AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29978

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29978.t1 MTR_8g074420 94.828 290 15 0 1 290 1 290 0.0 538
MS.gene29978.t1 MTR_8g074450 81.379 290 54 0 1 290 1 290 3.07e-170 473
MS.gene29978.t1 MTR_8g074510 81.034 290 53 1 1 290 1 288 6.76e-166 462
MS.gene29978.t1 MTR_5g023350 69.097 288 83 2 2 289 3 284 5.15e-132 376
MS.gene29978.t1 MTR_5g023600 68.750 288 84 2 2 289 3 284 1.47e-131 375
MS.gene29978.t1 MTR_5g023370 67.361 288 88 2 2 289 3 284 6.74e-129 368
MS.gene29978.t1 MTR_5g023340 67.361 288 88 2 2 289 3 284 1.42e-128 367
MS.gene29978.t1 MTR_5g023390 66.319 288 91 2 2 289 3 284 3.83e-128 366
MS.gene29978.t1 MTR_5g023520 65.517 290 95 1 1 290 1 285 5.55e-128 365
MS.gene29978.t1 MTR_5g023550 65.398 289 94 2 1 289 1 283 6.78e-125 358
MS.gene29978.t1 MTR_5g023320 66.552 290 87 4 2 290 3 283 3.64e-124 356
MS.gene29978.t1 MTR_5g023530 64.605 291 95 4 1 289 1 285 4.82e-122 350
MS.gene29978.t1 MTR_5g023470 63.918 291 97 4 1 289 1 285 3.46e-120 346
MS.gene29978.t1 MTR_5g023580 64.685 286 99 1 2 287 3 286 5.81e-120 348
MS.gene29978.t1 MTR_8g074530 47.586 290 148 3 2 289 17 304 1.73e-78 241
MS.gene29978.t1 MTR_5g023460 61.979 192 63 2 99 290 11 192 4.97e-76 230
MS.gene29978.t1 MTR_5g023290 40.940 298 164 4 4 289 11 308 4.86e-64 204
MS.gene29978.t1 MTR_5g023650 33.106 293 184 4 7 289 14 304 3.69e-44 152
MS.gene29978.t1 MTR_8g074380 32.990 291 163 5 7 288 14 281 1.14e-41 147
MS.gene29978.t1 MTR_4g070530 34.028 288 179 5 7 289 14 295 1.60e-39 140
MS.gene29978.t1 MTR_5g023410 69.000 100 31 0 1 100 1 100 5.20e-38 134
MS.gene29978.t1 MTR_4g070570 31.164 292 190 6 5 289 15 302 9.55e-38 135
MS.gene29978.t1 MTR_4g070540 31.119 286 190 4 7 289 14 295 7.21e-36 130
MS.gene29978.t1 MTR_4g070590 33.904 292 178 7 7 289 15 300 3.90e-34 126
MS.gene29978.t1 MTR_3g116920 31.849 292 186 8 5 289 12 297 3.89e-31 118
MS.gene29978.t1 MTR_3g116950 33.219 292 180 10 5 289 12 295 5.16e-31 117
MS.gene29978.t1 MTR_3g115150 26.910 301 188 9 7 289 29 315 2.53e-23 97.4
MS.gene29978.t1 MTR_1g037820 28.750 240 147 6 51 289 9 225 2.07e-19 85.1
MS.gene29978.t1 MTR_5g023540 47.761 67 31 1 165 231 4 66 7.20e-12 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29978.t1 AT4G35690 36.949 295 165 7 1 289 4 283 2.52e-50 167
MS.gene29978.t1 AT2G17680 38.141 312 148 11 1 290 4 292 9.36e-46 156
MS.gene29978.t1 AT4G35710 35.906 298 166 8 1 289 1 282 6.23e-42 146
MS.gene29978.t1 AT2G17080 35.069 288 160 6 1 288 1 261 1.94e-40 141
MS.gene29978.t1 AT2G17070 34.965 286 159 6 1 286 1 259 1.79e-36 131
MS.gene29978.t1 AT4G35200 35.836 293 142 11 1 287 1 253 9.77e-34 124
MS.gene29978.t1 AT4G35210 33.333 288 153 9 1 287 1 250 4.81e-31 116
MS.gene29978.t1 AT4G35660 32.203 295 165 7 7 289 16 287 4.36e-30 115
MS.gene29978.t1 AT4G35720 31.761 318 177 9 5 289 14 324 4.54e-28 110
MS.gene29978.t1 AT4G35680 28.523 298 194 7 6 289 17 309 1.13e-22 95.9
MS.gene29978.t1 AT3G51400 30.169 295 179 9 1 289 1 274 4.01e-19 85.5
MS.gene29978.t1 AT1G76240 29.153 295 177 9 8 289 32 307 7.83e-19 85.1
MS.gene29978.t1 AT1G76210 27.111 225 141 5 65 289 24 225 1.16e-14 72.0
MS.gene29978.t1 AT3G51410 29.617 287 152 9 7 289 39 279 1.03e-13 70.1

Find 55 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGCATATGGATAGAAAATT+TGG 0.129322 8.4:-30319887 MS.gene29978:CDS
ATTTGGGGTGTCCCAAATTT+TGG 0.131611 8.4:-30319870 MS.gene29978:CDS
GATGATCAAGTTCCAAAATT+TGG 0.152831 8.4:+30319858 None:intergenic
CACTATTGGTGAAAAGTTTC+AGG 0.207067 8.4:-30319606 MS.gene29978:CDS
GGATAGTTCAATGAGAATTT+TGG 0.221029 8.4:-30320083 MS.gene29978:CDS
CAATAGTGGATTCACTTAAA+AGG 0.237225 8.4:+30319621 None:intergenic
CAATGCATTTCTCACCTCTA+TGG 0.309012 8.4:+30320116 None:intergenic
ATGATCAAGTTCCAAAATTT+GGG 0.315958 8.4:+30319859 None:intergenic
AGCATATGGATAGAAAATTT+GGG 0.332480 8.4:-30319886 MS.gene29978:CDS
GCTCTATAATTAGAGTGGTT+AGG 0.346875 8.4:-30319829 MS.gene29978:CDS
AAGCCCTTCACTCTTGTCTA+AGG 0.365459 8.4:-30320009 MS.gene29978:CDS
TGAAGAATTGTATATTTCAT+TGG 0.371711 8.4:-30320182 MS.gene29978:CDS
GATCACAAGTTTGAAGCATA+TGG 0.388619 8.4:-30319900 MS.gene29978:CDS
CTCTATAATTAGAGTGGTTA+GGG 0.390882 8.4:-30319828 MS.gene29978:CDS
GAAATCACTTGTTGGGTTGA+TGG 0.405774 8.4:+30320142 None:intergenic
ACATGAGAGATTGGAGGCTT+TGG 0.408989 8.4:-30319579 MS.gene29978:CDS
TACATCAAGCTCCATTCAAA+CGG 0.450991 8.4:-30320218 MS.gene29978:CDS
TCAGGCTGCACATGAGAGAT+TGG 0.452007 8.4:-30319588 MS.gene29978:CDS
CAAGGAAAGACCCGTTTGAA+TGG 0.453573 8.4:+30320207 None:intergenic
TGTGTCTTCATCAAAGTCTA+AGG 0.455083 8.4:-30319753 MS.gene29978:CDS
TGGATATTTGTGGCATCACT+AGG 0.456088 8.4:-30320063 MS.gene29978:CDS
AATAGTGGATTCACTTAAAA+GGG 0.456111 8.4:+30319622 None:intergenic
GCAATTGAAAGCATTGAGAA+TGG 0.463409 8.4:-30319551 MS.gene29978:CDS
ATGGTGAGAAATCACTTGTT+GGG 0.479630 8.4:+30320135 None:intergenic
TATGGTGAGAAATCACTTGT+TGG 0.484011 8.4:+30320134 None:intergenic
AATATACAATTCTTCAATCA+AGG 0.493373 8.4:+30320189 None:intergenic
GTGCTAGGATGAAATCTAGA+TGG 0.495612 8.4:+30320298 None:intergenic
GGATACAATTCTTCAAATCA+AGG 0.500801 8.4:-30320041 MS.gene29978:CDS
TCTTGTCTAAGGAGAAGAAA+AGG 0.505857 8.4:-30319998 MS.gene29978:CDS
ACATCAAGCTCCATTCAAAC+GGG 0.526245 8.4:-30320217 MS.gene29978:CDS
AGAGATTATGTTCAAGAGGA+AGG 0.527971 8.4:+30319490 None:intergenic
TTCTCCTTAGACAAGAGTGA+AGG 0.531189 8.4:+30320005 None:intergenic
TAAGGCAACCAAATGGTTGT+TGG 0.536702 8.4:-30319735 MS.gene29978:CDS
TCATGTACTCTAATTGTGCT+AGG 0.541777 8.4:+30320283 None:intergenic
GGCTGCACATGAGAGATTGG+AGG 0.542067 8.4:-30319585 MS.gene29978:CDS
CTTCAAACTTGTGATCAACT+TGG 0.545317 8.4:+30319907 None:intergenic
ATTGAGAGATTATGTTCAAG+AGG 0.553521 8.4:+30319486 None:intergenic
GAAATGCATTGAAGAGGTGT+TGG 0.557821 8.4:-30320104 MS.gene29978:CDS
TCTCCTTAGACAAGAGTGAA+GGG 0.564139 8.4:+30320006 None:intergenic
CCTTTGCTCTATAATTAGAG+TGG 0.572418 8.4:-30319834 MS.gene29978:CDS
CCACTCTAATTATAGAGCAA+AGG 0.574371 8.4:+30319834 None:intergenic
CAAAGTCTAAGGCAACCAAA+TGG 0.575102 8.4:-30319742 MS.gene29978:CDS
GGATATTTGTGGCATCACTA+GGG 0.577026 8.4:-30320062 MS.gene29978:CDS
AACAAGCTTAAAACATGGGA+AGG 0.577507 8.4:-30320253 MS.gene29978:CDS
AGGTGAGAAATGCATTGAAG+AGG 0.582191 8.4:-30320110 MS.gene29978:CDS
ATTGAACAAGCTTAAAACAT+GGG 0.608973 8.4:-30320257 MS.gene29978:CDS
AATTGAACAAGCTTAAAACA+TGG 0.616486 8.4:-30320258 MS.gene29978:CDS
AATGGAGCTTGATGTAGATG+TGG 0.620161 8.4:+30320225 None:intergenic
TTCAAGTGTTGAAAGAAGTG+TGG 0.622624 8.4:-30319972 MS.gene29978:CDS
TAGCACAATTAGAGTACATG+AGG 0.624704 8.4:-30320281 MS.gene29978:CDS
CAAGTGATTTCTCACCATAG+AGG 0.629127 8.4:-30320130 MS.gene29978:CDS
TATCAATGAGTTGCAATGTG+TGG 0.636179 8.4:-30319660 MS.gene29978:CDS
GCATATGGATAGAAAATTTG+GGG 0.662441 8.4:-30319885 MS.gene29978:CDS
GGTGACAAAACTAATGCACA+AGG 0.706638 8.4:-30319714 MS.gene29978:CDS
GTGACAAAACTAATGCACAA+GGG 0.759874 8.4:-30319713 MS.gene29978:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATACAATTCTTCAATCA+AGG + chr8.4:30319632-30319651 None:intergenic 20.0%
!! TGAAGAATTGTATATTTCAT+TGG - chr8.4:30319636-30319655 MS.gene29978:CDS 20.0%
! AAGCATATGGATAGAAAATT+TGG - chr8.4:30319931-30319950 MS.gene29978:CDS 25.0%
! AATTGAACAAGCTTAAAACA+TGG - chr8.4:30319560-30319579 MS.gene29978:CDS 25.0%
! AGCATATGGATAGAAAATTT+GGG - chr8.4:30319932-30319951 MS.gene29978:CDS 25.0%
! ATGATCAAGTTCCAAAATTT+GGG + chr8.4:30319962-30319981 None:intergenic 25.0%
! ATTGAACAAGCTTAAAACAT+GGG - chr8.4:30319561-30319580 MS.gene29978:CDS 25.0%
!! ATGAGAATTTTGGATATTTG+TGG - chr8.4:30319745-30319764 MS.gene29978:CDS 25.0%
!!! AATAGTGGATTCACTTAAAA+GGG + chr8.4:30320199-30320218 None:intergenic 25.0%
ATTGAGAGATTATGTTCAAG+AGG + chr8.4:30320335-30320354 None:intergenic 30.0%
CTCTATAATTAGAGTGGTTA+GGG - chr8.4:30319990-30320009 MS.gene29978:CDS 30.0%
GATGATCAAGTTCCAAAATT+TGG + chr8.4:30319963-30319982 None:intergenic 30.0%
GCATATGGATAGAAAATTTG+GGG - chr8.4:30319933-30319952 MS.gene29978:CDS 30.0%
GGATACAATTCTTCAAATCA+AGG - chr8.4:30319777-30319796 MS.gene29978:CDS 30.0%
! GGATAGTTCAATGAGAATTT+TGG - chr8.4:30319735-30319754 MS.gene29978:CDS 30.0%
!! CAATAGTGGATTCACTTAAA+AGG + chr8.4:30320200-30320219 None:intergenic 30.0%
!! CTTTTAAGTGAATCCACTAT+TGG - chr8.4:30320198-30320217 MS.gene29978:CDS 30.0%
AACAAGCTTAAAACATGGGA+AGG - chr8.4:30319565-30319584 MS.gene29978:CDS 35.0%
AGAGATTATGTTCAAGAGGA+AGG + chr8.4:30320331-30320350 None:intergenic 35.0%
ATGGTGAGAAATCACTTGTT+GGG + chr8.4:30319686-30319705 None:intergenic 35.0%
CACTATTGGTGAAAAGTTTC+AGG - chr8.4:30320212-30320231 MS.gene29978:CDS 35.0%
CCACTCTAATTATAGAGCAA+AGG + chr8.4:30319987-30320006 None:intergenic 35.0%
CCTTTGCTCTATAATTAGAG+TGG - chr8.4:30319984-30320003 MS.gene29978:CDS 35.0%
CTTCAAACTTGTGATCAACT+TGG + chr8.4:30319914-30319933 None:intergenic 35.0%
GCTCTATAATTAGAGTGGTT+AGG - chr8.4:30319989-30320008 MS.gene29978:CDS 35.0%
GTGACAAAACTAATGCACAA+GGG - chr8.4:30320105-30320124 MS.gene29978:CDS 35.0%
TACATCAAGCTCCATTCAAA+CGG - chr8.4:30319600-30319619 MS.gene29978:CDS 35.0%
TAGCACAATTAGAGTACATG+AGG - chr8.4:30319537-30319556 MS.gene29978:CDS 35.0%
TATCAATGAGTTGCAATGTG+TGG - chr8.4:30320158-30320177 MS.gene29978:CDS 35.0%
TATGGTGAGAAATCACTTGT+TGG + chr8.4:30319687-30319706 None:intergenic 35.0%
TCATGTACTCTAATTGTGCT+AGG + chr8.4:30319538-30319557 None:intergenic 35.0%
TCTTGTCTAAGGAGAAGAAA+AGG - chr8.4:30319820-30319839 MS.gene29978:CDS 35.0%
TGTGTCTTCATCAAAGTCTA+AGG - chr8.4:30320065-30320084 MS.gene29978:CDS 35.0%
! CTGAAACTTTTCACCAATAG+TGG + chr8.4:30320214-30320233 None:intergenic 35.0%
! GATCACAAGTTTGAAGCATA+TGG - chr8.4:30319918-30319937 MS.gene29978:CDS 35.0%
! TTTTGTCACCAACAACCATT+TGG + chr8.4:30320094-30320113 None:intergenic 35.0%
!! GCAATTGAAAGCATTGAGAA+TGG - chr8.4:30320267-30320286 MS.gene29978:CDS 35.0%
!! TTCAAGTGTTGAAAGAAGTG+TGG - chr8.4:30319846-30319865 MS.gene29978:CDS 35.0%
AATGGAGCTTGATGTAGATG+TGG + chr8.4:30319596-30319615 None:intergenic 40.0%
ACATCAAGCTCCATTCAAAC+GGG - chr8.4:30319601-30319620 MS.gene29978:CDS 40.0%
AGGTGAGAAATGCATTGAAG+AGG - chr8.4:30319708-30319727 MS.gene29978:CDS 40.0%
CAAGTGATTTCTCACCATAG+AGG - chr8.4:30319688-30319707 MS.gene29978:CDS 40.0%
CAATGCATTTCTCACCTCTA+TGG + chr8.4:30319705-30319724 None:intergenic 40.0%
GGATATTTGTGGCATCACTA+GGG - chr8.4:30319756-30319775 MS.gene29978:CDS 40.0%
GGTGACAAAACTAATGCACA+AGG - chr8.4:30320104-30320123 MS.gene29978:CDS 40.0%
GTGCTAGGATGAAATCTAGA+TGG + chr8.4:30319523-30319542 None:intergenic 40.0%
TAAGGCAACCAAATGGTTGT+TGG - chr8.4:30320083-30320102 MS.gene29978:CDS 40.0%
TCTCCTTAGACAAGAGTGAA+GGG + chr8.4:30319815-30319834 None:intergenic 40.0%
TGGATATTTGTGGCATCACT+AGG - chr8.4:30319755-30319774 MS.gene29978:CDS 40.0%
TTCTCCTTAGACAAGAGTGA+AGG + chr8.4:30319816-30319835 None:intergenic 40.0%
! CAAAGTCTAAGGCAACCAAA+TGG - chr8.4:30320076-30320095 MS.gene29978:CDS 40.0%
! GAAATGCATTGAAGAGGTGT+TGG - chr8.4:30319714-30319733 MS.gene29978:CDS 40.0%
!! ATTTGGGGTGTCCCAAATTT+TGG - chr8.4:30319948-30319967 MS.gene29978:CDS 40.0%
!! GAAATCACTTGTTGGGTTGA+TGG + chr8.4:30319679-30319698 None:intergenic 40.0%
AAGCCCTTCACTCTTGTCTA+AGG - chr8.4:30319809-30319828 MS.gene29978:CDS 45.0%
ACATGAGAGATTGGAGGCTT+TGG - chr8.4:30320239-30320258 MS.gene29978:CDS 45.0%
CAAGGAAAGACCCGTTTGAA+TGG + chr8.4:30319614-30319633 None:intergenic 45.0%
TCAGGCTGCACATGAGAGAT+TGG - chr8.4:30320230-30320249 MS.gene29978:CDS 50.0%
GGCTGCACATGAGAGATTGG+AGG - chr8.4:30320233-30320252 MS.gene29978:CDS 55.0%


Chromosome Type Strat End Strand Name
chr8.4 gene 30319484 30320356 30319484 ID=MS.gene29978
chr8.4 mRNA 30319484 30320356 30319484 ID=MS.gene29978.t1;Parent=MS.gene29978
chr8.4 exon 30319484 30320356 30319484 ID=MS.gene29978.t1.exon1;Parent=MS.gene29978.t1
chr8.4 CDS 30319484 30320356 30319484 ID=cds.MS.gene29978.t1;Parent=MS.gene29978.t1
Gene Sequence

>MS.gene29978

ATGGCAAACAAGTATAGTGTTCGATCAATTAGTTTGCCATCTAGATTTCATCCTAGCACAATTAGAGTACATGAGGAATTGAACAAGCTTAAAACATGGGAAGGAACATCCACATCTACATCAAGCTCCATTCAAACGGGTCTTTCCTTGATTGAAGAATTGTATATTTCATTGGAAGATCTTCTCAACATGCCATCAACCCAACAAGTGATTTCTCACCATAGAGGTGAGAAATGCATTGAAGAGGTGTTGGATAGTTCAATGAGAATTTTGGATATTTGTGGCATCACTAGGGATACAATTCTTCAAATCAAGGAAAATGTTCAAGCCCTTCACTCTTGTCTAAGGAGAAGAAAAGGTGATTCAAGTGTTGAAAGAAGTGTGGAAGAATACAAATTTTTCACAAAAAAGATGAAGAAAAATCTCACCAAGTTGATCACAAGTTTGAAGCATATGGATAGAAAATTTGGGGTGTCCCAAATTTTGGAACTTGATCATCACCTTTGCTCTATAATTAGAGTGGTTAGGGAAGTGATTACAATGAACTTGTCTGTTTTTCAATTCATTTTGTCATTTTTGAATGTGTCTTCATCAAAGTCTAAGGCAACCAAATGGTTGTTGGTGACAAAACTAATGCACAAGGGTGTTATAACATCTCAACATAACTCACAGAATATCAATGAGTTGCAATGTGTGGAAGCTACTTTAAATACCCTTTTAAGTGAATCCACTATTGGTGAAAAGTTTCAGGCTGCACATGAGAGATTGGAGGCTTTGGAGAATGCAATTGAAAGCATTGAGAATGGTTTAGAGAACTTATATAGACACTTAATTAAATTTAGATCCTTCCTCTTGAACATAATCTCTCAATAG
Protein sequence

>MS.gene29978.t1

MANKYSVRSISLPSRFHPSTIRVHEELNKLKTWEGTSTSTSSSIQTGLSLIEELYISLEDLLNMPSTQQVISHHRGEKCIEEVLDSSMRILDICGITRDTILQIKENVQALHSCLRRRKGDSSVERSVEEYKFFTKKMKKNLTKLITSLKHMDRKFGVSQILELDHHLCSIIRVVREVITMNLSVFQFILSFLNVSSSKSKATKWLLVTKLMHKGVITSQHNSQNINELQCVEATLNTLLSESTIGEKFQAAHERLEALENAIESIENGLENLYRHLIKFRSFLLNIISQ