RetrogeneDB ID: retro_atau_37

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold260505:16053..16656(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_30198
• Aliases: None
• Description: None

Sequence

>retro_atau_37
ATCATGACTATTCTCGTTACTGGTGGAGCAGGCTACATTGGTTCACATGCATTGGTTGAGCTTGCCTCGGCGGGTTTTGA
TTTTGTTGTGCTGGATAACCTGTGTAATTCATCTTCGGTTTCTTTACAGCGTGTGCAGGCCATTACTGGCAAGTCGGTTG
AGTTTGTGCAGGGTGATATTCGTAATGCTGAACTCTTAAAGCAGCTATTTACTCGTTACTCCATCAGTGCGGTCATGCAT
TTTGCCGGTTTGAAATCCGTGGGCGAAAGTGTGGCGCAGCCGCTACGTTATTACGATAACAACGTATGTGGCAGCCAAGT
GTTGTTCCAAGCCATGGCCGATGCGTGTGTGTTTAACATCGTATTCAGCTCGTCGGCGACCGTGTATGGTGACCCGGCTG
AAATGCCTATCTCCGAGCAGTGCCCGGTTGGCCGGCCAACGAATCCCTATGGTCGGTCAAAGTTGATGGTCGAAGATATT
CTGCGCGATTTAGCGTTGTCTGACCCACGTTGGCGGGTGGCACTTTTGCGCTATTTTAACCCGGTGGGAGCGCATGAGAG
TGGCAGCATAGGGGAGGATCCGAACGGTATTCCGGATAATCTG

Alignment

ORF - retro_atau_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.9 %
• Parental protein coverage: 55.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRTILVTGGAGYIGSHTVLQLLLQGFRVLVVDSLDNASEEAIRRVRQLANAPQNSLDFRKVDLRDKEALD
          ..TILVTGGAGYIGSH....L...GF...V.D.L.N.S.....RV.........S..F...D.R..E.L.
Retrocopy IMTILVTGGAGYIGSHALVELASAGFDFVVLDNLCNSSSVSLQRVQAITG---KSVEFVQGDIRNAELLK

Parental  QIFSSQRFEAVIHFAGLKAVGESVDKPLLYYDNNLIGTITLLQVMAAHGCKKLVFSSSATVYGWPKEVPC
          Q.F......AV.HFAGLK.VGESV..PL.YYDNN..G...L.Q.MA.......VFSSSATVYG.P.E.P.
Retrocopy QLFTRYSISAVMHFAGLKSVGESVAQPLRYYDNNVCGSQVLFQAMADACVFNIVFSSSATVYGDPAEMPI

Parental  TEEFPLS-ATNPYGRTKLVIEDICRDLQRSDPDWKIILLRYFNPVGAHPSGYIGEDPLGVPNNL
          .E..P....TNPYGR.KL..EDI.RDL..SDP.W...LLRYFNPVGAH.SG.IGEDP.G.P.NL
Retrocopy SEQCPVGRPTNPYGRSKLMVEDILRDLALSDPRWRVALLRYFNPVGAHESGSIGEDPNGIPDNL

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_37 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_30198	1 retrocopy	retro_atau_37 ,