RetrogeneDB ID: retro_atau_25

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: C141224876:5..509(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_25997
• Aliases: None
• Description: None

Sequence

>retro_atau_25
TCGCCGTCGACGGACCGGTCGCCGGGGTTCCAGGCGGAGTGCCTGGCCGCCGCGCTCGGGAAGCTGGGCGTGGACGAGTG
CACGGTGGTGGGGTTCAGCTACGGCGGGATGGTGGCCTTCAAGATGGCCGAGTCGCGCCCCGACCTCGTCCGCTCGCTCG
TCGTGTCGGGCTCCGTCGTCGCCATGACCGACTCAATCAGCGACGCCACGCTCGAGCGGATCGGCGTCCGGTCGTCGGCG
GAGCTGCTGCTGCCGGAGTCCGTCAAGGGGCTCAAGGCGCTGCTCTCCATCGCCGCCCACCGGAGGCTCTGGTTCCCGGA
ACGCCTTCACAGGGACTTCCTGGAGGTGATGTTCACCAACCGCAAGGAAAGGGCGGAGCTGCTGGAAGGTCTGGTGGTCA
GCAACAAAGACGCCACCGTCCCCGTTTTGCCGCAGAAAATACTCCTGCTCTGGGGACACAACGACAACATCTTCAACATA
GAGCTCGCCAAGACGATGAAAGAG

Alignment

ORF - retro_atau_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.67 %
• Parental protein coverage: 50.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPSTDRSPGFQAECLVAALGKLGVERCTVVGFSYGGMGAFKMAEAHPGLVRSLVVSGSVVAMTDSISETT
          SPSTDRSPGFQAECL.AALGKLGV..CTVVGFSYGGM.AFKMAE..P.LVRSLVVSGSVVAMTDSIS..T
Retrocopy SPSTDRSPGFQAECLAAALGKLGVDECTVVGFSYGGMVAFKMAESRPDLVRSLVVSGSVVAMTDSISDAT

Parental  LERIGVKSSAELLLPDSVKGLKALLSIAAHRKLWFPERLHRDYLQVMFTNRKERAELLEGLVVSNKDATV
          LERIGV.SSAELLLP.SVKGLKALLSIAAHR.LWFPERLHRD.L.VMFTNRKERAELLEGLVVSNKDATV
Retrocopy LERIGVRSSAELLLPESVKGLKALLSIAAHRRLWFPERLHRDFLEVMFTNRKERAELLEGLVVSNKDATV

Parental  PVLPQKILLLWGHNDNIFNIELAKTMKE
          PVLPQKILLLWGHNDNIFNIELAKTMKE
Retrocopy PVLPQKILLLWGHNDNIFNIELAKTMKE

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_25 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_08492	1 retrocopy	retro_atau_54,
Aegilops tauschii	F775_25997	1 retrocopy	retro_atau_25 ,