AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene23301

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene23301.t1 MTR_4g070570 97.000 300 9 0 2 301 4 303 0.0 591
MS.gene23301.t1 MTR_4g070590 58.333 300 113 6 8 301 8 301 2.06e-110 322
MS.gene23301.t1 MTR_3g116950 55.814 301 119 7 6 301 5 296 5.81e-102 300
MS.gene23301.t1 MTR_3g116920 56.333 300 121 6 6 301 5 298 2.31e-99 294
MS.gene23301.t1 MTR_4g070540 43.253 289 154 4 16 301 15 296 7.33e-63 201
MS.gene23301.t1 MTR_4g070530 41.176 289 160 4 16 301 15 296 1.03e-59 192
MS.gene23301.t1 MTR_8g074530 34.576 295 182 6 10 300 17 304 1.33e-46 159
MS.gene23301.t1 MTR_5g023550 31.525 295 185 8 11 301 3 284 4.57e-39 139
MS.gene23301.t1 MTR_8g074510 29.655 290 195 5 13 300 5 287 9.91e-39 138
MS.gene23301.t1 MTR_8g074450 32.646 291 185 6 13 299 5 288 1.06e-38 138
MS.gene23301.t1 MTR_5g023290 30.573 314 198 9 1 300 1 308 7.88e-38 136
MS.gene23301.t1 MTR_5g023390 30.847 295 187 8 9 299 2 283 1.69e-37 135
MS.gene23301.t1 MTR_5g023600 31.081 296 185 9 9 299 2 283 6.08e-37 133
MS.gene23301.t1 MTR_5g023370 30.847 295 187 8 9 299 2 283 8.17e-37 133
MS.gene23301.t1 MTR_8g074420 30.479 292 192 6 13 300 5 289 8.24e-37 133
MS.gene23301.t1 MTR_5g023340 30.612 294 189 6 9 299 2 283 1.04e-36 132
MS.gene23301.t1 MTR_5g023350 29.831 295 190 8 9 299 2 283 1.68e-35 129
MS.gene23301.t1 MTR_5g023520 30.872 298 184 11 11 301 3 285 1.70e-35 129
MS.gene23301.t1 MTR_5g023530 30.743 296 190 8 7 299 1 284 2.38e-35 129
MS.gene23301.t1 MTR_5g023470 30.743 296 190 8 7 299 1 284 1.72e-34 127
MS.gene23301.t1 MTR_5g023320 29.966 297 185 10 9 299 2 281 3.02e-34 126
MS.gene23301.t1 MTR_5g023580 29.592 294 192 7 10 298 3 286 5.64e-34 127
MS.gene23301.t1 MTR_8g074380 31.475 305 174 9 4 299 3 281 7.69e-27 107
MS.gene23301.t1 MTR_3g116940 43.307 127 46 1 1 127 1 101 4.12e-24 95.9
MS.gene23301.t1 MTR_5g023650 30.519 308 189 7 9 301 8 305 6.82e-23 96.3
MS.gene23301.t1 MTR_1g037820 32.900 231 126 8 72 301 24 226 8.57e-21 89.4
MS.gene23301.t1 MTR_5g023460 31.633 196 117 6 105 299 11 190 5.58e-19 83.2
MS.gene23301.t1 MTR_3g115150 26.144 306 197 11 9 299 23 314 5.55e-13 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene23301.t1 AT2G17080 40.625 288 137 9 16 301 8 263 5.47e-51 169
MS.gene23301.t1 AT2G17070 38.889 288 142 8 16 301 8 263 7.56e-51 169
MS.gene23301.t1 AT4G35210 39.576 283 131 9 16 298 8 250 1.32e-48 162
MS.gene23301.t1 AT4G35200 39.223 283 135 9 16 298 8 253 1.95e-46 157
MS.gene23301.t1 AT4G35690 34.783 299 163 11 13 301 8 284 3.63e-42 147
MS.gene23301.t1 AT4G35710 31.313 297 173 9 14 301 9 283 5.33e-29 112
MS.gene23301.t1 AT2G17680 29.642 307 168 11 16 300 11 291 8.20e-27 107
MS.gene23301.t1 AT4G35680 29.618 314 196 11 4 301 6 310 2.22e-20 89.7
MS.gene23301.t1 AT4G35720 28.308 325 196 11 7 300 6 324 2.27e-20 89.7
MS.gene23301.t1 AT1G76210 29.555 247 143 6 57 301 9 226 1.93e-19 85.5
MS.gene23301.t1 AT3G51400 29.412 204 130 4 100 300 82 274 8.48e-18 82.0
MS.gene23301.t1 AT4G35660 27.815 302 182 7 9 299 10 286 6.88e-15 73.9
MS.gene23301.t1 AT1G20520 26.506 249 152 6 54 300 6 225 9.10e-13 67.0

Find 49 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAGAACCAATTGGAAAATT+TGG 0.112535 4.3:+34555249 MS.gene23301:CDS
TGAGAAAATTCTTGGCTTCT+AGG 0.199154 4.3:+34554864 MS.gene23301:CDS
ATTTATACAACTAGTGATTA+AGG 0.290293 4.3:-34555354 None:intergenic
AATCGAAACCAAGTAATTAT+TGG 0.313179 4.3:+34555083 MS.gene23301:CDS
GGCCGAGGTGAGAAAATTCT+TGG 0.322610 4.3:+34554856 MS.gene23301:CDS
ACATGATTGCGTCGAAAGTT+TGG 0.329591 4.3:+34554640 MS.gene23301:CDS
TGATGTGATGTTGGACTAAT+AGG 0.335874 4.3:-34554476 None:intergenic
ATTATCTCCTAGCAACAATA+AGG 0.373881 4.3:+34554961 MS.gene23301:CDS
TCAAATTCTCCAAAGCTTTG+AGG 0.381031 4.3:-34554907 None:intergenic
CAATCATTTGCAGAACCAAT+TGG 0.396017 4.3:+34555240 MS.gene23301:CDS
GAAAGCAATCCTCAAAGCTT+TGG 0.399242 4.3:+34554898 MS.gene23301:CDS
CAAAGCTTTGGAGAATTTGA+AGG 0.400637 4.3:+34554910 MS.gene23301:CDS
ACCAAGGACCAATAATTACT+TGG 0.401947 4.3:-34555091 None:intergenic
TCCACGCACGTCAAGAGAAA+TGG 0.417810 4.3:+34554693 MS.gene23301:CDS
ACCAAGTAATTATTGGTCCT+TGG 0.430617 4.3:+34555090 MS.gene23301:CDS
TTTAATCTTTATATCTGGAC+CGG 0.469654 4.3:+34555057 MS.gene23301:CDS
ATCAACTCTTCATCGTTGTT+CGG 0.473180 4.3:+34554590 MS.gene23301:CDS
TTGCTACAGAACACACATCT+AGG 0.484586 4.3:-34554748 None:intergenic
GTCTGTTGTTCAAGGGTTTG+TGG 0.488801 4.3:+34555273 MS.gene23301:CDS
AGTGATCACTCTTTCAATGT+TGG 0.496374 4.3:+34555027 MS.gene23301:CDS
ACAAGGACTTGTTGAGTAAG+AGG 0.502400 4.3:-34554671 None:intergenic
ATTTGGAGTCTGTTGTTCAA+GGG 0.504312 4.3:+34555266 MS.gene23301:CDS
CGAAATGGAGGTGACGGCCG+AGG 0.520093 4.3:+34554841 MS.gene23301:CDS
AAAATTCTTGGCTTCTAGGA+AGG 0.521847 4.3:+34554868 MS.gene23301:CDS
TCTCTTGACGTGCGTGGACA+AGG 0.524756 4.3:-34554688 None:intergenic
TCATGATCCTTATTGTTGCT+AGG 0.526232 4.3:-34554968 None:intergenic
TTGAAGGCTAATGTGAAGAA+AGG 0.526883 4.3:+34554926 MS.gene23301:CDS
GCTAATGTGAAGAAAGGTAA+AGG 0.528831 4.3:+34554932 MS.gene23301:CDS
AATTTGGAGTCTGTTGTTCA+AGG 0.538470 4.3:+34555265 MS.gene23301:CDS
TCCATTTCTCTTGACGTGCG+TGG 0.539554 4.3:-34554694 None:intergenic
CATTGTAGAATGAGAGGGTG+TGG 0.553149 4.3:-34554530 None:intergenic
CGAGGTTGGTGATGTGATGT+TGG 0.563264 4.3:-34554485 None:intergenic
AGGAGGCGAAATGGAGGTGA+CGG 0.564930 4.3:+34554835 MS.gene23301:CDS
ATGAGAGGGTGTGGTTTCGA+TGG 0.575082 4.3:-34554521 None:intergenic
GAAGAGTTGATTGCGTCGAA+AGG 0.582245 4.3:-34554578 None:intergenic
GCTTATGATGCAGAGCAAGA+AGG 0.582612 4.3:+34555120 MS.gene23301:CDS
TCTACAATGCAATCAACACT+TGG 0.582703 4.3:+34554544 MS.gene23301:CDS
AGATGTGTGTTCTGTAGCAA+AGG 0.585332 4.3:+34554751 MS.gene23301:CDS
CATCATAAGCTTTGAAACCA+AGG 0.589484 4.3:-34555107 None:intergenic
AGTGATTAAGGACATTGAGA+AGG 0.590750 4.3:-34555342 None:intergenic
GTGATTAAGGACATTGAGAA+GGG 0.597371 4.3:-34555341 None:intergenic
TTACTTGGTTTCGATTGCGC+CGG 0.602841 4.3:-34555076 None:intergenic
GGTTAGTTTGTTAAGAGACG+TGG 0.607951 4.3:+34555003 MS.gene23301:CDS
TGATTGCATTGTAGAATGAG+AGG 0.610266 4.3:-34554536 None:intergenic
ATCATGTAAAGCTTGTAGAT+CGG 0.622289 4.3:-34554624 None:intergenic
GGATTCTCTAATTCATACGA+AGG 0.644514 4.3:+34554772 MS.gene23301:CDS
TGATGTTGGACTAATAGGAA+TGG 0.654192 4.3:-34554471 None:intergenic
AGATCCGTCTAAAAGCTCAT+CGG 0.663380 4.3:-34554717 None:intergenic
GATTGCATTGTAGAATGAGA+GGG 0.668472 4.3:-34554535 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCACTTTTAATCTTTATATC+TGG + chr4.3:34555052-34555071 MS.gene23301:CDS 20.0%
! AATCGAAACCAAGTAATTAT+TGG + chr4.3:34555083-34555102 MS.gene23301:CDS 25.0%
! TTTAATCTTTATATCTGGAC+CGG + chr4.3:34555057-34555076 MS.gene23301:CDS 25.0%
ATCATGTAAAGCTTGTAGAT+CGG - chr4.3:34554627-34554646 None:intergenic 30.0%
ATTATCTCCTAGCAACAATA+AGG + chr4.3:34554961-34554980 MS.gene23301:CDS 30.0%
ACCAAGGACCAATAATTACT+TGG - chr4.3:34555094-34555113 None:intergenic 35.0%
ACCAAGTAATTATTGGTCCT+TGG + chr4.3:34555090-34555109 MS.gene23301:CDS 35.0%
AGTGATCACTCTTTCAATGT+TGG + chr4.3:34555027-34555046 MS.gene23301:CDS 35.0%
AGTGATTAAGGACATTGAGA+AGG - chr4.3:34555345-34555364 None:intergenic 35.0%
ATCAACTCTTCATCGTTGTT+CGG + chr4.3:34554590-34554609 MS.gene23301:CDS 35.0%
ATTATGCGAAGAAAAAGAGG+AGG + chr4.3:34554818-34554837 MS.gene23301:CDS 35.0%
CAATCATTTGCAGAACCAAT+TGG + chr4.3:34555240-34555259 MS.gene23301:CDS 35.0%
GATTGCATTGTAGAATGAGA+GGG - chr4.3:34554538-34554557 None:intergenic 35.0%
GCAGAACCAATTGGAAAATT+TGG + chr4.3:34555249-34555268 MS.gene23301:CDS 35.0%
GCTAATGTGAAGAAAGGTAA+AGG + chr4.3:34554932-34554951 MS.gene23301:CDS 35.0%
GGATCATGAAAAAGTGACTT+TGG + chr4.3:34554982-34555001 MS.gene23301:CDS 35.0%
GGATTCTCTAATTCATACGA+AGG + chr4.3:34554772-34554791 MS.gene23301:CDS 35.0%
GTGATTAAGGACATTGAGAA+GGG - chr4.3:34555344-34555363 None:intergenic 35.0%
TCAAATTCTCCAAAGCTTTG+AGG - chr4.3:34554910-34554929 None:intergenic 35.0%
TCATGATCCTTATTGTTGCT+AGG - chr4.3:34554971-34554990 None:intergenic 35.0%
TCGATTATGCGAAGAAAAAG+AGG + chr4.3:34554815-34554834 MS.gene23301:CDS 35.0%
TCTACAATGCAATCAACACT+TGG + chr4.3:34554544-34554563 MS.gene23301:CDS 35.0%
TGAGAAAATTCTTGGCTTCT+AGG + chr4.3:34554864-34554883 MS.gene23301:CDS 35.0%
TGATGTGATGTTGGACTAAT+AGG - chr4.3:34554479-34554498 None:intergenic 35.0%
TGATGTTGGACTAATAGGAA+TGG - chr4.3:34554474-34554493 None:intergenic 35.0%
TGATTGCATTGTAGAATGAG+AGG - chr4.3:34554539-34554558 None:intergenic 35.0%
TTGAAGGCTAATGTGAAGAA+AGG + chr4.3:34554926-34554945 MS.gene23301:CDS 35.0%
! AAAATTCTTGGCTTCTAGGA+AGG + chr4.3:34554868-34554887 MS.gene23301:CDS 35.0%
! AATTTGGAGTCTGTTGTTCA+AGG + chr4.3:34555265-34555284 MS.gene23301:CDS 35.0%
! AGCTTTTAGACGGATCTTTA+AGG + chr4.3:34554723-34554742 MS.gene23301:CDS 35.0%
! ATTTGGAGTCTGTTGTTCAA+GGG + chr4.3:34555266-34555285 MS.gene23301:CDS 35.0%
! CAGACTCCAAATTTTCCAAT+TGG - chr4.3:34555258-34555277 None:intergenic 35.0%
!! CAAAGCTTTGGAGAATTTGA+AGG + chr4.3:34554910-34554929 MS.gene23301:CDS 35.0%
!! CATCATAAGCTTTGAAACCA+AGG - chr4.3:34555110-34555129 None:intergenic 35.0%
AAGAAAAAGAGGAGGCGAAA+TGG + chr4.3:34554826-34554845 MS.gene23301:CDS 40.0%
ACATGATTGCGTCGAAAGTT+TGG + chr4.3:34554640-34554659 MS.gene23301:CDS 40.0%
AGATCCGTCTAAAAGCTCAT+CGG - chr4.3:34554720-34554739 None:intergenic 40.0%
AGATGTGTGTTCTGTAGCAA+AGG + chr4.3:34554751-34554770 MS.gene23301:CDS 40.0%
GAAAGCAATCCTCAAAGCTT+TGG + chr4.3:34554898-34554917 MS.gene23301:CDS 40.0%
TTGCTACAGAACACACATCT+AGG - chr4.3:34554751-34554770 None:intergenic 40.0%
! AGCCAAGAATTTTCTCACCT+CGG - chr4.3:34554861-34554880 None:intergenic 40.0%
!! ACAAGGACTTGTTGAGTAAG+AGG - chr4.3:34554674-34554693 None:intergenic 40.0%
!! GGTTAGTTTGTTAAGAGACG+TGG + chr4.3:34555003-34555022 MS.gene23301:CDS 40.0%
AAAAAGAGGAGGCGAAATGG+AGG + chr4.3:34554829-34554848 MS.gene23301:CDS 45.0%
CATTGTAGAATGAGAGGGTG+TGG - chr4.3:34554533-34554552 None:intergenic 45.0%
GCTTATGATGCAGAGCAAGA+AGG + chr4.3:34555120-34555139 MS.gene23301:CDS 45.0%
GTCTGTTGTTCAAGGGTTTG+TGG + chr4.3:34555273-34555292 MS.gene23301:CDS 45.0%
TTACTTGGTTTCGATTGCGC+CGG - chr4.3:34555079-34555098 None:intergenic 45.0%
! GAAGAGTTGATTGCGTCGAA+AGG - chr4.3:34554581-34554600 None:intergenic 45.0%
! TGGACCGATGAGCTTTTAGA+CGG + chr4.3:34554713-34554732 MS.gene23301:CDS 45.0%
GGCCGAGGTGAGAAAATTCT+TGG + chr4.3:34554856-34554875 MS.gene23301:CDS 50.0%
TCCACGCACGTCAAGAGAAA+TGG + chr4.3:34554693-34554712 MS.gene23301:CDS 50.0%
TCCATTTCTCTTGACGTGCG+TGG - chr4.3:34554697-34554716 None:intergenic 50.0%
! ATGAGAGGGTGTGGTTTCGA+TGG - chr4.3:34554524-34554543 None:intergenic 50.0%
!! CGAGGTTGGTGATGTGATGT+TGG - chr4.3:34554488-34554507 None:intergenic 50.0%
AGGAGGCGAAATGGAGGTGA+CGG + chr4.3:34554835-34554854 MS.gene23301:CDS 55.0%
TCTCTTGACGTGCGTGGACA+AGG - chr4.3:34554691-34554710 None:intergenic 55.0%
!! GATGGCAAGCTTTTCGAGCG+AGG - chr4.3:34554506-34554525 None:intergenic 55.0%
!! GCAAGCTTTTCGAGCGAGGT+TGG - chr4.3:34554502-34554521 None:intergenic 55.0%
! CGAAATGGAGGTGACGGCCG+AGG + chr4.3:34554841-34554860 MS.gene23301:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 34554461 34555366 34554461 ID=MS.gene23301
chr4.3 mRNA 34554461 34555366 34554461 ID=MS.gene23301.t1;Parent=MS.gene23301
chr4.3 exon 34554461 34555366 34554461 ID=MS.gene23301.t1.exon1;Parent=MS.gene23301.t1
chr4.3 CDS 34554461 34555366 34554461 ID=cds.MS.gene23301.t1;Parent=MS.gene23301.t1
Gene Sequence

>MS.gene23301

ATGGCTACTACCATTCCTATTAGTCCAACATCACATCACCAACCTCGCTCGAAAAGCTTGCCATCGAAACCACACCCTCTCATTCTACAATGCAATCAACACTTGGCAAATTTAGAGCCTTTCGACGCAATCAACTCTTCATCGTTGTTCGGTAAAAAACTAACCGATCTACAAGCTTTACATGATTGCGTCGAAAGTTTGGTATTGCTACCTCTTACTCAACAAGTCCTTGTCCACGCACGTCAAGAGAAATGGACCGATGAGCTTTTAGACGGATCTTTAAGGCTCCTAGATGTGTGTTCTGTAGCAAAGGATTCTCTAATTCATACGAAGGAATGTGCACGCGAACTTCAATCGATTATGCGAAGAAAAAGAGGAGGCGAAATGGAGGTGACGGCCGAGGTGAGAAAATTCTTGGCTTCTAGGAAGGTAGTAAAGAAAGCAATCCTCAAAGCTTTGGAGAATTTGAAGGCTAATGTGAAGAAAGGTAAAGGAAAACTATTATCTCCTAGCAACAATAAGGATCATGAAAAAGTGACTTTGGTTAGTTTGTTAAGAGACGTGGAAGTGATCACTCTTTCAATGTTGGAGTCACTTTTAATCTTTATATCTGGACCGGCGCAATCGAAACCAAGTAATTATTGGTCCTTGGTTTCAAAGCTTATGATGCAGAGCAAGAAGGTTTCTTCTACACAAGAAGCTGATATCAACGAGTTTTCTAATGTTGATGCTGCATTGCAGTCTTTTGTGTTTAATGTCGCAAGAAAATCAGATAATGTCAATCATTTGCAGAACCAATTGGAAAATTTGGAGTCTGTTGTTCAAGGGTTTGTGGAAGCACTTGAAGCTCTTTTTAAACGCTTTATTAAGATTAGAGTTTCCCTTCTCAATGTCCTTAATCACTAG
Protein sequence

>MS.gene23301.t1

MATTIPISPTSHHQPRSKSLPSKPHPLILQCNQHLANLEPFDAINSSSLFGKKLTDLQALHDCVESLVLLPLTQQVLVHARQEKWTDELLDGSLRLLDVCSVAKDSLIHTKECARELQSIMRRKRGGEMEVTAEVRKFLASRKVVKKAILKALENLKANVKKGKGKLLSPSNNKDHEKVTLVSLLRDVEVITLSMLESLLIFISGPAQSKPSNYWSLVSKLMMQSKKVSSTQEADINEFSNVDAALQSFVFNVARKSDNVNHLQNQLENLESVVQGFVEALEALFKRFIKIRVSLLNVLNH