RetrogeneDB ID: retro_atau_16

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold88348:28321..29671(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_18404
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_06160
• Aliases: None
• Description: None

Sequence

>retro_atau_16
ATGGAGGAGCTCCGCAAGTCTATGTTTGTGGCTCTGATCCTCGCGGTCATCTGCTCCGTGGCGGTTGCGTATGATCCCCT
CGACCCGACAGGCAACATTACAATCAAGTGGGATATCCAGTCATGGACGCCTGACGGGTACGTCGCCATGGTGGCGATGA
ACAACTATCAGCAGTACCGTCAGATCATGGCGCCCGGGTGGACGCTGGGGTGGTCGTGGGCCAAGAAGGAGGTGATCTGG
TCCATCGTGGGAGCGCAGGCGACCGAGCAGGGCGACTGCTCCAAGTTCAAGGGCGGCATCCCGCACTGCTGCAAGCACAC
GCCCTCCGTCGTCGACCTCCTCCCCGGCGTCCCCTACAACCAGCAGATCGCCAACTGCTGCCGTGGCGGCGTCATCTCCG
CCTACGGCCAGGACCCCGCCGGCTCGCTCTCGGCGTTCCAGGTCTCCGTGGGGCTCGCCGGGACCACCAACAAGACCGTG
AAGCTGCCCAAGAACTTCACGCTCATGGGCCCCGGGCTCGGCTACACCTGCGGCCCGGCCACCATCGTCCCCTCCACCGT
CTACTGGAGCGCCGACCACCGGCGCAAGACTCAGGCGCTGATGACGTGGACGGTGACCTGCACCTACTCGCAGCAGCTGG
CGTCCAGGTACCCGACCTGCTGCGTCTCCTTCTCCTCCTTCTACAACAGCACCATCGTGCCGTGCGCCAAGTGCGCGTGC
GGCTGCGGCGCCCACAAGAGCATGGGCGGCCGCGGCGGCAAGAGCCACAGCGACGGCTGCATCATGGGCGACTCCAAGCG
GGCGCTCACCCCCGGGGTGAACACGCCCAAGAAGGACGGGGCGCAGCTGCTGCAGTGCACCAACCACATGTGCCCCATCC
GGGTGCACTGGCACGTGAAGCTCAACTACAAGGACTACTGGCGCGCCAAGATCGCCGTCACCAACTTCAACTACCGCATG
AACTACACGCAGTGGACCCTCGTCGCCCAGCACCCCAACCTCAACAACGTCACCGAGGTCTTCAGCTTCCAGTACAAACC
CCTCCTCCCCTACGGGAACATCAACGACACCGGCATGTTCTACGGCCTCAAGCTCTACAACGACCTGCTCATGGAGGCCG
GCCCCTTCGGCAACGTGCAGTCGGAGGTGCTCATGCGCAAGGACGACAGAACCTTCACCTTCAGCCAGGGATGGGCGTTC
CCGCGCAAGATCTACTTCAACGGCGACGAGTGCAAGATGCCGCCGCCCGACTCCTACCCCTACCTGCCCAACTCCGCGCC
GCTTGTGACGCCGCGTTCCCTCATCACCGCTGCCTCGGCGTGCTTGCTCGTGCTGCTCCTGGTGGCATGA

Alignment

ORF - retro_atau_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.51 %
• Parental protein coverage: 54.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MELPHAALALIVAAAATLSVAVAYDPLDPNGNITIKWDVLSWTPDGYVATVTINNFQTYRQIMAPGWTVG
          ME............A...SVAVAYDPLDP.GNITIKWD..SWTPDGYVA.V..NN.Q.YRQIMAPGWT.G
Retrocopy MEELRKSMFVALILAVICSVAVAYDPLDPTGNITIKWDIQSWTPDGYVAMVAMNNYQQYRQIMAPGWTLG

Parental  WTWAKREVIWSMVGAQATEQGDCSKFKANLPHSCKRTPAVVDLLPGVPYNQQIANCCRGGVVSAYGQDPS
          W.WAK.EVIWS.VGAQATEQGDCSKFK...PH.CK.TP.VVDLLPGVPYNQQIANCCRGGV.SAYGQDP.
Retrocopy WSWAKKEVIWSIVGAQATEQGDCSKFKGGIPHCCKHTPSVVDLLPGVPYNQQIANCCRGGVISAYGQDPA

Parental  GAVSSFQVSVGQAGTTNRTVKVPKNFTLLGPGPGYTCGPAKVVPSTVFLTADHRRKTQALMTWNVTCTYS
          G..S.FQVSVG.AGTTN.TVK.PKNFTL.GPG.GYTCGPA..VPSTV...ADHRRKTQALMTW.VTCTYS
Retrocopy GSLSAFQVSVGLAGTTNKTVKLPKNFTLMGPGLGYTCGPATIVPSTVYWSADHRRKTQALMTWTVTCTYS

Parental  QHLASKYPTCCVSFSSFYNDTIVPCAKCACGC
          Q.LAS.YPTCCVSFSSFYN.TIVPCAKCACGC
Retrocopy QQLASRYPTCCVSFSSFYNSTIVPCAKCACGC

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_16 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_06160	1 retrocopy	retro_atau_16 ,
Hordeum vulgare	MLOC_75040	1 retrocopy	retro_hvul_24,