AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene59232

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene59232.t1 MTR_5g080880 81.641 256 42 3 1 253 1 254 2.33e-138 392
MS.gene59232.t1 MTR_5g080870 68.898 254 45 5 1 254 1 220 1.09e-112 327
MS.gene59232.t1 MTR_7g063520 42.629 251 122 6 8 253 20 253 2.30e-58 186
MS.gene59232.t1 MTR_4g006560 32.075 159 100 3 97 253 83 235 1.40e-22 93.2
MS.gene59232.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.gene59232.t1 AT5G05990 37.879 264 141 6 5 253 3 258 4.67e-54 175
MS.gene59232.t1 AT3G55605 41.328 271 127 9 1 253 1 257 1.53e-51 169
MS.gene59232.t1 AT2G39795 43.077 195 102 3 63 253 60 249 2.63e-49 163
MS.gene59232.t1 AT5G02050 36.803 269 151 6 1 253 1 266 6.36e-43 147
MS.gene59232.t1 AT2G39790 30.172 232 144 4 31 254 19 240 6.39e-28 107
MS.gene59232.t1 AT1G15870 29.255 188 120 5 69 253 63 240 1.59e-20 87.8
MS.gene59232.t1 AT1G80720 30.120 166 104 5 92 253 31 188 5.90e-16 74.3
MS.gene59232.t1 AT1G80720 30.120 166 104 5 92 253 83 240 9.47e-16 74.7
MS.gene59232.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:-68694671 None:intergenic
AGTGTTATTGTCTGATTTCC+TGG 0.252098 5.2:-68694692 None:intergenic
ATCAGACAATAACACTTAAA+AGG 0.289378 5.2:+68694699 MS.gene59232:CDS
TTATCAAGGTGAAGAAATTC+AGG 0.325526 5.2:+68694724 MS.gene59232:CDS
CCAAGTCAAGCACTTTCCTT+AGG 0.334931 5.2:+68694184 MS.gene59232:CDS
TGCAAGAAATTTACTGTGCT+TGG 0.359052 5.2:-68695396 None:intergenic
CAGCGAATAACCATCTCATC+TGG 0.375769 5.2:-68694911 None:intergenic
TTAGAAACCTTGACTGAAAG+TGG 0.404401 5.2:-68694848 None:intergenic
CTCTTATTTCTAAGTACTTG+TGG 0.408675 5.2:-68695365 None:intergenic
TGCAAGAGTACATGATCAAC+AGG 0.410602 5.2:+68695415 MS.gene59232:CDS
TTCAGTCAAGGTTTCTAAGA+AGG 0.418352 5.2:+68694853 MS.gene59232:CDS
CACAAGTACTTAGAAATAAG+AGG 0.434165 5.2:+68695366 MS.gene59232:CDS
GATTATCAACTATCTTAAAT+GGG 0.456111 5.2:-68694670 None:intergenic
TAATCATCAAAAGGATGATA+AGG 0.475586 5.2:+68694790 MS.gene59232:CDS
GAGAAAAGTCTCATCGGAGT+TGG 0.476774 5.2:-68694343 None:intergenic
CAGGAAAAGTAGAGACTACT+TGG 0.480599 5.2:+68695434 MS.gene59232:CDS
CAAGTCAAGCACTTTCCTTA+GGG 0.487750 5.2:+68694185 MS.gene59232:CDS
ATCGAAAATCACTTGTGCTC+AGG 0.490320 5.2:+68694377 MS.gene59232:CDS
GTCAAGGTTTCTAAGAAGGA+TGG 0.493043 5.2:+68694857 MS.gene59232:CDS
AGAAAAGTCTCATCGGAGTT+GGG 0.497268 5.2:-68694342 None:intergenic
CTCGTAGCGGTTGACGGCAG+CGG 0.497835 5.2:-68694268 None:intergenic
TTTAAGATAGTTGATAATCC+AGG 0.504200 5.2:+68694674 MS.gene59232:CDS
TGAACCCTCGTAGCGGTTGA+CGG 0.507166 5.2:-68694274 None:intergenic
AGAACATGATAATCATCAAA+AGG 0.514345 5.2:+68694781 MS.gene59232:CDS
ATCTTAAATGGGAAATTGCT+CGG 0.515748 5.2:-68694659 None:intergenic
GAAAGCACGGCGCGATGACC+CGG 0.519271 5.2:-68694246 None:intergenic
ACACTTAAAAGGACTTATCA+AGG 0.527097 5.2:+68694710 MS.gene59232:CDS
AAGCATTCCACTTTCAGTCA+AGG 0.530679 5.2:+68694841 MS.gene59232:CDS
AACACATTTGAATTTCAAAG+AGG 0.535659 5.2:-68694882 None:intergenic
GTTTACAGCGCGGAACTCAT+CGG 0.541419 5.2:-68694403 None:intergenic
CGCTGCCGTCAACCGCTACG+AGG 0.550566 5.2:+68694269 MS.gene59232:CDS
GTTGACGGCAGCGGAAAGCA+CGG 0.551406 5.2:-68694259 None:intergenic
TGATTATCATGTTCTTCACC+AGG 0.551810 5.2:-68694773 None:intergenic
CCTAAGGAAAGTGCTTGACT+TGG 0.566876 5.2:-68694184 None:intergenic
TCAAGGTTTCTAAGAAGGAT+GGG 0.576019 5.2:+68694858 MS.gene59232:CDS
AATCTTGCAACAAGCAGCTG+CGG 0.606350 5.2:-68694964 None:intergenic
AGCGAATAACCATCTCATCT+GGG 0.609542 5.2:-68694910 None:intergenic
TAAACGGAGAAAAGTCTCAT+CGG 0.611707 5.2:-68694349 None:intergenic
GCTGCCGTCAACCGCTACGA+GGG 0.613894 5.2:+68694270 MS.gene59232:CDS
TGTTGCTTACCCAGATGAGA+TGG 0.638083 5.2:+68694901 MS.gene59232:CDS
TCAGAAGAAAAGTGAAACGT+AGG 0.644962 5.2:-68694303 None:intergenic
AAAGTAGAGACTACTTGGTG+TGG 0.647167 5.2:+68695439 MS.gene59232:CDS
AAGTGCTTGACTTGGAACGA+AGG 0.662607 5.2:-68694176 None:intergenic
GAACAAATGAACCCTCGTAG+CGG 0.717050 5.2:-68694281 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATGTTGAAAATTTGATTT+TGG + chr5.2:68694615-68694634 MS.gene59232:intron 15.0%
!!! TGAGATTATGATTTTTAATT+TGG + chr5.2:68694748-68694767 MS.gene59232:CDS 15.0%
!! AATTGAAAGTAATACAAACA+GGG - chr5.2:68695264-68695283 None:intergenic 20.0%
!! ATGGTATGAAAATTTGAATT+TGG + chr5.2:68694560-68694579 MS.gene59232:intron 20.0%
!! GATTATCAACTATCTTAAAT+GGG - chr5.2:68694673-68694692 None:intergenic 20.0%
!! TAATTGAAAGTAATACAAAC+AGG - chr5.2:68695265-68695284 None:intergenic 20.0%
!!! AATTTGATTTTGGTTGATAT+AGG + chr5.2:68694625-68694644 MS.gene59232:intron 20.0%
!!! ATTTGATTTTGGTTGATATA+GGG + chr5.2:68694626-68694645 MS.gene59232:intron 20.0%
!!! TGATTTTCGATTCAATTAAA+CGG - chr5.2:68694368-68694387 None:intergenic 20.0%
! AACACATTTGAATTTCAAAG+AGG - chr5.2:68694885-68694904 None:intergenic 25.0%
! AGAACATGATAATCATCAAA+AGG + chr5.2:68694781-68694800 MS.gene59232:CDS 25.0%
! AGAATAAAATAATCAGAACG+AGG - chr5.2:68695001-68695020 None:intergenic 25.0%
! ATCAGACAATAACACTTAAA+AGG + chr5.2:68694699-68694718 MS.gene59232:CDS 25.0%
! ATCATGAGTCTAGTAAATTA+AGG - chr5.2:68694437-68694456 None:intergenic 25.0%
! GGATTATCAACTATCTTAAA+TGG - chr5.2:68694674-68694693 None:intergenic 25.0%
! TAATCATCAAAAGGATGATA+AGG + chr5.2:68694790-68694809 MS.gene59232:CDS 25.0%
! TTTAATCATACCAGCTTATA+AGG - chr5.2:68694524-68694543 None:intergenic 25.0%
!! ATTTTCATACCATTACGAAA+TGG - chr5.2:68694553-68694572 None:intergenic 25.0%
!! TTTTCATACCATTACGAAAT+GGG - chr5.2:68694552-68694571 None:intergenic 25.0%
!!! ATGATTTTTAATTTGGTTCC+TGG + chr5.2:68694755-68694774 MS.gene59232:CDS 25.0%
!!! TTTAAGATAGTTGATAATCC+AGG + chr5.2:68694674-68694693 MS.gene59232:CDS 25.0%
AAAAAAGACCCATTTCGTAA+TGG + chr5.2:68694541-68694560 MS.gene59232:intron 30.0%
ACACTTAAAAGGACTTATCA+AGG + chr5.2:68694710-68694729 MS.gene59232:CDS 30.0%
ATCTTAAATGGGAAATTGCT+CGG - chr5.2:68694662-68694681 None:intergenic 30.0%
ATTGATCAGAAAAACTCAAC+CGG + chr5.2:68694227-68694246 MS.gene59232:CDS 30.0%
CACAAGTACTTAGAAATAAG+AGG + chr5.2:68695366-68695385 MS.gene59232:CDS 30.0%
TGAACTTATACCTTATAAGC+TGG + chr5.2:68694511-68694530 MS.gene59232:intron 30.0%
TTATCAAGGTGAAGAAATTC+AGG + chr5.2:68694724-68694743 MS.gene59232:CDS 30.0%
! GTGCATTCAATATTTGAAAC+CGG + chr5.2:68695033-68695052 MS.gene59232:intron 30.0%
! TGCATTCAATATTTGAAACC+GGG + chr5.2:68695034-68695053 MS.gene59232:intron 30.0%
!! CTCTTATTTCTAAGTACTTG+TGG - chr5.2:68695368-68695387 None:intergenic 30.0%
CCAATCTCAATTTCAAATCG+CGG - chr5.2:68695144-68695163 None:intergenic 35.0%
TAAACGGAGAAAAGTCTCAT+CGG - chr5.2:68694352-68694371 None:intergenic 35.0%
TCAGAAGAAAAGTGAAACGT+AGG - chr5.2:68694306-68694325 None:intergenic 35.0%
TCCAAATCCCTGGAAAAAAA+TGG - chr5.2:68695324-68695343 None:intergenic 35.0%
TGATTATCATGTTCTTCACC+AGG - chr5.2:68694776-68694795 None:intergenic 35.0%
TGCAAGAAATTTACTGTGCT+TGG - chr5.2:68695399-68695418 None:intergenic 35.0%
TTAGAAACCTTGACTGAAAG+TGG - chr5.2:68694851-68694870 None:intergenic 35.0%
TTGATCAGAAAAACTCAACC+GGG + chr5.2:68694228-68694247 MS.gene59232:CDS 35.0%
TTGCAGTTCAGAATCAGATT+GGG + chr5.2:68695217-68695236 MS.gene59232:intron 35.0%
! AGTGTTATTGTCTGATTTCC+TGG - chr5.2:68694695-68694714 None:intergenic 35.0%
! CGCGATTTGAAATTGAGATT+GGG + chr5.2:68695142-68695161 MS.gene59232:intron 35.0%
! GATTTGAAATTGAGATTGGG+TGG + chr5.2:68695145-68695164 MS.gene59232:intron 35.0%
! GCATTCAATATTTGAAACCG+GGG + chr5.2:68695035-68695054 MS.gene59232:intron 35.0%
! TCAAGGTTTCTAAGAAGGAT+GGG + chr5.2:68694858-68694877 MS.gene59232:CDS 35.0%
! TCAGAATCAGATTGGGATTT+TGG + chr5.2:68695224-68695243 MS.gene59232:intron 35.0%
! TTCAGTCAAGGTTTCTAAGA+AGG + chr5.2:68694853-68694872 MS.gene59232:CDS 35.0%
!!! AGATTCTGCCATTTTTTTCC+AGG + chr5.2:68695313-68695332 MS.gene59232:intron 35.0%
!!! ATTTTGGTTGATATAGGGTG+AGG + chr5.2:68694631-68694650 MS.gene59232:intron 35.0%
!!! GATTCTGCCATTTTTTTCCA+GGG + chr5.2:68695314-68695333 MS.gene59232:intron 35.0%
AAGCATTCCACTTTCAGTCA+AGG + chr5.2:68694841-68694860 MS.gene59232:CDS 40.0%
AGAAAAGTCTCATCGGAGTT+GGG - chr5.2:68694345-68694364 None:intergenic 40.0%
AGCGAATAACCATCTCATCT+GGG - chr5.2:68694913-68694932 None:intergenic 40.0%
ATCGAAAATCACTTGTGCTC+AGG + chr5.2:68694377-68694396 MS.gene59232:CDS 40.0%
CAAGTCAAGCACTTTCCTTA+GGG + chr5.2:68694185-68694204 MS.gene59232:CDS 40.0%
CAGGAAAAGTAGAGACTACT+TGG + chr5.2:68695434-68695453 MS.gene59232:CDS 40.0%
CCACTATAGCTGCTATGATA+TGG - chr5.2:68695073-68695092 None:intergenic 40.0%
CCATATCATAGCAGCTATAG+TGG + chr5.2:68695070-68695089 MS.gene59232:intron 40.0%
GTTGCAGTTCAGAATCAGAT+TGG + chr5.2:68695216-68695235 MS.gene59232:intron 40.0%
! AAAGTAGAGACTACTTGGTG+TGG + chr5.2:68695439-68695458 MS.gene59232:CDS 40.0%
! CCGCGATTTGAAATTGAGAT+TGG + chr5.2:68695141-68695160 MS.gene59232:intron 40.0%
! GTCAAGGTTTCTAAGAAGGA+TGG + chr5.2:68694857-68694876 MS.gene59232:CDS 40.0%
! TGCAAGAGTACATGATCAAC+AGG + chr5.2:68695415-68695434 MS.gene59232:CDS 40.0%
! TTTTTCCAGGGATTTGGATG+AGG + chr5.2:68695326-68695345 MS.gene59232:intron 40.0%
!!! GCCATTTTTTTCCAGGGATT+TGG + chr5.2:68695320-68695339 MS.gene59232:intron 40.0%
AATCTTGCAACAAGCAGCTG+CGG - chr5.2:68694967-68694986 None:intergenic 45.0%
CAGCGAATAACCATCTCATC+TGG - chr5.2:68694914-68694933 None:intergenic 45.0%
CCAAGTCAAGCACTTTCCTT+AGG + chr5.2:68694184-68694203 MS.gene59232:CDS 45.0%
GAACAAATGAACCCTCGTAG+CGG - chr5.2:68694284-68694303 None:intergenic 45.0%
GAGAAAAGTCTCATCGGAGT+TGG - chr5.2:68694346-68694365 None:intergenic 45.0%
GCTATAGCACCTTTGCATAG+CGG + chr5.2:68695096-68695115 MS.gene59232:intron 45.0%
GTTCAAACTCCGCTATGCAA+AGG - chr5.2:68695108-68695127 None:intergenic 45.0%
TATGGTCACTGATGTAACCC+CGG - chr5.2:68695055-68695074 None:intergenic 45.0%
TCGCAGAAGAAAAAGCCCTA+AGG - chr5.2:68694203-68694222 None:intergenic 45.0%
TCTCTACAACCAAGCAGTAC+AGG - chr5.2:68695180-68695199 None:intergenic 45.0%
TGTTGCTAACCTGTACTGCT+TGG + chr5.2:68695168-68695187 MS.gene59232:intron 45.0%
! TGTTGCTTACCCAGATGAGA+TGG + chr5.2:68694901-68694920 MS.gene59232:CDS 45.0%
!! AAGTGCTTGACTTGGAACGA+AGG - chr5.2:68694179-68694198 None:intergenic 45.0%
!! CCTAAGGAAAGTGCTTGACT+TGG - chr5.2:68694187-68694206 None:intergenic 45.0%
GGAAGACGAAGTTTACAGCG+CGG - chr5.2:68694416-68694435 None:intergenic 50.0%
GTTTACAGCGCGGAACTCAT+CGG - chr5.2:68694406-68694425 None:intergenic 50.0%
CAACGCCTCATCCAAATCCC+TGG - chr5.2:68695334-68695353 None:intergenic 55.0%
TGAACCCTCGTAGCGGTTGA+CGG - chr5.2:68694277-68694296 None:intergenic 55.0%
GTTGACGGCAGCGGAAAGCA+CGG - chr5.2:68694262-68694281 None:intergenic 60.0%
CTCGTAGCGGTTGACGGCAG+CGG - chr5.2:68694271-68694290 None:intergenic 65.0%
GCTGCCGTCAACCGCTACGA+GGG + chr5.2:68694270-68694289 MS.gene59232:CDS 65.0%
! GAAAGCACGGCGCGATGACC+CGG - chr5.2:68694249-68694268 None:intergenic 65.0%
CGCTGCCGTCAACCGCTACG+AGG + chr5.2:68694269-68694288 MS.gene59232:CDS 70.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 68694159 68695494 68694159 ID=MS.gene59232
chr5.2 mRNA 68694159 68695494 68694159 ID=MS.gene59232.t1;Parent=MS.gene59232
chr5.2 exon 68694159 68694419 68694159 ID=MS.gene59232.t1.exon1;Parent=MS.gene59232.t1
chr5.2 CDS 68694159 68694419 68694159 ID=cds.MS.gene59232.t1;Parent=MS.gene59232.t1
chr5.2 exon 68694647 68694990 68694647 ID=MS.gene59232.t1.exon2;Parent=MS.gene59232.t1
chr5.2 CDS 68694647 68694990 68694647 ID=cds.MS.gene59232.t1;Parent=MS.gene59232.t1
chr5.2 exon 68695335 68695494 68695335 ID=MS.gene59232.t1.exon3;Parent=MS.gene59232.t1
chr5.2 CDS 68695335 68695494 68695335 ID=cds.MS.gene59232.t1;Parent=MS.gene59232.t1
Gene Sequence

>MS.gene59232

ATGGCGTTCAATTCAATCCTTCGTTCCAAGTCAAGCACTTTCCTTAGGGCTTTTTCTTCTGCGACTCAATTGATCAGAAAAACTCAACCGGGTCATCGCGCCGTGCTTTCCGCTGCCGTCAACCGCTACGAGGGTTCATTTGTTCCTACGTTTCACTTTTCTTCTGAAGCTGTCAAAAACGAACCCAACTCCGATGAGACTTTTCTCCGTTTAATTGAATCGAAAATCACTTGTGCTCAGGAAACCGATGAGTTCCGCGCTGTAAACTTCGTCTTCCTTAATTTACTAGACTCATGATTGTAGTAATAGAAACAATGTTTTTCTTTTTAATTTCATTAGCTAGACACAATTTTGAACTTATACCTTATAAGCTGGTATGATTAAAAAAGACCCATTTCGTAATGGTATGAAAATTTGAATTTGGTTGTTAATTATGATAATTATTATTATGTTGTGAAATGTTGAAAATTTGATTTTGGTTGATATAGGGTGAGGAAGTTCCGAGCAATTTCCCATTTAAGATAGTTGATAATCCAGGAAATCAGACAATAACACTTAAAAGGACTTATCAAGGTGAAGAAATTCAGGTTGAGATTATGATTTTTAATTTGGTTCCTGGTGAAGAACATGATAATCATCAAAAGGATGATAAGGATGATGAGAGTGAGAGAGCAACTCAATCAAGCATTCCACTTTCAGTCAAGGTTTCTAAGAAGGATGGGACCTCTTTGAAATTCAAATGTGTTGCTTACCCAGATGAGATGGTTATTCGCTGCTTGTTTATTAAGAATCGTGATGAACAGATCCGCAGCTGCTTGTTGCAAGATTTTCAGTATGTACCTCGTTCTGATTATTTTATTCTGTTTATAAATATGTGCATTCAATATTTGAAACCGGGGTTACATCAGTGACCATATCATAGCAGCTATAGTGGTGCGCTATAGCACCTTTGCATAGCGGAGTTTGAACAAATAACTATTTTCCGCGATTTGAAATTGAGATTGGGTGGTGTTGCTAACCTGTACTGCTTGGTTGTAGAGACATGAAAAATATTGATGTTGCAGTTCAGAATCAGATTGGGATTTTGGAGCTTTTTGTAAAACCCTGTTTGTATTACTTTCAATTAATGTTGTAGCTTATACATTGTTTGATTGAGATTCTGCCATTTTTTTCCAGGGATTTGGATGAGGCGTTGCAAAAGTCATTCCACAAGTACTTAGAAATAAGAGGAATCAAACCAAGCACAGTAAATTTCTTGCAAGAGTACATGATCAACAGGAAAAGTAGAGACTACTTGGTGTGGTTGAATAAGCTCAAGAATTTCATTAAAGCATGA
Protein sequence

>MS.gene59232.t1

MAFNSILRSKSSTFLRAFSSATQLIRKTQPGHRAVLSAAVNRYEGSFVPTFHFSSEAVKNEPNSDETFLRLIESKITCAQETDEFRAGEEVPSNFPFKIVDNPGNQTITLKRTYQGEEIQVEIMIFNLVPGEEHDNHQKDDKDDESERATQSSIPLSVKVSKKDGTSLKFKCVAYPDEMVIRCLFIKNRDEQIRSCLLQDFQDLDEALQKSFHKYLEIRGIKPSTVNFLQEYMINRKSRDYLVWLNKLKNFIKA