RetrogeneDB ID: retro_taes_72

Retrocopy location

• Organism: Wheat (Triticum aestivum)
• Coordinates: IWGSC_CSS_7DL_scaff_3332001:199..1708(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Traes_7DL_988A0B630
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Traes_6DS_A593093E1
• Aliases: None
• Description: None

Sequence

>retro_taes_72
ATGGTGCTCACTAGGATGAAGGAGACCGCCGAGGCCTACCTCGGCGAGAAGGTCACGCACGCCGTCGTCACCGTGCCGGC
CTACTTCAACGACGCGCAGCGCCAGGCCACCAAGGACGCCGGCGTCATCGCCGGGCTCAACGTCATCCGCATCGTCAACG
AGCCCACCGCCGCGGCCATCGCCTACGGCATCGACGAGAAGGGCCCCGAGAAGAACGTCCTCGTCTTCGACCTCGGCGGC
GGCACCTTTGACGTCAGCGTGCTCTCCATCGACAATGGCGTCTTCGAGGTCCTGGCCACCAACGGCGACACGCACCTCGG
CGGTGAGGATTTCGACCAGCGCCTCATGGACTACTTCATCAAGCTCATCAAGCGCAAGCACGGCCGGGACATCGCCGGCG
ACCTGCGCGCGCTGGGGAAGCTGCGGCGGGAGTGCGAGCGCGCAAAGCGTGCGCTCAGCAACCAGCATCAGGTGCGCGTC
GAGATCGAATCGCTCTTCGACGGCGTCGACTTCTCGGAGCCGCTCACCAGGGCACGGTTCGAGGAGCTCAACAATGACCT
TTTCCGCAAGACAATGGTGCCGGTGAAGAAGGCCATGGCGGACGCTGGGCTAAGCAAGGCTGACATCGACGAGATCGTGC
TCGTCGGTGGCAGCACCAGGATTCCCAAGGTGCAGCAGCTCCTCAAGGACTACTTCAACGGCAAGGAACCCAACAAGGGG
GTCAACCCCGACGAGGCCGTTGCGTACGGCGCCGCCGTGCAGGCCAGCATCGTGAGCGGACACGTCGACGAGAACACCAA
AACCATGATCCTGCTCGACGTCGCGCCGCTTACACTAGGCATGGAGACTGTCGGCGGGGTGATGACGAAGCTGATCCCGA
GGAACACGGTGGTGCCGACAAAGAAGACGCAGGTGTTCACCACGTACCAGGACAAGCAGACCACCGTGTCCATCAAGGTC
TACGAGGGCGAGCGGAGCATGACCAAGGACAACAGGCTCCTCGGCAAGTTTGACCTCTCCGGGATCCCGCCGGCTCCGAG
GGGTACGCCACAGATTGAGGTGACGTTCGAGGTGGACGTCAACGGCATCCTGCACGTGAAGGCCGCCGACAAGGGCACCG
GCAAGTCGGAGAAGATCACCATCACCAACGAGGACCGTCGGCATAGCCAGGAGGACATCGACCGGATGGTGCGCGAGGCA
GAGGAGTTCGCCGAGGCGGATCACAAGCTCAAGGAGCGGGTCGACGCTCGGAACAAGCTAGAGACGTATGTGTACGGCGT
CAAGAACACAGTCGACGGCAAGATGGCCGACGCAATGGAGAGGGATGAGAAGGAGAAGGTTCAGGATGCAGTGAGGGAGG
TGAACGAGTGGCTCGACGACAACGCGGAAGCGGAGAAGGAGGACTACGATGAGAAGCTCCAGGAGCTTGAAGACGTGTGC
AACCCTATCCTCACGACGGTGTACCAGAGGTCTGGAGGAGCACCAACCGAGGAAGACGAACATGATGAG

Alignment

ORF - retro_taes_72 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.4 %
• Parental protein coverage: 75.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MILGKMKETAEAYLGKKINDAVVTVPAYFNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGLDKRGGE
          M.L..MKETAEAYLG.K...AVVTVPAYFNDAQRQATKDAGVIAGLNV.RI.NEPTAAAIAYG.D..G.E
Retrocopy MVLTRMKETAEAYLGEKVTHAVVTVPAYFNDAQRQATKDAGVIAGLNVIRIVNEPTAAAIAYGIDEKGPE

Parental  KNILVFDLGGGTFDVSILTIDNGVFEVLATNGDTHLGGEDFDHRIMDYFIKLIKKKHGKDISKDNRALGK
          KN.LVFDLGGGTFDVS.L.IDNGVFEVLATNGDTHLGGEDFD.R.MDYFIKLIK.KHG.DI..D.RALGK
Retrocopy KNVLVFDLGGGTFDVSVLSIDNGVFEVLATNGDTHLGGEDFDQRLMDYFIKLIKRKHGRDIAGDLRALGK

Parental  LRREAERAKRALSNQHQVRVEIESLFDGTDFSEPLTRARFEELNNDLFRKTMGPVKKAMDDAGLEKTQIH
          LRRE.ERAKRALSNQHQVRVEIESLFDG.DFSEPLTRARFEELNNDLFRKTM.PVKKAM.DAGL.K..I.
Retrocopy LRRECERAKRALSNQHQVRVEIESLFDGVDFSEPLTRARFEELNNDLFRKTMVPVKKAMADAGLSKADID

Parental  EIVLVGGSTRIPKVQQLLRDYFDGKEPNKGVNPDEAVAFGAAVQGSILSGEGGDETKDILLLDVAPLTLG
          EIVLVGGSTRIPKVQQLL.DYF.GKEPNKGVNPDEAVA.GAAVQ.SI.SG.....TK...LLDVAPLTLG
Retrocopy EIVLVGGSTRIPKVQQLLKDYFNGKEPNKGVNPDEAVAYGAAVQASIVSGHVDENTKTMILLDVAPLTLG

Parental  IETVGGVMTKLIPRNTVIPTKKSQVFTTYQDQQTTVSIQVFEGERSMTKDCRLLGKFDLSGIPPAPRGTP
          .ETVGGVMTKLIPRNTV.PTKK.QVFTTYQD.QTTVSI.V.EGERSMTKD.RLLGKFDLSGIPPAPRGTP
Retrocopy METVGGVMTKLIPRNTVVPTKKTQVFTTYQDKQTTVSIKVYEGERSMTKDNRLLGKFDLSGIPPAPRGTP

Parental  QIEVTFEVDANGILNVKAEDKGTGKSEKITITNEKGRLSQEEIDRMVKEAEEFAEEDKKVKERIDARNQL
          QIEVTFEVD.NGIL.VKA.DKGTGKSEKITITNE..R.SQE.IDRMV.EAEEFAE.D.K.KER.DARN.L
Retrocopy QIEVTFEVDVNGILHVKAADKGTGKSEKITITNEDRRHSQEDIDRMVREAEEFAEADHKLKERVDARNKL

Parental  ETYVYNMKNTVGDKDKLADKLESEEKEKVEEALKEALEWLDENQTAEKEDYEEKLKEVEAVCNPIVSAVY
          ETYVY..KNTV....K.AD..E..EKEKV..A..E..EWLD.N..AEKEDY.EKL.E.E.VCNPI...VY
Retrocopy ETYVYGVKNTV--DGKMADAMERDEKEKVQDAVREVNEWLDDNAEAEKEDYDEKLQELEDVCNPILTTVY

Parental  QRSGGAPGGE
          QRSGGAP..E
Retrocopy QRSGGAPTEE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Triticum aestivum was not studied using RNA-Seq expression data.

ChIP-Seq

Triticum aestivum was not studied using ChIP-Seq data.

EST

Triticum aestivum was not studied using EST data.

TSS

Triticum aestivum was not studied using FANTOM5 data.

Lab

retro_taes_72 was not experimentally validated.

Homology

Retrocopy orthology:

Triticum aestivum 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 ,