RetrogeneDB ID: retro_atau_1

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold65995:40081..41389(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_06159
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_19450
• Aliases: None
• Description: None

Sequence

>retro_atau_1
ATGGCCGTGCCCACCAATGACTCCGCCGTGCGCGCGCGCCTCCGCCGTCTCGGCGAGCCCATCACGCTCTTCGGCGAGGG
CGCGATGGAGCGCCGCGACCGCCTGCGCGCGCTCATGGCCCGCCTCGAGGCCGAGGGCCAGTTCGACCGCCTCCTCCGCG
CGCAGGAGGACGAACGGGGAGCCTCGGGCGACGACGACGACGAGGGCACGGAGCAGATCAAGTACCCGTTCTTCACCGAG
GGGACCAACCAACTGCTCCAGGCGCGCATTGACATCGCCATGTACTCACTGCCCCGCGCCAAGGCCAGGGTCGAGAGGGC
CAAGCGACGCCTCGCCGACCCCGACGAGGACCCCGAGGCAGAGGCCGCCCTTGTTGTGAAGCAGGCGGCGGACTTCGCGC
TTGAGCGCAGCGAGATTGGAGACGACCGCCCGCTCACCGGCTGCTCCTTCTCCCGGGATGCCTCGATGCTCGCCACAAGT
TCCTGGAGTGGGATCGTCAAAGTGTGGAGCATGCCACAGATAGCCAAGATTGCAACCCTGAAAGGCCATACAGAACGTGC
AACTGATGTTGCCTTCTCCCCAGTCGACAACTGCTTAGCGACAGCCTCAGCTGATAAAACTGCCAAATTGTGGAACAGCG
ATGGCTCACTTCTGATGTCTTTTGATGGTCACCTGGATCGTCTTGCTCGCCTTGCTTTTCATCCATCTGGAAAGTACCTT
GGTACAGCTAGCTTTGACAAGACCTGGAGATTGTGGGACATCAACACTGGAACTGAACTTCTACTCCAGGAGGGACATAG
CAGAAGTGTATATGGTGTCAGCTTTCACCCAGACGGTTCTTTAGCTGCATCTTGTGGGTTTGATGCGAGTGCTCGAGTTT
GGGATTTAAGGTCAGGAAGATTGTACTGTACCCTCATTGGAAATGTGAAACCTGTCCTAGGAGTCGGCTTCTCCCCTAAT
GGTCATCTGGTTGCAACCACAAGTGAAGACAATTTCTGTCGAATATGGGATTTGAGGACCAGACAAATGTTATATTCTAT
ACCAGCACATAAGAGTCTCATCTCGCATGTGAAATTCGAACCCCAGGAGGGTTATTATTTAGCAACATCTTCCTATGACA
CTAAAGCAGCGCTATGGTCAACTCGGGATTACAAACCAATTAAAAGCTTGTCAGGCCATGAGTCAAACGTTACTAGTCTG
GATATTAGTGGAGATGGACAACAGATTGTGACTGTTTCACTTGATAGAACGATAAAGATCTGGTCATGCAGAGGCAGTGC
GCGGGATAATGAGATGGAGTTGGATTAA

Alignment

ORF - retro_atau_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.1 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVPTNDSAVRARLRRLGEPITLFGEREMERRDRLRALMVRLEADGQFDRLLRVQEDEQGAPGDDDD--M
          MAVPTNDSAVRARLRRLGEPITLFGE..MERRDRLRALM.RLEA.GQFDRLLR.QEDE.GA.GDDDD...
Retrocopy MAVPTNDSAVRARLRRLGEPITLFGEGAMERRDRLRALMARLEAEGQFDRLLRAQEDERGASGDDDDEGT

Parental  EQIQYPFFTEGTNQLLQARVDIAMYSLPRAKARVDRAKRRLADLDEDPEAEADLVVKQAGDFVLECSEIG
          EQI.YPFFTEGTNQLLQAR.DIAMYSLPRAKARV.RAKRRLAD.DEDPEAEA.LVVKQA.DF.LE.SEIG
Retrocopy EQIKYPFFTEGTNQLLQARIDIAMYSLPRAKARVERAKRRLADPDEDPEAEAALVVKQAADFALERSEIG

Parental  DDRPLTGCSFSRDASMLATSSWSGILKVWSMPQITKIATLKGHTERATDVAFSPVDNCLATASADKTAKL
          DDRPLTGCSFSRDASMLATSSWSGI.KVWSMPQI.KIATLKGHTERATDVAFSPVDNCLATASADKTAKL
Retrocopy DDRPLTGCSFSRDASMLATSSWSGIVKVWSMPQIAKIATLKGHTERATDVAFSPVDNCLATASADKTAKL

Parental  WNSDGSLLMSFDGHLDRLARVAFHPSGKYLGTASFDKTWRLWDINTGTELLLQEGHSRSVYGVSFHPDGS
          WNSDGSLLMSFDGHLDRLAR.AFHPSGKYLGTASFDKTWRLWDINTGTELLLQEGHSRSVYGVSFHPDGS
Retrocopy WNSDGSLLMSFDGHLDRLARLAFHPSGKYLGTASFDKTWRLWDINTGTELLLQEGHSRSVYGVSFHPDGS

Parental  LAASCGLDANARVWDLRSGRLYCTLIGHVKPVLGVGFSPNGHLVATASEDNFCRIWDLRTRQMLYSIPAH
          LAASCG.DA.ARVWDLRSGRLYCTLIG.VKPVLGVGFSPNGHLVAT.SEDNFCRIWDLRTRQMLYSIPAH
Retrocopy LAASCGFDASARVWDLRSGRLYCTLIGNVKPVLGVGFSPNGHLVATTSEDNFCRIWDLRTRQMLYSIPAH

Parental  KSLISHVKFEPQEGYYLATSSYDTKAALWSTRDYKPIKCLAGHESKVTSLDISGDGQQIVTVSHDRTIKI
          KSLISHVKFEPQEGYYLATSSYDTKAALWSTRDYKPIK.L.GHES.VTSLDISGDGQQIVTVS.DRTIKI
Retrocopy KSLISHVKFEPQEGYYLATSSYDTKAALWSTRDYKPIKSLSGHESNVTSLDISGDGQQIVTVSLDRTIKI

Parental  WSCRGTARDNEMELD
          WSCRG.ARDNEMELD
Retrocopy WSCRGSARDNEMELD

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_1 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_19450	1 retrocopy	retro_atau_1 ,
Hordeum vulgare	MLOC_50327	1 retrocopy	retro_hvul_8,
Triticum aestivum	Traes_4AL_060131441	1 retrocopy	retro_taes_21,