AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0296720

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0296720 MtrunA17_Chr6g0453811 100.000 65 0 0 1 65 1 65 6.66e-42 130
Msa0296720 MtrunA17_Chr4g0041861 90.769 65 6 0 1 65 1 65 3.30e-37 118
Msa0296720 MtrunA17_Chr6g0453911 81.538 65 11 1 1 65 1 64 1.49e-31 103
Msa0296720 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
Msa0296720 AT5G03850.1 90.769 65 5 1 1 65 1 64 1.33e-35 114
Msa0296720 AT3G10090.1 90.769 65 5 1 1 65 1 64 1.33e-35 114
Msa0296720 AT5G64140.1 89.231 65 6 1 1 65 1 64 1.14e-34 112

Find 36 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGAAGTTGGTTGCTAAAA+TGG 0.117951 2_3:+50195829 None:intergenic
ACCTGCTATTCAAGGAAATT+AGG 0.247464 2_3:+50194424 None:intergenic
TGATTGATATTTGATTAGTT+TGG 0.323942 2_3:-50194393 Msa0296720:three_prime_UTR
TTCTTATAACCTGCTATTCA+AGG 0.363273 2_3:+50194416 None:intergenic
ACCTAATTTCCTTGAATAGC+AGG 0.397759 2_3:-50194425 Msa0296720:three_prime_UTR
GCTGTTGTTGTGAAAGTTAT+GGG 0.420809 2_3:-50194877 Msa0296720:CDS
AGGATGTCTCCCTCCCTAAC+TGG 0.425936 2_3:+50194766 None:intergenic
TGCTGTTGTTGTGAAAGTTA+TGG 0.441002 2_3:-50194878 Msa0296720:CDS
TTATGGGTCGTACTGGATCC+AGG 0.451262 2_3:-50194861 Msa0296720:CDS
AACCTGAGTGACTTGTCCCC+TGG 0.461687 2_3:+50194843 None:intergenic
GAATGTGAAGGGACCAGTTA+GGG 0.464736 2_3:-50194779 Msa0296720:CDS
AGCTCTTAAAACTGTTGTGT+TGG 0.468388 2_3:-50194643 Msa0296720:three_prime_UTR
GGAATGTGAAGGGACCAGTT+AGG 0.473428 2_3:-50194780 Msa0296720:CDS
TGTGACTTAGATATAAAATC+TGG 0.474524 2_3:-50194515 Msa0296720:three_prime_UTR
TAAAATGGAAAGTGCAGAAT+CGG 0.485027 2_3:+50195844 None:intergenic
TCTCAGACTCGAGGAGGGTA+AGG 0.488938 2_3:+50194746 None:intergenic
AGGAAATTAGGTTTGAGACT+TGG 0.499121 2_3:+50194436 None:intergenic
TATATGTTGTTCAATATGTC+AGG 0.499645 2_3:-50194492 Msa0296720:three_prime_UTR
GAGAGAAACGAACTTGAAGT+TGG 0.505451 2_3:+50195817 None:intergenic
GTGAAAGTTATGGGTCGTAC+TGG 0.530087 2_3:-50194868 Msa0296720:CDS
GCGAAGAAGCTAGCTGCGTA+TGG 0.560787 2_3:+50195882 None:intergenic
TGTGAAGGGACCAGTTAGGG+AGG 0.582336 2_3:-50194776 Msa0296720:CDS
ATCAGAATCGTCACATCATG+AGG 0.584464 2_3:-50194801 Msa0296720:CDS
TTGCTTCTCTCTCAGACTCG+AGG 0.586554 2_3:+50194737 None:intergenic
AAACATCGAGACTCTTCTAT+CGG 0.589119 2_3:+50194707 None:intergenic
CTTCTCTCTCAGACTCGAGG+AGG 0.606831 2_3:+50194740 None:intergenic
TATGGGTCGTACTGGATCCA+GGG 0.613108 2_3:-50194860 Msa0296720:CDS
GGAAAGTGCAGAATCGGCGT+GGG 0.619085 2_3:+50195850 None:intergenic
TCACATCATGAGGAATGTGA+AGG 0.626309 2_3:-50194791 Msa0296720:CDS
TGGAAAGTGCAGAATCGGCG+TGG 0.632732 2_3:+50195849 None:intergenic
CACATCATGAGGAATGTGAA+GGG 0.632733 2_3:-50194790 Msa0296720:CDS
ATCCAGGGGACAAGTCACTC+AGG 0.638739 2_3:-50194845 Msa0296720:CDS
TTCTCTCTCAGACTCGAGGA+GGG 0.644799 2_3:+50194741 None:intergenic
GTGAAGGGACCAGTTAGGGA+GGG 0.647685 2_3:-50194775 Msa0296720:CDS
ATGCTGTCTTGTTTATACGA+TGG 0.664216 2_3:-50194464 Msa0296720:three_prime_UTR
ATGGGTCGTACTGGATCCAG+GGG 0.674814 2_3:-50194859 Msa0296720:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTATTTTGATTTTTTCA+TGG - chr2_3:50194579-50194598 Msa0296720:three_prime_UTR 10.0%
!!! TTATTTGTTTTAATTAATGA+AGG - chr2_3:50195732-50195751 Msa0296720:intron 10.0%
!!! TATTTGTTTTAATTAATGAA+GGG - chr2_3:50195733-50195752 Msa0296720:intron 10.0%
!!! TTTTTATTTTGATTTTTTCA+TGG - chr2_3:50194579-50194598 Msa0296720:three_prime_UTR 10.0%
!!! TTATTTGTTTTAATTAATGA+AGG - chr2_3:50195732-50195751 Msa0296720:intron 10.0%
!!! TATTTGTTTTAATTAATGAA+GGG - chr2_3:50195733-50195752 Msa0296720:intron 10.0%
!! TAGTTTAATAAAAATCAAAG+AGG + chr2_3:50195109-50195128 None:intergenic 15.0%
!! AAATTATGATTTAAATAGTC+TGG - chr2_3:50195218-50195237 Msa0296720:intron 15.0%
!! TAGTTTAATAAAAATCAAAG+AGG + chr2_3:50195109-50195128 None:intergenic 15.0%
!! AAATTATGATTTAAATAGTC+TGG - chr2_3:50195218-50195237 Msa0296720:intron 15.0%
!! AGTTAAAAAAGTCATTTCTA+AGG + chr2_3:50194912-50194931 None:intergenic 20.0%
!!! ATCAACTTCACTTTATTTTT+TGG + chr2_3:50195185-50195204 None:intergenic 20.0%
!!! TGATTGATATTTGATTAGTT+TGG - chr2_3:50195895-50195914 Msa0296720:five_prime_UTR 20.0%
!! AGTTAAAAAAGTCATTTCTA+AGG + chr2_3:50194912-50194931 None:intergenic 20.0%
!!! ATCAACTTCACTTTATTTTT+TGG + chr2_3:50195185-50195204 None:intergenic 20.0%
! GCTAAAACTATAGATCAATA+AGG + chr2_3:50194514-50194533 None:intergenic 25.0%
!!! GATTTTTTCATGGTTGATTT+AGG - chr2_3:50194589-50194608 Msa0296720:three_prime_UTR 25.0%
!! TTTAAAATGTGTGAAAGATG+AGG - chr2_3:50194763-50194782 Msa0296720:CDS 25.0%
!! TGATTGCTATTAATTGTGTT+TGG - chr2_3:50194943-50194962 Msa0296720:intron 25.0%
! TTGATTGCTTATATTGTGTT+TGG - chr2_3:50195134-50195153 Msa0296720:intron 25.0%
!!! GATAAAAAAGTGTTTTTCAG+TGG - chr2_3:50195254-50195273 Msa0296720:intron 25.0%
! ACACATTCACAATTGTTAAT+AGG + chr2_3:50195357-50195376 None:intergenic 25.0%
! TGTGACTTAGATATAAAATC+TGG - chr2_3:50195773-50195792 Msa0296720:intron 25.0%
! TATATGTTGTTCAATATGTC+AGG - chr2_3:50195796-50195815 Msa0296720:intron 25.0%
!!! TTGATATTTGATTAGTTTGG+AGG - chr2_3:50195898-50195917 Msa0296720:five_prime_UTR 25.0%
! GCTAAAACTATAGATCAATA+AGG + chr2_3:50194514-50194533 None:intergenic 25.0%
!!! GATTTTTTCATGGTTGATTT+AGG - chr2_3:50194589-50194608 Msa0296720:three_prime_UTR 25.0%
!! TTTAAAATGTGTGAAAGATG+AGG - chr2_3:50194763-50194782 Msa0296720:CDS 25.0%
!! TGATTGCTATTAATTGTGTT+TGG - chr2_3:50194943-50194962 Msa0296720:intron 25.0%
! TTGATTGCTTATATTGTGTT+TGG - chr2_3:50195134-50195153 Msa0296720:intron 25.0%
!!! GATAAAAAAGTGTTTTTCAG+TGG - chr2_3:50195254-50195273 Msa0296720:intron 25.0%
! ACACATTCACAATTGTTAAT+AGG + chr2_3:50195357-50195376 None:intergenic 25.0%
! TGTGACTTAGATATAAAATC+TGG - chr2_3:50195773-50195792 Msa0296720:intron 25.0%
! TATATGTTGTTCAATATGTC+AGG - chr2_3:50195796-50195815 Msa0296720:intron 25.0%
! TAAAATGGAAAGTGCAGAAT+CGG + chr2_3:50194447-50194466 None:intergenic 30.0%
!! TTTTCATGGTTGATTTAGGT+TGG - chr2_3:50194593-50194612 Msa0296720:three_prime_UTR 30.0%
TTCTTATAACCTGCTATTCA+AGG + chr2_3:50195875-50195894 None:intergenic 30.0%
! TAAAATGGAAAGTGCAGAAT+CGG + chr2_3:50194447-50194466 None:intergenic 30.0%
!! TTTTCATGGTTGATTTAGGT+TGG - chr2_3:50194593-50194612 Msa0296720:three_prime_UTR 30.0%
TTCTTATAACCTGCTATTCA+AGG + chr2_3:50195875-50195894 None:intergenic 30.0%
! CTTGAAGTTGGTTGCTAAAA+TGG + chr2_3:50194462-50194481 None:intergenic 35.0%
TCAACAAATTAAGCTGAAGC+TGG + chr2_3:50194848-50194867 None:intergenic 35.0%
CAATTGTTAATAGGAGAGCA+AGG + chr2_3:50195348-50195367 None:intergenic 35.0%
TGCTGTTGTTGTGAAAGTTA+TGG - chr2_3:50195410-50195429 Msa0296720:intron 35.0%
GCTGTTGTTGTGAAAGTTAT+GGG - chr2_3:50195411-50195430 Msa0296720:intron 35.0%
! TCAGGTTAGAGTGAAGTTTT+TGG - chr2_3:50195461-50195480 Msa0296720:intron 35.0%
AAACATCGAGACTCTTCTAT+CGG + chr2_3:50195584-50195603 None:intergenic 35.0%
AGCTCTTAAAACTGTTGTGT+TGG - chr2_3:50195645-50195664 Msa0296720:intron 35.0%
!! ATGCTGTCTTGTTTATACGA+TGG - chr2_3:50195824-50195843 Msa0296720:intron 35.0%
! AGGAAATTAGGTTTGAGACT+TGG + chr2_3:50195855-50195874 None:intergenic 35.0%
ACCTAATTTCCTTGAATAGC+AGG - chr2_3:50195863-50195882 Msa0296720:five_prime_UTR 35.0%
ACCTGCTATTCAAGGAAATT+AGG + chr2_3:50195867-50195886 None:intergenic 35.0%
! CTTGAAGTTGGTTGCTAAAA+TGG + chr2_3:50194462-50194481 None:intergenic 35.0%
TCAACAAATTAAGCTGAAGC+TGG + chr2_3:50194848-50194867 None:intergenic 35.0%
CAATTGTTAATAGGAGAGCA+AGG + chr2_3:50195348-50195367 None:intergenic 35.0%
TGCTGTTGTTGTGAAAGTTA+TGG - chr2_3:50195410-50195429 Msa0296720:intron 35.0%
GCTGTTGTTGTGAAAGTTAT+GGG - chr2_3:50195411-50195430 Msa0296720:intron 35.0%
! TCAGGTTAGAGTGAAGTTTT+TGG - chr2_3:50195461-50195480 Msa0296720:intron 35.0%
AAACATCGAGACTCTTCTAT+CGG + chr2_3:50195584-50195603 None:intergenic 35.0%
AGCTCTTAAAACTGTTGTGT+TGG - chr2_3:50195645-50195664 Msa0296720:intron 35.0%
!! ATGCTGTCTTGTTTATACGA+TGG - chr2_3:50195824-50195843 Msa0296720:intron 35.0%
! AGGAAATTAGGTTTGAGACT+TGG + chr2_3:50195855-50195874 None:intergenic 35.0%
ACCTAATTTCCTTGAATAGC+AGG - chr2_3:50195863-50195882 Msa0296720:five_prime_UTR 35.0%
ACCTGCTATTCAAGGAAATT+AGG + chr2_3:50195867-50195886 None:intergenic 35.0%
GAGAGAAACGAACTTGAAGT+TGG + chr2_3:50194474-50194493 None:intergenic 40.0%
ATCAGAATCGTCACATCATG+AGG - chr2_3:50195487-50195506 Msa0296720:intron 40.0%
TCACATCATGAGGAATGTGA+AGG - chr2_3:50195497-50195516 Msa0296720:intron 40.0%
CACATCATGAGGAATGTGAA+GGG - chr2_3:50195498-50195517 Msa0296720:intron 40.0%
GAGAGAAACGAACTTGAAGT+TGG + chr2_3:50194474-50194493 None:intergenic 40.0%
ATCAGAATCGTCACATCATG+AGG - chr2_3:50195487-50195506 Msa0296720:intron 40.0%
TCACATCATGAGGAATGTGA+AGG - chr2_3:50195497-50195516 Msa0296720:intron 40.0%
CACATCATGAGGAATGTGAA+GGG - chr2_3:50195498-50195517 Msa0296720:intron 40.0%
GTGAATGTGTGTGTTTGAGC+AGG - chr2_3:50195367-50195386 Msa0296720:intron 45.0%
ATGTGTGTGTTTGAGCAGGA+TGG - chr2_3:50195371-50195390 Msa0296720:intron 45.0%
GTGAAAGTTATGGGTCGTAC+TGG - chr2_3:50195420-50195439 Msa0296720:intron 45.0%
GAATGTGAAGGGACCAGTTA+GGG - chr2_3:50195509-50195528 Msa0296720:intron 45.0%
GTGAATGTGTGTGTTTGAGC+AGG - chr2_3:50195367-50195386 Msa0296720:intron 45.0%
ATGTGTGTGTTTGAGCAGGA+TGG - chr2_3:50195371-50195390 Msa0296720:intron 45.0%
GTGAAAGTTATGGGTCGTAC+TGG - chr2_3:50195420-50195439 Msa0296720:intron 45.0%
GAATGTGAAGGGACCAGTTA+GGG - chr2_3:50195509-50195528 Msa0296720:intron 45.0%
!! TCAAAATAAAAAAATTAATA+TGG + chr2_3:50194571-50194590 None:intergenic 5.0%
!! TCAAAATAAAAAAATTAATA+TGG + chr2_3:50194571-50194590 None:intergenic 5.0%
TTATGGGTCGTACTGGATCC+AGG - chr2_3:50195427-50195446 Msa0296720:intron 50.0%
TATGGGTCGTACTGGATCCA+GGG - chr2_3:50195428-50195447 Msa0296720:intron 50.0%
GGAATGTGAAGGGACCAGTT+AGG - chr2_3:50195508-50195527 Msa0296720:intron 50.0%
TTCTCTCTCAGACTCGAGGA+GGG + chr2_3:50195550-50195569 None:intergenic 50.0%
TTGCTTCTCTCTCAGACTCG+AGG + chr2_3:50195554-50195573 None:intergenic 50.0%
TTATGGGTCGTACTGGATCC+AGG - chr2_3:50195427-50195446 Msa0296720:intron 50.0%
TATGGGTCGTACTGGATCCA+GGG - chr2_3:50195428-50195447 Msa0296720:intron 50.0%
GGAATGTGAAGGGACCAGTT+AGG - chr2_3:50195508-50195527 Msa0296720:intron 50.0%
TTCTCTCTCAGACTCGAGGA+GGG + chr2_3:50195550-50195569 None:intergenic 50.0%
TTGCTTCTCTCTCAGACTCG+AGG + chr2_3:50195554-50195573 None:intergenic 50.0%
GCGAAGAAGCTAGCTGCGTA+TGG + chr2_3:50194409-50194428 None:intergenic 55.0%
! GGAAAGTGCAGAATCGGCGT+GGG + chr2_3:50194441-50194460 None:intergenic 55.0%
! TGGAAAGTGCAGAATCGGCG+TGG + chr2_3:50194442-50194461 None:intergenic 55.0%
ATGGGTCGTACTGGATCCAG+GGG - chr2_3:50195429-50195448 Msa0296720:intron 55.0%
ATCCAGGGGACAAGTCACTC+AGG - chr2_3:50195443-50195462 Msa0296720:intron 55.0%
! AACCTGAGTGACTTGTCCCC+TGG + chr2_3:50195448-50195467 None:intergenic 55.0%
TGTGAAGGGACCAGTTAGGG+AGG - chr2_3:50195512-50195531 Msa0296720:intron 55.0%
GTGAAGGGACCAGTTAGGGA+GGG - chr2_3:50195513-50195532 Msa0296720:intron 55.0%
AGGATGTCTCCCTCCCTAAC+TGG + chr2_3:50195525-50195544 None:intergenic 55.0%
TCTCAGACTCGAGGAGGGTA+AGG + chr2_3:50195545-50195564 None:intergenic 55.0%
CTTCTCTCTCAGACTCGAGG+AGG + chr2_3:50195551-50195570 None:intergenic 55.0%
GCGAAGAAGCTAGCTGCGTA+TGG + chr2_3:50194409-50194428 None:intergenic 55.0%
! GGAAAGTGCAGAATCGGCGT+GGG + chr2_3:50194441-50194460 None:intergenic 55.0%
! TGGAAAGTGCAGAATCGGCG+TGG + chr2_3:50194442-50194461 None:intergenic 55.0%
ATGGGTCGTACTGGATCCAG+GGG - chr2_3:50195429-50195448 Msa0296720:intron 55.0%
ATCCAGGGGACAAGTCACTC+AGG - chr2_3:50195443-50195462 Msa0296720:intron 55.0%
! AACCTGAGTGACTTGTCCCC+TGG + chr2_3:50195448-50195467 None:intergenic 55.0%
TGTGAAGGGACCAGTTAGGG+AGG - chr2_3:50195512-50195531 Msa0296720:intron 55.0%
GTGAAGGGACCAGTTAGGGA+GGG - chr2_3:50195513-50195532 Msa0296720:intron 55.0%
AGGATGTCTCCCTCCCTAAC+TGG + chr2_3:50195525-50195544 None:intergenic 55.0%
TCTCAGACTCGAGGAGGGTA+AGG + chr2_3:50195545-50195564 None:intergenic 55.0%
CTTCTCTCTCAGACTCGAGG+AGG + chr2_3:50195551-50195570 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 50194393 50195917 50194393 ID=Msa0296720;Name=Msa0296720
chr2_3 mRNA 50194393 50195917 50194393 ID=Msa0296720-mRNA-1;Parent=Msa0296720;Name=Msa0296720-mRNA-1;_AED=0.12;_eAED=0.12;_QI=88|0|0.5|1|0|0.5|2|330|65
chr2_3 exon 50194393 50194920 50194393 ID=Msa0296720-mRNA-1:exon:15785;Parent=Msa0296720-mRNA-1
chr2_3 exon 50195830 50195917 50195830 ID=Msa0296720-mRNA-1:exon:15784;Parent=Msa0296720-mRNA-1
chr2_3 five_prime_UTR 50195830 50195917 50195830 ID=Msa0296720-mRNA-1:five_prime_utr;Parent=Msa0296720-mRNA-1
chr2_3 CDS 50194723 50194920 50194723 ID=Msa0296720-mRNA-1:cds;Parent=Msa0296720-mRNA-1
chr2_3 three_prime_UTR 50194393 50194722 50194393 ID=Msa0296720-mRNA-1:three_prime_utr;Parent=Msa0296720-mRNA-1
Gene Sequence

>Msa0296720

ATGGAATCACAGATTAAGCATGCTGTTGTTGTGAAAGTTATGGGTCGTACTGGATCCAGGGGACAAGTCACTCAGGTTAGAGTGAAGTTTTTGGATGATCAGAATCGTCACATCATGAGGAATGTGAAGGGACCAGTTAGGGAGGGAGACATCCTTACCCTCCTCGAGTCTGAGAGAGAAGCAAGAAGACTCCGATAG
Protein sequence

>Msa0296720

MESQIKHAVVVKVMGRTGSRGQVTQVRVKFLDDQNRHIMRNVKGPVREGDILTLLESEREARRLR*