RetrogeneDB ID: retro_atau_43

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold267898:1032..1563(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_28795
• Aliases: None
• Description: None

Sequence

>retro_atau_43
GGCGCCTTGACTGGTGAGCTGGCGGTTAGTCAGTTGGTCGACGGCGGTTGTGAGCTGGTGCTGGTTGGTCACTCGGAGCG
TCGCCTGATTCTGGGTGAAAGTGACGAAGTGGTCGTGCTCAAGTTTGCAGCGGTACAGGCTGCAGGTTTGACTCCCGTGC
TCTGTGTGGGTGAAACCCGCGAGCAGCGTGAAGCGAATACAACGCTGGGTGTGGTGGGTGGCCAGTTGGCCGCAGTGATC
GACGCGCTGGGTGTCGATGCGCTGAAAAACGCCGTAGTGGCCTATGAGCCTGTATGGGCCATTGGTACCGGGTTGACCGC
TACGCCCGAGCAGGCTCAGGAAGTGCACGCAGCGATCCGCGCGCAAGTTGCGCTGCTCGATGCTGGTGTCGCGAGTGGGT
TGAGAATTCTTTATGGTGGCAGTGTGAAGGCCGCCAGTGCTGCCGAGTTGTTCGGCATGCGGGATATCGATGGGGGGCTC
GTAGGTGGCGCCTCTCTGAATGCGGATGAATTCGGTGCGATCTGTCGCGCT

Alignment

ORF - retro_atau_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.69 %
• Parental protein coverage: 68.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAFTGEISAEQLVDIGCQWVILGHSERRHVIGEDDQFIGKKAAYALSQNLKVMACIGELLEEREAGKTFD
          GA.TGE....QLVD.GC..V..GHSERR...GE.D.....K.A......L....C.GE..E.REA..T..
Retrocopy GALTGELAVSQLVDGGCELVLVGHSERRLILGESDEVVVLKFAAVQAAGLTPVLCVGETREQREANTTLG

Parental  VCFKQMKAFAD--NITDWKNVVIAYEPVWAIGTGKVASPEQAQEVHAAVRDWLKTNVSADVASTVRIIYG
          V...Q..A..D.......KN.V.AYEPVWAIGTG..A.PEQAQEVHAA.R........A.VAS..RI.YG
Retrocopy VVGGQLAAVIDALGVDALKNAVVAYEPVWAIGTGLTATPEQAQEVHAAIRAQVAL-LDAGVASGLRILYG

Parental  GSVNAANCAELAKKEDIDGFLVGGASLKGPDFATICNS
          GSV.AA..AEL....DIDG.LVGGASL....F..IC..
Retrocopy GSVKAASAAELFGMRDIDGGLVGGASLNADEFGAICRA

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_43 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_28795	1 retrocopy	retro_atau_43 ,