RetrogeneDB ID: retro_taes_144

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: 5B:239894408..239895173(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_7BL_FE6ED9DF9
• Aliases: None
• Description: None

Sequence

>retro_taes_144
GAGAAAGCTGATAAAGGACATACAATTGACTCCTCAACAATGGCAGGTACTCCAGTTTTAACACTAAAGATCCTTCTTAT
GTATTCGCTTATTCTCGATGGAATAAGTCCTTTCTTTCTAAAGCTTTTCACTAATGGCATGAAAGAATCCGATGAGACGC
ATCCAAGAATTAGGATTGCTGATTCGGAGGAAAATTCCCTTATGGAGCTTCTAAGATTCATTTATAGTGGAAAGTTGACA
ACAATTGAGCCCATTCTTCTGCTCGACATCTTGATGGCGGCCGATAAATTTGAGGTTCTTGCTTGCATGAGGCACTGCAG
TCAGTTGCTCACAAGCCTGCCTATGACCACATAATTTGCATTGCTATACCTAGACCATCCATGCTCCTCTTTAATGGTTG
CTGAAGTACAAAGTGTAGTATGTGTAGCCAGCCAAGGAATTCCTTGCTGACAAATACAAGGATTTTCGTAAGTTCGAAGC
TGAAGTGATGAACATCTCTCTTGTTGGGACCGAGGCCATCTTTTCGAGTATTGACATGATGTTACTATCTGAAGATGAGG
CATATTACTTCTTGCTCAAGTGGGCCAGTCTACGATACCCAGAATTTGAGGAAAGATGGAAGATCTAAAGCTGTCATTTA
CTTCCGCTGGTATGCTCAGTCATATGACAGGTTTGTCACTTCAGAATACCCTAGGATGCACTAATGATGATATAGACCAT
GAGCAATTAGCTCAACGTATTGTTGAGGTACTTCTATACAAATCT

Alignment

ORF - retro_taes_144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.43 %
• Parental protein coverage: 58.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QDGEDGENSDSSWNMECNQVLRVKSIYISSAILAAKSPFFYKLFSNGMKESDQRHATLRITTSEESALME
          .....G...DSS..M....VL..K.....S.IL...SPFF.KLF.NGMKESD..H...RI..SEE..LME
Retrocopy EKADKGHTIDSS-TMAGTPVLTLKILLMYSLILDGISPFFLKLFTNGMKESDETHPRIRIADSEENSLME

Parental  LLSFIYSGKLTTNEPTLLLDILMISDKFEVVSCMRHCSQLLRSLPMTTESALLYLDLP-SSISMAAAVQP
          LL.FIYSGKLTT.EP.LLLDILM..DKFEV..CMRHCSQLL.SLPMTT..ALLYLD.P.SS...A.....
Retrocopy LLRFIYSGKLTTIEPILLLDILMAADKFEVLACMRHCSQLLTSLPMTT*FALLYLDHPCSSLMVAEVQSV

Parental  LTDA-AKEFLANKYKDLTKFQDEVMNIPLAGIEAILCSNDLQVASEDAVYDFVIKWVRAQYPRTEERREI
          ...A.AKEFLA.KYKD..KF..EVMNI.L.G.EAI..S.D....SED..Y.F..KW....YP..EER..I
Retrocopy VCVA>AKEFLADKYKDFRKFEAEVMNISLVGTEAIFSSIDMMLLSEDEAYYFLLKWASLRYPEFEERWKI

Parental  LGTRLLPLV-RFSHMTCRKLRKVLACS--DLDHEQASKSVTDALLYKA
          ....LLPLV...SHMT...L...L.C...D.DHEQ........LLYK.
Retrocopy *SCHLLPLV<MLSHMTGLSLQNTLGCTNDDIDHEQLAQRIVEVLLYKS

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_144 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Triticum aestivum	Traes_7BL_FE6ED9DF9	2 retrocopies	retro_taes_144 , retro_taes_145,