RetrogeneDB ID: retro_atau_23

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold104841:15124..16699(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: F775_30457
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_14124
• Aliases: None
• Description: None

Sequence

>retro_atau_23
ATGGCGTTCAACGACGACGAGAAGCCTCCTGCTTCTAACGCAGGTAACACCAAGGGTCTGGTGACCATCACCGAGCCCAA
GTTCAGCAAGGACGAGGCGGCCCTGTCGGCGGACGAGGTGACGGCGGTGGTAGAGCTCAAAGCCACGTCGTCGACGGCCG
TCCGGGAAGGGCTGGACCTGGTGGCGGTGCTGGACGTGAGCGGCAGCATGCAGGGCGACAAGCTCCAGAGCATGAAGATG
GCGATGCAGTTCGTCATCATGAAGCTCACCCCCGTCGACCGCCTCTCCGTCGTCTCCTTCTCCGGCTCCGCCACCAGGCA
CTGCCCACTCCGCTCCGTCACGCAGCAAGCGCAGGCCGACCTCAAGGCCATCGTCGACGGCCTTGTCGCCAACGGCGGGA
CCAACATCAAGGCCGGCCTGGACACCGCCCTGGCCATCGTCGCCGGCCGCGCCACCACCAAAGCCCGCACGCCCAATGTC
TTCCTCATGTCCGACGGCCAGCAGAGCGACGGCGACGCCAGGCAAGTCGATCCCGGGAACGTGGCGGTCTACACGTTCGG
CTTCGGCAAGGACGCCGACCACGCCTTGCTCAGCGACGTCGCCAGGAAGTCCCCCGGCGGCACGTTCAACTCGGTGCCGG
ACGGCGGCAACGTGACCGCGCCCTTCTCGCAGCTCCTCGGCGGGCTCCTCACCATCGTCGCGCAGGACGTGCAGCTCACG
CTGACGCCCAAGGCGGAAGATCCCAGCGCCCCGGACCTGGACACCATGACCGTGGCGCCAGGGACCGACTACACGCAGAC
CACCGACGGCGGCACGGGCGTCATCACCATCAAGTTCGGCACCCTCTTCAGCGGCGAGACCCGCAAGGTGGCCATCAACT
TCAAGCTCCTGGAGAGCACCTTGACGACGCCGTACGACGGGTTGGTGGCGGAGGCCCAGCACAGCTACAACGTGCAGGGT
AGCCCGCAGGGCCAGACCCCGCAGGACGTCGTGATACCCCGCTCCCCGGACGCGCCCGGCGAGGAAGCCGTGAGCGTCAA
GGCGCGGGGGGTGCTGGCGGAGATGGCGCGTCGGCAGCACGCCGGCGCGATCGGCGAGGCGAGGCAGATGGCCGACGGGA
AGAACCTGGAGGAGGCGCGGTACAAGCTGGCGGACGCGCAGAACGCGCTGGAGGACATCGTGCTGAACGACGGGGAGAAG
CTGGTGGGCATGCTCCGGGCGGAGCTGCAGCAGCTGCTGGACCTGATGGAGACGCAGGAGCTGTACGAGGCGGAGGGGCG
GCCGTACGCGCTGGCCTCCGAGACGTCGCACGGCCGGCAGCGGTACGCGGCGAGGGGCGGCGACATGGACGCCGTGCGGC
TGTTCGCCACCCCGCGCATGGACACGTACCTGGAGCAGGCCAAGAAGTTCGAGGAGGACCCGACGGCGCCGCTGCCGTCC
GCCGACGACGACGCCAAGGAGGAGATGGCCGCCAACCCGCTGGCCGCCATCTCGGCGCCCATCGCCTTCTACATCAAGGT
GGCCATCCAGGCGCTGCAGGAGATCGAGAAGCTCGTCGCCCCGCCCACCAAATAA

Alignment

ORF - retro_atau_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.05 %
• Parental protein coverage: 92.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMFADDENPAPLNKGSTKGLVKIKKPAYSRDDVSLKADEVTAVVELNAAPSAVVREGLDLVVVLDVSGSM
          M.F.DDE.P...N.G.TKGLV.I..P..S.D...L.ADEVTAVVEL.A..S..VREGLDLV.VLDVSGSM
Retrocopy MAFNDDEKPPASNAGNTKGLVTITEPKFSKDEAALSADEVTAVVELKATSSTAVREGLDLVAVLDVSGSM

Parental  AAEKLVSMKQAMQFVIMKLTPVDRLSIVTCNNSAKRHCALRSMTVDAQKELKAMVDGLEAYGGTNIKSGL
          ...KL.SMK.AMQFVIMKLTPVDRLS.V....SA.RHC.LRS.T..AQ..LKA.VDGL.A.GGTNIK.GL
Retrocopy QGDKLQSMKMAMQFVIMKLTPVDRLSVVSFSGSATRHCPLRSVTQQAQADLKAIVDGLVANGGTNIKAGL

Parental  ETARAIFAARNIVKSRSANVFLLSDGQQTANEATDVDLGSAGVYTFGLGKDSDHKLLSDIAKKSPGGTFS
          .TA.AI.A.R...K.R..NVFL.SDGQQ....A..VD.G...VYTFG.GKD.DH.LLSD.A.KSPGGTF.
Retrocopy DTALAIVAGRATTKARTPNVFLMSDGQQSDGDARQVDPGNVAVYTFGFGKDADHALLSDVARKSPGGTFN

Parental  TVVDGSNLTKPFAQMLGGLLTVVAQDVRLILTPKKAD----GLKDMVVPEDTDYTKTTD-AAGVITIHFG
          .V.DG.N.T.PF.Q.LGGLLT.VAQDV.L.LTPK..D.....L..M.V...TDYT.TTD...GVITI.FG
Retrocopy SVPDGGNVTAPFSQLLGGLLTIVAQDVQLTLTPKAEDPSAPDLDTMTVAPGTDYTQTTDGGTGVITIKFG

Parental  TLFSGESRKVTVKMTLSECAVGTTRHDAVLAEAQHSYSAQSIVQGLQTPENLKIFRTPN-PATVAGS-KA
          TLFSGE.RKV.....L.E....TT..D...AEAQHSY..Q...QG.QTP....I.R.P..P...A.S.KA
Retrocopy TLFSGETRKVAINFKLLESTL-TTPYDGLVAEAQHSYNVQGSPQG-QTPQDVVIPRSPDAPGEEAVSVKA

Parental  RWVLAELARRRQAEAIRKAMALADTGDLDGARYLLVDAQNALEDVLLDDGQKLIDSLRAELVQLIKLMAS
          R.VLAE.ARR..A.AI..A...AD...L..ARY.L.DAQNALED..L.DG.KL...LRAEL.QL..LM..
Retrocopy RGVLAEMARRQHAGAIGEARQMADGKNLEEARYKLADAQNALEDIVLNDGEKLVGMLRAELQQLLDLMET

Parental  KQLYEAQGRPYALASDTSHARQRFADRGDVTDTVRLFATPRMDTYLEQAKPFDKDPTKPLPSAADDVKEE
          ..LYEA.GRPYALAS.TSH.RQR.A.RG...D.VRLFATPRMDTYLEQAK.F..DPT.PLPSA.DD.KEE
Retrocopy QELYEAEGRPYALASETSHGRQRYAARGGDMDAVRLFATPRMDTYLEQAKKFEEDPTAPLPSADDDAKEE

Parental  IAANPMAAFSSELAFYLRNAIEALQAIEKMVAAPT
          .AANP.AA.S...AFY...AI.ALQ.IEK.VA.PT
Retrocopy MAANPLAAISAPIAFYIKVAIQALQEIEKLVAPPT

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_23 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_14124	1 retrocopy	retro_atau_23 ,
Triticum aestivum	TRAES3BF072500070CFD_g	1 retrocopy	retro_taes_70,