AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0477010

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0477010 MtrunA17_Chr6g0477991 43.269 104 55 3 8 111 3 102 3.61e-22 83.6
Msa0477010 MtrunA17_Chr3g0138201 97.297 37 1 0 12 48 43 79 1.30e-21 81.6
Msa0477010 MtrunA17_Chr3g0137931 42.574 101 54 2 12 112 55 151 1.22e-20 80.9
Msa0477010 MtrunA17_Chr6g0476161 44.737 76 37 4 27 101 6 77 3.12e-12 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0477010 AT4G30380.2 34.314 102 54 4 10 109 33 123 3.23e-12 58.9
Msa0477010 AT4G30380.1 36.471 85 45 3 27 109 44 121 6.48e-12 58.2

Find 41 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTCTGAAACTTATTTAAA+TGG 0.172664 3_3:-81074525 Msa0477010:three_prime_UTR
TTAGTCAATGTAATTTAAAA+AGG 0.192566 3_3:+81074415 None:intergenic
GAGCACAATCTTCTGTTTCT+AGG 0.213213 3_3:-81075016 Msa0477010:CDS
GTTCAGCTGGAGAAGGTATA+TGG 0.236425 3_3:-81075145 Msa0477010:CDS
AAGACAGCGACGGCGTGTTT+TGG 0.285235 3_3:-81075206 Msa0477010:CDS
AACTTAGATGGCGGCATTAT+AGG 0.308157 3_3:-81074570 Msa0477010:three_prime_UTR
GTTCCTCGGACTTGCATTCC+TGG 0.318288 3_3:-81075068 Msa0477010:CDS
GATGGCGGCATTATAGGAAT+TGG 0.338158 3_3:-81074564 Msa0477010:three_prime_UTR
TATTTGAAAACAACAAAGTT+AGG 0.351896 3_3:-81074286 Msa0477010:three_prime_UTR
AGGGTTTGAAAATTTGAAAT+AGG 0.368924 3_3:-81074598 Msa0477010:exon
TTAGATGAGTAGTATTTGTA+TGG 0.372297 3_3:-81074480 Msa0477010:three_prime_UTR
AAATAGGCAATGAACTTAGA+TGG 0.389567 3_3:-81074582 Msa0477010:three_prime_UTR
AAGAAAACAGGCTGTCCTCT+TGG 0.405308 3_3:+81074448 None:intergenic
AGCAACATGTTTGGTTCAGC+TGG 0.419911 3_3:-81075158 Msa0477010:CDS
ATCGAAACATACAGTAATAC+AGG 0.436841 3_3:+81074312 None:intergenic
AGAAAACAGGCTGTCCTCTT+GGG 0.444172 3_3:+81074449 None:intergenic
TTTCCGTCGAGCAACATGTT+TGG 0.450035 3_3:-81075167 Msa0477010:CDS
TTGGAATTCGATGTTTATCA+AGG 0.457331 3_3:+81074923 None:intergenic
TTCTGTTTCTAGGCCTTCAT+CGG 0.477067 3_3:-81075006 Msa0477010:CDS
ACAATGGTGCAGCGTGTGGG+AGG 0.533075 3_3:-81075121 Msa0477010:CDS
GTATAAGTGCAGCTGTTCCT+CGG 0.534469 3_3:-81075082 Msa0477010:CDS
TTCAGCTGGAGAAGGTATAT+GGG 0.539255 3_3:-81075144 Msa0477010:CDS
ATGTTTGGTTCAGCTGGAGA+AGG 0.553087 3_3:-81075152 Msa0477010:CDS
AACATTTGCAATGATCTGAA+AGG 0.560268 3_3:+81074953 None:intergenic
ATGGAAGTATCATCCGATGA+AGG 0.570347 3_3:+81074993 None:intergenic
TTCATCGGATGATACTTCCA+TGG 0.589310 3_3:-81074991 Msa0477010:CDS
CAGGCAATAGCATTAGCTGA+TGG 0.593510 3_3:+81074331 None:intergenic
TGGGACAATGGTGCAGCGTG+TGG 0.603898 3_3:-81075125 Msa0477010:CDS
TTAATCTGAATAGTTTGACC+AGG 0.609627 3_3:+81075050 None:intergenic
ATGGCGATCTCTCGCTGCAG+AGG 0.609698 3_3:-81074506 Msa0477010:three_prime_UTR
GGGACAATGGTGCAGCGTGT+GGG 0.613332 3_3:-81075124 Msa0477010:CDS
TGCAATGATCTGAAAGGCAG+TGG 0.623356 3_3:+81074959 None:intergenic
GGCAGTGGTGGAAAGAACCA+TGG 0.636283 3_3:+81074974 None:intergenic
GAACCAAACATGTTGCTCGA+CGG 0.639586 3_3:+81075164 None:intergenic
GGAGAAGGTATATGGGACAA+TGG 0.640344 3_3:-81075137 Msa0477010:CDS
AGCGTGTGGGAGGCTGTATG+AGG 0.663788 3_3:-81075111 Msa0477010:CDS
AATGATCTGAAAGGCAGTGG+TGG 0.664140 3_3:+81074962 None:intergenic
GTGGGAGGCTGTATGAGGTG+AGG 0.677893 3_3:-81075106 Msa0477010:CDS
TGACCAGGAATGCAAGTCCG+AGG 0.678065 3_3:+81075065 None:intergenic
GGAACGTGACAAGACAGCGA+CGG 0.706963 3_3:-81075216 Msa0477010:CDS
TAGGCAATGAACTTAGATGG+CGG 0.714699 3_3:-81074579 Msa0477010:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATAATATAACTTACTGT+TGG + chr3_3:81074609-81074628 None:intergenic 15.0%
!! TAGTCAATGTAATTTAAAAA+GGG + chr3_3:81075097-81075116 None:intergenic 15.0%
!! TTAGTCAATGTAATTTAAAA+AGG + chr3_3:81075098-81075117 None:intergenic 15.0%
!! ATAATAATATAACTTACTGT+TGG + chr3_3:81074609-81074628 None:intergenic 15.0%
!! TAGTCAATGTAATTTAAAAA+GGG + chr3_3:81075097-81075116 None:intergenic 15.0%
!! TTAGTCAATGTAATTTAAAA+AGG + chr3_3:81075098-81075117 None:intergenic 15.0%
!! ATATGATATGATGAATCATT+AGG - chr3_3:81074631-81074650 Msa0477010:intron 20.0%
!! TTGAAAAATCAAATGTTGAA+TGG - chr3_3:81074760-81074779 Msa0477010:intron 20.0%
!!! ACAACAATATTTTTCTAGTT+AGG - chr3_3:81074861-81074880 Msa0477010:intron 20.0%
!! AGTCAATGTAATTTAAAAAG+GGG + chr3_3:81075096-81075115 None:intergenic 20.0%
!! TATTTGAAAACAACAAAGTT+AGG - chr3_3:81075224-81075243 Msa0477010:CDS 20.0%
!! ATATGATATGATGAATCATT+AGG - chr3_3:81074631-81074650 Msa0477010:intron 20.0%
!! TTGAAAAATCAAATGTTGAA+TGG - chr3_3:81074760-81074779 Msa0477010:intron 20.0%
!!! ACAACAATATTTTTCTAGTT+AGG - chr3_3:81074861-81074880 Msa0477010:intron 20.0%
!! AGTCAATGTAATTTAAAAAG+GGG + chr3_3:81075096-81075115 None:intergenic 20.0%
!! TATTTGAAAACAACAAAGTT+AGG - chr3_3:81075224-81075243 Msa0477010:CDS 20.0%
!!! TTATTGTTTATTTTCCGTGT+TGG - chr3_3:81074682-81074701 Msa0477010:intron 25.0%
! AAAAATCAAATGTTGAATGG+TGG - chr3_3:81074763-81074782 Msa0477010:intron 25.0%
!! AGGGTTTGAAAATTTGAAAT+AGG - chr3_3:81074912-81074931 Msa0477010:intron 25.0%
!!! TGCTCTGAAACTTATTTAAA+TGG - chr3_3:81074985-81075004 Msa0477010:CDS 25.0%
! TTAGATGAGTAGTATTTGTA+TGG - chr3_3:81075030-81075049 Msa0477010:CDS 25.0%
! GTCAATGTAATTTAAAAAGG+GGG + chr3_3:81075095-81075114 None:intergenic 25.0%
!!! TTATTGTTTATTTTCCGTGT+TGG - chr3_3:81074682-81074701 Msa0477010:intron 25.0%
! AAAAATCAAATGTTGAATGG+TGG - chr3_3:81074763-81074782 Msa0477010:intron 25.0%
!! AGGGTTTGAAAATTTGAAAT+AGG - chr3_3:81074912-81074931 Msa0477010:intron 25.0%
!!! TGCTCTGAAACTTATTTAAA+TGG - chr3_3:81074985-81075004 Msa0477010:CDS 25.0%
! TTAGATGAGTAGTATTTGTA+TGG - chr3_3:81075030-81075049 Msa0477010:CDS 25.0%
! GTCAATGTAATTTAAAAAGG+GGG + chr3_3:81075095-81075114 None:intergenic 25.0%
TTAATCTGAATAGTTTGACC+AGG + chr3_3:81074463-81074482 None:intergenic 30.0%
AACATTTGCAATGATCTGAA+AGG + chr3_3:81074560-81074579 None:intergenic 30.0%
TTGGAATTCGATGTTTATCA+AGG + chr3_3:81074590-81074609 None:intergenic 30.0%
AATGAATTTGTGAAAACGAG+AGG - chr3_3:81074802-81074821 Msa0477010:intron 30.0%
!! TCTAGTTAGGTACTGAAATA+TGG - chr3_3:81074874-81074893 Msa0477010:intron 30.0%
!!! TATGGTATTTTTTCATGTGC+AGG - chr3_3:81074892-81074911 Msa0477010:intron 30.0%
!!! ATGGTATTTTTTCATGTGCA+GGG - chr3_3:81074893-81074912 Msa0477010:intron 30.0%
AAATAGGCAATGAACTTAGA+TGG - chr3_3:81074928-81074947 Msa0477010:CDS 30.0%
ATCGAAACATACAGTAATAC+AGG + chr3_3:81075201-81075220 None:intergenic 30.0%
TTAATCTGAATAGTTTGACC+AGG + chr3_3:81074463-81074482 None:intergenic 30.0%
AACATTTGCAATGATCTGAA+AGG + chr3_3:81074560-81074579 None:intergenic 30.0%
TTGGAATTCGATGTTTATCA+AGG + chr3_3:81074590-81074609 None:intergenic 30.0%
AATGAATTTGTGAAAACGAG+AGG - chr3_3:81074802-81074821 Msa0477010:intron 30.0%
!! TCTAGTTAGGTACTGAAATA+TGG - chr3_3:81074874-81074893 Msa0477010:intron 30.0%
!!! TATGGTATTTTTTCATGTGC+AGG - chr3_3:81074892-81074911 Msa0477010:intron 30.0%
!!! ATGGTATTTTTTCATGTGCA+GGG - chr3_3:81074893-81074912 Msa0477010:intron 30.0%
AAATAGGCAATGAACTTAGA+TGG - chr3_3:81074928-81074947 Msa0477010:CDS 30.0%
ATCGAAACATACAGTAATAC+AGG + chr3_3:81075201-81075220 None:intergenic 30.0%
TATTACTCCACATCACAAGT+TGG - chr3_3:81074730-81074749 Msa0477010:intron 35.0%
TATTACTCCACATCACAAGT+TGG - chr3_3:81074730-81074749 Msa0477010:intron 35.0%
! TTCAGCTGGAGAAGGTATAT+GGG - chr3_3:81074366-81074385 Msa0477010:three_prime_UTR 40.0%
! GAGCACAATCTTCTGTTTCT+AGG - chr3_3:81074494-81074513 Msa0477010:three_prime_UTR 40.0%
!! TTCTGTTTCTAGGCCTTCAT+CGG - chr3_3:81074504-81074523 Msa0477010:three_prime_UTR 40.0%
!! ATGGAAGTATCATCCGATGA+AGG + chr3_3:81074520-81074539 None:intergenic 40.0%
TTCATCGGATGATACTTCCA+TGG - chr3_3:81074519-81074538 Msa0477010:three_prime_UTR 40.0%
!!! TTTCCGTGTTGGTTGTGTTT+TGG - chr3_3:81074693-81074712 Msa0477010:intron 40.0%
TCACCAAAACACAACCAACA+CGG + chr3_3:81074699-81074718 None:intergenic 40.0%
CAACTAACCAACTTGTGATG+TGG + chr3_3:81074740-81074759 None:intergenic 40.0%
TAGGCAATGAACTTAGATGG+CGG - chr3_3:81074931-81074950 Msa0477010:CDS 40.0%
! AACTTAGATGGCGGCATTAT+AGG - chr3_3:81074940-81074959 Msa0477010:CDS 40.0%
! GTATGGATTTTGTTCCCAAG+AGG - chr3_3:81075047-81075066 Msa0477010:CDS 40.0%
GGGGGTAATTTGAAGAAAAC+AGG + chr3_3:81075077-81075096 None:intergenic 40.0%
! TTCAGCTGGAGAAGGTATAT+GGG - chr3_3:81074366-81074385 Msa0477010:three_prime_UTR 40.0%
! GAGCACAATCTTCTGTTTCT+AGG - chr3_3:81074494-81074513 Msa0477010:three_prime_UTR 40.0%
!! TTCTGTTTCTAGGCCTTCAT+CGG - chr3_3:81074504-81074523 Msa0477010:three_prime_UTR 40.0%
!! ATGGAAGTATCATCCGATGA+AGG + chr3_3:81074520-81074539 None:intergenic 40.0%
TTCATCGGATGATACTTCCA+TGG - chr3_3:81074519-81074538 Msa0477010:three_prime_UTR 40.0%
!!! TTTCCGTGTTGGTTGTGTTT+TGG - chr3_3:81074693-81074712 Msa0477010:intron 40.0%
TCACCAAAACACAACCAACA+CGG + chr3_3:81074699-81074718 None:intergenic 40.0%
CAACTAACCAACTTGTGATG+TGG + chr3_3:81074740-81074759 None:intergenic 40.0%
TAGGCAATGAACTTAGATGG+CGG - chr3_3:81074931-81074950 Msa0477010:CDS 40.0%
! AACTTAGATGGCGGCATTAT+AGG - chr3_3:81074940-81074959 Msa0477010:CDS 40.0%
! GTATGGATTTTGTTCCCAAG+AGG - chr3_3:81075047-81075066 Msa0477010:CDS 40.0%
GGGGGTAATTTGAAGAAAAC+AGG + chr3_3:81075077-81075096 None:intergenic 40.0%
TTTCCGTCGAGCAACATGTT+TGG - chr3_3:81074343-81074362 Msa0477010:three_prime_UTR 45.0%
GAACCAAACATGTTGCTCGA+CGG + chr3_3:81074349-81074368 None:intergenic 45.0%
! AGCAACATGTTTGGTTCAGC+TGG - chr3_3:81074352-81074371 Msa0477010:three_prime_UTR 45.0%
! ATGTTTGGTTCAGCTGGAGA+AGG - chr3_3:81074358-81074377 Msa0477010:three_prime_UTR 45.0%
! GTTCAGCTGGAGAAGGTATA+TGG - chr3_3:81074365-81074384 Msa0477010:three_prime_UTR 45.0%
! GGAGAAGGTATATGGGACAA+TGG - chr3_3:81074373-81074392 Msa0477010:three_prime_UTR 45.0%
GTATAAGTGCAGCTGTTCCT+CGG - chr3_3:81074428-81074447 Msa0477010:three_prime_UTR 45.0%
AATGATCTGAAAGGCAGTGG+TGG + chr3_3:81074551-81074570 None:intergenic 45.0%
TGCAATGATCTGAAAGGCAG+TGG + chr3_3:81074554-81074573 None:intergenic 45.0%
! GATGGCGGCATTATAGGAAT+TGG - chr3_3:81074946-81074965 Msa0477010:CDS 45.0%
AGAAAACAGGCTGTCCTCTT+GGG + chr3_3:81075064-81075083 None:intergenic 45.0%
AAGAAAACAGGCTGTCCTCT+TGG + chr3_3:81075065-81075084 None:intergenic 45.0%
CAGGCAATAGCATTAGCTGA+TGG + chr3_3:81075182-81075201 None:intergenic 45.0%
TTTCCGTCGAGCAACATGTT+TGG - chr3_3:81074343-81074362 Msa0477010:three_prime_UTR 45.0%
GAACCAAACATGTTGCTCGA+CGG + chr3_3:81074349-81074368 None:intergenic 45.0%
! AGCAACATGTTTGGTTCAGC+TGG - chr3_3:81074352-81074371 Msa0477010:three_prime_UTR 45.0%
! ATGTTTGGTTCAGCTGGAGA+AGG - chr3_3:81074358-81074377 Msa0477010:three_prime_UTR 45.0%
! GTTCAGCTGGAGAAGGTATA+TGG - chr3_3:81074365-81074384 Msa0477010:three_prime_UTR 45.0%
! GGAGAAGGTATATGGGACAA+TGG - chr3_3:81074373-81074392 Msa0477010:three_prime_UTR 45.0%
GTATAAGTGCAGCTGTTCCT+CGG - chr3_3:81074428-81074447 Msa0477010:three_prime_UTR 45.0%
AATGATCTGAAAGGCAGTGG+TGG + chr3_3:81074551-81074570 None:intergenic 45.0%
TGCAATGATCTGAAAGGCAG+TGG + chr3_3:81074554-81074573 None:intergenic 45.0%
! GATGGCGGCATTATAGGAAT+TGG - chr3_3:81074946-81074965 Msa0477010:CDS 45.0%
AGAAAACAGGCTGTCCTCTT+GGG + chr3_3:81075064-81075083 None:intergenic 45.0%
AAGAAAACAGGCTGTCCTCT+TGG + chr3_3:81075065-81075084 None:intergenic 45.0%
CAGGCAATAGCATTAGCTGA+TGG + chr3_3:81075182-81075201 None:intergenic 45.0%
GGAACGTGACAAGACAGCGA+CGG - chr3_3:81074294-81074313 Msa0477010:three_prime_UTR 55.0%
! AAGACAGCGACGGCGTGTTT+TGG - chr3_3:81074304-81074323 Msa0477010:three_prime_UTR 55.0%
! AGACAGCGACGGCGTGTTTT+GGG - chr3_3:81074305-81074324 Msa0477010:three_prime_UTR 55.0%
GTTCCTCGGACTTGCATTCC+TGG - chr3_3:81074442-81074461 Msa0477010:three_prime_UTR 55.0%
TGACCAGGAATGCAAGTCCG+AGG + chr3_3:81074448-81074467 None:intergenic 55.0%
! GGCAGTGGTGGAAAGAACCA+TGG + chr3_3:81074539-81074558 None:intergenic 55.0%
GGAACGTGACAAGACAGCGA+CGG - chr3_3:81074294-81074313 Msa0477010:three_prime_UTR 55.0%
! AAGACAGCGACGGCGTGTTT+TGG - chr3_3:81074304-81074323 Msa0477010:three_prime_UTR 55.0%
! AGACAGCGACGGCGTGTTTT+GGG - chr3_3:81074305-81074324 Msa0477010:three_prime_UTR 55.0%
GTTCCTCGGACTTGCATTCC+TGG - chr3_3:81074442-81074461 Msa0477010:three_prime_UTR 55.0%
TGACCAGGAATGCAAGTCCG+AGG + chr3_3:81074448-81074467 None:intergenic 55.0%
! GGCAGTGGTGGAAAGAACCA+TGG + chr3_3:81074539-81074558 None:intergenic 55.0%
! GACAGCGACGGCGTGTTTTG+GGG - chr3_3:81074306-81074325 Msa0477010:three_prime_UTR 60.0%
!! ACAGCGACGGCGTGTTTTGG+GGG - chr3_3:81074307-81074326 Msa0477010:three_prime_UTR 60.0%
TGGGACAATGGTGCAGCGTG+TGG - chr3_3:81074385-81074404 Msa0477010:three_prime_UTR 60.0%
GGGACAATGGTGCAGCGTGT+GGG - chr3_3:81074386-81074405 Msa0477010:three_prime_UTR 60.0%
ACAATGGTGCAGCGTGTGGG+AGG - chr3_3:81074389-81074408 Msa0477010:three_prime_UTR 60.0%
AGCGTGTGGGAGGCTGTATG+AGG - chr3_3:81074399-81074418 Msa0477010:three_prime_UTR 60.0%
GTGGGAGGCTGTATGAGGTG+AGG - chr3_3:81074404-81074423 Msa0477010:three_prime_UTR 60.0%
ATGGCGATCTCTCGCTGCAG+AGG - chr3_3:81075004-81075023 Msa0477010:CDS 60.0%
! GACAGCGACGGCGTGTTTTG+GGG - chr3_3:81074306-81074325 Msa0477010:three_prime_UTR 60.0%
!! ACAGCGACGGCGTGTTTTGG+GGG - chr3_3:81074307-81074326 Msa0477010:three_prime_UTR 60.0%
TGGGACAATGGTGCAGCGTG+TGG - chr3_3:81074385-81074404 Msa0477010:three_prime_UTR 60.0%
GGGACAATGGTGCAGCGTGT+GGG - chr3_3:81074386-81074405 Msa0477010:three_prime_UTR 60.0%
ACAATGGTGCAGCGTGTGGG+AGG - chr3_3:81074389-81074408 Msa0477010:three_prime_UTR 60.0%
AGCGTGTGGGAGGCTGTATG+AGG - chr3_3:81074399-81074418 Msa0477010:three_prime_UTR 60.0%
GTGGGAGGCTGTATGAGGTG+AGG - chr3_3:81074404-81074423 Msa0477010:three_prime_UTR 60.0%
ATGGCGATCTCTCGCTGCAG+AGG - chr3_3:81075004-81075023 Msa0477010:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 81074280 81075252 81074280 ID=Msa0477010;Name=Msa0477010
chr3_3 mRNA 81074280 81075252 81074280 ID=Msa0477010-mRNA-1;Parent=Msa0477010;Name=Msa0477010-mRNA-1;_AED=0.33;_eAED=0.33;_QI=0|1|0.5|1|0|0|2|332|112
chr3_3 exon 81074280 81074618 81074280 ID=Msa0477010-mRNA-1:exon:22299;Parent=Msa0477010-mRNA-1
chr3_3 exon 81074921 81075252 81074921 ID=Msa0477010-mRNA-1:exon:22298;Parent=Msa0477010-mRNA-1
chr3_3 CDS 81074921 81075252 81074921 ID=Msa0477010-mRNA-1:cds;Parent=Msa0477010-mRNA-1
chr3_3 CDS 81074612 81074618 81074612 ID=Msa0477010-mRNA-1:cds;Parent=Msa0477010-mRNA-1
chr3_3 three_prime_UTR 81074280 81074611 81074280 ID=Msa0477010-mRNA-1:three_prime_utr;Parent=Msa0477010-mRNA-1
Gene Sequence

>Msa0477010

TTGTTGTGTTTTGTGGAACGTGACAAGACAGCGACGGCGTGTTTTGGGGGAGATGCGTCACAATTTCCGTCGAGCAACATGTTTGGTTCAGCTGGAGAAGGTATATGGGACAATGGTGCAGCGTGTGGGAGGCTGTATGAGGTGAGGTGTATAAGTGCAGCTGTTCCTCGGACTTGCATTCCTGGTCAAACTATTCAGATTAAGATTGTTGATAGAGCACAATCTTCTGTTTCTAGGCCTTCATCGGATGATACTTCCATGGTTCTTTCCACCACTGCCTTTCAGATCATTGCAAATGTTTCTTCATCCTTGATAAACATCGAATTCCAACAGGTTTGA
Protein sequence

>Msa0477010

LLCFVERDKTATACFGGDASQFPSSNMFGSAGEGIWDNGAACGRLYEVRCISAAVPRTCIPGQTIQIKIVDRAQSSVSRPSSDDTSMVLSTTAFQIIANVSSSLINIEFQQV*