTATGCTTCAGTCATATGACAGGTTTGTCACTTCAGAATG
TCCTAGCATGCACTGATGATGATATAGACCATGAGCAAGTAGCTCAATGTATTGCTGAGGTACTTTTATACAAAGCTTAT
CCAACACAGATGGAAGGTACTCCTGCAGTAGAAGTAGCAACCCATCATAATTTTCTGAGCAAACTTATGAGTTGAGGACC
ATGAAAGTTGTTGCGTTCAGTCGACCCTGCCCACATGTTACAGTTTATATGGCATTAGAACGA

Alignment

ORF - retro_taes_140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.75 %
• Parental protein coverage: 62.45 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGSSANQERRREEQGEKEQSVDSSSMMVGTPVLREKNIHINSAILASRSPFFLKFFSNGMKESDQTNPTI
          GGS.........E...K....DSSS.M.G.PVL..K.I..N..IL..RSPFF.K.F.NGMKESD.T.P.I
Retrocopy GGSVPDLVSNNDEKADKGHTIDSSSTMAGRPVLILKSILMNLLILTGRSPFFVKLFTNGMKESDETHPRI

Parental  RITDSEENAFMELLSYMYSGKLTTAEPTRLLDILMAADKFEVLSCMRHCSQLLISLPMTTESALLYIDHP
          RI.DSEENA..ELL..MYSGKLTT.EPT.LLDILMA.DKFEVL.CMRH..QLL.SLPMTT..A.LY.DHP
Retrocopy RIVDSEENALTELLRFMYSGKLTTIEPTLLLDILMAVDKFEVLACMRH-NQLLTSLPMTT*FAFLYLDHP

Parental  CSVSMVNEVRPLIDASKEFLANKYKDFYEFKSELMNISLAGIEAI-FSSTDIQVETEDDVYYFMLDWARA
          ....MV.EV.......KEFLA.KYKDF..F..E.MNI.L.GIEAI.F.ST......ED..YYF.L.WA..
Retrocopy *PSLMVAEV*SVVRVAKEFLADKYKDFRKFPAEVMNIALVGIEAI<FLSTNLILLSEDEAYYFFLKWASL

Parental  RYVELEERRKILSSRLLPLVRFSHMTCMTLQEILASTDNDIDREQVTHRIAEALLPKAYPKQLEGALAAE
          RY.E.EER.KI.S.RLLPLV.FSHMT...LQ..LA.TD.DID.EQV...IAE.LL.KAYP.Q.EG..A.E
Retrocopy RYLEYEERPKI*SCRLLPLVCFSHMTGLSLQNVLACTDDDIDHEQVAQCIAEVLLYKAYPTQMEGTPAVE

Parental  VTT-CSRFAERAYEYKPVKLVAFDQPCPQIIVYLDLTR
          V.T..S.F.E..YE....K.VAF..PCP...VY..L.R
Retrocopy VAT<PS*FSEQTYELRTMKVVAFSRPCPHVTVYMALER

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_140 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Triticum aestivum	Traes_5DL_DEAE3B117	4 retrocopies	retro_taes_138, retro_taes_140 , retro_taes_143, retro_taes_218,