AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0686030

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0686030 MtrunA17_Chr4g0034761 92.708 96 5 1 1 96 11 104 2.26e-61 182
Msa0686030 MtrunA17_Chr5g0446661 67.089 79 20 1 1 73 1 79 2.12e-26 93.6
Msa0686030 MtrunA17_Chr3g0078771 62.025 79 24 1 1 73 1 79 4.44e-23 85.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0686030 AT1G49310.1 43.284 67 34 2 8 70 12 78 1.49e-12 58.2

Find 30 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTTCTTCTTCTGCTTCT+TGG 0.153872 4_4:-50370739 None:intergenic
TTAATATCTTATATGTTATA+TGG 0.245081 4_4:+50370829 Msa0686030:three_prime_UTR
GAAAAGACTTGGGAGATTAT+TGG 0.261061 4_4:+50370583 Msa0686030:CDS
AATTAGATTTGTTAGTTTGA+TGG 0.285742 4_4:-50370325 None:intergenic
CTCCCCAGATGTATTGTGTT+TGG 0.312718 4_4:+50371073 Msa0686030:three_prime_UTR
TTGTTGCCACCAGTTGAAAT+TGG 0.319097 4_4:+50370233 None:intergenic
ACAAGTTCTTTGATTGCTTC+AGG 0.324229 4_4:-50370633 None:intergenic
AAATACATCTATAGATAAAA+AGG 0.351346 4_4:-50370931 None:intergenic
AATACCAAACACAATACATC+TGG 0.373946 4_4:-50371077 None:intergenic
AACTCTGAACAAGAGCTTCA+TGG 0.403904 4_4:+50370777 Msa0686030:CDS
GATACATCAATCAAATCTAT+TGG 0.418852 4_4:-50371009 None:intergenic
CTCTTATGCAAGAAAAGACT+TGG 0.442343 4_4:+50370572 Msa0686030:CDS
GAGTATGAGAGAAGCAAAGA+TGG 0.451907 4_4:-50370382 None:intergenic
GATTTGTTAGTTTGATGGCT+AGG 0.457950 4_4:-50370320 None:intergenic
GAAGAAACAACATGTCTTTG+TGG 0.469784 4_4:+50370752 Msa0686030:CDS
TCTTTGATTGCTTCAGGCAT+AGG 0.472850 4_4:-50370627 None:intergenic
ACGGTTGTACCAATTTCAAC+TGG 0.472939 4_4:-50370242 None:intergenic
AGTCAAAAGACAGTGAAACT+TGG 0.478801 4_4:+50371107 Msa0686030:three_prime_UTR
GTGTGATATAATATGACATT+AGG 0.480243 4_4:-50370705 None:intergenic
TGATTGCTTCAGGCATAGGT+TGG 0.514568 4_4:-50370623 None:intergenic
TGGTACAACCGTGTATAAAG+TGG 0.539054 4_4:+50370253 Msa0686030:five_prime_UTR
AGAACTTGTTCAAAATCAAG+AGG 0.539159 4_4:+50370647 Msa0686030:CDS
TTTGATTGATGTATCTAGTG+TGG 0.552142 4_4:+50371017 Msa0686030:three_prime_UTR
ATACCAAACACAATACATCT+GGG 0.600413 4_4:-50371076 None:intergenic
AAAAGACAGTGAAACTTGGA+TGG 0.605833 4_4:+50371111 Msa0686030:three_prime_UTR
TCTTATGCAAGAAAAGACTT+GGG 0.611202 4_4:+50370573 Msa0686030:CDS
TAAAAGTCCACATCTTAGCA+AGG 0.615141 4_4:+50370347 Msa0686030:five_prime_UTR
GGTACAACCGTGTATAAAGT+GGG 0.640534 4_4:+50370254 Msa0686030:five_prime_UTR
AAAGGGGCCCACTTTATACA+CGG 0.655601 4_4:-50370261 None:intergenic
TACCAAACACAATACATCTG+GGG 0.678240 4_4:-50371075 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATATCTTATATGTTATA+TGG + chr4_4:50370829-50370848 Msa0686030:three_prime_UTR 10.0%
!! TTAATATCTTATATGTTATA+TGG + chr4_4:50370829-50370848 Msa0686030:three_prime_UTR 10.0%
!! ACAATATAGTATAAATTGAT+TGG - chr4_4:50370507-50370526 None:intergenic 15.0%
!!! AATTTTCTTTGTACTAAAAT+AGG + chr4_4:50370539-50370558 Msa0686030:intron 15.0%
!!! TATTTAAGGTTTATTTTGTA+GGG + chr4_4:50370864-50370883 Msa0686030:three_prime_UTR 15.0%
!! AAATACATCTATAGATAAAA+AGG - chr4_4:50370934-50370953 None:intergenic 15.0%
!!! TATCTATAGATGTATTTTTA+TGG + chr4_4:50370937-50370956 Msa0686030:three_prime_UTR 15.0%
!! ACAATATAGTATAAATTGAT+TGG - chr4_4:50370507-50370526 None:intergenic 15.0%
!!! AATTTTCTTTGTACTAAAAT+AGG + chr4_4:50370539-50370558 Msa0686030:intron 15.0%
!!! TATTTAAGGTTTATTTTGTA+GGG + chr4_4:50370864-50370883 Msa0686030:three_prime_UTR 15.0%
!! AAATACATCTATAGATAAAA+AGG - chr4_4:50370934-50370953 None:intergenic 15.0%
!!! TATCTATAGATGTATTTTTA+TGG + chr4_4:50370937-50370956 Msa0686030:three_prime_UTR 15.0%
!!! AATTAGATTTGTTAGTTTGA+TGG - chr4_4:50370328-50370347 None:intergenic 20.0%
!! TTAGTACAAAGAAAATTGAA+AGG - chr4_4:50370536-50370555 None:intergenic 20.0%
!! GGAAAAAGAATTAGTATTTA+AGG + chr4_4:50370850-50370869 Msa0686030:three_prime_UTR 20.0%
!!! GTATTTAAGGTTTATTTTGT+AGG + chr4_4:50370863-50370882 Msa0686030:three_prime_UTR 20.0%
!!! TAAAGTTGTATTTTTGTTGA+TGG + chr4_4:50370902-50370921 Msa0686030:three_prime_UTR 20.0%
!!! AATTAGATTTGTTAGTTTGA+TGG - chr4_4:50370328-50370347 None:intergenic 20.0%
!! TTAGTACAAAGAAAATTGAA+AGG - chr4_4:50370536-50370555 None:intergenic 20.0%
!! GGAAAAAGAATTAGTATTTA+AGG + chr4_4:50370850-50370869 Msa0686030:three_prime_UTR 20.0%
!!! GTATTTAAGGTTTATTTTGT+AGG + chr4_4:50370863-50370882 Msa0686030:three_prime_UTR 20.0%
!!! TAAAGTTGTATTTTTGTTGA+TGG + chr4_4:50370902-50370921 Msa0686030:three_prime_UTR 20.0%
!! TTCTTTTTATAGGCCAAAAA+GGG - chr4_4:50370281-50370300 None:intergenic 25.0%
!! TTTCTTTTTATAGGCCAAAA+AGG - chr4_4:50370282-50370301 None:intergenic 25.0%
!!! CTCTGACTATTTCTTTTTAT+AGG - chr4_4:50370291-50370310 None:intergenic 25.0%
! CTATAAAAAGAAATAGTCAG+AGG + chr4_4:50370289-50370308 Msa0686030:five_prime_UTR 25.0%
! GTGTGATATAATATGACATT+AGG - chr4_4:50370708-50370727 None:intergenic 25.0%
!!! TTTTTTGCTGCATCTATTTT+TGG + chr4_4:50370968-50370987 Msa0686030:three_prime_UTR 25.0%
!!! TTTTTGCTGCATCTATTTTT+GGG + chr4_4:50370969-50370988 Msa0686030:three_prime_UTR 25.0%
! GATACATCAATCAAATCTAT+TGG - chr4_4:50371012-50371031 None:intergenic 25.0%
!! TTCTTTTTATAGGCCAAAAA+GGG - chr4_4:50370281-50370300 None:intergenic 25.0%
!! TTTCTTTTTATAGGCCAAAA+AGG - chr4_4:50370282-50370301 None:intergenic 25.0%
!!! CTCTGACTATTTCTTTTTAT+AGG - chr4_4:50370291-50370310 None:intergenic 25.0%
! CTATAAAAAGAAATAGTCAG+AGG + chr4_4:50370289-50370308 Msa0686030:five_prime_UTR 25.0%
! GTGTGATATAATATGACATT+AGG - chr4_4:50370708-50370727 None:intergenic 25.0%
!!! TTTTTTGCTGCATCTATTTT+TGG + chr4_4:50370968-50370987 Msa0686030:three_prime_UTR 25.0%
!!! TTTTTGCTGCATCTATTTTT+GGG + chr4_4:50370969-50370988 Msa0686030:three_prime_UTR 25.0%
! GATACATCAATCAAATCTAT+TGG - chr4_4:50371012-50371031 None:intergenic 25.0%
! TCTTTTTATAGGCCAAAAAG+GGG - chr4_4:50370280-50370299 None:intergenic 30.0%
!!! ATTTTTTCCTTGCTAAGATG+TGG - chr4_4:50370357-50370376 None:intergenic 30.0%
TCTTATGCAAGAAAAGACTT+GGG + chr4_4:50370573-50370592 Msa0686030:CDS 30.0%
! AGAACTTGTTCAAAATCAAG+AGG + chr4_4:50370647-50370666 Msa0686030:CDS 30.0%
CTTCATGGAACATAAAAACA+TGG + chr4_4:50370792-50370811 Msa0686030:exon 30.0%
ATGGAACATAAAAACATGGT+TGG + chr4_4:50370796-50370815 Msa0686030:exon 30.0%
TTTGATTGATGTATCTAGTG+TGG + chr4_4:50371017-50371036 Msa0686030:three_prime_UTR 30.0%
ATACCAAACACAATACATCT+GGG - chr4_4:50371079-50371098 None:intergenic 30.0%
AATACCAAACACAATACATC+TGG - chr4_4:50371080-50371099 None:intergenic 30.0%
! TCTTTTTATAGGCCAAAAAG+GGG - chr4_4:50370280-50370299 None:intergenic 30.0%
!!! ATTTTTTCCTTGCTAAGATG+TGG - chr4_4:50370357-50370376 None:intergenic 30.0%
TCTTATGCAAGAAAAGACTT+GGG + chr4_4:50370573-50370592 Msa0686030:CDS 30.0%
! AGAACTTGTTCAAAATCAAG+AGG + chr4_4:50370647-50370666 Msa0686030:CDS 30.0%
CTTCATGGAACATAAAAACA+TGG + chr4_4:50370792-50370811 Msa0686030:exon 30.0%
ATGGAACATAAAAACATGGT+TGG + chr4_4:50370796-50370815 Msa0686030:exon 30.0%
TTTGATTGATGTATCTAGTG+TGG + chr4_4:50371017-50371036 Msa0686030:three_prime_UTR 30.0%
ATACCAAACACAATACATCT+GGG - chr4_4:50371079-50371098 None:intergenic 30.0%
AATACCAAACACAATACATC+TGG - chr4_4:50371080-50371099 None:intergenic 30.0%
!! GATTTGTTAGTTTGATGGCT+AGG - chr4_4:50370323-50370342 None:intergenic 35.0%
TAAAAGTCCACATCTTAGCA+AGG + chr4_4:50370347-50370366 Msa0686030:five_prime_UTR 35.0%
! CATACTCTTTTCTCTTCTTC+TGG + chr4_4:50370398-50370417 Msa0686030:CDS 35.0%
! AGTCTTTTCTTGCATAAGAG+AGG - chr4_4:50370572-50370591 None:intergenic 35.0%
CTCTTATGCAAGAAAAGACT+TGG + chr4_4:50370572-50370591 Msa0686030:CDS 35.0%
GAAAAGACTTGGGAGATTAT+TGG + chr4_4:50370583-50370602 Msa0686030:CDS 35.0%
ACAAGTTCTTTGATTGCTTC+AGG - chr4_4:50370636-50370655 None:intergenic 35.0%
! TTGTTTCTTCTTCTGCTTCT+TGG - chr4_4:50370742-50370761 None:intergenic 35.0%
GAAGAAACAACATGTCTTTG+TGG + chr4_4:50370752-50370771 Msa0686030:CDS 35.0%
TACCAAACACAATACATCTG+GGG - chr4_4:50371078-50371097 None:intergenic 35.0%
AGTCAAAAGACAGTGAAACT+TGG + chr4_4:50371107-50371126 Msa0686030:three_prime_UTR 35.0%
AAAAGACAGTGAAACTTGGA+TGG + chr4_4:50371111-50371130 Msa0686030:three_prime_UTR 35.0%
GAAACTTGGATGGTATTTGA+TGG + chr4_4:50371121-50371140 Msa0686030:three_prime_UTR 35.0%
!! GATTTGTTAGTTTGATGGCT+AGG - chr4_4:50370323-50370342 None:intergenic 35.0%
TAAAAGTCCACATCTTAGCA+AGG + chr4_4:50370347-50370366 Msa0686030:five_prime_UTR 35.0%
! CATACTCTTTTCTCTTCTTC+TGG + chr4_4:50370398-50370417 Msa0686030:CDS 35.0%
! AGTCTTTTCTTGCATAAGAG+AGG - chr4_4:50370572-50370591 None:intergenic 35.0%
CTCTTATGCAAGAAAAGACT+TGG + chr4_4:50370572-50370591 Msa0686030:CDS 35.0%
GAAAAGACTTGGGAGATTAT+TGG + chr4_4:50370583-50370602 Msa0686030:CDS 35.0%
ACAAGTTCTTTGATTGCTTC+AGG - chr4_4:50370636-50370655 None:intergenic 35.0%
! TTGTTTCTTCTTCTGCTTCT+TGG - chr4_4:50370742-50370761 None:intergenic 35.0%
GAAGAAACAACATGTCTTTG+TGG + chr4_4:50370752-50370771 Msa0686030:CDS 35.0%
TACCAAACACAATACATCTG+GGG - chr4_4:50371078-50371097 None:intergenic 35.0%
AGTCAAAAGACAGTGAAACT+TGG + chr4_4:50371107-50371126 Msa0686030:three_prime_UTR 35.0%
AAAAGACAGTGAAACTTGGA+TGG + chr4_4:50371111-50371130 Msa0686030:three_prime_UTR 35.0%
TGGTACAACCGTGTATAAAG+TGG + chr4_4:50370253-50370272 Msa0686030:five_prime_UTR 40.0%
GGTACAACCGTGTATAAAGT+GGG + chr4_4:50370254-50370273 Msa0686030:five_prime_UTR 40.0%
GAGTATGAGAGAAGCAAAGA+TGG - chr4_4:50370385-50370404 None:intergenic 40.0%
TCTTTGATTGCTTCAGGCAT+AGG - chr4_4:50370630-50370649 None:intergenic 40.0%
AACTCTGAACAAGAGCTTCA+TGG + chr4_4:50370777-50370796 Msa0686030:CDS 40.0%
TGGTACAACCGTGTATAAAG+TGG + chr4_4:50370253-50370272 Msa0686030:five_prime_UTR 40.0%
GGTACAACCGTGTATAAAGT+GGG + chr4_4:50370254-50370273 Msa0686030:five_prime_UTR 40.0%
GAGTATGAGAGAAGCAAAGA+TGG - chr4_4:50370385-50370404 None:intergenic 40.0%
TCTTTGATTGCTTCAGGCAT+AGG - chr4_4:50370630-50370649 None:intergenic 40.0%
AACTCTGAACAAGAGCTTCA+TGG + chr4_4:50370777-50370796 Msa0686030:CDS 40.0%
AAAGGGGCCCACTTTATACA+CGG - chr4_4:50370264-50370283 None:intergenic 45.0%
! GTATAAAGTGGGCCCCTTTT+TGG + chr4_4:50370265-50370284 Msa0686030:five_prime_UTR 45.0%
TGATTGCTTCAGGCATAGGT+TGG - chr4_4:50370626-50370645 None:intergenic 45.0%
CTCCCCAGATGTATTGTGTT+TGG + chr4_4:50371073-50371092 Msa0686030:three_prime_UTR 45.0%
AAAGGGGCCCACTTTATACA+CGG - chr4_4:50370264-50370283 None:intergenic 45.0%
! GTATAAAGTGGGCCCCTTTT+TGG + chr4_4:50370265-50370284 Msa0686030:five_prime_UTR 45.0%
TGATTGCTTCAGGCATAGGT+TGG - chr4_4:50370626-50370645 None:intergenic 45.0%
CTCCCCAGATGTATTGTGTT+TGG + chr4_4:50371073-50371092 Msa0686030:three_prime_UTR 45.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 50370245 50371142 50370245 ID=Msa0686030;Name=Msa0686030
chr4_4 mRNA 50370245 50371142 50370245 ID=Msa0686030-mRNA-1;Parent=Msa0686030;Name=Msa0686030-mRNA-1;_AED=0.08;_eAED=0.08;_QI=130|1|1|1|1|1|2|336|96
chr4_4 exon 50370245 50370419 50370245 ID=Msa0686030-mRNA-1:exon:12846;Parent=Msa0686030-mRNA-1
chr4_4 exon 50370561 50371142 50370561 ID=Msa0686030-mRNA-1:exon:12847;Parent=Msa0686030-mRNA-1
chr4_4 five_prime_UTR 50370245 50370374 50370245 ID=Msa0686030-mRNA-1:five_prime_utr;Parent=Msa0686030-mRNA-1
chr4_4 CDS 50370375 50370419 50370375 ID=Msa0686030-mRNA-1:cds;Parent=Msa0686030-mRNA-1
chr4_4 CDS 50370561 50370806 50370561 ID=Msa0686030-mRNA-1:cds;Parent=Msa0686030-mRNA-1
chr4_4 three_prime_UTR 50370807 50371142 50370807 ID=Msa0686030-mRNA-1:three_prime_utr;Parent=Msa0686030-mRNA-1
Gene Sequence

>Msa0686030

ATGAAGTCCATCTTTGCTTCTCTCATACTCTTTTCTCTTCTTCTGGTTGCTGACCTCTCTTATGCAAGAAAAGACTTGGGAGATTATTGGAAGAATATGATGAATGACCAACCTATGCCTGAAGCAATCAAAGAACTTGTTCAAAATCAAGAGGTTTCAGATGACTTTATTAGAGACTTTGATGTAAAGCCTAATGTCATATTATATCACACACATGTTGAATCCAAGAAGCAGAAGAAGAAACAACATGTCTTTGTGGAAAACTCTGAACAAGAGCTTCATGGAACATAA
Protein sequence

>Msa0686030

MKSIFASLILFSLLLVADLSYARKDLGDYWKNMMNDQPMPEAIKELVQNQEVSDDFIRDFDVKPNVILYHTHVESKKQKKKQHVFVENSEQELHGT*