AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004417

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004417.t1 MTR_0010s0370 71.111 180 52 0 1 180 1 180 3.66e-92 270
MS.gene004417.t1 MTR_0010s0350 71.111 180 52 0 1 180 1 180 3.66e-92 270
MS.gene004417.t1 MTR_1g036720 72.222 108 30 0 1 108 1 108 1.16e-54 172
MS.gene004417.t1 MTR_1g036710 50.877 114 22 1 132 245 1 80 5.16e-29 112
MS.gene004417.t1 MTR_6g033215 30.952 168 116 0 32 199 127 294 1.41e-28 110
MS.gene004417.t1 MTR_7g089990 47.872 94 47 1 118 209 100 193 1.28e-20 87.8
MS.gene004417.t1 MTR_3g053920 31.928 166 94 3 4 169 8 154 3.61e-20 87.8
MS.gene004417.t1 MTR_2g061500 33.884 121 78 1 7 127 11 129 4.03e-16 73.6
MS.gene004417.t1 MTR_3g024240 37.190 121 74 2 82 200 55 175 1.03e-15 73.9
MS.gene004417.t1 MTR_4g103530 38.202 89 55 0 57 145 5 93 2.84e-15 72.8
MS.gene004417.t1 MTR_7g106180 28.966 145 96 2 34 175 26 166 2.43e-14 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004417.t1 AT2G17920 26.512 215 150 2 4 215 9 218 3.65e-21 91.3
MS.gene004417.t1 AT3G57587 26.977 215 149 2 4 215 9 218 1.03e-20 90.5
MS.gene004417.t1 AT3G31430 23.944 213 158 1 3 215 103 311 1.56e-20 89.7
MS.gene004417.t1 AT2G41590 25.943 212 155 1 4 215 9 218 2.16e-20 89.7
MS.gene004417.t1 AT5G18636 26.291 213 153 3 4 215 9 218 9.43e-19 85.1
MS.gene004417.t1 AT5G25200 26.291 213 153 3 4 215 9 218 1.02e-18 85.1
MS.gene004417.t1 AT2G02103 26.291 213 153 3 4 215 9 218 1.19e-18 85.1
MS.gene004417.t1 AT5G36228 23.246 228 165 2 3 226 8 229 1.34e-18 84.7
MS.gene004417.t1 AT2G13450 23.502 217 154 2 4 215 9 218 5.86e-18 83.2
MS.gene004417.t1 AT3G47920 28.472 144 95 2 75 215 9 147 6.36e-14 70.9
MS.gene004417.t1 AT2G17905 27.976 168 110 6 3 166 8 168 1.34e-12 65.1
MS.gene004417.t1 AT2G13510 25.568 176 123 2 4 176 9 179 2.28e-12 66.2
MS.gene004417.t1 AT4G02000 25.714 140 92 2 81 215 6 138 4.11e-12 65.5
MS.gene004417.t1 AT2G13500 24.299 214 153 3 4 214 9 216 6.89e-12 65.1

Find 65 sgRNAs with CRISPR-Local

Find 78 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTCACTCAAGGAAAGATTT+TGG 0.193818 2.3:+67309527 None:intergenic
GTCCTTTCTTGAGAATTCTT+TGG 0.257282 2.3:+67309290 None:intergenic
AAAGATATAGCAAATTATAT+TGG 0.289746 2.3:-67309127 MS.gene004417:CDS
TGGAAAAGATTGAAACATTC+TGG 0.297865 2.3:-67309390 MS.gene004417:CDS
AAGATATAGCAAATTATATT+GGG 0.311021 2.3:-67309126 MS.gene004417:CDS
CACAACACCGGAGGAGGAAG+GGG 0.318322 2.3:-67308821 MS.gene004417:CDS
CTTGACTTCATGCCAGAAAA+AGG 0.328446 2.3:-67309238 MS.gene004417:CDS
CTGATGACGGCACAAGACTA+TGG 0.332428 2.3:-67308871 MS.gene004417:CDS
CGCCGCTAGCTTCTGAATTC+CGG 0.340329 2.3:+67308793 None:intergenic
GACCCTCGCCTCTGTCTTGT+AGG 0.359953 2.3:-67309454 MS.gene004417:CDS
CATGTATGTTCTGAGATAGT+TGG 0.368459 2.3:+67309072 None:intergenic
AAAGTTCAAATACGAGCGTC+TGG 0.379441 2.3:-67308966 MS.gene004417:CDS
TGAGAATTCTTTGGAGGTCT+AGG 0.380201 2.3:+67309299 None:intergenic
TGTTACTATTGCGGCTGCTT+AGG 0.383883 2.3:-67308935 MS.gene004417:CDS
CTTTCTTGAGAATTCTTTGG+AGG 0.429302 2.3:+67309293 None:intergenic
GCACAACACCGGAGGAGGAA+GGG 0.433388 2.3:-67308822 MS.gene004417:CDS
GGTCTAGGTGATGGTTGAAT+TGG 0.452367 2.3:+67309314 None:intergenic
GTACTTTGATAACCACCTCT+TGG 0.453645 2.3:-67309263 MS.gene004417:CDS
CGGCTGCTTAGGACATATAG+AGG 0.455299 2.3:-67308924 MS.gene004417:CDS
AGCACAACACCGGAGGAGGA+AGG 0.456576 2.3:-67308823 MS.gene004417:CDS
GGAAATTTCTGTTACTATTG+CGG 0.473358 2.3:-67308944 MS.gene004417:CDS
TTCTTTGGAGGTCTAGGTGA+TGG 0.494027 2.3:+67309305 None:intergenic
TGTCTGTCCACTCGTAGCTC+TGG 0.494136 2.3:+67308845 None:intergenic
TATTCGCTCTTACATGATGA+TGG 0.497534 2.3:-67309410 MS.gene004417:CDS
CTCCAAAGAATTCTCAAGAA+AGG 0.506456 2.3:-67309292 MS.gene004417:CDS
TGATGACGGCACAAGACTAT+GGG 0.506567 2.3:-67308870 MS.gene004417:CDS
ATCAGTTTCAGATGCAAACA+AGG 0.512705 2.3:-67308754 MS.gene004417:CDS
AAAATTCAAGAGATCGAGCC+AGG 0.513249 2.3:-67309349 MS.gene004417:CDS
AGACAGCACAACACCGGAGG+AGG 0.527402 2.3:-67308827 MS.gene004417:CDS
ATCATCATGTAAGAGCGAAT+AGG 0.527476 2.3:+67309412 None:intergenic
TTCATCATCTTCGTCACTCA+AGG 0.547309 2.3:+67309516 None:intergenic
GGTTTCATGACAGAGAAAGT+TGG 0.553601 2.3:-67309151 MS.gene004417:CDS
TGAAACTGATGCTGAAACGC+TGG 0.560635 2.3:+67308767 None:intergenic
ACAACACCGGAGGAGGAAGG+GGG 0.563226 2.3:-67308820 MS.gene004417:CDS
ACTTTCTCTGTCATGAAACC+TGG 0.564600 2.3:+67309154 None:intergenic
CGAGGGTCAACAGATTGTGC+AGG 0.567187 2.3:+67309469 None:intergenic
CAAGTCCACAATATTCCACC+AGG 0.581515 2.3:-67309172 MS.gene004417:CDS
TGTGCCGTCATCAGACTCGT+TGG 0.581519 2.3:+67308880 None:intergenic
ACATTCTGGAATCCTGTCAA+AGG 0.589990 2.3:-67309376 MS.gene004417:CDS
ATTGTGGACTTGTATCCAGA+AGG 0.590531 2.3:+67309183 None:intergenic
AGATTGTGCAGGTAATTCAT+CGG 0.592821 2.3:+67309480 None:intergenic
AGATATAGCAAATTATATTG+GGG 0.594767 2.3:-67309125 MS.gene004417:CDS
TTCTCTGTCATGAAACCTGG+TGG 0.595858 2.3:+67309157 None:intergenic
GGCCTACAAGACAGAGGCGA+GGG 0.598187 2.3:+67309452 None:intergenic
TGAAACCTGGTGGAATATTG+TGG 0.600443 2.3:+67309167 None:intergenic
TATTCCAACGAGTCTGATGA+CGG 0.608340 2.3:-67308884 MS.gene004417:CDS
AAGTTCAAATACGAGCGTCT+GGG 0.608367 2.3:-67308965 MS.gene004417:CDS
TTGTGGACTTGTATCCAGAA+GGG 0.618904 2.3:+67309184 None:intergenic
GTGGACAGACAGCACAACAC+CGG 0.621246 2.3:-67308833 MS.gene004417:CDS
GGCCGGAATTCAGAAGCTAG+CGG 0.622168 2.3:-67308795 MS.gene004417:CDS
GACAGACAGCACAACACCGG+AGG 0.631280 2.3:-67308830 MS.gene004417:CDS
GAATTCTCAAGAAAGGACCT+TGG 0.641093 2.3:-67309285 MS.gene004417:CDS
AATTGGAAGGTGTATAGACC+TGG 0.641746 2.3:+67309331 None:intergenic
CGGCCTACAAGACAGAGGCG+AGG 0.659419 2.3:+67309451 None:intergenic
TCAGTTTCAGATGCAAACAA+GGG 0.662707 2.3:-67308753 MS.gene004417:CDS
TGAAGTCAAGGACCAAGAGG+TGG 0.664947 2.3:+67309251 None:intergenic
GATGACGGCACAAGACTATG+GGG 0.665680 2.3:-67308869 MS.gene004417:CDS
TAGGTCGATTTGTGAGAAAG+CGG 0.673154 2.3:+67309431 None:intergenic
GCATGAAGTCAAGGACCAAG+AGG 0.676582 2.3:+67309248 None:intergenic
GGCTGCTTAGGACATATAGA+GGG 0.678201 2.3:-67308923 MS.gene004417:CDS
TAGGTGATGGTTGAATTGGA+AGG 0.679656 2.3:+67309318 None:intergenic
AACTGATGCTGAAACGCTGG+CGG 0.694912 2.3:+67308770 None:intergenic
ATGACGGCACAAGACTATGG+GGG 0.722221 2.3:-67308868 MS.gene004417:CDS
AGGTGGTTATCAAAGTACCA+AGG 0.724627 2.3:+67309268 None:intergenic
GAAAGCGGCCTACAAGACAG+AGG 0.744498 2.3:+67309446 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGATATAGCAAATTATAT+TGG - chr2.3:67309159-67309178 MS.gene004417:CDS 15.0%
!! AAGATATAGCAAATTATATT+GGG - chr2.3:67309160-67309179 MS.gene004417:CDS 15.0%
!! AGATATAGCAAATTATATTG+GGG - chr2.3:67309161-67309180 MS.gene004417:CDS 20.0%
GGAAATTTCTGTTACTATTG+CGG - chr2.3:67309342-67309361 MS.gene004417:CDS 30.0%
TGGAAAAGATTGAAACATTC+TGG - chr2.3:67308896-67308915 MS.gene004417:CDS 30.0%
!!! ATTTTTTTCTGACGCTTCAA+AGG + chr2.3:67309270-67309289 None:intergenic 30.0%
AGATTGTGCAGGTAATTCAT+CGG + chr2.3:67308809-67308828 None:intergenic 35.0%
AGCGTCAGAAAAAAATCAAG+AGG - chr2.3:67309274-67309293 MS.gene004417:CDS 35.0%
ATCAGTTTCAGATGCAAACA+AGG - chr2.3:67309532-67309551 MS.gene004417:CDS 35.0%
ATCATCATGTAAGAGCGAAT+AGG + chr2.3:67308877-67308896 None:intergenic 35.0%
CAGAAAAAAATCAAGAGGCA+GGG - chr2.3:67309279-67309298 MS.gene004417:CDS 35.0%
CTCCAAAGAATTCTCAAGAA+AGG - chr2.3:67308994-67309013 MS.gene004417:CDS 35.0%
CTTTCTTGAGAATTCTTTGG+AGG + chr2.3:67308996-67309015 None:intergenic 35.0%
GTCCTTTCTTGAGAATTCTT+TGG + chr2.3:67308999-67309018 None:intergenic 35.0%
TATTCGCTCTTACATGATGA+TGG - chr2.3:67308876-67308895 MS.gene004417:CDS 35.0%
TCAGAAAAAAATCAAGAGGC+AGG - chr2.3:67309278-67309297 MS.gene004417:CDS 35.0%
TCAGTTTCAGATGCAAACAA+GGG - chr2.3:67309533-67309552 MS.gene004417:CDS 35.0%
! CAAGGAAAGATTTTGGATTG+TGG + chr2.3:67308755-67308774 None:intergenic 35.0%
!! CATGTATGTTCTGAGATAGT+TGG + chr2.3:67309217-67309236 None:intergenic 35.0%
!! TGAATTTTGATGCCTTTGAC+AGG + chr2.3:67308925-67308944 None:intergenic 35.0%
AAAATTCAAGAGATCGAGCC+AGG - chr2.3:67308937-67308956 MS.gene004417:CDS 40.0%
AAAGTTCAAATACGAGCGTC+TGG - chr2.3:67309320-67309339 MS.gene004417:CDS 40.0%
AAGTTCAAATACGAGCGTCT+GGG - chr2.3:67309321-67309340 MS.gene004417:CDS 40.0%
ACTTTCTCTGTCATGAAACC+TGG + chr2.3:67309135-67309154 None:intergenic 40.0%
ATTGTGGACTTGTATCCAGA+AGG + chr2.3:67309106-67309125 None:intergenic 40.0%
CTTGACTTCATGCCAGAAAA+AGG - chr2.3:67309048-67309067 MS.gene004417:CDS 40.0%
GAATTCTCAAGAAAGGACCT+TGG - chr2.3:67309001-67309020 MS.gene004417:CDS 40.0%
GGTTTCATGACAGAGAAAGT+TGG - chr2.3:67309135-67309154 MS.gene004417:CDS 40.0%
TATTCCAACGAGTCTGATGA+CGG - chr2.3:67309402-67309421 MS.gene004417:CDS 40.0%
TGAAACCTGGTGGAATATTG+TGG + chr2.3:67309122-67309141 None:intergenic 40.0%
TTCATCATCTTCGTCACTCA+AGG + chr2.3:67308773-67308792 None:intergenic 40.0%
TTGTGGACTTGTATCCAGAA+GGG + chr2.3:67309105-67309124 None:intergenic 40.0%
! AATTGGAAGGTGTATAGACC+TGG + chr2.3:67308958-67308977 None:intergenic 40.0%
! AGGTGGTTATCAAAGTACCA+AGG + chr2.3:67309021-67309040 None:intergenic 40.0%
! CACTAAATTTTGTGCCCTTC+TGG - chr2.3:67309088-67309107 MS.gene004417:CDS 40.0%
! CGTCACTCAAGGAAAGATTT+TGG + chr2.3:67308762-67308781 None:intergenic 40.0%
! GTACTTTGATAACCACCTCT+TGG - chr2.3:67309023-67309042 MS.gene004417:CDS 40.0%
! TAGGTGATGGTTGAATTGGA+AGG + chr2.3:67308971-67308990 None:intergenic 40.0%
! TGAGAATTCTTTGGAGGTCT+AGG + chr2.3:67308990-67309009 None:intergenic 40.0%
! TGCTCATGCTTACCTTTTTC+TGG + chr2.3:67309063-67309082 None:intergenic 40.0%
!! ACATTCTGGAATCCTGTCAA+AGG - chr2.3:67308910-67308929 MS.gene004417:CDS 40.0%
!! CTTTTTCTGGCATGAAGTCA+AGG + chr2.3:67309050-67309069 None:intergenic 40.0%
!! TAGGTCGATTTGTGAGAAAG+CGG + chr2.3:67308858-67308877 None:intergenic 40.0%
CAAGTCCACAATATTCCACC+AGG - chr2.3:67309114-67309133 MS.gene004417:CDS 45.0%
GGCTGCTTAGGACATATAGA+GGG - chr2.3:67309363-67309382 MS.gene004417:CDS 45.0%
TGAAACTGATGCTGAAACGC+TGG + chr2.3:67309522-67309541 None:intergenic 45.0%
TGTTACTATTGCGGCTGCTT+AGG - chr2.3:67309351-67309370 MS.gene004417:CDS 45.0%
TTCTCTGTCATGAAACCTGG+TGG + chr2.3:67309132-67309151 None:intergenic 45.0%
! GGTCTAGGTGATGGTTGAAT+TGG + chr2.3:67308975-67308994 None:intergenic 45.0%
! TTCTTTGGAGGTCTAGGTGA+TGG + chr2.3:67308984-67309003 None:intergenic 45.0%
!! TGATGACGGCACAAGACTAT+GGG - chr2.3:67309416-67309435 MS.gene004417:CDS 45.0%
AACTGATGCTGAAACGCTGG+CGG + chr2.3:67309519-67309538 None:intergenic 50.0%
ATGACGGCACAAGACTATGG+GGG - chr2.3:67309418-67309437 MS.gene004417:CDS 50.0%
CGGCTGCTTAGGACATATAG+AGG - chr2.3:67309362-67309381 MS.gene004417:CDS 50.0%
GCATGAAGTCAAGGACCAAG+AGG + chr2.3:67309041-67309060 None:intergenic 50.0%
TGAAGTCAAGGACCAAGAGG+TGG + chr2.3:67309038-67309057 None:intergenic 50.0%
! GATGACGGCACAAGACTATG+GGG - chr2.3:67309417-67309436 MS.gene004417:CDS 50.0%
!! CTGATGACGGCACAAGACTA+TGG - chr2.3:67309415-67309434 MS.gene004417:CDS 50.0%
CGAGGGTCAACAGATTGTGC+AGG + chr2.3:67308820-67308839 None:intergenic 55.0%
GAAAGCGGCCTACAAGACAG+AGG + chr2.3:67308843-67308862 None:intergenic 55.0%
GGCCGGAATTCAGAAGCTAG+CGG - chr2.3:67309491-67309510 MS.gene004417:CDS 55.0%
GTGGACAGACAGCACAACAC+CGG - chr2.3:67309453-67309472 MS.gene004417:CDS 55.0%
TGTCTGTCCACTCGTAGCTC+TGG + chr2.3:67309444-67309463 None:intergenic 55.0%
TGTGCCGTCATCAGACTCGT+TGG + chr2.3:67309409-67309428 None:intergenic 55.0%
! CGCCGCTAGCTTCTGAATTC+CGG + chr2.3:67309496-67309515 None:intergenic 55.0%
ACAACACCGGAGGAGGAAGG+GGG - chr2.3:67309466-67309485 MS.gene004417:CDS 60.0%
AGACAGCACAACACCGGAGG+AGG - chr2.3:67309459-67309478 MS.gene004417:CDS 60.0%
AGCACAACACCGGAGGAGGA+AGG - chr2.3:67309463-67309482 MS.gene004417:CDS 60.0%
CACAACACCGGAGGAGGAAG+GGG - chr2.3:67309465-67309484 MS.gene004417:CDS 60.0%
GACAGACAGCACAACACCGG+AGG - chr2.3:67309456-67309475 MS.gene004417:CDS 60.0%
GACCCTCGCCTCTGTCTTGT+AGG - chr2.3:67308832-67308851 MS.gene004417:CDS 60.0%
GCACAACACCGGAGGAGGAA+GGG - chr2.3:67309464-67309483 MS.gene004417:CDS 60.0%
GGCCTACAAGACAGAGGCGA+GGG + chr2.3:67308837-67308856 None:intergenic 60.0%
ATGGGGGCCAGAGCTACGAG+TGG - chr2.3:67309434-67309453 MS.gene004417:CDS 65.0%
CGGCCTACAAGACAGAGGCG+AGG + chr2.3:67308838-67308857 None:intergenic 65.0%
CACCGGAGGAGGAAGGGGGC+TGG - chr2.3:67309470-67309489 MS.gene004417:CDS 75.0%
GGCCAGCCCCCTTCCTCCTC+CGG + chr2.3:67309475-67309494 None:intergenic 75.0%
! GGAGGAGGAAGGGGGCTGGC+CGG - chr2.3:67309474-67309493 MS.gene004417:CDS 75.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 67308748 67309560 67308748 ID=MS.gene004417
chr2.3 mRNA 67308748 67309560 67308748 ID=MS.gene004417.t1;Parent=MS.gene004417
chr2.3 exon 67308748 67309560 67308748 ID=MS.gene004417.t1.exon1;Parent=MS.gene004417.t1
chr2.3 CDS 67308748 67309560 67308748 ID=cds.MS.gene004417.t1;Parent=MS.gene004417.t1
Gene Sequence

>MS.gene004417

ATGGCCACAATCCAAAATCTTTCCTTGAGTGACGAAGATGATGAACTCATAATACAAGCCGATGAATTACCTGCACAATCTGTTGACCCTCGCCTCTGTCTTGTAGGCCGCTTTCTCACAAATCGACCTATTCGCTCTTACATGATGATGGAAAAGATTGAAACATTCTGGAATCCTGTCAAAGGCATCAAAATTCAAGAGATCGAGCCAGGTCTATACACCTTCCAATTCAACCATCACCTAGACCTCCAAAGAATTCTCAAGAAAGGACCTTGGTACTTTGATAACCACCTCTTGGTCCTTGACTTCATGCCAGAAAAAGGTAAGCATGAGCAAGTTGCACTAAATTTTGTGCCCTTCTGGATACAAGTCCACAATATTCCACCAGGTTTCATGACAGAGAAAGTTGGAAAAGATATAGCAAATTATATTGGGGAATTTCTTGAATATGATGACAAAAACAATTCCAACTATCTCAGAACATACATGAAAATTAGAGTTCTGCTCAATGTCACTAAGCCTTTGAAGCGTCAGAAAAAAATCAAGAGGCAGGGAGAAGAAGCAACTTTCATAAAGTTCAAATACGAGCGTCTGGGAAATTTCTGTTACTATTGCGGCTGCTTAGGACATATAGAGGGTTATTGTGAAAAACTTTATTCCAACGAGTCTGATGACGGCACAAGACTATGGGGGCCAGAGCTACGAGTGGACAGACAGCACAACACCGGAGGAGGAAGGGGGCTGGCCGGAATTCAGAAGCTAGCGGCGCCGCCAGCGTTTCAGCATCAGTTTCAGATGCAAACAAGGGATTAA
Protein sequence

>MS.gene004417.t1

MATIQNLSLSDEDDELIIQADELPAQSVDPRLCLVGRFLTNRPIRSYMMMEKIETFWNPVKGIKIQEIEPGLYTFQFNHHLDLQRILKKGPWYFDNHLLVLDFMPEKGKHEQVALNFVPFWIQVHNIPPGFMTEKVGKDIANYIGEFLEYDDKNNSNYLRTYMKIRVLLNVTKPLKRQKKIKRQGEEATFIKFKYERLGNFCYYCGCLGHIEGYCEKLYSNESDDGTRLWGPELRVDRQHNTGGGRGLAGIQKLAAPPAFQHQFQMQTRD