RetrogeneDB ID: retro_atau_47

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold33259:165601..167948(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_25618
• Aliases: None
• Description: None

Sequence

>retro_atau_47
GGGAAAGGTTGTAGTGCTCCTACTGGCACTAAGCCTGAGGAAAGCTATGTGTCCTCATCCCCTCTATCTTCTGTTGTTAA
ATTAGTACGCAGCACCACAAGCCAAATAACAGATTGGATCTCACGCGGCAGAAAAAGGAAACGTGAAGAGGAGGGGCCAG
CTCATTGTAACATGCTGCCTTTTGAGATGAAAGATAGCATTTCTAAGAGGATCAATGTAATAGTGAATCTTCTACGCAGT
AATGGCAATTCTGTGCAGGGGGCTCTTCAGCTTGAGATCTTGCGCCCCATTGCAACATCAAGTAAGTGTCAGAATATTTC
AAGGAATACTTGCATGACAACTTCTCTTTCAACTGAATGTCAGATGTACGGAAGGGATGCAGAAAGGGACGATATAATAG
CTCAGTTGATAAAGGGGGGATCTAGTGATCTGAATGTTTTTCCAGTGGTTGGCATTGGTGGTATTGGGAAGACGACGCTT
GCTAGATATGTATACCATGATAAAAGAATTAAAGATCATTTTGATTTGCAAATGTGGGTCTGTGTATCCACTAACTTCGA
TATAGTGGGGCTAACAATTCAGATCCTAGAGCATGTATGTGAAGATAGACCGTATGAGAAAAAAAGCAGCTTGAATAAAT
TGCAGGAGATCCTTTTGGAAAATATTAGAAACAAAAGATTTCTGCTTGTATTGGATGATATGTGGGAAGACAAGGACAGG
AGTGGATGATTAAACTCTTGGCTCCATTGAAAAGTAACCAAGCAAACGGTTGCATGGTACTAGCAACAACTAGAACAAAA
TCAGTGGCAAAAATGATAGGAACTATGGGTGAAATCACATTGAGTGGTCTGGATGAAAAGGAGTTTTGGCTGTTCTTCAA
GGCATGTGCATTTCGCAATGTCAACTGCAAGCACCATCCTAGTTTACAATTTATTGGGAAACAAATTGCTAAAGTGCTAA
AAGGCTGCCCACTAGCTGCACGAAGTGTTGGTGCACTTCTGAGCACAGATGTTAGCTATCAGCACTGGACGGCAGTTCGG
GACAAATGGAAATCTCTTCAAGAATATGATGATGATATTTTACCCATCTTGAAGCTCAGTTATGATCATCTACCAGTCCA
CCTTCAGCGCTGTTTCTCATATTGCTCTTTGTTTCCAGAGGACTACCAATTTAATGGGAAAGAATTGGTCCATGCTTGGA
TATCACAAAATTTTGTGCAGCGCAAAGATCCTACCATAAGATTGGAGGAAACAGGGCACGCATATTTGGAAAGATTAGTG
GATTTGGGCTTCTTCCAAAAGGATGGCTCACACTATATTATGCATGACCTAATGCACGTACTGGCTGGGACGGTTTCAGC
AAATGAGTGTGCTACTATTGATGGATTGAAATCTGAATCAATTCAAGCAACTGTTCGGCATTTGTCTATCATAACTACTG
ATTTTGAGGAAGATGAACATGGCAACAATTCTAGTGAGAAGTTTGACAAAATACTTCAGAAGGTTAGTTCTTGGCACAAA
TTGAGGACCTTGATGTTGTTTGGGCAAAGCAGCATACATTATTAGGGTCCTTGCGTACTTTATGCAAGAGGGCTAAATGT
TTAAGGTTCCTAAGTGTGTCAGGTGTTGATATCGGCTCTACAAACAGCTTGTTAAATCTGTTCCATCTTCGTTATATAAT
GGCATACGGAGTCAACAACCCTGCATTTTGTCAAGCTTTGACAAGTTGTTATCACCTTCAAGTACTGGATGTGGGCATTT
CAGGCTATCTTGATGTACCTGCTGATATGAATAATCTTGTTAATCTGCGCCATCTTATTGCTCATGAGAAAGTGCACCAT
GCAATAGATTGTGTCGGCAACATGACCTCTCTCCAGGAGTTAAAATTCAAGGTTCAAAATGTTGGCAGGTTTCAGATAGG
ACAACTTCAGTCCATGAATAAGCTTGTATTACTTGGAATTTCTCAACTTGAAAATGCGAAGACTAAAGAAGAGGCGAGGG
GGGCCAGGCTGATAGACAAAGAGTATCTAGACAAATTGTCGTTATCATGGGAGAATAGTAGCATGAATCTTCAACCTGAG
GCTGTGAAAGATGTGCTTGATGGTCTTCAACCACATCAAAACCTCAAAAATCTAGAAATAACTGGATATGGTGGTGTTAC
CTCCCCAACCTGGCTTTCCAGTACTTTCTCAGTTACCTCACTGCAGATACTTCATCTAGAGAATTGCAGGGAATGGAAAA
TTCTTCGATCTATTGAAATGCCTTCCCTTAGGAAACTAACATTGATCAGGATGTTGAATATAATGGAAATCTCAGTTCCT
TCTTTGGAAGAGTTGATCTTGATTGAG

Alignment

ORF - retro_atau_47 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.14 %
• Parental protein coverage: 64.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKGCTAASDDNSDGSYVSSSAPSSASELVYSATSQITRWASCGRKRRREEEGPAHSIMLTYEIKHDISQR
          GKGC.A........SYVSSS..SS...LV.S.TSQIT.W.S.GRKR.REEEGPAH..ML..E.K..IS.R
Retrocopy GKGCSAPTGTKPEESYVSSSPLSSVVKLVRSTTSQITDWISRGRKRKREEEGPAHCNMLPFEMKDSISKR

Parental  INGIVKHLCTIGNSVQRVLQLEISRPTATSNESQNICRNARLTTSVPIECKVYGRDAERDKIIELLINGG
          IN.IV..L...GNSVQ..LQLEI.RP.ATS...QNI.RN...TTS...EC..YGRDAERD.II..LI.GG
Retrocopy INVIVNLLRSNGNSVQGALQLEILRPIATSSKCQNISRNTCMTTSLSTECQMYGRDAERDDIIAQLIKGG

Parental  SSELNVLPVVGIGGVGKTTLARYVYRDERITNHFDLQMWVCVSTNFNEVRLTLEILEHVCKDRQEYEKIS
          SS.LNV.PVVGIGG.GKTTLARYVY.D.RI..HFDLQMWVCVSTNF..V.LT..ILEHVC.DR..YE...
Retrocopy SSDLNVFPVVGIGGIGKTTLARYVYHDKRIKDHFDLQMWVCVSTNFDIVGLTIQILEHVCEDRP-YEXXX

Parental  NFNVLQEILLKNIRNKRFLLVLDDVWEDKNISG-WIKLLAPLKNNQVNGCMVLATTRTKSVAKMIGTVDE
          ..N.LQEILL.NIRNKRFLLVLDD.WEDK..SG..IKLLAPLK.NQ.NGCMVLATTRTKSVAKMIGT..E
Retrocopy SLNKLQEILLENIRNKRFLLVLDDMWEDKDRSG<MIKLLAPLKSNQANGCMVLATTRTKSVAKMIGTMGE

Parental  VRLSGLDEKEFWLFFKACAFGNENYEGHPSLQSIGKQIAKALKGCPLAARSVGALLNTNVSDKHWRIVRD
          ..LSGLDEKEFWLFFKACAF.N.N...HPSLQ.IGKQIAK.LKGCPLAARSVGALL.T.VS..HW..VRD
Retrocopy ITLSGLDEKEFWLFFKACAFRNVNCKHHPSLQFIGKQIAKVLKGCPLAARSVGALLSTDVSYQHWTAVRD

Parental  KWKSFQEDSDDILPILKLSYDYLPVHLQRCFSHCSLFPEDYPFDGEQLVHAWISQDFVQCEDRTVRLEET
          KWKS.QE..DDILPILKLSYD.LPVHLQRCFS.CSLFPEDY.F.G..LVHAWISQ.FVQ..D.T.RLEET
Retrocopy KWKSLQEYDDDILPILKLSYDHLPVHLQRCFSYCSLFPEDYQFNGKELVHAWISQNFVQRKDPTIRLEET

Parental  GQEYLDRLVDLGFFQMVNSHYVMHDLMHELAGKVSLNECATIHGLKPEAIRPSVRHLSIITTAFDKDNGG
          G..YL.RLVDLGFFQ...SHY.MHDLMH.LAG.VS.NECATI.GLK.E.I...VRHLSIITT.F..D..G
Retrocopy GHAYLERLVDLGFFQKDGSHYIMHDLMHVLAGTVSANECATIDGLKSESIQATVRHLSIITTDFEEDEHG

Parental  NFPNERFEKILQKVRPLQKLRTLMLFGRSSIN-LLGSLRDLCKEAKCLRFLRIFVTGADISSINRLLNPC
          N...E.F.KILQKV....KLRTLMLFG.SSI..LLGSLR.LCK.AKCLRFL...V.G.DI.S.N.LLN..
Retrocopy NNSSEKFDKILQKVSSWHKLRTLMLFGQSSIH<LLGSLRTLCKRAKCLRFLS--VSGVDIGSTNSLLNLF

Parental  HLRYLEYVCVVTTTMSLFPQALTRFYHLQVLNVGISGNLAVPTDMHKLVNLRHLISHEKVHHAIACVGNM
          HLR...Y..........F.QALT..YHLQVL.VGISG.L.VP.DM..LVNLRHLI.HEKVHHAI.CVGNM
Retrocopy HLR---YIMAYGVNNPAFCQALTSCYHLQVLDVGISGYLDVPADMNNLVNLRHLIAHEKVHHAIDCVGNM

Parental  TSLQKLRFKVQNVGSFEIRQLQSMNELVLLEISQLQIVKTKEEACGARLLDKEYLEKLSLSWEDSSMSLE
          TSLQ.L.FKVQNVG.F.I.QLQSMN.LVLL.ISQL...KTKEEA.GARL.DKEYL.KLSLSWE.SSM.L.
Retrocopy TSLQELKFKVQNVGRFQIGQLQSMNKLVLLGISQLENAKTKEEARGARLIDKEYLDKLSLSWENSSMNLQ

Parental  PVMAEDVLEGLQPHSNLKTLEITGYSGAIPPTWLS----IPSLEELILINMP--KLEKCIGSYGMELTSH
          P....DVL.GLQPH.NLK.LEITGY.G...PTWLS......SL..L.L.N....K....I..........
Retrocopy PEAVKDVLDGLQPHQNLKNLEITGYGGVTSPTWLSSTFSVTSLQILHLENCREWKILRSIEMPSLRKLTL

Parental  LRVLMIMK--CPQLNDITLFQ
          .R.L.IM....P.L....L..
Retrocopy IRMLNIMEISVPSLEELILIE

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_47 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_25618	1 retrocopy	retro_atau_47 ,