RetrogeneDB ID: retro_atau_4

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold30437:26367..27213(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_20323
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_27787
• Aliases: None
• Description: None

Sequence

>retro_atau_4
ATGCGCTCCGACGAGCTCCCCGTCGACTCCGCCGGAGTGGAGCTGCAGCTCTTTCACGGGCACAACGACGGCGACGGCAG
CGCCAGGTTCGTGGACGAGGAAGCCTGGGCAGAGTCATCATCGGCGACGGCTCTGGATGTGGCGAAGCGGGCGGCGGTGG
GAGTGGGCGCGCGGGTGCTCTTCTACCCGAAGCTGGCCTACAAGCTGGTGGCCGGCCGGTCGGCTCCGGGTAAAGCCTCG
GAGGAGTCGTCGTCATCGTCATCGGCGACGACTCTAGACGCCGCGAAGCAAGCGGCGGTGGGCGTGGGCGCGCGGGCGCT
CTTCTACCCGACGCTCGCCTACAGCCTGGCCCGGAACCGCCTCTCGCCGGCCGGCTTCAAGTGGTGGCACAAGATCACGG
ACACCCACATGCTCCTCGGCGCTGTCCCGTTCCCGAGCGACGTGCCGCGCCTCCGCGCCCTGGGCGTCACCGCCGTGGTC
ACGCTCACCGAGCCCTACGAGCGGCTCGTCGACGCGAAGCTGTACAAGGCCCACGGCATGGAGAACCTGGTGCTGCCCAC
CACGGACTACCTCTACGCGCCGTCGCAGAAGGACCTCCGCGACGCCACGGCGTTCATCCACGGCAAGGAGGGCGGCGGGC
TGACCTACGTGCATTGCAAGGCCGGGCGCGCGCGCAGCGCCACGGTGGTGATGTGCTACCTGGTGCGGTACAAGGGGATG
ACGACGAAGCAGGCGTACGATCACGTGCGGTCGTGCCGGTCCAGGGTGTCGCTGGCTCCGGCGCAGTGGCAGGCGGTCCA
GGACTTCGAGGACTTCTACCGGCGGCCGGCCGGTAGCTCGGAGTGA

Alignment

ORF - retro_atau_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.91 %
• Parental protein coverage: 55.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AKRAAVGVGARMLFYPTLVYNVVRNQCE-SHFHWWDQV-DEHVLLGAVPFPSDVLRLQKLGVCGVVTLNE
          AK.AAVGVGAR.LFYPTL.Y...RN......F.WW....D.H.LLGAVPFPSDV.RL..LGV..VVTL.E
Retrocopy AKQAAVGVGARALFYPTLAYSLARNRLSPAGFKWWHKITDTHMLLGAVPFPSDVPRLRALGVTAVVTLTE

Parental  SYERLVSKSLYEAHGIENLVLPTRDYLYAPSFDNLCKAADFIHRNASCGKLTYVHCKAGRGRSTTVVLCY
          .YERLV...LY.AHG.ENLVLPT.DYLYAPS...L..A..FIH.....G.LTYVHCKAGR.RS.TVV.CY
Retrocopy PYERLVDAKLYKAHGMENLVLPTTDYLYAPSQKDLRDATAFIHGKEG-GGLTYVHCKAGRARSATVVMCY

Parental  LVQYKQMTPAGAFEHVRSCRPRVLLASAQWKAVQEF
          LV.YK.MT...A..HVRSCR.RV.LA.AQW.AVQ.F
Retrocopy LVRYKGMTTKQAYDHVRSCRSRVSLAPAQWQAVQDF

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_4 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_27787	1 retrocopy	retro_atau_4 ,
Hordeum vulgare	MLOC_37833	1 retrocopy	retro_hvul_75,