RetrogeneDB ID: retro_atau_38

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold260651:12986..14159(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_06769
• Aliases: None
• Description: None

Sequence

>retro_atau_38
TTCGAACGTAACAAACCGCACGTCAACGTTGGCACCATCGGTCACGTTGACCACGGTAAAACCACTCTGACCGCTGCTCT
GACCCGTGTCTGCTCCGAAGTTTTCGGTTCCGCTCGCGTTGACTTCGACAAGATCGACAGCGCCCCGGAAGAGAAGGCTC
GTGGTATCACCATCAACACTGCCCACGTAGAGTACGATTCCAACATTCGTCACTACGCGCACGTTGACTGCCCGGGTCAC
GCCGACTACGTGAAGAACATGATCACCGGTGCTGCCCAGATGGACGGCGCGATCCTGGTCTGCTCGGCTGCCGACGGCCC
GATGCCGCAAACTCGTGAGCACATCCTGCTGTCCCGTCAGGTTGGCGTACCGTACATCGTTGTCTTCCTGAACAAGGCTG
ACATGGTTGACGACGCTGAGCTGCTGGAGCTGGTCGAGATGGAAGTTCGCGACCTGCTGAGCACCTACGATTTCCCGGGT
GACGACACTCCGATCATCATCGGCTCGGCGCTGATGGCTCTGAACGGCCAGGACGACAACGAGATGGGCACCACTGCCGT
CAAGAAGCTCGTCGAGACTCTGGATACTTATATCCCTGAGCCGGTTCGTGCCATCGACAAGCCGTTCCTGATGCCGATCG
AAGACGTATTCTCGATCTCCGGCCGCGGTACTGTAGTGACCGGTCGTGTAGAGCGCGGTATCGTCCGTATCCAGGAAGAA
ATCGAAATCGTTGGTCTGCGTCCGACCACCAAGACCACCTGCACCGGCGTTGAGATGTTCCGCAAGCTGCTGGACGAAGG
TCGTGCTGGTGAGAACTGCGGCGTGCTGCTGCGCGGCACCAAGCGTGATGAAGTCGAGCGTGGTCAGGTTCTGGCCAAGC
CGGGCACCATCAAGCCGCACACCAAGTTCGAAGCTGAAGTGTACGTTCTGTCCAAAGAAGAAGGTGGTCGTCACACCCCG
TTCTTCAAGGGCTACCGTCCTCAGTTCTACTTCCGTACCACTGACGTGACCGGTTCGTGCGAACTGCCGGAAGGCGTTGA
GATGGTAATGCCGGGCGACAACATCAAAATGGTTGTTACCCTGATCAAGCCGATCGCCATGGAAGATGGCCTGCGTTTCG
CAATTCGCGAAGGCGGCCGTACCGTTGGTGCTGGCGTGGTTGCCAAGATCGTC

Alignment

ORF - retro_atau_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.45 %
• Parental protein coverage: 98.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FTRTKPHVNVGTIGHVDHGKTTLTAAITKVLSEAGSAKAVAFDEIDKAPEEKARGITISTAHVEYETAKR
          F.R.KPHVNVGTIGHVDHGKTTLTAA.T.V.SE......V.FD.ID.APEEKARGITI.TAHVEY....R
Retrocopy FERNKPHVNVGTIGHVDHGKTTLTAALTRVCSEVFGSARVDFDKIDSAPEEKARGITINTAHVEYDSNIR

Parental  HYAHVDCPGHADYVKNMITGAAQMDGGILVVSAPDGPMPQTKEHILLARQVGVPSLVCFLNKVDAVEDEE
          HYAHVDCPGHADYVKNMITGAAQMDG.ILV.SA.DGPMPQT.EHILL.RQVGVP..V.FLNK.D.V.D.E
Retrocopy HYAHVDCPGHADYVKNMITGAAQMDGAILVCSAADGPMPQTREHILLSRQVGVPYIVVFLNKADMVDDAE

Parental  LLELVEMELRELLSFYKFPGDDIPIIRGSALSALNGTNE-EIGKNAILKLMDAVDSYIPDPVRVLDKSFL
          LLELVEME.R.LLS.Y.FPGDD.PII.GSAL.ALNG....E.G..A..KL....D.YIP.PVR..DK.FL
Retrocopy LLELVEMEVRDLLSTYDFPGDDTPIIIGSALMALNGQDDNEMGTTAVKKLVETLDTYIPEPVRAIDKPFL

Parental  MPIEGIFSIQGRGTVVTGRIEQGVIKTGEDVEVIGLTESGPVKTTVTGVEMFKKMMDHGEAGDNVGLLLR
          MPIE..FSI.GRGTVVTGR.E.G.....E..E..GL......KTT.TGVEMF.K..D.G.AG.N.G.LLR
Retrocopy MPIEDVFSISGRGTVVTGRVERGIVRIQEEIEIVGLRPT--TKTTCTGVEMFRKLLDEGRAGENCGVLLR

Parental  GLKRGDVERGQVVCKPGTVKTYKKFEAEIYVLTKDEGGRHTAFFSNYSPQFYFRTADICGKIELPPDVKM
          G.KR..VERGQV..KPGT.K...KFEAE.YVL.K.EGGRHT.FF..Y.PQFYFRT.D..G..ELP..V.M
Retrocopy GTKRDEVERGQVLAKPGTIKPHTKFEAEVYVLSKEEGGRHTPFFKGYRPQFYFRTTDVTGSCELPEGVEM

Parental  VMPGDNVTAIFELMLPVPLEPGLRFALREGGRTVGAGVVAKVM
          VMPGDN......L..P...E.GLRFA.REGGRTVGAGVVAK..
Retrocopy VMPGDNIKMVVTLIKPIAMEDGLRFAIREGGRTVGAGVVAKIV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Aegilops tauschii was not studied using RNA-Seq expression data.

ChIP-Seq

Aegilops tauschii was not studied using ChIP-Seq data.

EST

Aegilops tauschii was not studied using EST data.

TSS

Aegilops tauschii was not studied using FANTOM5 data.

Lab

retro_atau_38 was not experimentally validated.

Homology

Retrocopy orthology:

Aegilops tauschii 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_06769	1 retrocopy	retro_atau_38 ,
Triticum aestivum	Traes_4AL_766B299B11	1 retrocopy	retro_taes_180,