RetrogeneDB ID: retro_atau_11

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold119313:2835..4767(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_11379
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_27431
• Aliases: None
• Description: None

Sequence

>retro_atau_11
ATGTGGATGTTCGCTACGCTCGTCGCGGCATTGTTTCTCGTGATGCCAGCCGCTTCCGCTGCGCCCACCGCCCTCGGAGG
GCAACACGGGCACCGTCATCGGCATCGACCTCGGCACCACCTACTCGTGCGTCGGCGTCTACCGCAACGGCCGCGTCGAG
ATCATCGCCAACGACCAGGGCAACCGGATCACCCCCTCCTGGGTCGCCTTCACCGACGGCGGCGAGCGGCTCATCGGCGA
GGCCGCCAAGAGGCAGCGGCCAACCCCGAGCGCACCATCTACGACGCCAAGCGCCTCATCGGCCGCGACTTCGCCGACGC
CGTCGTGCAGCGGGACATCAAGCTGCTGCCCTACTCCGTCGTCGACCGGAATGGCAAGCCGCACGTCCAGGTGCAGGTCA
AGGACGGCGACGTGCGCGTCTTCAGCCCCGAGGAGGTCAGCGCCATGGTGCTCACCAGGATGAAGGAGACCGCCGAGGCC
TACCTCGGCGAGAAGGTCACGCACGCCGTCGTCACCGTCCCCGCCTACTTCAACGACGCGCAGCGACAGGCCACCAAGGA
CGCCGGCGTCATCGCCGGGCGCAACGTCATCCGCATCGTCAACGAGCCCACCGCCGCGGCCATCGCCTACGGCATCGACG
AGAAGGGGCCCGAGAAGAACGTCCTGGTGTTCGACCTCGGCGGCGGCACCTTTGACGTCAGCGTGCTCTCCATCGACAAT
GGCGTCTTCGAGGTCCTCGCCACCAACGGCGACACGCACCTCGGCGGCGAGGATTTCGACCAGCGCCTCATGGACTACTT
CATCAAGCTCATCAAGCGCAAGCACGGCCGCGACATCGCCGGCGACCTGCGCGCGCTGGGGAAGCTGCGCCGGGAGTGCG
AGCGCGCCAAGCGTGCGCTCAGCAACCAGTACCAGGTGCGCGTCGAGATCGAATCGCTCTTCGACGGCGTCGACTTCTCG
GAGCCGCTCACCAGGGCACGGTTCGAGGAGCTCAACAACGACCTTTTCCGCAAGACGATGGTGCCCGTGAAGAAGGCCAT
GGCGGATGCCGGGCTCAACAAGGCTGACATCGACGAGATCGTGCTCGTCGGTGGCAGCACCAGGATTCCCAAGGTGCAGC
AGCTTCTCAAGGACTACTTCAACGGCAAGGAACCTAACAAGGGGGTCAACCCCGACGAGGCCGTCGCGTACGGCGCTGCC
GTGCAGGCCAGCATCGTGAGCGGACACGTCGACGAGAACACCAAAACCATGATCCTGCTCGACGTCGCGCCGCTTACACT
AGGCATGGAGACGGTCGGCGGCGTGATGACGAAGCTGATCCCGAGGAACACGGTGGTGCCGACAAAGAAGACACAGGTGT
TCACCACGTACCAGGACAAGCAGACCACCGTGTCCATCAAGGTCTACGAGGGCGAGCGGAGCATGACCAAGGACAACAGG
CTCCTCGGTAAGTTTGACCTCTCCGGGATCCCGCCGTCTCCGAGGGGCACGCCACAGCTTGAGGTGACGTTCGACGTGGA
CGTCAACGGCATCCTGCACGTGAAGGCGGCGGACAAGGGCACCGGCAAATCGGAGAAGATCACCATCACCAACGAGGACC
GTCGGCATAGCCAGGAGGACATCGACCGGATGGTGCGCGAGGCAGAGGAGTTCGCCGAGGCGGATCACAAGCTCAAGGAG
CGGGTCGACGCTCGGAACAAGCTAGAGACGTACGTGTACAGCATCAAGAACACCGTCGACACCAAGATGGCCGATGCCAT
GGAGAGGGATGAGAAGGAGAAGGTCCAGGATGCGCTGAGGGAGGTAAACGAGTGGCTCGATGACAACACAGAGGCAGAGA
AGGAGGACTACGATGAGAAGCTTCGGGAGATGGAAGACGTGTGCAACCCTATCATCACTAGTAGAAAAACGACTTTTAGT
ACCGGTTCGTAA

Alignment

ORF - retro_atau_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.2 %
• Parental protein coverage: 83.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNQAAVNPERTVFDVKRLIGRKFEDKEVQRDMKLVPYKIVNKEGKPYIQVKIKDGETKVFSPEEISAMIL
          ...AA.NPERT..D.KRLIGR.F.D..VQRD.KL.PY..V...GKP..QV..KDG...VFSPEE.SAM.L
Retrocopy RQEAAANPERTIYDAKRLIGRDFADAVVQRDIKLLPYSVVDRNGKPHVQVQVKDGDVRVFSPEEVSAMVL

Parental  GKMKETAEAYLGKKINDAVVTVPAYFNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGLDKRGGEKNI
          ..MKETAEAYLG.K...AVVTVPAYFNDAQRQATKDAGVIAG.NV.RI.NEPTAAAIAYG.D..G.EKN.
Retrocopy TRMKETAEAYLGEKVTHAVVTVPAYFNDAQRQATKDAGVIAGRNVIRIVNEPTAAAIAYGIDEKGPEKNV

Parental  LVFDLGGGTFDVSILTIDNGVFEVLATNGDTHLGGEDFDHRIMDYFIKLIKKKHGKDISKDNRALGKLRR
          LVFDLGGGTFDVS.L.IDNGVFEVLATNGDTHLGGEDFD.R.MDYFIKLIK.KHG.DI..D.RALGKLRR
Retrocopy LVFDLGGGTFDVSVLSIDNGVFEVLATNGDTHLGGEDFDQRLMDYFIKLIKRKHGRDIAGDLRALGKLRR

Parental  EAERAKRALSNQHQVRVEIESLFDGTDFSEPLTRARFEELNNDLFRKTMGPVKKAMDDAGLEKTQIHEIV
          E.ERAKRALSNQ.QVRVEIESLFDG.DFSEPLTRARFEELNNDLFRKTM.PVKKAM.DAGL.K..I.EIV
Retrocopy ECERAKRALSNQYQVRVEIESLFDGVDFSEPLTRARFEELNNDLFRKTMVPVKKAMADAGLNKADIDEIV

Parental  LVGGSTRIPKVQQLLRDYFDGKEPNKGVNPDEAVAFGAAVQGSILSGEGGDETKDILLLDVAPLTLGIET
          LVGGSTRIPKVQQLL.DYF.GKEPNKGVNPDEAVA.GAAVQ.SI.SG.....TK...LLDVAPLTLG.ET
Retrocopy LVGGSTRIPKVQQLLKDYFNGKEPNKGVNPDEAVAYGAAVQASIVSGHVDENTKTMILLDVAPLTLGMET

Parental  VGGVMTKLIPRNTVIPTKKSQVFTTYQDQQTTVSIQVFEGERSMTKDCRLLGKFDLSGIPPAPRGTPQIE
          VGGVMTKLIPRNTV.PTKK.QVFTTYQD.QTTVSI.V.EGERSMTKD.RLLGKFDLSGIPP.PRGTPQ.E
Retrocopy VGGVMTKLIPRNTVVPTKKTQVFTTYQDKQTTVSIKVYEGERSMTKDNRLLGKFDLSGIPPSPRGTPQLE

Parental  VTFEVDANGILNVKAEDKGTGKSEKITITNEKGRLSQEEIDRMVKEAEEFAEEDKKVKERIDARNQLETY
          VTF.VD.NGIL.VKA.DKGTGKSEKITITNE..R.SQE.IDRMV.EAEEFAE.D.K.KER.DARN.LETY
Retrocopy VTFDVDVNGILHVKAADKGTGKSEKITITNEDRRHSQEDIDRMVREAEEFAEADHKLKERVDARNKLETY

Parental  VYNMKNTVGDKDKLADKLESEEKEKVEEALKEALEWLDENQTAEKEDYEEKLKEVEAVCNPIVSA
          VY..KNTV....K.AD..E..EKEKV..AL.E..EWLD.N..AEKEDY.EKL.E.E.VCNPI...
Retrocopy VYSIKNTV--DTKMADAMERDEKEKVQDALREVNEWLDDNTEAEKEDYDEKLREMEDVCNPIITS

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_11 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G01477	1 retrocopy	retro_bdis_30,
Aegilops tauschii	F775_27431	1 retrocopy	retro_atau_11 ,
Oryza longistaminata	KN538684.1_FG046	1 retrocopy	retro_olon_13,
Hordeum vulgare	MLOC_55999	1 retrocopy	retro_hvul_1,
Oryza nivara	ONIVA01G37420	1 retrocopy	retro_oniv_8,
Oryza rufipogon	ORUFI02G01160	1 retrocopy	retro_oruf_18,
Sorghum bicolor	Sb04g001140	1 retrocopy	retro_sbic_39,
Triticum aestivum	Traes_6DS_A593093E1	1 retrocopy	retro_taes_72,