RetrogeneDB ID: retro_atau_12

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold17807:100545..101433(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_06129
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_06457
• Aliases: None
• Description: None

Sequence

>retro_atau_12
ATGGCGCTGAACGAGAGCCTCGCCAGGTTCCGGCTGCTGCAGGAGAGGAACCAGGCGGCTCTGTCCGCCATCGCCGCAAC
CAGAACCTCATCATCGTCATGCACCAAGCCGTCCCAGCAGCAACCCGCTCCAACTCCACGGCCGGCAGCCAAGCCATCCC
CGCCCGCGCCTGCCGCCGCTGTCGTCAGATTCTCCGATGACACGGCGCGGCTACGGAAGATCAACGAGGTGAGGAGGTCC
ACGGTCGGGCACCAGATGAAAAACGTGATCGACCTGCTCGACAAGACGAGGGAAGCTCTTACGACGCATCAGATCAACCA
ATGGACCTACGTCGACATCGACGGCAGCAGGACCCTCGCCGAGAGCCTGAGGAACAACCCCAAGGTGCGCTTCGACGGGC
GGCGCTACTCCTACAAGCCCACGCACGACGTCAAGGCCAAAGGCGAGCTGCTGACACTGATCAAGAGCTTCCCGGACGGC
CTCCCGGCGTCCGAGGTGGATGACGCGTATCCAGCCGTCTTGGAAGATCTGCAGGCCTTGAAATCCTCGGGCGACGTCTA
TCTGCTGCCGGGCGAGGGAGGCATCATAGCGTACCCGAACGACGACCCGAGGTCGAAGATCGGGGTGGACACCGAGCTCA
AGAAGCTGTTCCACGACATCAAGCTCCCGCGGGAGATGATCGACATCGAGAAGGAGCTCAGGAAGAACGGCGAGAGGCCG
GCCACCGATACTATGAAGCGGCGCGCGGCGGAGCAGCTCAATGGCCGGCAGCCCAAGCCGAAGAAGGCCAAGAAGAAGTC
GCGCGGGCTCACCAGCAGGACCAAGCTCACCAACGTTCATCTCCCGTGGCTCATGGACCTGCCTGTGGATTCGAAGGATA
TCATCTGA

Alignment

ORF - retro_atau_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.26 %
• Parental protein coverage: 64.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALNERLSKFK---QQQERCQTTLSSIAATQASTTKSHN---APRSRPANAPSAPAKQIQAIKFSNDTER
          MALNE.L..F......................S.TK......AP..RPA..PS.PA.......FS.DT.R
Retrocopy MALNESLARFRLLQERNQAALSAIAATRTSSSSCTKPSQQQPAPTPRPAAKPSPPAPAAAVVRFSDDTAR

Parental  LQHINSVRKSPVGAQIKLVIELLYKTRLAYTAEQINEATYVAINSNKAVFDSLTNNPKVQFDGKRFSYKS
          L..IN.VR.S.VG.Q.K.VI.LL.KTR.A.T..QIN..TYV.I........SL.NNPKV.FDG.R.SYK.
Retrocopy LRKINEVRRSTVGHQMKNVIDLLDKTREALTTHQINQWTYVDIDGSRTLAESLRNNPKVRFDGRRYSYKP

Parental  KHDLKGKDQLLHLIRRFPEGLPVVEVKDSYPTVLDDLQALKASGDVWWL
          .HD.K.K..LL.LI..FP.GLP..EV.D.YP.VL.DLQALK.SGDV..L
Retrocopy THDVKAKGELLTLIKSFPDGLPASEVDDAYPAVLEDLQALKSSGDVYLL

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_12 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_06457	1 retrocopy	retro_atau_12 ,
Hordeum vulgare	MLOC_10618	1 retrocopy	retro_hvul_52,
Triticum aestivum	Traes_4AS_90C3255FC	1 retrocopy	retro_taes_119,