RetrogeneDB ID: retro_atau_60

Retrocopy location

• Organism: Tausch goatgrass (Aegilops tauschii)
• Coordinates: Scaffold5664:6799..8374(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: F775_12909
• Aliases: None
• Description: None

Sequence

>retro_atau_60
ATGATGATGACCACCAACGGCATGTGGCAGGACGAGGGCGTGAACCCGCTCGAGTTCTCCCTCCCGCTCTTCATCGTCCA
GGTGGCCGTCATCGTCATCACCACCCGCCTCCTCGTCCTCCTCCTCCGGCCCTTCCGCCAGCCGCGCGTCATCGCTGAGA
TCCTCGCCGGCGTCGTGCTGGGCCCGTCCATGATCGGGCAGAGCGAGCTGTGGGCCAGCCTGGTGTTCCCCGTGCGCAGC
CTGCTCACGCTCGAGACGGTGGCGCACCTGGGGCTGCTCTTCTTCCTCTTCCTCGTCGGCCTGGAGATGGACGTCGACGT
CATCCGCCGGTCCGGGGACAAGGCGGTGTTTGTCGCCATGGCCGGCATGGCGCTGCCCTTCTGCATGGGCATCGCCACCT
CCTTCATATTCCGGCACCAGGTGTCCCGGAACGTGCACCAGACCTCCTTCCTGCTCTTCCTCGGCGTCGCCCTCTCCGTC
ACGGCCTTCCCCGTGCTCGCCCGCATCCTCGCCGAGATCAAGCTGCTCAACTCGGAGCTCGGCCGCACCGCCATGTCCGC
CGCCATCGTCAACGACATGTGCGCCTGGATCCTGCTCGCGCTTGCCATCTCCATTTCGGAGGTGGACAGCACCGCGCTGT
CGTCACTTTGGGTGCTCCTCGCCGGGGTCACCTTCGTGCTCTTCTGCTTCTACGCCGTGCGCCCCTTGATGTGGCGGATC
ATCCGCAGCATCCCCGAGGGCGACGACGTCAGCAACGCGCAGATCACCCTCATTCTCACGGGCGTCATGATCGCCGGCGC
GTGCACCGACGCCATCGGCATCCACTCCGTCTTCGGCGCCTTCGTCTACGGGCTGGTCATCCCGAGCGCGCCGCTAGGCG
TGACGCTGATCGAGAAGCTCGAGGACTTCGTCACCGGGCTCCTCCTCCCGCTCTTCTTCGCCATGAGCGGCCTCCGCACC
AACGTTCGCATGATACGCGACCCCGTCACCGTCGGCCTGCTCGTGCTCGTGTTCGTGATGGCCAGCTTCGCCAAGATCAT
GGGCACCATCATCATCGCGGCGCTCTACGCCATGCCGTTCCGCGAGGGCATCGCCCTCGGCTTCCTCATGAACACCAGGG
GGCTGGTGGAGATGATCGTGCTCAACATCGGGAGGGACAAGCAGGTGCTGGACGACGAGTCGTTCGCGGTGATGGTGCTA
GTGTCGGTGGCGATGACGTCGCTGGTGACGCCGGTGGTGACCGGCGTGTACCGGCCGTCGCGGCGGCTCGTCGGCTACAA
GCGGCGGAACCTGCAGCGCATCCGGCACGACAGCGAGCTCCGCATGCTGGCCTGCGTGCACACCACCCGCAACGTGCCGT
CCGTGCTGTCGCTGCTCGAGCTCTCCAACCCGTCCAAGCGCTCCCCCATCTTCATCTACGCGCTCCACATCATCGAGCTC
ACCGGCCGAGCCTCCAACATGCTCGCCGCCGCGGCTGCCTCCTCCTCCAGCCGGACAAGCTCGTCCTCCGCCTTGCCCGC
CACCACGGAGCACATCTTCAACGCCTTTGAGAACTACGAGAGGCTCACCGGTCAG

Alignment

ORF - retro_atau_60 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKVTTYGIW--EGVNPLEFSLPIFILQTAVIVATTRLLVLLLKPFRQPRVIAEILAGVILGPSVMGQVGT
          M..TT.G.W..EGVNPLEFSLP.FI.Q.AVIV.TTRLLVLLL.PFRQPRVIAEILAGV.LGPS..GQ...
Retrocopy MMMTTNGMWQDEGVNPLEFSLPLFIVQVAVIVITTRLLVLLLRPFRQPRVIAEILAGVVLGPSMIGQSEL

Parental  WAGTVFPGRSLLTLETVAHLGLLYFLFLVGLEMDVNVIKRSGKKAVIIAVAGMALPFCIGTATSFIFRHQ
          WA..VFP.RSLLTLETVAHLGLL.FLFLVGLEMDV.VI.RSG.KAV..A.AGMALPFC.G.ATSFIFRHQ
Retrocopy WASLVFPVRSLLTLETVAHLGLLFFLFLVGLEMDVDVIRRSGDKAVFVAMAGMALPFCMGIATSFIFRHQ

Parental  VSKNVHQASFLLFLGVALSVTAFPVLARILAEIKLLNSELGKIAMSAAIVNDMCAWILLALAIAISDVNS
          VS.NVHQ.SFLLFLGVALSVTAFPVLARILAEIKLLNSELG..AMSAAIVNDMCAWILLALAI.IS.V.S
Retrocopy VSRNVHQTSFLLFLGVALSVTAFPVLARILAEIKLLNSELGRTAMSAAIVNDMCAWILLALAISISEVDS

Parental  TPFSSLYVLLSGVAFVLACFYVVRPVMWWIVRRIPEGETISDVQITLILTGVMISGVCTDAIGIHSVFGA
          T..SSL.VLL.GV.FVL.CFY.VRP.MW.I.R.IPEG...S..QITLILTGVMI.G.CTDAIGIHSVFGA
Retrocopy TALSSLWVLLAGVTFVLFCFYAVRPLMWRIIRSIPEGDDVSNAQITLILTGVMIAGACTDAIGIHSVFGA

Parental  FVYGLVIPSGELGVVLIEKLEDFVMGLLLPLFFAISGLRTNVTRVSDPVTAGLLVLVFVMASFAKIMGTI
          FVYGLVIPS..LGV.LIEKLEDFV.GLLLPLFFA.SGLRTNV....DPVT.GLLVLVFVMASFAKIMGTI
Retrocopy FVYGLVIPSAPLGVTLIEKLEDFVTGLLLPLFFAMSGLRTNVRMIRDPVTVGLLVLVFVMASFAKIMGTI

Parental  LIAISYTMTFRDGVALGFLMNTRGLVEMIVLNIGRDKQVLDDESFAVMVLVSVAMTALVTPVVTTVYRPA
          .IA..Y.M.FR.G.ALGFLMNTRGLVEMIVLNIGRDKQVLDDESFAVMVLVSVAMT.LVTPVVT.VYRP.
Retrocopy IIAALYAMPFREGIALGFLMNTRGLVEMIVLNIGRDKQVLDDESFAVMVLVSVAMTSLVTPVVTGVYRPS

Parental  RRLVGYKRRNLQRSKHDAELRMLACVHTTRNVPSIISLLELSNPSKRSPLFIYALHLVELTGRASNMLAA
          RRLVGYKRRNLQR..HD.ELRMLACVHTTRNVPS..SLLELSNPSKRSP.FIYALH..ELTGRASNMLAA
Retrocopy RRLVGYKRRNLQRIRHDSELRMLACVHTTRNVPSVLSLLELSNPSKRSPIFIYALHIIELTGRASNMLAA

Parental  HHTAANQNRSASTSA----SEHIFNAFENYEESVGQ
          ...A....R..S.SA.....EHIFNAFENYE...GQ
Retrocopy -AAASSSSRTSSSSALPATTEHIFNAFENYERLTGQ

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_60 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_12909	1 retrocopy	retro_atau_60 ,