AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene006970


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene006970.t1 MTR_4g085100 98.578 211 2 1 1 211 1 210 3.01e-150 416
MS.gene006970.t1 MTR_1g030740 64.651 215 68 5 1 211 1 211 1.14e-83 247
MS.gene006970.t1 MTR_3g067730 46.512 215 103 5 1 206 1 212 5.54e-53 169
MS.gene006970.t1 MTR_5g079610 48.077 208 89 6 1 199 1 198 1.31e-52 168
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene006970.t1 AT2G01340 53.182 220 88 3 1 210 1 215 6.00e-64 197
MS.gene006970.t1 AT1G71015 51.497 167 69 3 1 163 1 159 1.01e-44 147
MS.gene006970.t1 AT1G71015 51.497 167 69 3 1 163 1 159 1.01e-44 147
MS.gene006970.t1 AT1G66480 46.067 178 78 5 1 164 1 174 4.47e-42 142
MS.gene006970.t1 AT5G37840 42.373 177 88 5 1 170 1 170 3.11e-36 126

Find 52 sgRNAs with CRISPR-Local

Find 95 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCTTGGTTTGGTTTCTTT+TGG 0.198709 4.2:+25353291 None:intergenic
GATGATTATGCGTTTGTATA+AGG 0.275789 4.2:-25353040 MS.gene006970:CDS
ACAAGAAAATAAAGCCTCTT+TGG 0.283419 4.2:+25353321 None:intergenic
CAAAGATAGACTTGATAATT+TGG 0.287354 4.2:-25353241 MS.gene006970:CDS
CAGTTAAGCATTATGGTGTT+AGG 0.299381 4.2:-25353377 MS.gene006970:CDS
CAAATTATCAAGTCTATCTT+TGG 0.302648 4.2:+25353242 None:intergenic
GTACTAATGGGGAACACTTT+TGG 0.306983 4.2:-25353519 None:intergenic
TCTGAAGCAGTTAAGCATTA+TGG 0.310517 4.2:-25353384 MS.gene006970:CDS
TTTGGCACTCATTTGAATTC+CGG 0.326729 4.2:+25353260 None:intergenic
ATTCCGGAACGAATTCTTCT+TGG 0.341703 4.2:+25353276 None:intergenic
GGAACGAATTCTTCTTGGTT+TGG 0.362859 4.2:+25353281 None:intergenic
CAAACCTGTCGTGGTGTTCT+CGG 0.372324 4.2:+25352955 None:intergenic
GAATGATAATAGTGGTGAAT+TGG 0.372478 4.2:-25353166 MS.gene006970:CDS
CGTGGTGTTCTCGGAGTTCT+CGG 0.376858 4.2:+25352964 None:intergenic
TGAATCCCTCCTTCGTTGCT+TGG 0.382019 4.2:+25352241 None:intergenic
TTGATAATTTGGTGCTTACT+AGG 0.395266 4.2:-25353230 MS.gene006970:CDS
GGAAAAGGAGACTATAGTTA+AGG 0.420314 4.2:-25353004 MS.gene006970:CDS
ACAAAGGTCATGAAAATAGA+TGG 0.431872 4.2:-25353483 MS.gene006970:CDS
CTCGGAGTTCTCGGAGTCCT+CGG 0.435508 4.2:+25352973 None:intergenic
TAGTGGTGAATTGGAAAGTA+AGG 0.435680 4.2:-25353157 MS.gene006970:CDS
AGGAGAATGGTGGTGGGGTG+AGG 0.452868 4.2:-25353137 MS.gene006970:CDS
TTGTATAAGGCCAGTGGCAA+AGG 0.455846 4.2:-25353027 MS.gene006970:CDS
AAAAGCTGGAGAAGTGCTTA+AGG 0.461047 4.2:-25353433 MS.gene006970:CDS
AGTAAAATGAATGATAATAG+TGG 0.471671 4.2:-25353174 MS.gene006970:CDS
TGTATAAGGCCAGTGGCAAA+GGG 0.475209 4.2:-25353026 MS.gene006970:CDS
AGTTAAGCATTATGGTGTTA+GGG 0.475824 4.2:-25353376 MS.gene006970:CDS
AACTTCTCCACCTCTGCCTT+AGG 0.479167 4.2:+25353099 None:intergenic
GAAAGTAAGGAGAATGGTGG+TGG 0.482857 4.2:-25353144 MS.gene006970:CDS
GGCCAGTGGCAAAGGGGAAA+AGG 0.487730 4.2:-25353019 MS.gene006970:CDS
AAAGGAGACTATAGTTAAGG+AGG 0.500505 4.2:-25353001 MS.gene006970:CDS
AACTCCGAGAACACCACGAC+AGG 0.518893 4.2:-25352959 MS.gene006970:intron
GTTGAAAGTTAGACTTCCTA+AGG 0.523556 4.2:-25353115 MS.gene006970:CDS
GCATTATGGTGTTAGGGCAA+AGG 0.538688 4.2:-25353370 MS.gene006970:CDS
AAAGTAAGGAGAATGGTGGT+GGG 0.541122 4.2:-25353143 MS.gene006970:CDS
TAGACTTCCTAAGGCAGAGG+TGG 0.572018 4.2:-25353106 MS.gene006970:CDS
TTATGCCAAGCAACGAAGGA+GGG 0.580061 4.2:-25352246 MS.gene006970:CDS
AAACCAAGAAGAATTCGTTC+CGG 0.593057 4.2:-25353279 MS.gene006970:CDS
AGTTAGACTTCCTAAGGCAG+AGG 0.603968 4.2:-25353109 MS.gene006970:CDS
GAATCTAACAAAACAAGACC+TGG 0.606823 4.2:+25353405 None:intergenic
ATTCGAAAACAAACCTGTCG+TGG 0.610738 4.2:+25352946 None:intergenic
TAGTTAAGGAGGAGAGTCCG+AGG 0.610786 4.2:-25352990 MS.gene006970:CDS
GATGAGAGATTGTAAAGATG+AGG 0.620097 4.2:-25353076 MS.gene006970:CDS
TTTATGCCAAGCAACGAAGG+AGG 0.621866 4.2:-25352247 MS.gene006970:CDS
ACAAAGAGTTACAACCAAAG+AGG 0.621866 4.2:-25353335 MS.gene006970:CDS
AGATTGTAAAGATGAGGCTG+AGG 0.623789 4.2:-25353070 MS.gene006970:CDS
ATGCGTTTGTATAAGGCCAG+TGG 0.639943 4.2:-25353033 MS.gene006970:CDS
GAAGTGCTTAAGGATCATCC+AGG 0.665688 4.2:-25353423 MS.gene006970:CDS
GAATTGGAAAGTAAGGAGAA+TGG 0.667558 4.2:-25353150 MS.gene006970:CDS
AGGAGGGATTCAAATAGCTG+TGG 0.671981 4.2:-25352230 MS.gene006970:CDS
AAGTAAGGAGAATGGTGGTG+GGG 0.675900 4.2:-25353142 MS.gene006970:CDS
GTATAAGGCCAGTGGCAAAG+GGG 0.732700 4.2:-25353025 MS.gene006970:CDS
TTGGAAAGTAAGGAGAATGG+TGG 0.733038 4.2:-25353147 MS.gene006970:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTCTTGAAAGAATTTAAAA+GGG + chr4.2:25353031-25353050 None:intergenic 15.0%
!! ATTTGAACATATTATTCATT+TGG - chr4.2:25352937-25352956 MS.gene006970:intron 15.0%
!!! AATTTTTTTAAAGTCAACAT+TGG + chr4.2:25353369-25353388 None:intergenic 15.0%
!!! ATTTTCTCTTTAAAAAAGTT+AGG - chr4.2:25353289-25353308 MS.gene006970:CDS 15.0%
!!! GTAATTAATTTTACAGAAAA+GGG - chr4.2:25353460-25353479 MS.gene006970:CDS 15.0%
!!! TGTAATTAATTTTACAGAAA+AGG - chr4.2:25353459-25353478 MS.gene006970:CDS 15.0%
!! AATACAAAATTCTGCATTAA+CGG + chr4.2:25352871-25352890 None:intergenic 20.0%
!! AGTAAAATGAATGATAATAG+TGG - chr4.2:25352561-25352580 MS.gene006970:intron 20.0%
!! ATGTGTTGAAAAAATTAGTT+TGG - chr4.2:25353105-25353124 MS.gene006970:CDS 20.0%
!! ATTAATTACACAAACACTTT+AGG + chr4.2:25353449-25353468 None:intergenic 20.0%
!! GATTCTTGAAAGAATTTAAA+AGG + chr4.2:25353032-25353051 None:intergenic 20.0%
!! TTAAATTATCTTAAACACAC+AGG + chr4.2:25353202-25353221 None:intergenic 20.0%
!!! ATGCAGAATTTTGTATTATT+TGG - chr4.2:25352874-25352893 MS.gene006970:intron 20.0%
!!! GTGTGTTTAAGATAATTTAA+AGG - chr4.2:25353202-25353221 MS.gene006970:CDS 20.0%
! ATACAAAATTCTGCATTAAC+GGG + chr4.2:25352870-25352889 None:intergenic 25.0%
! ATTAGTACTTCTCTTCTAAA+AGG + chr4.2:25353252-25353271 None:intergenic 25.0%
! CAAATTATCAAGTCTATCTT+TGG + chr4.2:25352496-25352515 None:intergenic 25.0%
! CTAATTATCTTAGAATTGGA+GGG + chr4.2:25352846-25352865 None:intergenic 25.0%
! TCTTATGAATATTCAATCTG+TGG + chr4.2:25353334-25353353 None:intergenic 25.0%
!! CAAAGATAGACTTGATAATT+TGG - chr4.2:25352494-25352513 MS.gene006970:intron 25.0%
!! TGCTTAATGAGTTTTTAATG+AGG + chr4.2:25352918-25352937 None:intergenic 25.0%
ACAAAGGTCATGAAAATAGA+TGG - chr4.2:25352252-25352271 MS.gene006970:CDS 30.0%
ACAAGAAAATAAAGCCTCTT+TGG + chr4.2:25352417-25352436 None:intergenic 30.0%
CTAAAAACACCAATAAAAGC+TGG - chr4.2:25352288-25352307 MS.gene006970:intron 30.0%
GAATGATAATAGTGGTGAAT+TGG - chr4.2:25352569-25352588 MS.gene006970:intron 30.0%
GATGATTATGCGTTTGTATA+AGG - chr4.2:25352695-25352714 MS.gene006970:intron 30.0%
GCTAATTATCTTAGAATTGG+AGG + chr4.2:25352847-25352866 None:intergenic 30.0%
TACAAAATTCTGCATTAACG+GGG + chr4.2:25352869-25352888 None:intergenic 30.0%
! ACACAAACACTTTAGGAAAA+TGG + chr4.2:25353442-25353461 None:intergenic 30.0%
! AGTTAAGCATTATGGTGTTA+GGG - chr4.2:25352359-25352378 MS.gene006970:intron 30.0%
! ATCTATTTTCATGACCTTTG+TGG + chr4.2:25352253-25352272 None:intergenic 30.0%
! GAGTTTTTAATGAGGATGAA+TGG + chr4.2:25352910-25352929 None:intergenic 30.0%
! GGTGATTTTTACCCAAAAAT+GGG - chr4.2:25353126-25353145 MS.gene006970:CDS 30.0%
! GTGATTTTTACCCAAAAATG+GGG - chr4.2:25353127-25353146 MS.gene006970:CDS 30.0%
! TGATTTTTACCCAAAAATGG+GGG - chr4.2:25353128-25353147 MS.gene006970:CDS 30.0%
! TGGTGATTTTTACCCAAAAA+TGG - chr4.2:25353125-25353144 MS.gene006970:CDS 30.0%
!! TTGATAATTTGGTGCTTACT+AGG - chr4.2:25352505-25352524 MS.gene006970:intron 30.0%
!!! AAAGAGGCTTTATTTTCTTG+TGG - chr4.2:25352416-25352435 MS.gene006970:intron 30.0%
AAACCAAGAAGAATTCGTTC+CGG - chr4.2:25352456-25352475 MS.gene006970:intron 35.0%
AAAGGAGACTATAGTTAAGG+AGG - chr4.2:25352734-25352753 MS.gene006970:intron 35.0%
ACAAAGAGTTACAACCAAAG+AGG - chr4.2:25352400-25352419 MS.gene006970:intron 35.0%
CAGTTAAGCATTATGGTGTT+AGG - chr4.2:25352358-25352377 MS.gene006970:intron 35.0%
GAATCTAACAAAACAAGACC+TGG + chr4.2:25352333-25352352 None:intergenic 35.0%
GAATTGGAAAGTAAGGAGAA+TGG - chr4.2:25352585-25352604 MS.gene006970:intron 35.0%
GATGAGAGATTGTAAAGATG+AGG - chr4.2:25352659-25352678 MS.gene006970:intron 35.0%
GGAAAAGGAGACTATAGTTA+AGG - chr4.2:25352731-25352750 MS.gene006970:intron 35.0%
GGGGCTAATTATCTTAGAAT+TGG + chr4.2:25352850-25352869 None:intergenic 35.0%
GGTGAATTTAGGCTATTTAG+TGG - chr4.2:25353167-25353186 MS.gene006970:CDS 35.0%
GTTGAAAGTTAGACTTCCTA+AGG - chr4.2:25352620-25352639 MS.gene006970:intron 35.0%
TAGTGGTGAATTGGAAAGTA+AGG - chr4.2:25352578-25352597 MS.gene006970:intron 35.0%
TATAAATGAGCATCACTACG+AGG - chr4.2:25353412-25353431 MS.gene006970:CDS 35.0%
TCTTAAACACACAGGCATTT+AGG + chr4.2:25353194-25353213 None:intergenic 35.0%
TGGTTCAAAAAAGACCACAA+AGG - chr4.2:25352236-25352255 MS.gene006970:CDS 35.0%
TTTGGCACTCATTTGAATTC+CGG + chr4.2:25352478-25352497 None:intergenic 35.0%
TTTGGTTAAGGGGTGAATTT+AGG - chr4.2:25353156-25353175 MS.gene006970:CDS 35.0%
! TCTGAAGCAGTTAAGCATTA+TGG - chr4.2:25352351-25352370 MS.gene006970:intron 35.0%
!! CAAATTCTTCCCCCATTTTT+GGG + chr4.2:25353140-25353159 None:intergenic 35.0%
!!! CTTCTTGGTTTGGTTTCTTT+TGG + chr4.2:25352447-25352466 None:intergenic 35.0%
AAAGTAAGGAGAATGGTGGT+GGG - chr4.2:25352592-25352611 MS.gene006970:intron 40.0%
AGATTGTAAAGATGAGGCTG+AGG - chr4.2:25352665-25352684 MS.gene006970:intron 40.0%
ATGGGGGAAGAATTTGGTTA+AGG - chr4.2:25353144-25353163 MS.gene006970:CDS 40.0%
ATTCCGGAACGAATTCTTCT+TGG + chr4.2:25352462-25352481 None:intergenic 40.0%
ATTCGAAAACAAACCTGTCG+TGG + chr4.2:25352792-25352811 None:intergenic 40.0%
CCAAAAATGGGGGAAGAATT+TGG - chr4.2:25353138-25353157 MS.gene006970:CDS 40.0%
GGAACGAATTCTTCTTGGTT+TGG + chr4.2:25352457-25352476 None:intergenic 40.0%
TGGGGGAAGAATTTGGTTAA+GGG - chr4.2:25353145-25353164 MS.gene006970:CDS 40.0%
TTGGAAAGTAAGGAGAATGG+TGG - chr4.2:25352588-25352607 MS.gene006970:intron 40.0%
! AGCACTTCTCCAGCTTTTAT+TGG + chr4.2:25352300-25352319 None:intergenic 40.0%
! CCAAATTCTTCCCCCATTTT+TGG + chr4.2:25353141-25353160 None:intergenic 40.0%
!! AAAAGCTGGAGAAGTGCTTA+AGG - chr4.2:25352302-25352321 MS.gene006970:intron 40.0%
!! AGTTTTATGCCAAGCAACGA+AGG - chr4.2:25353485-25353504 MS.gene006970:CDS 40.0%
AGGAGGGATTCAAATAGCTG+TGG - chr4.2:25353505-25353524 MS.gene006970:CDS 45.0%
AGTTAGACTTCCTAAGGCAG+AGG - chr4.2:25352626-25352645 MS.gene006970:intron 45.0%
ATGCGTTTGTATAAGGCCAG+TGG - chr4.2:25352702-25352721 MS.gene006970:intron 45.0%
GAAAGTAAGGAGAATGGTGG+TGG - chr4.2:25352591-25352610 MS.gene006970:intron 45.0%
GGGGGAAGAATTTGGTTAAG+GGG - chr4.2:25353146-25353165 MS.gene006970:CDS 45.0%
TGTATAAGGCCAGTGGCAAA+GGG - chr4.2:25352709-25352728 MS.gene006970:intron 45.0%
TTATGCCAAGCAACGAAGGA+GGG - chr4.2:25353489-25353508 MS.gene006970:CDS 45.0%
TTGTATAAGGCCAGTGGCAA+AGG - chr4.2:25352708-25352727 MS.gene006970:intron 45.0%
TTTATGCCAAGCAACGAAGG+AGG - chr4.2:25353488-25353507 MS.gene006970:CDS 45.0%
! AAGTAAGGAGAATGGTGGTG+GGG - chr4.2:25352593-25352612 MS.gene006970:intron 45.0%
! GAAGTGCTTAAGGATCATCC+AGG - chr4.2:25352312-25352331 MS.gene006970:intron 45.0%
! GCATTATGGTGTTAGGGCAA+AGG - chr4.2:25352365-25352384 MS.gene006970:intron 45.0%
AACTTCTCCACCTCTGCCTT+AGG + chr4.2:25352639-25352658 None:intergenic 50.0%
CAAACCTGTCGTGGTGTTCT+CGG + chr4.2:25352783-25352802 None:intergenic 50.0%
GTATAAGGCCAGTGGCAAAG+GGG - chr4.2:25352710-25352729 MS.gene006970:intron 50.0%
TAGACTTCCTAAGGCAGAGG+TGG - chr4.2:25352629-25352648 MS.gene006970:intron 50.0%
TAGTTAAGGAGGAGAGTCCG+AGG - chr4.2:25352745-25352764 MS.gene006970:intron 50.0%
TGAATCCCTCCTTCGTTGCT+TGG + chr4.2:25353497-25353516 None:intergenic 50.0%
AACTCCGAGAACACCACGAC+AGG - chr4.2:25352776-25352795 MS.gene006970:intron 55.0%
CGTGGTGTTCTCGGAGTTCT+CGG + chr4.2:25352774-25352793 None:intergenic 55.0%
! CTCCTTTTCCCCTTTGCCAC+TGG + chr4.2:25352721-25352740 None:intergenic 55.0%
CTCGGAGTTCTCGGAGTCCT+CGG + chr4.2:25352765-25352784 None:intergenic 60.0%
GGCCAGTGGCAAAGGGGAAA+AGG - chr4.2:25352716-25352735 MS.gene006970:intron 60.0%
!! AGGAGAATGGTGGTGGGGTG+AGG - chr4.2:25352598-25352617 MS.gene006970:intron 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 25352222 25353535 25352222 ID=MS.gene006970
chr4.2 mRNA 25352222 25353535 25352222 ID=MS.gene006970.t1;Parent=MS.gene006970
chr4.2 exon 25352960 25353535 25352960 ID=MS.gene006970.t1.exon1;Parent=MS.gene006970.t1
chr4.2 CDS 25352960 25353535 25352960 ID=cds.MS.gene006970.t1;Parent=MS.gene006970.t1
chr4.2 exon 25352222 25352281 25352222 ID=MS.gene006970.t1.exon2;Parent=MS.gene006970.t1
chr4.2 CDS 25352222 25352281 25352222 ID=cds.MS.gene006970.t1;Parent=MS.gene006970.t1
Gene Sequence

>MS.gene006970

ATGGGGAACACTTTTGGTTCAAAAAAGACCACAAAGGTCATGAAAATAGATGGTGAAACAATGAAGCTAAAAACACCAATAAAAGCTGGAGAAGTGCTTAAGGATCATCCAGGTCTTGTTTTGTTAGATTCTGAAGCAGTTAAGCATTATGGTGTTAGGGCAAAGGCAATTGAAGCACACAAAGAGTTACAACCAAAGAGGCTTTATTTTCTTGTGGAGCTTCCAAAAGAAACCAAACCAAGAAGAATTCGTTCCGGAATTCAAATGAGTGCCAAAGATAGACTTGATAATTTGGTGCTTACTAGGAGATCTGCTTCTGATTTGTCAATTTTGAAACAAAGTAAAATGAATGATAATAGTGGTGAATTGGAAAGTAAGGAGAATGGTGGTGGGGTGAGGTTGAAAGTTAGACTTCCTAAGGCAGAGGTGGAGAAGTTGATGAGAGATTGTAAAGATGAGGCTGAGGCTGCAGAGATGATTATGCGTTTGTATAAGGCCAGTGGCAAAGGGGAAAAGGAGACTATAGTTAAGGAGGAGAGTCCGAGGACTCCGAGAACTCCGAGAACACCACGACAGGTTTGTTTTCGAATAATTTTGCATGCTAATTTTTTTTTGTCTTAACCCTCCAATTCTAAGATAATTAGCCCCGTTAATGCAGAATTTTGTATTATTTGGTTCTCTCGAACCATTCATCCTCATTAAAAACTCATTAAGCATTTGAACATATTATTCATTTGGTTTAGCATGACTTATTTAAACTTAAAATTTGAATTGAAATTTTTTAATGTATGAATTACTCAAGCATACCCTTTTAAATTCTTTCAAGAATCATTGAAACTTTTCTAACAGTCACATGTGAAATTTTTAATTTTTGTCACTCATTATGTGTTGAAAAAATTAGTTTGGTGATTTTTACCCAAAAATGGGGGAAGAATTTGGTTAAGGGGTGAATTTAGGCTATTTAGTGGTCCTAAATGCCTGTGTGTTTAAGATAATTTAAAGGTCAACTATCAACTTTATGTTTATTCCTTTTAGAAGAGAAGTACTAATAAAATTTGTGATCATTAATTTTCTCTTTAAAAAAGTTAGGACAATGATGTTTAAACTCACCACAGATTGAATATTCATAAGAAAATAAATCTTACCAATGTTGACTTTAAAAAAATTGTGTGACTACATTATAATCATATTATAAATGAGCATCACTACGAGGTTTTCCATTTTCCTAAAGTGTTTGTGTAATTAATTTTACAGAAAAGGGTGAGTTTTATGCCAAGCAACGAAGGAGGGATTCAAATAGCTGTGGCTTCATAA

Protein sequence

>MS.gene006970.t1

MGNTFGSKKTTKVMKIDGETMKLKTPIKAGEVLKDHPGLVLLDSEAVKHYGVRAKAIEAHKELQPKRLYFLVELPKETKPRRIRSGIQMSAKDRLDNLVLTRRSASDLSILKQSKMNDNSGELESKENGGGVRLKVRLPKAEVEKLMRDCKDEAEAAEMIMRLYKASGKGEKETIVKEESPRTPRTPRTPRQKRVSFMPSNEGGIQIAVAS