AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1244600


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1244600 MtrunA17_Chr8g0360281 98.160 163 3 0 3 165 364 526 3.34e-115 336
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1244600 AT3G15180.1 58.896 163 65 2 3 165 359 519 1.07e-58 191
Msa1244600 AT3G15180.2 58.896 163 65 2 3 165 391 551 2.00e-58 191

Find 33 sgRNAs with CRISPR-Local

Find 129 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAATTTATGAATATCATTT+TGG 0.264813 8_2:+33284032 Msa1244600:three_prime_UTR
TAATAGTTTGTTATGACTTC+AGG 0.296563 8_2:+33283891 Msa1244600:three_prime_UTR
AGTCATAACAAACTATTATT+AGG 0.330833 8_2:-33283886 None:intergenic
TTAAATGTCTCACCGCTATA+CGG 0.368585 8_2:-33282694 None:intergenic
TGGTGTCAGCTTTGAGCTCC+TGG 0.386617 8_2:-33281677 None:intergenic
GTCTCGACCGTGGTGCTTGA+TGG 0.390375 8_2:+33283288 Msa1244600:CDS
TTGATCTAGACTTGAGCGTT+TGG 0.409997 8_2:+33283951 Msa1244600:three_prime_UTR
CTATCAGCCGTCATCACAAT+AGG 0.428327 8_2:-33283786 None:intergenic
TATGACGTCATTCTCAGATC+TGG 0.444701 8_2:-33281602 None:intergenic
CTATTATTAGGTAAAGAGTA+AGG 0.459022 8_2:-33283874 None:intergenic
TTTCATAAAGTAAGCGAAGC+AGG 0.475520 8_2:-33281648 None:intergenic
GCAGCTGTTCCTGCAAAAGC+AGG 0.484395 8_2:-33283576 None:intergenic
GTCTAGATCAAAAGTTGTAA+AGG 0.490892 8_2:-33283939 None:intergenic
GTTTGTTATGACTTCAGGAT+TGG 0.491099 8_2:+33283896 Msa1244600:three_prime_UTR
CAGGGTTATAGAATGATAAG+TGG 0.493664 8_2:+33283259 Msa1244600:intron
TAAGACTTAAATTGGTACAT+TGG 0.501633 8_2:+33284001 Msa1244600:three_prime_UTR
CTGCAAGAAGCCGTAGGAAT+GGG 0.511865 8_2:+33283726 Msa1244600:CDS
CAGGCTGCACTGCATGCTCT+AGG 0.517824 8_2:+33281562 Msa1244600:intron
CGCTTTCGATGATGAAGATA+CGG 0.525676 8_2:-33283750 None:intergenic
GCTGCAAGAAGCCGTAGGAA+TGG 0.539955 8_2:+33283725 Msa1244600:intron
GCATGCTCTAGGAAACATCT+CGG 0.550660 8_2:+33281573 Msa1244600:CDS
TGTAGTTTCAGTACTTGGGT+CGG 0.550899 8_2:-33283347 None:intergenic
TACTTTATGAAACAGCATCC+AGG 0.554953 8_2:+33281659 Msa1244600:CDS
TTATAGAATGATAAGTGGAT+TGG 0.557998 8_2:+33283264 Msa1244600:CDS
AGCTCAACCTATTGTGATGA+CGG 0.603732 8_2:+33283779 Msa1244600:CDS
CATGCTCTAGGAAACATCTC+GGG 0.609327 8_2:+33281574 Msa1244600:CDS
GAGCTCAAAGCTGACACCAT+CGG 0.619703 8_2:+33281681 Msa1244600:CDS
AAGATACGGACCCATTCCTA+CGG 0.635459 8_2:-33283736 None:intergenic
CTAGATATAACTGCTGCATG+CGG 0.647515 8_2:+33283511 Msa1244600:CDS
GTGCAGCTGCAAGAAGCCGT+AGG 0.664105 8_2:+33283720 Msa1244600:intron
AGATTCAGAAATCCGTATAG+CGG 0.690364 8_2:+33282682 Msa1244600:CDS
CATATCTCCATCAAGCACCA+CGG 0.693939 8_2:-33283295 None:intergenic
GTGGATTGGTGTCTCGACCG+TGG 0.710959 8_2:+33283278 Msa1244600:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTATTATATTTAGATGAA+AGG - chr8_2:33282066-33282085 None:intergenic 10.0%
!! ATAAAAATATTATTTGTCAA+GGG - chr8_2:33282396-33282415 None:intergenic 10.0%
!! TATAAAAATATTATTTGTCA+AGG - chr8_2:33282397-33282416 None:intergenic 10.0%
!! GAAAATAAAATAGTAATATT+CGG - chr8_2:33283442-33283461 None:intergenic 10.0%
!!! TTTTTTTTTAAGACTTAAAT+TGG + chr8_2:33283993-33284012 Msa1244600:three_prime_UTR 10.0%
!!! TTAATTTATGAATATCATTT+TGG + chr8_2:33284032-33284051 Msa1244600:three_prime_UTR 10.0%
!!! CTTAATTTGATGATATTATT+GGG - chr8_2:33282900-33282919 None:intergenic 15.0%
!!! TGTATTATTTTAACACAAAT+CGG + chr8_2:33283469-33283488 Msa1244600:intron 15.0%
!! CTATTTAAGCTAAAGATATT+CGG + chr8_2:33281786-33281805 Msa1244600:intron 20.0%
!!! AACTGTTTTTATTAGAGATA+TGG + chr8_2:33281987-33282006 Msa1244600:intron 20.0%
!!! ACTGTTTTTATTAGAGATAT+GGG + chr8_2:33281988-33282007 Msa1244600:intron 20.0%
!! ACTTTATTATCTTATTCAAC+AGG + chr8_2:33282178-33282197 Msa1244600:intron 20.0%
!! AAAATACCTCTAATAAAGAA+GGG - chr8_2:33282209-33282228 None:intergenic 20.0%
!! TAAAATACCTCTAATAAAGA+AGG - chr8_2:33282210-33282229 None:intergenic 20.0%
!!! TCAAATTTTCATAAAGTACA+GGG - chr8_2:33282521-33282540 None:intergenic 20.0%
!!! ATCAAATTTTCATAAAGTAC+AGG - chr8_2:33282522-33282541 None:intergenic 20.0%
!! GTAATTTCAATTTCATATGA+TGG + chr8_2:33282813-33282832 Msa1244600:intron 20.0%
!!! CCTTAATTTGATGATATTAT+TGG - chr8_2:33282901-33282920 None:intergenic 20.0%
!! CCAATAATATCATCAAATTA+AGG + chr8_2:33282898-33282917 Msa1244600:intron 20.0%
!! TAATATCATCAAATTAAGGA+AGG + chr8_2:33282902-33282921 Msa1244600:intron 20.0%
!!! ATAGGTAAAAAACTTTTTGT+AGG - chr8_2:33283009-33283028 None:intergenic 20.0%
!!! ATACTAGATTTTCTAATATC+AGG + chr8_2:33283123-33283142 Msa1244600:intron 20.0%
!! AGTCATAACAAACTATTATT+AGG - chr8_2:33283889-33283908 None:intergenic 20.0%
!! TAATTTCAAATGCTATTTGC+TGG + chr8_2:33281722-33281741 Msa1244600:intron 25.0%
!! GATCAGAAATTTTCAATTAC+TGG - chr8_2:33281866-33281885 None:intergenic 25.0%
!!! TATATCTGAAATGATTTTGG+AGG - chr8_2:33281951-33281970 None:intergenic 25.0%
!!! ACGTATATCTGAAATGATTT+TGG - chr8_2:33281954-33281973 None:intergenic 25.0%
! GGAATGAAAGAAATAAAAGT+GGG - chr8_2:33282045-33282064 None:intergenic 25.0%
! AGGAATGAAAGAAATAAAAG+TGG - chr8_2:33282046-33282065 None:intergenic 25.0%
! AAAGCTTATTCCTTAGATTA+AGG + chr8_2:33282232-33282251 Msa1244600:intron 25.0%
!! ATAGAACTGCTATTTAATCA+GGG - chr8_2:33282440-33282459 None:intergenic 25.0%
! TATAAAGCTATGTTATGTTC+AGG - chr8_2:33282778-33282797 None:intergenic 25.0%
!! ATGCTACATAATTGAGTTTT+GGG - chr8_2:33282863-33282882 None:intergenic 25.0%
!! AATGCTACATAATTGAGTTT+TGG - chr8_2:33282864-33282883 None:intergenic 25.0%
! TGCAAAGTTATATTACTAGT+AGG + chr8_2:33282935-33282954 Msa1244600:intron 25.0%
!! GATGATGTCTAAGATAAAAT+AGG - chr8_2:33283027-33283046 None:intergenic 25.0%
!! TTCCTGAATTTTCTTTACAA+CGG - chr8_2:33283149-33283168 None:intergenic 25.0%
! GACTTTCTTTAGTGAATTTA+AGG - chr8_2:33283212-33283231 None:intergenic 25.0%
!! TTTTTGTGTGACATATTTTC+AGG + chr8_2:33283240-33283259 Msa1244600:intron 25.0%
!! TTTTGTGTGACATATTTTCA+GGG + chr8_2:33283241-33283260 Msa1244600:intron 25.0%
! TTATAGAATGATAAGTGGAT+TGG + chr8_2:33283264-33283283 Msa1244600:CDS 25.0%
!! TTTTTGTAGTTTCAGTACTT+GGG - chr8_2:33283354-33283373 None:intergenic 25.0%
!! ATTTTTGTAGTTTCAGTACT+TGG - chr8_2:33283355-33283374 None:intergenic 25.0%
!! AGTACTGAAACTACAAAAAT+AGG + chr8_2:33283355-33283374 Msa1244600:CDS 25.0%
! AAACACAAGCAATACATAAT+GGG - chr8_2:33283623-33283642 None:intergenic 25.0%
!!! ACTGTTTTCTTGATTTGTTT+AGG - chr8_2:33283661-33283680 None:intergenic 25.0%
! CTATTATTAGGTAAAGAGTA+AGG - chr8_2:33283877-33283896 None:intergenic 25.0%
!!! TAATAGTTTGTTATGACTTC+AGG + chr8_2:33283891-33283910 Msa1244600:three_prime_UTR 25.0%
! TAAGACTTAAATTGGTACAT+TGG + chr8_2:33284001-33284020 Msa1244600:three_prime_UTR 25.0%
!!! CACTAAACTTTTTCTAGTTG+TGG + chr8_2:33281813-33281832 Msa1244600:intron 30.0%
TGATCTAAATCAAAAAGACC+AGG + chr8_2:33281881-33281900 Msa1244600:intron 30.0%
! GTTTTTATTAGAGATATGGG+TGG + chr8_2:33281991-33282010 Msa1244600:intron 30.0%
TCCTTAGATTAAGGAAAGAT+AGG + chr8_2:33282241-33282260 Msa1244600:intron 30.0%
TCCTATCTTTCCTTAATCTA+AGG - chr8_2:33282245-33282264 None:intergenic 30.0%
TTTAATCAGGGTCATTTGTT+GGG - chr8_2:33282428-33282447 None:intergenic 30.0%
ATTTAATCAGGGTCATTTGT+TGG - chr8_2:33282429-33282448 None:intergenic 30.0%
! GATAGAACTGCTATTTAATC+AGG - chr8_2:33282441-33282460 None:intergenic 30.0%
GTAACTGATCAACAAAATCT+TGG - chr8_2:33282468-33282487 None:intergenic 30.0%
TTTGTTGATCAGTTACTTGT+AGG + chr8_2:33282472-33282491 Msa1244600:intron 30.0%
! CATATGATGGAAATGAAATC+AGG + chr8_2:33282826-33282845 Msa1244600:intron 30.0%
TATCTTAGACATCATCATAG+AGG + chr8_2:33283031-33283050 Msa1244600:intron 30.0%
TCTTTAGTGAATTTAAGGAC+AGG - chr8_2:33283207-33283226 None:intergenic 30.0%
! CAATACATAATGGGAAAGTT+TGG - chr8_2:33283614-33283633 None:intergenic 30.0%
CAAACACAAGCAATACATAA+TGG - chr8_2:33283624-33283643 None:intergenic 30.0%
AGTGTAAATGCTAAACTTTC+CGG + chr8_2:33283678-33283697 Msa1244600:intron 30.0%
! TGTAATTTTGCAATTTGCAG+TGG + chr8_2:33283838-33283857 Msa1244600:three_prime_UTR 30.0%
GTCTAGATCAAAAGTTGTAA+AGG - chr8_2:33283942-33283961 None:intergenic 30.0%
ATTTCTTCAAACGCAATCAC+AGG + chr8_2:33281543-33281562 Msa1244600:intron 35.0%
TTTCATAAAGTAAGCGAAGC+AGG - chr8_2:33281651-33281670 None:intergenic 35.0%
TACTTTATGAAACAGCATCC+AGG + chr8_2:33281659-33281678 Msa1244600:CDS 35.0%
GAGTGTAAAAAAATGACCGA+TGG - chr8_2:33281700-33281719 None:intergenic 35.0%
!! TCTGAAATGATTTTGGAGGA+TGG - chr8_2:33281947-33281966 None:intergenic 35.0%
TATTAGAGATATGGGTGGTT+CGG + chr8_2:33281996-33282015 Msa1244600:intron 35.0%
AGGAAAGATAGGAACAAAAG+AGG + chr8_2:33282252-33282271 Msa1244600:intron 35.0%
TGATCTCTGGATTGAGAAAT+CGG - chr8_2:33282327-33282346 None:intergenic 35.0%
GCACTTTCTGTAGAAAAGTT+GGG - chr8_2:33282359-33282378 None:intergenic 35.0%
TGCACTTTCTGTAGAAAAGT+TGG - chr8_2:33282360-33282379 None:intergenic 35.0%
! TTTCTACAGAAAGTGCATCT+TGG + chr8_2:33282363-33282382 Msa1244600:intron 35.0%
TTAGAACCTAAGATCCTCTA+GGG + chr8_2:33282546-33282565 Msa1244600:intron 35.0%
! ATGCGTCAGTTTTTAAACAC+TGG + chr8_2:33282605-33282624 Msa1244600:intron 35.0%
!! CAATTTGCATGATAATGGTG+AGG - chr8_2:33282633-33282652 None:intergenic 35.0%
ACCATTATCATGCAAATTGC+AGG + chr8_2:33282634-33282653 Msa1244600:intron 35.0%
CCATTATCATGCAAATTGCA+GGG + chr8_2:33282635-33282654 Msa1244600:intron 35.0%
AGATTCAGAAATCCGTATAG+CGG + chr8_2:33282682-33282701 Msa1244600:CDS 35.0%
TTAAATGTCTCACCGCTATA+CGG - chr8_2:33282697-33282716 None:intergenic 35.0%
CAGGGTTATAGAATGATAAG+TGG + chr8_2:33283259-33283278 Msa1244600:intron 35.0%
ATATTCGGACTGTAAACATG+TGG - chr8_2:33283427-33283446 None:intergenic 35.0%
! AACACAAATCGGAGTATTTC+AGG + chr8_2:33283480-33283499 Msa1244600:intron 35.0%
! AAATCGGAGTATTTCAGGAA+TGG + chr8_2:33283485-33283504 Msa1244600:intron 35.0%
ACAAGATACACAAACACAAC+CGG - chr8_2:33283700-33283719 None:intergenic 35.0%
!! GTTTGTTATGACTTCAGGAT+TGG + chr8_2:33283896-33283915 Msa1244600:three_prime_UTR 35.0%
TATGACGTCATTCTCAGATC+TGG - chr8_2:33281605-33281624 None:intergenic 40.0%
GTCCCATCTTAATCATGACT+CGG + chr8_2:33281840-33281859 Msa1244600:intron 40.0%
GACATGCCCTTCTTTATTAG+AGG + chr8_2:33282200-33282219 Msa1244600:intron 40.0%
GTTAGAACCTAAGATCCTCT+AGG + chr8_2:33282545-33282564 Msa1244600:intron 40.0%
ATTGTACCCTAGAGGATCTT+AGG - chr8_2:33282555-33282574 None:intergenic 40.0%
CAATGAACATTGTACCCTAG+AGG - chr8_2:33282563-33282582 None:intergenic 40.0%
CCCTGCAATTTGCATGATAA+TGG - chr8_2:33282638-33282657 None:intergenic 40.0%
! AGTCTTGTATTTGCAGCAAG+AGG - chr8_2:33282985-33283004 None:intergenic 40.0%
GGCCGTTGTAAAGAAAATTC+AGG + chr8_2:33283144-33283163 Msa1244600:intron 40.0%
TGTAGTTTCAGTACTTGGGT+CGG - chr8_2:33283350-33283369 None:intergenic 40.0%
CTAGATATAACTGCTGCATG+CGG + chr8_2:33283511-33283530 Msa1244600:CDS 40.0%
CGCTTTCGATGATGAAGATA+CGG - chr8_2:33283753-33283772 None:intergenic 40.0%
AGCTCAACCTATTGTGATGA+CGG + chr8_2:33283779-33283798 Msa1244600:CDS 40.0%
!!! GATTTTAGTTTGCACAGCAC+AGG + chr8_2:33283808-33283827 Msa1244600:exon 40.0%
! TTTTGCAATTTGCAGTGGTG+TGG + chr8_2:33283843-33283862 Msa1244600:three_prime_UTR 40.0%
TTGATCTAGACTTGAGCGTT+TGG + chr8_2:33283951-33283970 Msa1244600:three_prime_UTR 40.0%
!! GCATGCTCTAGGAAACATCT+CGG + chr8_2:33281573-33281592 Msa1244600:CDS 45.0%
!! CATGCTCTAGGAAACATCTC+GGG + chr8_2:33281574-33281593 Msa1244600:CDS 45.0%
GGCCGAGTCATGATTAAGAT+GGG - chr8_2:33281845-33281864 None:intergenic 45.0%
TGGCCGAGTCATGATTAAGA+TGG - chr8_2:33281846-33281865 None:intergenic 45.0%
TGGGAGACATTTCTGATCTC+TGG - chr8_2:33282340-33282359 None:intergenic 45.0%
GCAGCAAGAGGAAGATTCTT+AGG - chr8_2:33282973-33282992 None:intergenic 45.0%
CATATCTCCATCAAGCACCA+CGG - chr8_2:33283298-33283317 None:intergenic 45.0%
CGGACTGTAAACATGTGGAA+TGG - chr8_2:33283422-33283441 None:intergenic 45.0%
! TTTTGCAGGAACAGCTGCAA+AGG + chr8_2:33283581-33283600 Msa1244600:CDS 45.0%
AAGATACGGACCCATTCCTA+CGG - chr8_2:33283739-33283758 None:intergenic 45.0%
CTATCAGCCGTCATCACAAT+AGG - chr8_2:33283789-33283808 None:intergenic 45.0%
GAGCTCAAAGCTGACACCAT+CGG + chr8_2:33281681-33281700 Msa1244600:CDS 50.0%
TAGAAAGACACTGCTCAGCC+TGG - chr8_2:33281902-33281921 None:intergenic 50.0%
!! TCTGCTGATCCTGCTTTTGC+AGG + chr8_2:33283567-33283586 Msa1244600:CDS 50.0%
CTGCAAGAAGCCGTAGGAAT+GGG + chr8_2:33283726-33283745 Msa1244600:CDS 50.0%
!! TGGTGTCAGCTTTGAGCTCC+TGG - chr8_2:33281680-33281699 None:intergenic 55.0%
GCAGCTGTTCCTGCAAAAGC+AGG - chr8_2:33283579-33283598 None:intergenic 55.0%
GCTGCAAGAAGCCGTAGGAA+TGG + chr8_2:33283725-33283744 Msa1244600:intron 55.0%
CAGGCTGCACTGCATGCTCT+AGG + chr8_2:33281562-33281581 Msa1244600:intron 60.0%
!! GTGGATTGGTGTCTCGACCG+TGG + chr8_2:33283278-33283297 Msa1244600:CDS 60.0%
GTCTCGACCGTGGTGCTTGA+TGG + chr8_2:33283288-33283307 Msa1244600:CDS 60.0%
GTGCAGCTGCAAGAAGCCGT+AGG + chr8_2:33283720-33283739 Msa1244600:intron 60.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 33281507 33284059 33281507 ID=Msa1244600;Name=Msa1244600
chr8_2 mRNA 33281507 33284059 33281507 ID=Msa1244600-mRNA-1;Parent=Msa1244600;Name=Msa1244600-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|0.8|0.66|0.83|0.8|0.83|6|244|165
chr8_2 exon 33281507 33281512 33281507 ID=Msa1244600-mRNA-1:exon:10739;Parent=Msa1244600-mRNA-1
chr8_2 exon 33281565 33281702 33281565 ID=Msa1244600-mRNA-1:exon:10740;Parent=Msa1244600-mRNA-1
chr8_2 exon 33282656 33282703 33282656 ID=Msa1244600-mRNA-1:exon:10741;Parent=Msa1244600-mRNA-1
chr8_2 exon 33283262 33283376 33283262 ID=Msa1244600-mRNA-1:exon:10742;Parent=Msa1244600-mRNA-1
chr8_2 exon 33283502 33283602 33283502 ID=Msa1244600-mRNA-1:exon:10743;Parent=Msa1244600-mRNA-1
chr8_2 exon 33283726 33284059 33283726 ID=Msa1244600-mRNA-1:exon:10744;Parent=Msa1244600-mRNA-1
chr8_2 CDS 33281507 33281512 33281507 ID=Msa1244600-mRNA-1:cds;Parent=Msa1244600-mRNA-1
chr8_2 CDS 33281565 33281702 33281565 ID=Msa1244600-mRNA-1:cds;Parent=Msa1244600-mRNA-1
chr8_2 CDS 33282656 33282703 33282656 ID=Msa1244600-mRNA-1:cds;Parent=Msa1244600-mRNA-1
chr8_2 CDS 33283262 33283376 33283262 ID=Msa1244600-mRNA-1:cds;Parent=Msa1244600-mRNA-1
chr8_2 CDS 33283502 33283602 33283502 ID=Msa1244600-mRNA-1:cds;Parent=Msa1244600-mRNA-1
chr8_2 CDS 33283726 33283815 33283726 ID=Msa1244600-mRNA-1:cds;Parent=Msa1244600-mRNA-1
chr8_2 three_prime_UTR 33283816 33284059 33283816 ID=Msa1244600-mRNA-1:three_prime_utr;Parent=Msa1244600-mRNA-1
Gene Sequence

>Msa1244600

TTCGATGCTGCACTGCATGCTCTAGGAAACATCTCGGGTGAAACCAGATCTGAGAATGACGTCATACTTGATGCTGAAGCAGAAGAAAACCTGCTTCGCTTACTTTATGAAACAGCATCCAGGAGCTCAAAGCTGACACCATCGGGTCTATTTCTATCAGTTTTGCAGCAAGATTCAGAAATCCGTATAGCGGGTTATAGAATGATAAGTGGATTGGTGTCTCGACCGTGGTGCTTGATGGAGATATGCTCAAGACAAGAGATTATAAATATTGTGACCGACCCAAGTACTGAAACTACAAAAATAGGAATGGAAGCTAGATATAACTGCTGCATGCGGATAAACAAATCACTGACACAGTCAAGTAGAGTCTCTGCTGATCCTGCTTTTGCAGGAACAGCTGCAAAGCTGCAAGAAGCCGTAGGAATGGGTCCGTATCTTCATCATCGAAAGCGTGTTGAAGCTCAACCTATTGTGATGACGGCTGATAGATTTTAG

Protein sequence

>Msa1244600

FDAALHALGNISGETRSENDVILDAEAEENLLRLLYETASRSSKLTPSGLFLSVLQQDSEIRIAGYRMISGLVSRPWCLMEICSRQEIINIVTDPSTETTKIGMEARYNCCMRINKSLTQSSRVSADPAFAGTAAKLQEAVGMGPYLHHRKRVEAQPIVMTADRF*