AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0217620

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0217620 MtrunA17_Chr6g0453811 100.000 65 0 0 1 65 1 65 6.66e-42 130
Msa0217620 MtrunA17_Chr4g0041861 90.769 65 6 0 1 65 1 65 3.30e-37 118
Msa0217620 MtrunA17_Chr6g0453911 81.538 65 11 1 1 65 1 64 1.49e-31 103
Msa0217620 MtrunA17_Chr8g0381481 83.673 49 8 0 1 49 1 49 8.05e-25 86.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0217620 AT5G03850.1 90.769 65 5 1 1 65 1 64 1.33e-35 114
Msa0217620 AT3G10090.1 90.769 65 5 1 1 65 1 64 1.33e-35 114
Msa0217620 AT5G64140.1 89.231 65 6 1 1 65 1 64 1.14e-34 112

Find 36 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGAAGTTGGTTGCTAAAA+TGG 0.117951 2_1:+64542039 None:intergenic
ACCTGCTATTCAAGGAAATT+AGG 0.247464 2_1:+64540588 None:intergenic
TGATTGATATTTGATTAGTT+TGG 0.323942 2_1:-64540557 Msa0217620:three_prime_UTR
TTCTTATAACCTGCTATTCA+AGG 0.363273 2_1:+64540580 None:intergenic
ACCTAATTTCCTTGAATAGC+AGG 0.397759 2_1:-64540589 Msa0217620:three_prime_UTR
GCTGTTGTTGTGAAAGTTAT+GGG 0.420809 2_1:-64541041 Msa0217620:CDS
AGGATGTCTCCCTCCCTAAC+TGG 0.425936 2_1:+64540930 None:intergenic
TGCTGTTGTTGTGAAAGTTA+TGG 0.441002 2_1:-64541042 Msa0217620:CDS
TTATGGGTCGTACTGGATCC+AGG 0.451262 2_1:-64541025 Msa0217620:CDS
AACCTGAGTGACTTGTCCCC+TGG 0.461687 2_1:+64541007 None:intergenic
GAATGTGAAGGGACCAGTTA+GGG 0.464736 2_1:-64540943 Msa0217620:CDS
AGCTCTTAAAACTGTTGTGT+TGG 0.468388 2_1:-64540807 Msa0217620:three_prime_UTR
TGTGACTTAGATATAAAATC+TGG 0.471929 2_1:-64540679 Msa0217620:three_prime_UTR
GGAATGTGAAGGGACCAGTT+AGG 0.473428 2_1:-64540944 Msa0217620:CDS
TAAAATGGAAAGTGCAGAAT+CGG 0.485027 2_1:+64542054 None:intergenic
TCTCAGACTCGAGGAGGGTA+AGG 0.488938 2_1:+64540910 None:intergenic
AGGAAATTAGGTTTGAGACT+TGG 0.499121 2_1:+64540600 None:intergenic
TATATGTTGTTCAATATGTC+AGG 0.499645 2_1:-64540656 Msa0217620:three_prime_UTR
GAGAGAAACGAACTTGAAGT+TGG 0.505451 2_1:+64542027 None:intergenic
GTGAAAGTTATGGGTCGTAC+TGG 0.530087 2_1:-64541032 Msa0217620:CDS
TGTGAAGGGACCAGTTAGGG+AGG 0.582336 2_1:-64540940 Msa0217620:CDS
ATCAGAATCGTCACATCATG+AGG 0.584464 2_1:-64540965 Msa0217620:CDS
TTGCTTCTCTCTCAGACTCG+AGG 0.586554 2_1:+64540901 None:intergenic
AAACATCGAGACTCTTCTAT+CGG 0.589119 2_1:+64540871 None:intergenic
GAAGAGAAGCTAGCTGCGTA+TGG 0.602154 2_1:+64542094 None:intergenic
CTTCTCTCTCAGACTCGAGG+AGG 0.606831 2_1:+64540904 None:intergenic
TATGGGTCGTACTGGATCCA+GGG 0.613108 2_1:-64541024 Msa0217620:CDS
GGAAAGTGCAGAATCGGCGT+GGG 0.619085 2_1:+64542060 None:intergenic
TCACATCATGAGGAATGTGA+AGG 0.626309 2_1:-64540955 Msa0217620:CDS
TGGAAAGTGCAGAATCGGCG+TGG 0.632732 2_1:+64542059 None:intergenic
CACATCATGAGGAATGTGAA+GGG 0.632733 2_1:-64540954 Msa0217620:CDS
ATCCAGGGGACAAGTCACTC+AGG 0.638739 2_1:-64541009 Msa0217620:CDS
TTCTCTCTCAGACTCGAGGA+GGG 0.644799 2_1:+64540905 None:intergenic
GTGAAGGGACCAGTTAGGGA+GGG 0.647685 2_1:-64540939 Msa0217620:CDS
ATGCTGTCTTGTTTATACGA+TGG 0.664216 2_1:-64540628 Msa0217620:three_prime_UTR
ATGGGTCGTACTGGATCCAG+GGG 0.674814 2_1:-64541023 Msa0217620:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTATTTTGATTTTTTCA+TGG - chr2_1:64540785-64540804 Msa0217620:three_prime_UTR 10.0%
!!! TTATTTGTTTTAATTAATGA+AGG - chr2_1:64541944-64541963 Msa0217620:intron 10.0%
!!! TATTTGTTTTAATTAATGAA+GGG - chr2_1:64541945-64541964 Msa0217620:intron 10.0%
!!! TTTTTATTTTGATTTTTTCA+TGG - chr2_1:64540785-64540804 Msa0217620:three_prime_UTR 10.0%
!!! TTATTTGTTTTAATTAATGA+AGG - chr2_1:64541944-64541963 Msa0217620:intron 10.0%
!!! TATTTGTTTTAATTAATGAA+GGG - chr2_1:64541945-64541964 Msa0217620:intron 10.0%
!! TAGTTTAATAAAAATCAAAG+AGG + chr2_1:64541319-64541338 None:intergenic 15.0%
!! ATTATGATTTAAATATAGTC+TGG - chr2_1:64541430-64541449 Msa0217620:intron 15.0%
!!! AAAGATAAAAAAGTGTTTTT+CGG - chr2_1:64541463-64541482 Msa0217620:intron 15.0%
!! TAGTTTAATAAAAATCAAAG+AGG + chr2_1:64541319-64541338 None:intergenic 15.0%
!! ATTATGATTTAAATATAGTC+TGG - chr2_1:64541430-64541449 Msa0217620:intron 15.0%
!!! AAAGATAAAAAAGTGTTTTT+CGG - chr2_1:64541463-64541482 Msa0217620:intron 15.0%
!! GCTAAAAATATAGATCAATA+AGG + chr2_1:64540720-64540739 None:intergenic 20.0%
!! AGTTAAAAAAGTCATTTCTA+AGG + chr2_1:64541123-64541142 None:intergenic 20.0%
!!! ATCAACTTCACTTTATTTTT+TGG + chr2_1:64541395-64541414 None:intergenic 20.0%
!!! TGATTGATATTTGATTAGTT+TGG - chr2_1:64542107-64542126 Msa0217620:five_prime_UTR 20.0%
!! GCTAAAAATATAGATCAATA+AGG + chr2_1:64540720-64540739 None:intergenic 20.0%
!! AGTTAAAAAAGTCATTTCTA+AGG + chr2_1:64541123-64541142 None:intergenic 20.0%
!!! ATCAACTTCACTTTATTTTT+TGG + chr2_1:64541395-64541414 None:intergenic 20.0%
!!! GATTTTTTCATGGTTGATTT+AGG - chr2_1:64540795-64540814 Msa0217620:three_prime_UTR 25.0%
!! TTTAAAATGTGTGAAAGATG+AGG - chr2_1:64540970-64540989 Msa0217620:CDS 25.0%
!! TGATTGCTATTAATTGTGTT+TGG - chr2_1:64541154-64541173 Msa0217620:intron 25.0%
! TTGATTGCTTATATTGTGTT+TGG - chr2_1:64541344-64541363 Msa0217620:intron 25.0%
! ACACATTCACAATTGTTAAT+AGG + chr2_1:64541569-64541588 None:intergenic 25.0%
! TGTGACTTAGATATAAAATC+TGG - chr2_1:64541985-64542004 Msa0217620:intron 25.0%
! TATATGTTGTTCAATATGTC+AGG - chr2_1:64542008-64542027 Msa0217620:intron 25.0%
!!! TTGATATTTGATTAGTTTGG+AGG - chr2_1:64542110-64542129 Msa0217620:five_prime_UTR 25.0%
!!! GATTTTTTCATGGTTGATTT+AGG - chr2_1:64540795-64540814 Msa0217620:three_prime_UTR 25.0%
!! TTTAAAATGTGTGAAAGATG+AGG - chr2_1:64540970-64540989 Msa0217620:CDS 25.0%
!! TGATTGCTATTAATTGTGTT+TGG - chr2_1:64541154-64541173 Msa0217620:intron 25.0%
! TTGATTGCTTATATTGTGTT+TGG - chr2_1:64541344-64541363 Msa0217620:intron 25.0%
! ACACATTCACAATTGTTAAT+AGG + chr2_1:64541569-64541588 None:intergenic 25.0%
! TGTGACTTAGATATAAAATC+TGG - chr2_1:64541985-64542004 Msa0217620:intron 25.0%
! TATATGTTGTTCAATATGTC+AGG - chr2_1:64542008-64542027 Msa0217620:intron 25.0%
! TAAAATGGAAAGTGCAGAAT+CGG + chr2_1:64540613-64540632 None:intergenic 30.0%
!! TTTTCATGGTTGATTTAGGT+TGG - chr2_1:64540799-64540818 Msa0217620:three_prime_UTR 30.0%
!!! GATAAAAAAGTGTTTTTCGG+TGG - chr2_1:64541466-64541485 Msa0217620:intron 30.0%
TTCTTATAACCTGCTATTCA+AGG + chr2_1:64542087-64542106 None:intergenic 30.0%
! TAAAATGGAAAGTGCAGAAT+CGG + chr2_1:64540613-64540632 None:intergenic 30.0%
!! TTTTCATGGTTGATTTAGGT+TGG - chr2_1:64540799-64540818 Msa0217620:three_prime_UTR 30.0%
!!! GATAAAAAAGTGTTTTTCGG+TGG - chr2_1:64541466-64541485 Msa0217620:intron 30.0%
TTCTTATAACCTGCTATTCA+AGG + chr2_1:64542087-64542106 None:intergenic 30.0%
! CTTGAAGTTGGTTGCTAAAA+TGG + chr2_1:64540628-64540647 None:intergenic 35.0%
TCAACAAATTAAGCTGAAGC+TGG + chr2_1:64541059-64541078 None:intergenic 35.0%
CAATTGTTAATAGGAGAGCA+AGG + chr2_1:64541560-64541579 None:intergenic 35.0%
TGCTGTTGTTGTGAAAGTTA+TGG - chr2_1:64541622-64541641 Msa0217620:intron 35.0%
GCTGTTGTTGTGAAAGTTAT+GGG - chr2_1:64541623-64541642 Msa0217620:intron 35.0%
! TCAGGTTAGAGTGAAGTTTT+TGG - chr2_1:64541673-64541692 Msa0217620:intron 35.0%
AAACATCGAGACTCTTCTAT+CGG + chr2_1:64541796-64541815 None:intergenic 35.0%
AGCTCTTAAAACTGTTGTGT+TGG - chr2_1:64541857-64541876 Msa0217620:intron 35.0%
!! ATGCTGTCTTGTTTATACGA+TGG - chr2_1:64542036-64542055 Msa0217620:intron 35.0%
! AGGAAATTAGGTTTGAGACT+TGG + chr2_1:64542067-64542086 None:intergenic 35.0%
ACCTAATTTCCTTGAATAGC+AGG - chr2_1:64542075-64542094 Msa0217620:five_prime_UTR 35.0%
ACCTGCTATTCAAGGAAATT+AGG + chr2_1:64542079-64542098 None:intergenic 35.0%
! CTTGAAGTTGGTTGCTAAAA+TGG + chr2_1:64540628-64540647 None:intergenic 35.0%
TCAACAAATTAAGCTGAAGC+TGG + chr2_1:64541059-64541078 None:intergenic 35.0%
CAATTGTTAATAGGAGAGCA+AGG + chr2_1:64541560-64541579 None:intergenic 35.0%
TGCTGTTGTTGTGAAAGTTA+TGG - chr2_1:64541622-64541641 Msa0217620:intron 35.0%
GCTGTTGTTGTGAAAGTTAT+GGG - chr2_1:64541623-64541642 Msa0217620:intron 35.0%
! TCAGGTTAGAGTGAAGTTTT+TGG - chr2_1:64541673-64541692 Msa0217620:intron 35.0%
AAACATCGAGACTCTTCTAT+CGG + chr2_1:64541796-64541815 None:intergenic 35.0%
AGCTCTTAAAACTGTTGTGT+TGG - chr2_1:64541857-64541876 Msa0217620:intron 35.0%
!! ATGCTGTCTTGTTTATACGA+TGG - chr2_1:64542036-64542055 Msa0217620:intron 35.0%
! AGGAAATTAGGTTTGAGACT+TGG + chr2_1:64542067-64542086 None:intergenic 35.0%
ACCTAATTTCCTTGAATAGC+AGG - chr2_1:64542075-64542094 Msa0217620:five_prime_UTR 35.0%
ACCTGCTATTCAAGGAAATT+AGG + chr2_1:64542079-64542098 None:intergenic 35.0%
GAGAGAAACGAACTTGAAGT+TGG + chr2_1:64540640-64540659 None:intergenic 40.0%
ATCAGAATCGTCACATCATG+AGG - chr2_1:64541699-64541718 Msa0217620:intron 40.0%
TCACATCATGAGGAATGTGA+AGG - chr2_1:64541709-64541728 Msa0217620:intron 40.0%
CACATCATGAGGAATGTGAA+GGG - chr2_1:64541710-64541729 Msa0217620:intron 40.0%
GAGAGAAACGAACTTGAAGT+TGG + chr2_1:64540640-64540659 None:intergenic 40.0%
ATCAGAATCGTCACATCATG+AGG - chr2_1:64541699-64541718 Msa0217620:intron 40.0%
TCACATCATGAGGAATGTGA+AGG - chr2_1:64541709-64541728 Msa0217620:intron 40.0%
CACATCATGAGGAATGTGAA+GGG - chr2_1:64541710-64541729 Msa0217620:intron 40.0%
GTGAATGTGTGTGTTTGAGC+AGG - chr2_1:64541579-64541598 Msa0217620:intron 45.0%
ATGTGTGTGTTTGAGCAGGA+TGG - chr2_1:64541583-64541602 Msa0217620:intron 45.0%
GTGAAAGTTATGGGTCGTAC+TGG - chr2_1:64541632-64541651 Msa0217620:intron 45.0%
GAATGTGAAGGGACCAGTTA+GGG - chr2_1:64541721-64541740 Msa0217620:intron 45.0%
GTGAATGTGTGTGTTTGAGC+AGG - chr2_1:64541579-64541598 Msa0217620:intron 45.0%
ATGTGTGTGTTTGAGCAGGA+TGG - chr2_1:64541583-64541602 Msa0217620:intron 45.0%
GTGAAAGTTATGGGTCGTAC+TGG - chr2_1:64541632-64541651 Msa0217620:intron 45.0%
GAATGTGAAGGGACCAGTTA+GGG - chr2_1:64541721-64541740 Msa0217620:intron 45.0%
!! TCAAAATAAAAAAATTAATA+TGG + chr2_1:64540777-64540796 None:intergenic 5.0%
!! TCAAAATAAAAAAATTAATA+TGG + chr2_1:64540777-64540796 None:intergenic 5.0%
GAAGAGAAGCTAGCTGCGTA+TGG + chr2_1:64540573-64540592 None:intergenic 50.0%
TTATGGGTCGTACTGGATCC+AGG - chr2_1:64541639-64541658 Msa0217620:intron 50.0%
TATGGGTCGTACTGGATCCA+GGG - chr2_1:64541640-64541659 Msa0217620:intron 50.0%
GGAATGTGAAGGGACCAGTT+AGG - chr2_1:64541720-64541739 Msa0217620:intron 50.0%
TTCTCTCTCAGACTCGAGGA+GGG + chr2_1:64541762-64541781 None:intergenic 50.0%
TTGCTTCTCTCTCAGACTCG+AGG + chr2_1:64541766-64541785 None:intergenic 50.0%
GAAGAGAAGCTAGCTGCGTA+TGG + chr2_1:64540573-64540592 None:intergenic 50.0%
TTATGGGTCGTACTGGATCC+AGG - chr2_1:64541639-64541658 Msa0217620:intron 50.0%
TATGGGTCGTACTGGATCCA+GGG - chr2_1:64541640-64541659 Msa0217620:intron 50.0%
GGAATGTGAAGGGACCAGTT+AGG - chr2_1:64541720-64541739 Msa0217620:intron 50.0%
TTCTCTCTCAGACTCGAGGA+GGG + chr2_1:64541762-64541781 None:intergenic 50.0%
TTGCTTCTCTCTCAGACTCG+AGG + chr2_1:64541766-64541785 None:intergenic 50.0%
! GGAAAGTGCAGAATCGGCGT+GGG + chr2_1:64540607-64540626 None:intergenic 55.0%
! TGGAAAGTGCAGAATCGGCG+TGG + chr2_1:64540608-64540627 None:intergenic 55.0%
ATGGGTCGTACTGGATCCAG+GGG - chr2_1:64541641-64541660 Msa0217620:intron 55.0%
ATCCAGGGGACAAGTCACTC+AGG - chr2_1:64541655-64541674 Msa0217620:intron 55.0%
! AACCTGAGTGACTTGTCCCC+TGG + chr2_1:64541660-64541679 None:intergenic 55.0%
TGTGAAGGGACCAGTTAGGG+AGG - chr2_1:64541724-64541743 Msa0217620:intron 55.0%
GTGAAGGGACCAGTTAGGGA+GGG - chr2_1:64541725-64541744 Msa0217620:intron 55.0%
AGGATGTCTCCCTCCCTAAC+TGG + chr2_1:64541737-64541756 None:intergenic 55.0%
TCTCAGACTCGAGGAGGGTA+AGG + chr2_1:64541757-64541776 None:intergenic 55.0%
CTTCTCTCTCAGACTCGAGG+AGG + chr2_1:64541763-64541782 None:intergenic 55.0%
! GGAAAGTGCAGAATCGGCGT+GGG + chr2_1:64540607-64540626 None:intergenic 55.0%
! TGGAAAGTGCAGAATCGGCG+TGG + chr2_1:64540608-64540627 None:intergenic 55.0%
ATGGGTCGTACTGGATCCAG+GGG - chr2_1:64541641-64541660 Msa0217620:intron 55.0%
ATCCAGGGGACAAGTCACTC+AGG - chr2_1:64541655-64541674 Msa0217620:intron 55.0%
! AACCTGAGTGACTTGTCCCC+TGG + chr2_1:64541660-64541679 None:intergenic 55.0%
TGTGAAGGGACCAGTTAGGG+AGG - chr2_1:64541724-64541743 Msa0217620:intron 55.0%
GTGAAGGGACCAGTTAGGGA+GGG - chr2_1:64541725-64541744 Msa0217620:intron 55.0%
AGGATGTCTCCCTCCCTAAC+TGG + chr2_1:64541737-64541756 None:intergenic 55.0%
TCTCAGACTCGAGGAGGGTA+AGG + chr2_1:64541757-64541776 None:intergenic 55.0%
CTTCTCTCTCAGACTCGAGG+AGG + chr2_1:64541763-64541782 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 64540557 64542129 64540557 ID=Msa0217620;Name=Msa0217620
chr2_1 mRNA 64540557 64542129 64540557 ID=Msa0217620-mRNA-1;Parent=Msa0217620;Name=Msa0217620-mRNA-1;_AED=0.12;_eAED=0.12;_QI=90|0|0.5|1|0|0.5|2|330|65
chr2_1 exon 64540557 64541084 64540557 ID=Msa0217620-mRNA-1:exon:17912;Parent=Msa0217620-mRNA-1
chr2_1 exon 64542040 64542129 64542040 ID=Msa0217620-mRNA-1:exon:17911;Parent=Msa0217620-mRNA-1
chr2_1 five_prime_UTR 64542040 64542129 64542040 ID=Msa0217620-mRNA-1:five_prime_utr;Parent=Msa0217620-mRNA-1
chr2_1 CDS 64540887 64541084 64540887 ID=Msa0217620-mRNA-1:cds;Parent=Msa0217620-mRNA-1
chr2_1 three_prime_UTR 64540557 64540886 64540557 ID=Msa0217620-mRNA-1:three_prime_utr;Parent=Msa0217620-mRNA-1
Gene Sequence

>Msa0217620

ATGGAATCACAGATTAAGCATGCTGTTGTTGTGAAAGTTATGGGTCGTACTGGATCCAGGGGACAAGTCACTCAGGTTAGAGTGAAGTTTTTGGATGATCAGAATCGTCACATCATGAGGAATGTGAAGGGACCAGTTAGGGAGGGAGACATCCTTACCCTCCTCGAGTCTGAGAGAGAAGCAAGAAGACTCCGATAG
Protein sequence

>Msa0217620

MESQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRHIMRNVKGPVREGDILTLLESEREARRLR*