RetrogeneDB ID: retro_atau_21

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold45110:53527..54517(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_52717
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_09413
• Aliases: None
• Description: None

Sequence

>retro_atau_21
ATGGTTGTCCCGGTCATCGACTTCTCCAAGCTCGACGGCGCCGAGAGGGCCGAGACCATGGCGCAGATCGCCGACGGCTG
CGAGAACTGGGGCTTCTTCCAGCTGGTGAACCACGGCATCCCGCTGGAGCTTCTTGACCGCGTCAAGAAGGTGTGCTCCG
AGAGCTACCGCCTCCGGGAGGCCGCGTTCCGGTCGTCCGAGCCGGTGCAGACGCTGGAGAGGCTGGTGGAGGCGGAGCGG
CGCGGCGAGGCGGTGGCGCCGGTGGACGACATGGACTGGGAGGACATCTTCTCCCTCCACGACGACAACCAGTGGCCCTC
CGACCCGCCGGCCTTCAAGGAGACCATGCGGGAGTACCGCGCCGAGCTCAAGAAGCTCGCGGAGCGGGTCATGGAGGCCA
TGGACGAGAACCTCGGCCTGGACAAGGGCCGCATGAAGGCCGCCTTCACTGGAGACGGCCTCCACGCGCCATTCTTCGGC
ACCAAGGTCAGCCACTACCCGCCGTGCCCGCGCCCGGACCTCATCACCGGGCTCCGCGCGCACACCGACGCCGGCGGCGG
CATCCTGCTGTTCCAGGACGACAAGGTAGGCGGCCTCGAGGTACTCAAGGACGGCGAGTGGCTCGACGTGCAGCCGCTCC
CCGACGCCATCGTCGTCAACACCGGCGACCAAGTGGAGGTGCTCAGCAACGGCCGCTACCGCAGCGCGTGGCACCGCGTC
CTGCCCATGCGCAACGGCAACCGCCGCTCCATCGCGTCTTTCTACAACCCGGCGTTCGAGGCGTGCCCGTGCCGCCTGCC
CCCCCGGCGCTCCATCGCGTCCTTCTACAACCCGGCGTTCGAGGTGGCCATCTCGCCGGCGGTGGGCGAAGGCGCCGCCG
CCGCGTACCCGGACTACGTGTTCGGGGATTACATGGACGTGTACAACAAGCAGAAGTTCGATGCCAAGGAGCCAAGGTTC
GAGGCCGTCAAGGCGCCAAAGTCAGCTTAA

Alignment

ORF - retro_atau_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.31 %
• Parental protein coverage: 82.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAIPVIDFSRLDGDERAAALAEIAAGFEQWGFFQLVNTGIPDELLERVKKVCSDCYKLREEGFNGSNPAV
          M..PVIDFS.LDG.ERA...A.IA.G.E.WGFFQLVN.GIP.ELL.RVKKVCS..Y.LRE..F..S.P.V
Retrocopy MVVPVIDFSKLDGAERAETMAQIADGCENWGFFQLVNHGIPLELLDRVKKVCSESYRLREAAFRSSEP-V

Parental  KALAALVEREGEGLAPRKVEGMDWEDVFTLHDDLPWPSIPPTFKETMMEYRTELKKLAEKLLGVMEELLG
          ..L..LVE.E..G.A...V..MDWED.F.LHDD..WPS.PP.FKETM.EYR.ELKKLAE.....M.E.LG
Retrocopy QTLERLVEAERRGEAVAPVDDMDWEDIFSLHDDNQWPSDPPAFKETMREYRAELKKLAERVMEAMDENLG

Parental  LAEGQITKVFSKDGDFKPFYGTKVSHYPPCPRPEMVDGLRAHTDAGGLILLFQDDRVGGLQVLGRDGRWA
          L..G.....F..DG...PF.GTKVSHYPPCPRP....GLRAHTDAGG.ILLFQDD.VGGL.VL..DG.W.
Retrocopy LDKGRMKAAFTGDGLHAPFFGTKVSHYPPCPRPDLITGLRAHTDAGGGILLFQDDKVGGLEVL-KDGEWL

Parental  DVQPVENAIVINTGDQIEVMSNGRYKSAWHRVLATRDGNRRSIASFYNPA
          DVQP...AIV.NTGDQ.EV.SNGRY.SAWHRVL..R.GNRRSIASFYNPA
Retrocopy DVQPLPDAIVVNTGDQVEVLSNGRYRSAWHRVLPMRNGNRRSIASFYNPA

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_21 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_09413	1 retrocopy	retro_atau_21 ,
Hordeum vulgare	MLOC_34709	1 retrocopy	retro_hvul_12,