RetrogeneDB ID: retro_atau_44

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold28265:33618..35292(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_28539
• Aliases: None
• Description: None

Sequence

>retro_atau_44
CGCGCGCAGTCGGCGCAGAAGTCGCGCGGCGACTCGCACCTCGCCGTCGACCAGCTGCTCATGGGCCTCCTCGAGGACCC
GCAGATCTCCGACGCGCTCAAGGAGGCCGGCATCTCCGCTGCGCGGGTGAAGGCCGAGGTCGAGAAGCTCCGGGGAGGCG
ACAACCGGCGCGTGGAGTCCGCGTCGGGGGACACCAACTTCCAGGCCCTCAAGACGTACGGCCGCGACCTCGTGGAGGTG
GCGGGCAAGCTGGACCCGGTCATCGGCCGCGACGAGGAGATCCGGCGCGTGGTGCGGATCCTGTCGCGGCGCACAAAGAA
CAACCCCGTCCTCATCGGCGAGCCCGGCGTGGGCAAGACGGCCGTCGTGGAGGGCCTCGCGCAGCGCGTCGTGCGCGGGG
ACGTGCCCAGCAACCTGCTCGACGTCCGCCTCGTCGCGCTCGACATGGGCGCGCTCGTCGCCGGCGCCAAGTACCGCGGC
GAGTTCGAGGAGCGGCTCAAGGCCGTGCTCAAGGAGGTGGAGGAGGCCGAGGGCAAGGTCATCCTCTTCATCGACGAGAT
ACACCTCGTCCTCGGCGCCGGGAGGACGGAGGGGTCCATGGACGCCGCCAACCTGTTCAAGCCGATGCTCGCCAGGGGCC
AGCTCCGGTGCATCGGCGCCACCACGCTGGAGGAGTACCGCAAGTACGTCGAGAAGGACGCCGCGTTCGAGCGGCGGTTC
CAGCAGGTGTACGTGGCCGAGCCGAGCGTCGCCGACACCATCAGCATCCTGCGAGGGCTCAAGGAGAAGTACGAGGGGCA
CCACGGCGTGCGCATCCAGGACCGCGCCATCGTCGTCGCGGCGCAGCTCTCGGCGAGGTACATCATGGGCCGGCACCTGC
CGGACAAGGCCATCGACCTGGTGGACGAGGCGTGCGCCAACGTGAGGGTGCAGCTGGACAGCCAGCCGGAGGAGATCGAC
AACCTGGAGAGGAAGCGGATTCAGCTGGAGGTGGAGCTGCACGCGCTGGAGAAGGAGAAGGACAAGGCCAGCAAGGCCCG
GCTGGTGGAGGTGAGGAAGGAGCTGGACGACCTGAGGGACAAGCTGCAGCCGCTGACCATGAAGTACAGGAAGGAGAAGG
AGCGGATCGACGAGATCCGGAAGCTGAAGCAGCGGCGCGAGGAGCTGCAGTTCACGCTGCAGGAGGCCGAGCGGCGCATG
GACCTGGCCCGGGTCGCCGACCTCAAGTACGGCGCCCTCCAGGAGATCGACGCCGCCATCGCCAAGCTGGAGGGCGAGAC
CGGCGAGAACCTGATGCTCACCGAGACCGTCGGCCCGGAGCAGATCGCGGAGGTGGTGAGCCGGTGGACCGGCATCCCGG
TGACCCGGCTCGGGCAGAACGACAAGGAGCGGCTCGTCGGCATGGCGGACAGGCTGCACACGAGGGTGGTCGGGCAGACG
GAGGCCGTGAACGCCGTCGCCGAGGCTGTGCTGAGGTCCAGGGCGGGGCTTGGACGGCCGCAGCAGCCCACCGGGTCGTT
CCTCTTCCTGGGCCCGACCGGCGTGGGCAAGACCGAGCTCGCCAAGGCCCTCGCCGAGCAGCTGTTCGACGACGAGAACC
TGCTCGTCCGCATCGACATGTCCGAGTACATGGAGCAGCACTCCGTCGCCCGCCTCATCGGAGCGCCACCTGGG

Alignment

ORF - retro_atau_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.12 %
• Parental protein coverage: 62.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KAMKYKKEYGDEFVSVEHMLRAFTADKRFGQQLFEDLQIGENELKEAISAVRG--SQRVTDQNPEGKFQA
          .A....K..GD....V...L.....D......L.....I.....K......RG....RV........FQA
Retrocopy RAQSAQKSRGDSHLAVDQLLMGLLEDPQISDAL-KEAGISAARVKAEVEKLRGGDNRRVESASGDTNFQA

Parental  LEKYGIDMTELARRGKLDPVIGRDDEVRRCIQILCRRTKNNPVIIGEPGVGKTAIAEGLAQRIVRGDVPE
          L..YG.D..E.A..GKLDPVIGRD.E.RR...IL.RRTKNNPV.IGEPGVGKTA..EGLAQR.VRGDVP.
Retrocopy LKTYGRDLVEVA--GKLDPVIGRDEEIRRVVRILSRRTKNNPVLIGEPGVGKTAVVEGLAQRVVRGDVPS

Parental  PLQNRKLISLDMGALLAGSKYRGEFEERLKAVLKEVTASNGQIILFIDEIHTVVGAGATGGSMDAGNLLK
          .L....L..LDMGAL.AG.KYRGEFEERLKAVLKEV....G..ILFIDEIH.V.GAG.T.GSMDA.NL.K
Retrocopy NLLDVRLVALDMGALVAGAKYRGEFEERLKAVLKEVEEAEGKVILFIDEIHLVLGAGRTEGSMDAANLFK

Parental  PMLGRGELRCIGATTLDEYRKYIEKDAALERRFQQVYCGEPAVEDTVSILRGLRERYEMHHGVKISDGAL
          PML.RG.LRCIGATTL.EYRKY.EKDAA.ERRFQQVY..EP.V.DT.SILRGL.E.YE.HHGV.I.D.A.
Retrocopy PMLARGQLRCIGATTLEEYRKYVEKDAAFERRFQQVYVAEPSVADTISILRGLKEKYEGHHGVRIQDRAI

Parental  VAAAALSDRYITGRFLPDKAIDLVDEAAAKLKMEITSKPIELDEVDREIIRFEMEKLSLKNDTDKASKER
          V.AA.LS.RYI.GR.LPDKAIDLVDEA.A.......S.P.E.D...R..I..E.E...L....DKASK.R
Retrocopy VVAAQLSARYIMGRHLPDKAIDLVDEACANVRVQLDSQPEEIDNLERKRIQLEVELHALEKEKDKASKAR

Parental  LSKLEAELESLKQKQKNLSEHWEYEKSLMTRIKSIKEEIDRVNLEIEAAEREYNLNRAAELKYSTLLTLQ
          L.....EL..L..K...L......EK.....I...K............AER...L.R.A.LKY..L....
Retrocopy LVEVRKELDDLRDKLQPLTMKYRKEKERIDEIRKLKQRREELQFTLQEAERRMDLARVADLKYGAL----

Parental  KQLDEAEENLTEFQQSGKSMLREEVTDVDIAEIVSKWTGIPVSNLQQSDREKLLLLEDVLHKRVIGQDIA
          ...D.A...L.E.......ML.E.V....IAE.VS.WTGIPV..L.Q.D.E.L....D.LH.RV.GQ..A
Retrocopy QEIDAAIAKL-EGETGENLMLTETVGPEQIAEVVSRWTGIPVTRLGQNDKERLVGMADRLHTRVVGQTEA

Parental  VKSVANAIRRSRAGLSDPNRPIASFMFMGPTGVGKTELGKTLAEFLFNTENALIRIDMSEYMEKHAVSRL
          V..VA.A..RSRAGL..P..P..SF.F.GPTGVGKTEL.K.LAE.LF..EN.L.RIDMSEYME.H.V.RL
Retrocopy VNAVAEAVLRSRAGLGRPQQPTGSFLFLGPTGVGKTELAKALAEQLFDDENLLVRIDMSEYMEQHSVARL

Parental  VGAPPG
          .GAPPG
Retrocopy IGAPPG

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_44 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_28539	1 retrocopy	retro_atau_44 ,