AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29525

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29525.t1 MTR_5g080880 81.641 256 42 3 1 253 1 254 2.33e-138 392
MS.gene29525.t1 MTR_5g080870 68.898 254 45 5 1 254 1 220 1.09e-112 327
MS.gene29525.t1 MTR_7g063520 42.629 251 122 6 8 253 20 253 2.30e-58 186
MS.gene29525.t1 MTR_4g006560 32.075 159 100 3 97 253 83 235 1.40e-22 93.2
MS.gene29525.t1 MTR_1g013120 30.041 243 143 9 24 253 4 232 2.28e-21 89.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29525.t1 AT5G05990 37.879 264 141 6 5 253 3 258 4.67e-54 175
MS.gene29525.t1 AT3G55605 41.328 271 127 9 1 253 1 257 1.53e-51 169
MS.gene29525.t1 AT2G39795 43.077 195 102 3 63 253 60 249 2.63e-49 163
MS.gene29525.t1 AT5G02050 36.803 269 151 6 1 253 1 266 6.36e-43 147
MS.gene29525.t1 AT2G39790 30.172 232 144 4 31 254 19 240 6.39e-28 107
MS.gene29525.t1 AT1G15870 29.255 188 120 5 69 253 63 240 1.59e-20 87.8
MS.gene29525.t1 AT1G80720 30.120 166 104 5 92 253 31 188 5.90e-16 74.3
MS.gene29525.t1 AT1G80720 30.120 166 104 5 92 253 83 240 9.47e-16 74.7
MS.gene29525.t1 AT4G31930 29.630 162 99 5 97 252 80 232 5.19e-13 67.0

Find 44 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGATTATCAACTATCTTAAA+TGG 0.175868 5.2:-68681719 None:intergenic
AGTGTTATTGTCTGATTTCC+TGG 0.252098 5.2:-68681740 None:intergenic
ATCAGACAATAACACTTAAA+AGG 0.289378 5.2:+68681747 MS.gene29525:CDS
TTATCAAGGTGAAGAAATTC+AGG 0.325526 5.2:+68681772 MS.gene29525:CDS
CCAAGTCAAGCACTTTCCTT+AGG 0.334931 5.2:+68681232 MS.gene29525:CDS
TGCAAGAAATTTACTGTGCT+TGG 0.359052 5.2:-68682444 None:intergenic
CAGCGAATAACCATCTCATC+TGG 0.375769 5.2:-68681959 None:intergenic
TTAGAAACCTTGACTGAAAG+TGG 0.404401 5.2:-68681896 None:intergenic
CTCTTATTTCTAAGTACTTG+TGG 0.408675 5.2:-68682413 None:intergenic
TGCAAGAGTACATGATCAAC+AGG 0.410602 5.2:+68682463 MS.gene29525:CDS
TTCAGTCAAGGTTTCTAAGA+AGG 0.418352 5.2:+68681901 MS.gene29525:CDS
CACAAGTACTTAGAAATAAG+AGG 0.434165 5.2:+68682414 MS.gene29525:CDS
GATTATCAACTATCTTAAAT+GGG 0.456111 5.2:-68681718 None:intergenic
TAATCATCAAAAGGATGATA+AGG 0.475586 5.2:+68681838 MS.gene29525:CDS
GAGAAAAGTCTCATCGGAGT+TGG 0.476774 5.2:-68681391 None:intergenic
CAGGAAAAGTAGAGACTACT+TGG 0.480599 5.2:+68682482 MS.gene29525:CDS
CAAGTCAAGCACTTTCCTTA+GGG 0.487750 5.2:+68681233 MS.gene29525:CDS
ATCGAAAATCACTTGTGCTC+AGG 0.490320 5.2:+68681425 MS.gene29525:CDS
GTCAAGGTTTCTAAGAAGGA+TGG 0.493043 5.2:+68681905 MS.gene29525:CDS
AGAAAAGTCTCATCGGAGTT+GGG 0.497268 5.2:-68681390 None:intergenic
CTCGTAGCGGTTGACGGCAG+CGG 0.497835 5.2:-68681316 None:intergenic
TTTAAGATAGTTGATAATCC+AGG 0.504200 5.2:+68681722 MS.gene29525:CDS
TGAACCCTCGTAGCGGTTGA+CGG 0.507166 5.2:-68681322 None:intergenic
AGAACATGATAATCATCAAA+AGG 0.514345 5.2:+68681829 MS.gene29525:CDS
ATCTTAAATGGGAAATTGCT+CGG 0.515748 5.2:-68681707 None:intergenic
GAAAGCACGGCGCGATGACC+CGG 0.519271 5.2:-68681294 None:intergenic
ACACTTAAAAGGACTTATCA+AGG 0.527097 5.2:+68681758 MS.gene29525:CDS
AAGCATTCCACTTTCAGTCA+AGG 0.530679 5.2:+68681889 MS.gene29525:CDS
AACACATTTGAATTTCAAAG+AGG 0.535659 5.2:-68681930 None:intergenic
GTTTACAGCGCGGAACTCAT+CGG 0.541419 5.2:-68681451 None:intergenic
CGCTGCCGTCAACCGCTACG+AGG 0.550566 5.2:+68681317 MS.gene29525:CDS
GTTGACGGCAGCGGAAAGCA+CGG 0.551406 5.2:-68681307 None:intergenic
TGATTATCATGTTCTTCACC+AGG 0.551810 5.2:-68681821 None:intergenic
CCTAAGGAAAGTGCTTGACT+TGG 0.566876 5.2:-68681232 None:intergenic
TCAAGGTTTCTAAGAAGGAT+GGG 0.576019 5.2:+68681906 MS.gene29525:CDS
AATCTTGCAACAAGCAGCTG+CGG 0.606350 5.2:-68682012 None:intergenic
AGCGAATAACCATCTCATCT+GGG 0.609542 5.2:-68681958 None:intergenic
TAAACGGAGAAAAGTCTCAT+CGG 0.611707 5.2:-68681397 None:intergenic
GCTGCCGTCAACCGCTACGA+GGG 0.613894 5.2:+68681318 MS.gene29525:CDS
TGTTGCTTACCCAGATGAGA+TGG 0.638083 5.2:+68681949 MS.gene29525:CDS
TCAGAAGAAAAGTGAAACGT+AGG 0.644962 5.2:-68681351 None:intergenic
AAAGTAGAGACTACTTGGTG+TGG 0.647167 5.2:+68682487 MS.gene29525:CDS
AAGTGCTTGACTTGGAACGA+AGG 0.662607 5.2:-68681224 None:intergenic
GAACAAATGAACCCTCGTAG+CGG 0.717050 5.2:-68681329 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATGTTGAAAATTTGATTT+TGG + chr5.2:68681663-68681682 MS.gene29525:intron 15.0%
!!! TGAGATTATGATTTTTAATT+TGG + chr5.2:68681796-68681815 MS.gene29525:CDS 15.0%
!! AATTGAAAGTAATACAAACA+GGG - chr5.2:68682312-68682331 None:intergenic 20.0%
!! ATGGTATGAAAATTTGAATT+TGG + chr5.2:68681608-68681627 MS.gene29525:intron 20.0%
!! GATTATCAACTATCTTAAAT+GGG - chr5.2:68681721-68681740 None:intergenic 20.0%
!! TAATTGAAAGTAATACAAAC+AGG - chr5.2:68682313-68682332 None:intergenic 20.0%
!!! AATTTGATTTTGGTTGATAT+AGG + chr5.2:68681673-68681692 MS.gene29525:intron 20.0%
!!! ATTTGATTTTGGTTGATATA+GGG + chr5.2:68681674-68681693 MS.gene29525:intron 20.0%
!!! TGATTTTCGATTCAATTAAA+CGG - chr5.2:68681416-68681435 None:intergenic 20.0%
! AACACATTTGAATTTCAAAG+AGG - chr5.2:68681933-68681952 None:intergenic 25.0%
! AGAACATGATAATCATCAAA+AGG + chr5.2:68681829-68681848 MS.gene29525:CDS 25.0%
! AGAATAAAATAATCAGAACG+AGG - chr5.2:68682049-68682068 None:intergenic 25.0%
! ATCAGACAATAACACTTAAA+AGG + chr5.2:68681747-68681766 MS.gene29525:CDS 25.0%
! ATCATGAGTCTAGTAAATTA+AGG - chr5.2:68681485-68681504 None:intergenic 25.0%
! GGATTATCAACTATCTTAAA+TGG - chr5.2:68681722-68681741 None:intergenic 25.0%
! TAATCATCAAAAGGATGATA+AGG + chr5.2:68681838-68681857 MS.gene29525:CDS 25.0%
! TTTAATCATACCAGCTTATA+AGG - chr5.2:68681572-68681591 None:intergenic 25.0%
!! ATTTTCATACCATTACGAAA+TGG - chr5.2:68681601-68681620 None:intergenic 25.0%
!! TTTTCATACCATTACGAAAT+GGG - chr5.2:68681600-68681619 None:intergenic 25.0%
!!! ATGATTTTTAATTTGGTTCC+TGG + chr5.2:68681803-68681822 MS.gene29525:CDS 25.0%
!!! TTTAAGATAGTTGATAATCC+AGG + chr5.2:68681722-68681741 MS.gene29525:CDS 25.0%
AAAAAAGACCCATTTCGTAA+TGG + chr5.2:68681589-68681608 MS.gene29525:intron 30.0%
ACACTTAAAAGGACTTATCA+AGG + chr5.2:68681758-68681777 MS.gene29525:CDS 30.0%
ATCTTAAATGGGAAATTGCT+CGG - chr5.2:68681710-68681729 None:intergenic 30.0%
ATTGATCAGAAAAACTCAAC+CGG + chr5.2:68681275-68681294 MS.gene29525:CDS 30.0%
CACAAGTACTTAGAAATAAG+AGG + chr5.2:68682414-68682433 MS.gene29525:CDS 30.0%
TGAACTTATACCTTATAAGC+TGG + chr5.2:68681559-68681578 MS.gene29525:intron 30.0%
TTATCAAGGTGAAGAAATTC+AGG + chr5.2:68681772-68681791 MS.gene29525:CDS 30.0%
! GTGCATTCAATATTTGAAAC+CGG + chr5.2:68682081-68682100 MS.gene29525:intron 30.0%
! TGCATTCAATATTTGAAACC+GGG + chr5.2:68682082-68682101 MS.gene29525:intron 30.0%
!! CTCTTATTTCTAAGTACTTG+TGG - chr5.2:68682416-68682435 None:intergenic 30.0%
CCAATCTCAATTTCAAATCG+CGG - chr5.2:68682192-68682211 None:intergenic 35.0%
TAAACGGAGAAAAGTCTCAT+CGG - chr5.2:68681400-68681419 None:intergenic 35.0%
TCAGAAGAAAAGTGAAACGT+AGG - chr5.2:68681354-68681373 None:intergenic 35.0%
TCCAAATCCCTGGAAAAAAA+TGG - chr5.2:68682372-68682391 None:intergenic 35.0%
TGATTATCATGTTCTTCACC+AGG - chr5.2:68681824-68681843 None:intergenic 35.0%
TGCAAGAAATTTACTGTGCT+TGG - chr5.2:68682447-68682466 None:intergenic 35.0%
TTAGAAACCTTGACTGAAAG+TGG - chr5.2:68681899-68681918 None:intergenic 35.0%
TTGATCAGAAAAACTCAACC+GGG + chr5.2:68681276-68681295 MS.gene29525:CDS 35.0%
TTGCAGTTCAGAATCAGATT+GGG + chr5.2:68682265-68682284 MS.gene29525:intron 35.0%
! AGTGTTATTGTCTGATTTCC+TGG - chr5.2:68681743-68681762 None:intergenic 35.0%
! CGCGATTTGAAATTGAGATT+GGG + chr5.2:68682190-68682209 MS.gene29525:intron 35.0%
! GATTTGAAATTGAGATTGGG+TGG + chr5.2:68682193-68682212 MS.gene29525:intron 35.0%
! GCATTCAATATTTGAAACCG+GGG + chr5.2:68682083-68682102 MS.gene29525:intron 35.0%
! TCAAGGTTTCTAAGAAGGAT+GGG + chr5.2:68681906-68681925 MS.gene29525:CDS 35.0%
! TCAGAATCAGATTGGGATTT+TGG + chr5.2:68682272-68682291 MS.gene29525:intron 35.0%
! TTCAGTCAAGGTTTCTAAGA+AGG + chr5.2:68681901-68681920 MS.gene29525:CDS 35.0%
!!! AGATTCTGCCATTTTTTTCC+AGG + chr5.2:68682361-68682380 MS.gene29525:intron 35.0%
!!! ATTTTGGTTGATATAGGGTG+AGG + chr5.2:68681679-68681698 MS.gene29525:intron 35.0%
!!! GATTCTGCCATTTTTTTCCA+GGG + chr5.2:68682362-68682381 MS.gene29525:intron 35.0%
AAGCATTCCACTTTCAGTCA+AGG + chr5.2:68681889-68681908 MS.gene29525:CDS 40.0%
AGAAAAGTCTCATCGGAGTT+GGG - chr5.2:68681393-68681412 None:intergenic 40.0%
AGCGAATAACCATCTCATCT+GGG - chr5.2:68681961-68681980 None:intergenic 40.0%
ATCGAAAATCACTTGTGCTC+AGG + chr5.2:68681425-68681444 MS.gene29525:CDS 40.0%
CAAGTCAAGCACTTTCCTTA+GGG + chr5.2:68681233-68681252 MS.gene29525:CDS 40.0%
CAGGAAAAGTAGAGACTACT+TGG + chr5.2:68682482-68682501 MS.gene29525:CDS 40.0%
CCACTATAGCTGCTATGATA+TGG - chr5.2:68682121-68682140 None:intergenic 40.0%
CCATATCATAGCAGCTATAG+TGG + chr5.2:68682118-68682137 MS.gene29525:intron 40.0%
GTTGCAGTTCAGAATCAGAT+TGG + chr5.2:68682264-68682283 MS.gene29525:intron 40.0%
! AAAGTAGAGACTACTTGGTG+TGG + chr5.2:68682487-68682506 MS.gene29525:CDS 40.0%
! CCGCGATTTGAAATTGAGAT+TGG + chr5.2:68682189-68682208 MS.gene29525:intron 40.0%
! GTCAAGGTTTCTAAGAAGGA+TGG + chr5.2:68681905-68681924 MS.gene29525:CDS 40.0%
! TGCAAGAGTACATGATCAAC+AGG + chr5.2:68682463-68682482 MS.gene29525:CDS 40.0%
! TTTTTCCAGGGATTTGGATG+AGG + chr5.2:68682374-68682393 MS.gene29525:intron 40.0%
!!! GCCATTTTTTTCCAGGGATT+TGG + chr5.2:68682368-68682387 MS.gene29525:intron 40.0%
AATCTTGCAACAAGCAGCTG+CGG - chr5.2:68682015-68682034 None:intergenic 45.0%
CAGCGAATAACCATCTCATC+TGG - chr5.2:68681962-68681981 None:intergenic 45.0%
CCAAGTCAAGCACTTTCCTT+AGG + chr5.2:68681232-68681251 MS.gene29525:CDS 45.0%
GAACAAATGAACCCTCGTAG+CGG - chr5.2:68681332-68681351 None:intergenic 45.0%
GAGAAAAGTCTCATCGGAGT+TGG - chr5.2:68681394-68681413 None:intergenic 45.0%
GCTATAGCACCTTTGCATAG+CGG + chr5.2:68682144-68682163 MS.gene29525:intron 45.0%
GTTCAAACTCCGCTATGCAA+AGG - chr5.2:68682156-68682175 None:intergenic 45.0%
TATGGTCACTGATGTAACCC+CGG - chr5.2:68682103-68682122 None:intergenic 45.0%
TCGCAGAAGAAAAAGCCCTA+AGG - chr5.2:68681251-68681270 None:intergenic 45.0%
TCTCTACAACCAAGCAGTAC+AGG - chr5.2:68682228-68682247 None:intergenic 45.0%
TGTTGCTAACCTGTACTGCT+TGG + chr5.2:68682216-68682235 MS.gene29525:intron 45.0%
! TGTTGCTTACCCAGATGAGA+TGG + chr5.2:68681949-68681968 MS.gene29525:CDS 45.0%
!! AAGTGCTTGACTTGGAACGA+AGG - chr5.2:68681227-68681246 None:intergenic 45.0%
!! CCTAAGGAAAGTGCTTGACT+TGG - chr5.2:68681235-68681254 None:intergenic 45.0%
GGAAGACGAAGTTTACAGCG+CGG - chr5.2:68681464-68681483 None:intergenic 50.0%
GTTTACAGCGCGGAACTCAT+CGG - chr5.2:68681454-68681473 None:intergenic 50.0%
CAACGCCTCATCCAAATCCC+TGG - chr5.2:68682382-68682401 None:intergenic 55.0%
TGAACCCTCGTAGCGGTTGA+CGG - chr5.2:68681325-68681344 None:intergenic 55.0%
GTTGACGGCAGCGGAAAGCA+CGG - chr5.2:68681310-68681329 None:intergenic 60.0%
CTCGTAGCGGTTGACGGCAG+CGG - chr5.2:68681319-68681338 None:intergenic 65.0%
GCTGCCGTCAACCGCTACGA+GGG + chr5.2:68681318-68681337 MS.gene29525:CDS 65.0%
! GAAAGCACGGCGCGATGACC+CGG - chr5.2:68681297-68681316 None:intergenic 65.0%
CGCTGCCGTCAACCGCTACG+AGG + chr5.2:68681317-68681336 MS.gene29525:CDS 70.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 68681207 68682542 68681207 ID=MS.gene29525
chr5.2 mRNA 68681207 68682542 68681207 ID=MS.gene29525.t1;Parent=MS.gene29525
chr5.2 exon 68681207 68681467 68681207 ID=MS.gene29525.t1.exon1;Parent=MS.gene29525.t1
chr5.2 CDS 68681207 68681467 68681207 ID=cds.MS.gene29525.t1;Parent=MS.gene29525.t1
chr5.2 exon 68681695 68682038 68681695 ID=MS.gene29525.t1.exon2;Parent=MS.gene29525.t1
chr5.2 CDS 68681695 68682038 68681695 ID=cds.MS.gene29525.t1;Parent=MS.gene29525.t1
chr5.2 exon 68682383 68682542 68682383 ID=MS.gene29525.t1.exon3;Parent=MS.gene29525.t1
chr5.2 CDS 68682383 68682542 68682383 ID=cds.MS.gene29525.t1;Parent=MS.gene29525.t1
Gene Sequence

>MS.gene29525

ATGGCGTTCAATTCAATCCTTCGTTCCAAGTCAAGCACTTTCCTTAGGGCTTTTTCTTCTGCGACTCAATTGATCAGAAAAACTCAACCGGGTCATCGCGCCGTGCTTTCCGCTGCCGTCAACCGCTACGAGGGTTCATTTGTTCCTACGTTTCACTTTTCTTCTGAAGCTGTCAAAAACGAACCCAACTCCGATGAGACTTTTCTCCGTTTAATTGAATCGAAAATCACTTGTGCTCAGGAAACCGATGAGTTCCGCGCTGTAAACTTCGTCTTCCTTAATTTACTAGACTCATGATTGTAGTAATAGAAACAATGTTTTTCTTTTTAATTTCATTAGCTAGACACAATTTTGAACTTATACCTTATAAGCTGGTATGATTAAAAAAGACCCATTTCGTAATGGTATGAAAATTTGAATTTGGTTGTTAATTATGATAATTATTATTATGTTGTGAAATGTTGAAAATTTGATTTTGGTTGATATAGGGTGAGGAAGTTCCGAGCAATTTCCCATTTAAGATAGTTGATAATCCAGGAAATCAGACAATAACACTTAAAAGGACTTATCAAGGTGAAGAAATTCAGGTTGAGATTATGATTTTTAATTTGGTTCCTGGTGAAGAACATGATAATCATCAAAAGGATGATAAGGATGATGAGAGTGAGAGAGCAACTCAATCAAGCATTCCACTTTCAGTCAAGGTTTCTAAGAAGGATGGGACCTCTTTGAAATTCAAATGTGTTGCTTACCCAGATGAGATGGTTATTCGCTGCTTGTTTATTAAGAATCGTGATGAACAGATCCGCAGCTGCTTGTTGCAAGATTTTCAGTATGTACCTCGTTCTGATTATTTTATTCTGTTTATAAATATGTGCATTCAATATTTGAAACCGGGGTTACATCAGTGACCATATCATAGCAGCTATAGTGGTGCGCTATAGCACCTTTGCATAGCGGAGTTTGAACAAATAACTATTTTCCGCGATTTGAAATTGAGATTGGGTGGTGTTGCTAACCTGTACTGCTTGGTTGTAGAGACATGAAAAATATTGATGTTGCAGTTCAGAATCAGATTGGGATTTTGGAGCTTTTTGTAAAACCCTGTTTGTATTACTTTCAATTAATGTTGTAGCTTATACATTGTTTGATTGAGATTCTGCCATTTTTTTCCAGGGATTTGGATGAGGCGTTGCAAAAGTCATTCCACAAGTACTTAGAAATAAGAGGAATCAAACCAAGCACAGTAAATTTCTTGCAAGAGTACATGATCAACAGGAAAAGTAGAGACTACTTGGTGTGGTTGAATAAGCTCAAGAATTTCATTAAAGCATGA
Protein sequence

>MS.gene29525.t1

MAFNSILRSKSSTFLRAFSSATQLIRKTQPGHRAVLSAAVNRYEGSFVPTFHFSSEAVKNEPNSDETFLRLIESKITCAQETDEFRAGEEVPSNFPFKIVDNPGNQTITLKRTYQGEEIQVEIMIFNLVPGEEHDNHQKDDKDDESERATQSSIPLSVKVSKKDGTSLKFKCVAYPDEMVIRCLFIKNRDEQIRSCLLQDFQDLDEALQKSFHKYLEIRGIKPSTVNFLQEYMINRKSRDYLVWLNKLKNFIKA