RetrogeneDB ID: retro_atau_32

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold16045:18153..18636(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_28326
• Aliases: None
• Description: None

Sequence

>retro_atau_32
ATGGGCGAGCGCAAGGTGCTGAACAAACACTACACGAACGACTTCGACCCGGCCAAGATCCCGCGGCGGCGGCAGCCCAA
GAACCGGCAGATCGTTGTGCGCATGATGCTCCCGATGAGCATCCGCTGCGGCACCTGCGGGACGTACATCGCCATGGGCA
CCAAATTCAACTCGCGGAAAGAGGACGCCGCCGGCGAGGCATACCTGGGCATACGAATACACAGGTTCTACATCAAGTGC
ACACGCTGCTCCGCCGAGATCGCCTTCAAGACGGACCCCAAGAATTCAGACTACGCGGTGGAGTCCGGGGCCAGCCGCAA
CTTCGAGCCATGGCGCGAGGCTGACGCTGTGGTGGACAGGGAGAAGAGGAAACGCGCAGCAGAGGAGATGGGCGATCAGA
TGAGAGCGCTGGAGAACAGAGCGATGGATTCCAAGCGGGACATGGACGGACTCGCCGCTTTAGAGGAGACGCTGTCGATG
AGG

Alignment

ORF - retro_atau_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.23 %
• Parental protein coverage: 51.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGERKVLNKYYPPDFDPAKIPRRKQPKNQQIKVRMMLPMSIRCGTCGTYIYKGTKFNSRKEDCIGETYLG
          MGERKVLNK.Y..DFDPAKIPRR.QPKN.QI.VRMMLPMSIRCGTCGTYI..GTKFNSRKED..GE.YLG
Retrocopy MGERKVLNKHYTNDFDPAKIPRRRQPKNRQIVVRMMLPMSIRCGTCGTYIAMGTKFNSRKEDAAGEAYLG

Parental  IQIFRFYFKCTRCSAEITFKTDPQNSDYTVESGASRNFEPWREEDEVVDKEKRKREAEEMGDAMRALENR
          I.I.RFY.KCTRCSAEI.FKTDP.NSDY.VESGASRNFEPWRE.D.VVD.EKRKR.AEEMGD.MRALENR
Retrocopy IRIHRFYIKCTRCSAEIAFKTDPKNSDYAVESGASRNFEPWREADAVVDREKRKRAAEEMGDQMRALENR

Parental  AMDSKQDMDILAALEEMRSMK
          AMDSK.DMD.LAALEE..SM.
Retrocopy AMDSKRDMDGLAALEETLSMR

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_32 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_28326	1 retrocopy	retro_atau_32 ,
Hordeum vulgare	MLOC_44559	1 retrocopy	retro_hvul_103,
Medicago truncatula	MTR_2g070740	1 retrocopy	retro_mtru_38,