AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene025681


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025681.t1 MTR_7g109250 96.942 327 10 0 1 327 1 327 0.0 661
MS.gene025681.t1 MTR_7g109250 96.942 327 10 0 1 327 61 387 0.0 658
MS.gene025681.t1 MTR_7g108868 51.412 177 26 5 62 238 11 127 1.36e-46 156
MS.gene025681.t1 MTR_8g058593 51.412 177 26 5 62 238 11 127 1.36e-46 156
MS.gene025681.t1 MTR_8g058607 50.000 176 28 4 62 237 24 139 1.16e-45 152
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene025681.t1 AT1G01350 69.375 320 95 2 8 327 20 336 3.31e-163 459
MS.gene025681.t1 AT5G06420 68.125 320 96 2 8 327 58 371 3.17e-161 455
MS.gene025681.t1 AT5G06420 68.125 320 96 2 8 327 58 371 3.17e-161 455
MS.gene025681.t1 AT4G01023 64.407 59 21 0 258 316 76 134 2.53e-26 104
MS.gene025681.t1 AT4G01023 65.079 63 21 1 254 316 92 153 5.86e-26 104
MS.gene025681.t1 AT4G01023 64.407 59 21 0 258 316 95 153 8.26e-26 103

Find 66 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCATATTCTTCCTATTAAC+AGG 0.250339 7.1:+4956323 None:intergenic
TCTTCAGAAAACCTGTTAAT+AGG 0.277151 7.1:-4956334 MS.gene025681:CDS
TTGTAATCCTTGCATATATC+TGG 0.290645 7.1:+4955816 None:intergenic
GTGGGTCACACGGTCCTCTC+AGG 0.313412 7.1:-4955881 MS.gene025681:CDS
GATCGAGGTGATTACAAATC+TGG 0.331028 7.1:-4955747 MS.gene025681:CDS
TGCAAGGATTACAAGGAAAC+TGG 0.409524 7.1:-4955807 MS.gene025681:CDS
AAATGAAAGCTGGGTTTCTC+AGG 0.415855 7.1:+4956146 None:intergenic
CATTTGTCGAAACCCATTTG+TGG 0.418726 7.1:-4955586 MS.gene025681:CDS
CTTGCTTAAGAGCTCTTTCA+CGG 0.431115 7.1:+4956030 None:intergenic
CTGTGAGCATTGTGCATTGA+AGG 0.436410 7.1:-4955532 MS.gene025681:intron
TAGCAAAGCAACAGCAACTT+TGG 0.436558 7.1:-4956090 MS.gene025681:CDS
GTTGAGACAGGATCCACAAA+TGG 0.441292 7.1:+4955573 None:intergenic
AGAAGACTCGAAATGAAAGC+TGG 0.441893 7.1:+4956136 None:intergenic
ACACGGTCCTCTCAGGGCTT+CGG 0.450938 7.1:-4955874 MS.gene025681:CDS
TGCTTACACTTGGTTGAGAC+AGG 0.460245 7.1:+4955561 None:intergenic
GTCTGCAATCAGCCTACGCT+TGG 0.462383 7.1:-4955364 MS.gene025681:CDS
CAATAATTATACAGATCATA+AGG 0.469416 7.1:-4955946 MS.gene025681:CDS
GGTGGCAGATGGAGAAAGAA+TGG 0.469953 7.1:-4955725 MS.gene025681:CDS
TGCAGGTGAGGATGCGGAAG+AGG 0.471533 7.1:-4955667 MS.gene025681:CDS
CGAGGATGTAAAATTATACA+AGG 0.486690 7.1:-4955973 MS.gene025681:CDS
ACATACCTTGTTCAGTCGGC+TGG 0.489348 7.1:+4956472 None:intergenic
GCAAACAATTGCCAGTGAAA+AGG 0.499122 7.1:-4955907 MS.gene025681:CDS
CGACAAATGAAACACGCAAA+TGG 0.499537 7.1:+4955600 None:intergenic
GAAAGCAAGGAAGATGAGAT+TGG 0.507679 7.1:-4955691 MS.gene025681:CDS
TGCAGAGCTCTTCGAAGAGC+CGG 0.511210 7.1:+4956190 None:intergenic
AATTATACAGATCATAAGGC+TGG 0.520545 7.1:-4955942 MS.gene025681:CDS
ATCGAGGTGATTACAAATCT+GGG 0.520829 7.1:-4955746 MS.gene025681:CDS
GAGCTCTTTCACGGATGGCA+CGG 0.524231 7.1:+4956039 None:intergenic
TTGAGACAGGATCCACAAAT+GGG 0.525917 7.1:+4955574 None:intergenic
AGATATATGCAAGGATTACA+AGG 0.530308 7.1:-4955814 MS.gene025681:CDS
TGGGTCACACGGTCCTCTCA+GGG 0.532282 7.1:-4955880 MS.gene025681:CDS
CTTAAGAGCTCTTTCACGGA+TGG 0.538525 7.1:+4956034 None:intergenic
AGTCTCAAGGGAAAGAGTAC+TGG 0.538575 7.1:-4955999 MS.gene025681:CDS
GAAAACCAGCCGACTGAACA+AGG 0.548242 7.1:-4956477 MS.gene025681:intron
GTGGCAGATGGAGAAAGAAT+GGG 0.553122 7.1:-4955724 MS.gene025681:CDS
TTACAAATCTGGGTGGCAGA+TGG 0.553483 7.1:-4955736 MS.gene025681:CDS
GAAGACTCGAAATGAAAGCT+GGG 0.554193 7.1:+4956137 None:intergenic
AGCTCTTTCACGGATGGCAC+GGG 0.560125 7.1:+4956040 None:intergenic
GAAACTGGTTACTGTGGGTA+TGG 0.560524 7.1:-4955792 MS.gene025681:CDS
TATTGAGAATGAAGATAATG+AGG 0.560776 7.1:-4956291 MS.gene025681:CDS
TCATGAGATACGAAAGAAGA+TGG 0.563924 7.1:-4955326 MS.gene025681:CDS
ATAGGAAGAATATGAGGAAG+CGG 0.564756 7.1:-4956316 MS.gene025681:CDS
GGTGAGGATGCGGAAGAGGA+AGG 0.573050 7.1:-4955663 MS.gene025681:CDS
CTGTTAATAGGAAGAATATG+AGG 0.583376 7.1:-4956322 MS.gene025681:CDS
GGGATGAAGCTGAGAAAGCA+AGG 0.584805 7.1:-4955704 MS.gene025681:CDS
TACAAGGAAACTGGTTACTG+TGG 0.587264 7.1:-4955798 MS.gene025681:CDS
ACAATTGCCAGTGAAAAGGC+TGG 0.588175 7.1:-4955903 MS.gene025681:CDS
TTATACATACCTTGTTCAGT+CGG 0.588673 7.1:+4956468 None:intergenic
GATGAGATTGGCTGCAGGTG+AGG 0.590274 7.1:-4955679 MS.gene025681:CDS
GAAAAGGCTGGTGGGTCACA+CGG 0.600903 7.1:-4955891 MS.gene025681:CDS
AGGAAGATGAGATTGGCTGC+AGG 0.603143 7.1:-4955684 MS.gene025681:CDS
ATTGGCTGCAGGTGAGGATG+CGG 0.603342 7.1:-4955673 MS.gene025681:CDS
ATTGCCAGTGAAAAGGCTGG+TGG 0.607353 7.1:-4955900 MS.gene025681:CDS
GATACGAAAGAAGATGGCTG+AGG 0.623889 7.1:-4955320 MS.gene025681:CDS
TTGCCAGTGAAAAGGCTGGT+GGG 0.630138 7.1:-4955899 MS.gene025681:CDS
CAAGCGACTGAGAGTCTCAA+GGG 0.630489 7.1:-4956011 MS.gene025681:CDS
ACAGAAGTAGTGCTTACACT+TGG 0.630927 7.1:+4955551 None:intergenic
GCAAGCGACTGAGAGTCTCA+AGG 0.636269 7.1:-4956012 MS.gene025681:CDS
GGGAAAGAGTACTGGTTCCG+AGG 0.640397 7.1:-4955991 MS.gene025681:CDS
ACAAGGAAACTGGTTACTGT+GGG 0.647981 7.1:-4955797 MS.gene025681:CDS
TGTAAGTTTATGCATGATCG+AGG 0.650874 7.1:-4955762 MS.gene025681:CDS
TTATCAGCCAGATATATGCA+AGG 0.656472 7.1:-4955823 MS.gene025681:CDS
AGAGCTCTTCGAAGAGCCGG+TGG 0.686462 7.1:+4956193 None:intergenic
GAGGATGTAAAATTATACAA+GGG 0.688297 7.1:-4955972 MS.gene025681:CDS
ATGTGAGCCGAAGCCCTGAG+AGG 0.689295 7.1:+4955867 None:intergenic
GAGGTGATTACAAATCTGGG+TGG 0.758440 7.1:-4955743 MS.gene025681:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAAAAAAAAGGTTAATGA+TGG + chr7.1:4955433-4955452 None:intergenic 20.0%
!! CAATAATTATACAGATCATA+AGG - chr7.1:4955870-4955889 MS.gene025681:CDS 20.0%
! AGAAGTTAGGCATAATTAAA+AGG + chr7.1:4956388-4956407 None:intergenic 25.0%
! GAGGATGTAAAATTATACAA+GGG - chr7.1:4955844-4955863 MS.gene025681:CDS 25.0%
! TATTGAGAATGAAGATAATG+AGG - chr7.1:4955525-4955544 MS.gene025681:intron 25.0%
!! CTTGTATAATTTTACATCCT+CGG + chr7.1:4955845-4955864 None:intergenic 25.0%
!!! ACTTATTTGCTTTGAAGTTA+AGG + chr7.1:4956315-4956334 None:intergenic 25.0%
!!! CTTATTTGCTTTGAAGTTAA+GGG + chr7.1:4956314-4956333 None:intergenic 25.0%
AAGTAAAATGAGCAGAAGTT+AGG + chr7.1:4956401-4956420 None:intergenic 30.0%
AATTATACAGATCATAAGGC+TGG - chr7.1:4955874-4955893 MS.gene025681:CDS 30.0%
ACAAACGCGTAGAAAAAAAA+AGG + chr7.1:4955443-4955462 None:intergenic 30.0%
AGATATATGCAAGGATTACA+AGG - chr7.1:4956002-4956021 MS.gene025681:CDS 30.0%
CGAGGATGTAAAATTATACA+AGG - chr7.1:4955843-4955862 MS.gene025681:CDS 30.0%
CTCATATTCTTCCTATTAAC+AGG + chr7.1:4955496-4955515 None:intergenic 30.0%
CTGTTAATAGGAAGAATATG+AGG - chr7.1:4955494-4955513 MS.gene025681:intron 30.0%
GATGGTACAAAAAAATGTAG+AGG + chr7.1:4955415-4955434 None:intergenic 30.0%
TCTTCAGAAAACCTGTTAAT+AGG - chr7.1:4955482-4955501 MS.gene025681:intron 30.0%
TGTTCAGAAAAAGAACATGA+AGG - chr7.1:4955579-4955598 MS.gene025681:CDS 30.0%
TTATACATACCTTGTTCAGT+CGG + chr7.1:4955351-4955370 None:intergenic 30.0%
TTGTAATCCTTGCATATATC+TGG + chr7.1:4956003-4956022 None:intergenic 30.0%
! AATAAGTTGTTCTTTTCCAC+CGG - chr7.1:4955607-4955626 MS.gene025681:CDS 30.0%
ACATTAAAAATGCCAAGCGT+AGG + chr7.1:4956467-4956486 None:intergenic 35.0%
ATAGGAAGAATATGAGGAAG+CGG - chr7.1:4955500-4955519 MS.gene025681:intron 35.0%
ATCGAGGTGATTACAAATCT+GGG - chr7.1:4956070-4956089 MS.gene025681:CDS 35.0%
TCATGAGATACGAAAGAAGA+TGG - chr7.1:4956490-4956509 MS.gene025681:CDS 35.0%
TGTAAGTTTATGCATGATCG+AGG - chr7.1:4956054-4956073 MS.gene025681:CDS 35.0%
TTATCAGCCAGATATATGCA+AGG - chr7.1:4955993-4956012 MS.gene025681:CDS 35.0%
! TACGCTTGGCATTTTTAATG+TGG - chr7.1:4956466-4956485 MS.gene025681:intron 35.0%
AAATGAAAGCTGGGTTTCTC+AGG + chr7.1:4955673-4955692 None:intergenic 40.0%
ACAAGGAAACTGGTTACTGT+GGG - chr7.1:4956019-4956038 MS.gene025681:CDS 40.0%
ACAGAAGTAGTGCTTACACT+TGG + chr7.1:4956268-4956287 None:intergenic 40.0%
AGAAGACTCGAAATGAAAGC+TGG + chr7.1:4955683-4955702 None:intergenic 40.0%
CATTTGTCGAAACCCATTTG+TGG - chr7.1:4956230-4956249 MS.gene025681:CDS 40.0%
CGACAAATGAAACACGCAAA+TGG + chr7.1:4956219-4956238 None:intergenic 40.0%
CTTGCTTAAGAGCTCTTTCA+CGG + chr7.1:4955789-4955808 None:intergenic 40.0%
GAAAGCAAGGAAGATGAGAT+TGG - chr7.1:4956125-4956144 MS.gene025681:CDS 40.0%
GAAGACTCGAAATGAAAGCT+GGG + chr7.1:4955682-4955701 None:intergenic 40.0%
GATCGAGGTGATTACAAATC+TGG - chr7.1:4956069-4956088 MS.gene025681:CDS 40.0%
GCAAACAATTGCCAGTGAAA+AGG - chr7.1:4955909-4955928 MS.gene025681:CDS 40.0%
TACAAGGAAACTGGTTACTG+TGG - chr7.1:4956018-4956037 MS.gene025681:CDS 40.0%
TAGCAAAGCAACAGCAACTT+TGG - chr7.1:4955726-4955745 MS.gene025681:CDS 40.0%
TGCAAGGATTACAAGGAAAC+TGG - chr7.1:4956009-4956028 MS.gene025681:CDS 40.0%
TTGAGACAGGATCCACAAAT+GGG + chr7.1:4956245-4956264 None:intergenic 40.0%
ACAATTGCCAGTGAAAAGGC+TGG - chr7.1:4955913-4955932 MS.gene025681:CDS 45.0%
CTTAAGAGCTCTTTCACGGA+TGG + chr7.1:4955785-4955804 None:intergenic 45.0%
GAAACTGGTTACTGTGGGTA+TGG - chr7.1:4956024-4956043 MS.gene025681:CDS 45.0%
GAGGTGATTACAAATCTGGG+TGG - chr7.1:4956073-4956092 MS.gene025681:CDS 45.0%
GATACGAAAGAAGATGGCTG+AGG - chr7.1:4956496-4956515 MS.gene025681:CDS 45.0%
GTGGCAGATGGAGAAAGAAT+GGG - chr7.1:4956092-4956111 MS.gene025681:CDS 45.0%
GTTGAGACAGGATCCACAAA+TGG + chr7.1:4956246-4956265 None:intergenic 45.0%
TGCTTACACTTGGTTGAGAC+AGG + chr7.1:4956258-4956277 None:intergenic 45.0%
TTACAAATCTGGGTGGCAGA+TGG - chr7.1:4956080-4956099 MS.gene025681:CDS 45.0%
! AGTCTCAAGGGAAAGAGTAC+TGG - chr7.1:4955817-4955836 MS.gene025681:CDS 45.0%
! CTGTGAGCATTGTGCATTGA+AGG - chr7.1:4956284-4956303 MS.gene025681:CDS 45.0%
ACATACCTTGTTCAGTCGGC+TGG + chr7.1:4955347-4955366 None:intergenic 50.0%
ATTGCCAGTGAAAAGGCTGG+TGG - chr7.1:4955916-4955935 MS.gene025681:CDS 50.0%
CAAGCGACTGAGAGTCTCAA+GGG - chr7.1:4955805-4955824 MS.gene025681:CDS 50.0%
GAAAACCAGCCGACTGAACA+AGG - chr7.1:4955339-4955358 MS.gene025681:CDS 50.0%
GGGATGAAGCTGAGAAAGCA+AGG - chr7.1:4956112-4956131 MS.gene025681:CDS 50.0%
GGTGGCAGATGGAGAAAGAA+TGG - chr7.1:4956091-4956110 MS.gene025681:CDS 50.0%
TTGCCAGTGAAAAGGCTGGT+GGG - chr7.1:4955917-4955936 MS.gene025681:CDS 50.0%
! AGGAAGATGAGATTGGCTGC+AGG - chr7.1:4956132-4956151 MS.gene025681:CDS 50.0%
!!! CGGCTGGTTTTCAGCAGATT+TGG + chr7.1:4955331-4955350 None:intergenic 50.0%
AGCTCTTTCACGGATGGCAC+GGG + chr7.1:4955779-4955798 None:intergenic 55.0%
ATTGGCTGCAGGTGAGGATG+CGG - chr7.1:4956143-4956162 MS.gene025681:CDS 55.0%
GAGCTCTTTCACGGATGGCA+CGG + chr7.1:4955780-4955799 None:intergenic 55.0%
GCAAGCGACTGAGAGTCTCA+AGG - chr7.1:4955804-4955823 MS.gene025681:CDS 55.0%
GTCTGCAATCAGCCTACGCT+TGG - chr7.1:4956452-4956471 MS.gene025681:intron 55.0%
TGCAGAGCTCTTCGAAGAGC+CGG + chr7.1:4955629-4955648 None:intergenic 55.0%
! GAAAAGGCTGGTGGGTCACA+CGG - chr7.1:4955925-4955944 MS.gene025681:CDS 55.0%
! GATGAGATTGGCTGCAGGTG+AGG - chr7.1:4956137-4956156 MS.gene025681:CDS 55.0%
! TGACCCACCAGCCTTTTCAC+TGG + chr7.1:4955923-4955942 None:intergenic 55.0%
!! GGGAAAGAGTACTGGTTCCG+AGG - chr7.1:4955825-4955844 MS.gene025681:CDS 55.0%
ACACGGTCCTCTCAGGGCTT+CGG - chr7.1:4955942-4955961 MS.gene025681:CDS 60.0%
AGAGCTCTTCGAAGAGCCGG+TGG + chr7.1:4955626-4955645 None:intergenic 60.0%
ATGTGAGCCGAAGCCCTGAG+AGG + chr7.1:4955952-4955971 None:intergenic 60.0%
GGTGAGGATGCGGAAGAGGA+AGG - chr7.1:4956153-4956172 MS.gene025681:CDS 60.0%
TGCAGGTGAGGATGCGGAAG+AGG - chr7.1:4956149-4956168 MS.gene025681:CDS 60.0%
TGGGTCACACGGTCCTCTCA+GGG - chr7.1:4955936-4955955 MS.gene025681:CDS 60.0%
GTGGGTCACACGGTCCTCTC+AGG - chr7.1:4955935-4955954 MS.gene025681:CDS 65.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 4955312 4956526 4955312 ID=MS.gene025681
chr7.1 mRNA 4955312 4956526 4955312 ID=MS.gene025681.t1;Parent=MS.gene025681
chr7.1 exon 4956478 4956526 4956478 ID=MS.gene025681.t1.exon1;Parent=MS.gene025681.t1
chr7.1 CDS 4956478 4956526 4956478 ID=cds.MS.gene025681.t1;Parent=MS.gene025681.t1
chr7.1 exon 4955533 4956365 4955533 ID=MS.gene025681.t1.exon2;Parent=MS.gene025681.t1
chr7.1 CDS 4955533 4956365 4955533 ID=cds.MS.gene025681.t1;Parent=MS.gene025681.t1
chr7.1 exon 4955312 4955413 4955312 ID=MS.gene025681.t1.exon3;Parent=MS.gene025681.t1
chr7.1 CDS 4955312 4955413 4955312 ID=cds.MS.gene025681.t1;Parent=MS.gene025681.t1
Gene Sequence

>MS.gene025681

ATGGAAAATTCTGAGGCCAAATCTGCTGAAAACCAGCCGACTGAACAAGGTATGTATAATATTTTGCATTATTAGACTCACAATCTTGTTATCTTATGCACCTCTACATTTTTTTGTACCATCATTAACCTTTTTTTTTCTACGCGTTTGTTTATCGTCAGTGTGTAGTTTCTTCAGAAAACCTGTTAATAGGAAGAATATGAGGAAGCGGACTATTGAGAATGAAGATAATGAGGATGACTCGAATAATGAAGAGTCTTTGATGCATGTTCAGAAAAAGAACATGAAGGCTGATAATAAGTTGTTCTTTTCCACCGGCTCTTCGAAGAGCTCTGCATCTGCTAAACTGAATGAAGAACCTGAGAAACCCAGCTTTCATTTCGAGTCTTCTAAAGAGATTCAAGTTCAACATGATAGCAAAGCAACAGCAACTTTGGAGACTGAGACTGATTTTTCAAGAGATGCCCGTGCCATCCGTGAAAGAGCTCTTAAGCAAGCGACTGAGAGTCTCAAGGGAAAGAGTACTGGTTCCGAGGATGTAAAATTATACAAGGGAATCAATAATTATACAGATCATAAGGCTGGATTTCGTAGAGAGCAAACAATTGCCAGTGAAAAGGCTGGTGGGTCACACGGTCCTCTCAGGGCTTCGGCTCACATAAGAGTTTCAGCAAGATTTGATTATCAGCCAGATATATGCAAGGATTACAAGGAAACTGGTTACTGTGGGTATGGTGATTCGTGTAAGTTTATGCATGATCGAGGTGATTACAAATCTGGGTGGCAGATGGAGAAAGAATGGGATGAAGCTGAGAAAGCAAGGAAGATGAGATTGGCTGCAGGTGAGGATGCGGAAGAGGAAGGTGCTAGTTTGAATGATGAAGATGATGATGAAGACGTATTACCATTTGCGTGTTTCATTTGTCGAAACCCATTTGTGGATCCTGTCTCAACCAAGTGTAAGCACTACTTCTGTGAGCATTGTGCATTGAAGGTACACCCTTAACTTCAAAGCAAATAAGTTTTAATTTATAACAGTTTCAAGTTATTCAGTAATGCTTAATTTCTTTTTTCCTTTTAATTATGCCTAACTTCTGCTCATTTTACTTGCAGCATCATGCGAAGAATAAGAAGTGTTTTGTCTGCAATCAGCCTACGCTTGGCATTTTTAATGTGGCTCATGAGATACGAAAGAAGATGGCTGAGGATAAATAG

Protein sequence

>MS.gene025681.t1

MENSEAKSAENQPTEQVCSFFRKPVNRKNMRKRTIENEDNEDDSNNEESLMHVQKKNMKADNKLFFSTGSSKSSASAKLNEEPEKPSFHFESSKEIQVQHDSKATATLETETDFSRDARAIRERALKQATESLKGKSTGSEDVKLYKGINNYTDHKAGFRREQTIASEKAGGSHGPLRASAHIRVSARFDYQPDICKDYKETGYCGYGDSCKFMHDRGDYKSGWQMEKEWDEAEKARKMRLAAGEDAEEEGASLNDEDDDEDVLPFACFICRNPFVDPVSTKCKHYFCEHCALKHHAKNKKCFVCNQPTLGIFNVAHEIRKKMAEDK