AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53262

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53262.t1 MTR_8g087450 96.918 292 9 0 1 292 1 292 0.0 566
MS.gene53262.t1 MTR_2g017960 71.379 290 66 6 1 289 1 274 3.09e-116 335
MS.gene53262.t1 MTR_2g017970 77.143 210 46 2 76 285 67 274 1.61e-109 318
MS.gene53262.t1 MTR_4g059840 55.187 241 93 6 58 288 53 288 3.51e-80 244
MS.gene53262.t1 MTR_4g053380 49.836 305 121 8 2 291 7 294 2.22e-78 240
MS.gene53262.t1 MTR_4g059790 60.199 201 70 3 58 248 53 253 5.49e-78 239
MS.gene53262.t1 MTR_2g093980 48.814 295 130 9 1 288 1 281 9.75e-76 233
MS.gene53262.t1 MTR_4g059780 49.815 271 115 5 21 284 45 301 8.99e-69 216
MS.gene53262.t1 MTR_2g093970 45.890 292 125 7 10 285 13 287 7.21e-68 213
MS.gene53262.t1 MTR_2g017950 43.345 293 139 8 6 285 12 290 2.67e-64 204
MS.gene53262.t1 MTR_8g087470 45.113 266 127 6 41 288 51 315 1.05e-62 201
MS.gene53262.t1 MTR_8g087460 46.212 264 121 7 45 288 53 315 1.05e-61 198
MS.gene53262.t1 MTR_4g059720 45.415 229 84 4 1 228 4 192 1.04e-56 183
MS.gene53262.t1 MTR_2g093990 46.117 206 101 3 77 279 41 239 7.22e-53 173
MS.gene53262.t1 MTR_7g101080 44.578 166 90 2 58 222 21 185 2.35e-41 144
MS.gene53262.t1 MTR_2g090765 35.565 239 132 4 50 286 29 247 1.41e-27 107
MS.gene53262.t1 MTR_5g098060 30.588 170 113 3 77 243 48 215 1.06e-15 75.5
MS.gene53262.t1 MTR_7g075453 31.746 189 113 4 68 250 175 353 3.68e-14 72.4
MS.gene53262.t1 MTR_2g437700 31.544 149 95 4 77 221 195 340 1.88e-12 67.4
MS.gene53262.t1 MTR_5g098420 30.270 185 114 5 55 235 177 350 7.20e-12 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53262.t1 AT5G60490 54.795 146 64 2 77 221 39 183 7.29e-47 158
MS.gene53262.t1 AT5G03170 46.023 176 93 2 70 244 29 203 7.20e-45 152
MS.gene53262.t1 AT5G44130 40.437 183 103 3 77 257 36 214 1.10e-33 123
MS.gene53262.t1 AT2G20520 41.622 185 95 5 77 249 38 221 1.34e-29 112
MS.gene53262.t1 AT1G03870 38.830 188 109 4 77 263 39 221 2.85e-29 112
MS.gene53262.t1 AT2G04780 31.544 149 96 3 75 221 44 188 2.65e-13 68.9
MS.gene53262.t1 AT2G04780 31.544 149 96 3 75 221 44 188 2.65e-13 68.9
MS.gene53262.t1 AT3G46550 28.495 186 120 8 63 243 194 371 1.06e-12 68.2
MS.gene53262.t1 AT3G60900 28.488 172 117 3 70 240 183 349 3.26e-12 67.0

Find 49 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTGCTGGAGCTTTAGCTTT+AGG 0.270473 4.3:+13409582 None:intergenic
TTCGAACTTGATACATATTC+AGG 0.279696 4.3:+13409807 None:intergenic
GAATTCTCTTTCTCAGCTTT+AGG 0.296501 4.3:+13409543 None:intergenic
TGCTATATATCATGTGAATA+AGG 0.305049 4.3:-13409631 MS.gene53262:CDS
CAGATTAATGTGACTGCATA+TGG 0.308276 4.3:-13409726 MS.gene53262:CDS
GGTGCTGGAGCAGGTGTTGA+AGG 0.331645 4.3:+13410122 None:intergenic
ATGCATGTTATTCAAGCTAA+TGG 0.337878 4.3:+13409470 None:intergenic
GAATAAGGTTCTTATTCCTT+TGG 0.338628 4.3:-13409616 MS.gene53262:CDS
TCTTGGTTTCCTGACGAATC+AGG 0.343060 4.3:+13410053 None:intergenic
AGCAGGTTACTTCAACTCCT+TGG 0.397163 4.3:-13409871 MS.gene53262:CDS
TGTGGTAATGCTGGGACTAA+TGG 0.407871 4.3:+13410092 None:intergenic
GATTAGTGTGTTGAATGATT+TGG 0.407894 4.3:+13410007 None:intergenic
TTAGAATCTTGATTATGTCT+TGG 0.417666 4.3:+13410036 None:intergenic
GCCTTAGCAAGAGCTGGTGC+TGG 0.431209 4.3:+13409567 None:intergenic
TCTGAAAAGGCACCATCATC+TGG 0.442423 4.3:+13409900 None:intergenic
AGAAGATAGAGGCAAGTAGT+AGG 0.446057 4.3:+13410234 None:intergenic
ATATCAGTGTTGGTTTCCCT+TGG 0.450067 4.3:-13409444 MS.gene53262:CDS
GCAGGTTACTTCAACTCCTT+GGG 0.455965 4.3:-13409870 MS.gene53262:CDS
AACAGTGTGAATATTTCAAC+TGG 0.459076 4.3:-13409702 MS.gene53262:CDS
GTAGGTGATTGTGGTAATGC+TGG 0.464029 4.3:+13410083 None:intergenic
GACGAATCAGGATTTGTTGT+AGG 0.471829 4.3:+13410065 None:intergenic
GTGCTGGAGCAGGTGTTGAA+GGG 0.481443 4.3:+13410123 None:intergenic
CATTAATCTGAAATCCTTGT+GGG 0.483229 4.3:+13409739 None:intergenic
ACCTGCTTTGAGTTCTGAAA+AGG 0.484192 4.3:+13409887 None:intergenic
TTAGGTGCCTTAGCAAGAGC+TGG 0.489973 4.3:+13409561 None:intergenic
GGATTTGTTGTAGGTGATTG+TGG 0.513333 4.3:+13410074 None:intergenic
ACAATTCTTGCACCAGATGA+TGG 0.514841 4.3:-13409912 MS.gene53262:CDS
GGAGCAGGTGTTGAAGGGGT+AGG 0.521942 4.3:+13410128 None:intergenic
ACAACAAATCCTGATTCGTC+AGG 0.522883 4.3:-13410062 MS.gene53262:CDS
AGTGGTGATTGAGAAGATAG+AGG 0.531658 4.3:+13410223 None:intergenic
TTTGTGTTGTCTTGAGCAAA+CGG 0.534377 4.3:+13409985 None:intergenic
TCCAGCACCAGCTCTTGCTA+AGG 0.542557 4.3:-13409568 MS.gene53262:CDS
AGCGTAAACGATTCCAGTGA+TGG 0.545525 4.3:+13409665 None:intergenic
TTACAAGCTGTGCATTGACT+TGG 0.551173 4.3:+13409955 None:intergenic
CATGCATGGAATATCAGTGT+TGG 0.573529 4.3:-13409454 MS.gene53262:CDS
TGCTGGAGCAGGTGTTGAAG+GGG 0.574142 4.3:+13410124 None:intergenic
ACATTAATCTGAAATCCTTG+TGG 0.574915 4.3:+13409738 None:intergenic
CTGCAAGCAGAGAAATTCCA+AGG 0.575775 4.3:+13409427 None:intergenic
AGCTGGTGATTGAGCTAAAG+TGG 0.578327 4.3:+13410205 None:intergenic
ATTAGCTTGAATAACATGCA+TGG 0.579278 4.3:-13409468 MS.gene53262:CDS
TAGGTGATTGTGGTAATGCT+GGG 0.582717 4.3:+13410084 None:intergenic
GTTGTTGATACAACCATCAC+TGG 0.593007 4.3:-13409678 MS.gene53262:CDS
TTAGGCTTAACAAAATCCAA+AGG 0.601169 4.3:+13409600 None:intergenic
CTAGCTAGTGATAGCCCACA+AGG 0.607212 4.3:-13409753 MS.gene53262:CDS
TGATCAGACTCAGGCACACA+AGG 0.622744 4.3:-13409505 MS.gene53262:CDS
AGATGATGATGATCAGACTC+AGG 0.626792 4.3:-13409514 MS.gene53262:CDS
CACTAGCTAGTGTCAACACA+GGG 0.648522 4.3:+13409766 None:intergenic
TGCAAGCAGAGAAATTCCAA+GGG 0.658685 4.3:+13409428 None:intergenic
TCACTAGCTAGTGTCAACAC+AGG 0.685638 4.3:+13409765 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGCTATATATCATGTGAATA+AGG - chr4.3:13410033-13410052 MS.gene53262:CDS 25.0%
! TTAGAATCTTGATTATGTCT+TGG + chr4.3:13409631-13409650 None:intergenic 25.0%
AACAGTGTGAATATTTCAAC+TGG - chr4.3:13409962-13409981 MS.gene53262:CDS 30.0%
ATGCATGTTATTCAAGCTAA+TGG + chr4.3:13410197-13410216 None:intergenic 30.0%
CAGCTTGTAACTACAAAAAA+TGG - chr4.3:13409722-13409741 MS.gene53262:CDS 30.0%
CTTGTAACTACAAAAAATGG+AGG - chr4.3:13409725-13409744 MS.gene53262:CDS 30.0%
GAATAAGGTTCTTATTCCTT+TGG - chr4.3:13410048-13410067 MS.gene53262:CDS 30.0%
GATTAGTGTGTTGAATGATT+TGG + chr4.3:13409660-13409679 None:intergenic 30.0%
TTAGGCTTAACAAAATCCAA+AGG + chr4.3:13410067-13410086 None:intergenic 30.0%
TTCGAACTTGATACATATTC+AGG + chr4.3:13409860-13409879 None:intergenic 30.0%
! ACATTAATCTGAAATCCTTG+TGG + chr4.3:13409929-13409948 None:intergenic 30.0%
! ATTAGCTTGAATAACATGCA+TGG - chr4.3:13410196-13410215 MS.gene53262:CDS 30.0%
! CATTAATCTGAAATCCTTGT+GGG + chr4.3:13409928-13409947 None:intergenic 30.0%
CAGATTAATGTGACTGCATA+TGG - chr4.3:13409938-13409957 MS.gene53262:CDS 35.0%
GAATTCTCTTTCTCAGCTTT+AGG + chr4.3:13410124-13410143 None:intergenic 35.0%
TTTGTGTTGTCTTGAGCAAA+CGG + chr4.3:13409682-13409701 None:intergenic 35.0%
!! TTTTTGTTGTCTTTCTCCCA+AGG + chr4.3:13409813-13409832 None:intergenic 35.0%
ACAATTCTTGCACCAGATGA+TGG - chr4.3:13409752-13409771 MS.gene53262:CDS 40.0%
AGAAGATAGAGGCAAGTAGT+AGG + chr4.3:13409433-13409452 None:intergenic 40.0%
AGTGGTGATTGAGAAGATAG+AGG + chr4.3:13409444-13409463 None:intergenic 40.0%
CATGCATGGAATATCAGTGT+TGG - chr4.3:13410210-13410229 MS.gene53262:CDS 40.0%
GTTGTTGATACAACCATCAC+TGG - chr4.3:13409986-13410005 MS.gene53262:CDS 40.0%
TGCAAGCAGAGAAATTCCAA+GGG + chr4.3:13410239-13410258 None:intergenic 40.0%
! ACAACAAATCCTGATTCGTC+AGG - chr4.3:13409602-13409621 MS.gene53262:CDS 40.0%
! AGATGATGATGATCAGACTC+AGG - chr4.3:13410150-13410169 MS.gene53262:CDS 40.0%
! TAGGTGATTGTGGTAATGCT+GGG + chr4.3:13409583-13409602 None:intergenic 40.0%
!! ACCTGCTTTGAGTTCTGAAA+AGG + chr4.3:13409780-13409799 None:intergenic 40.0%
!! ATATCAGTGTTGGTTTCCCT+TGG - chr4.3:13410220-13410239 MS.gene53262:CDS 40.0%
!! GACGAATCAGGATTTGTTGT+AGG + chr4.3:13409602-13409621 None:intergenic 40.0%
!! GGATTTGTTGTAGGTGATTG+TGG + chr4.3:13409593-13409612 None:intergenic 40.0%
!! TTACAAGCTGTGCATTGACT+TGG + chr4.3:13409712-13409731 None:intergenic 40.0%
!! TTGAAGGGGTAGGTTTTGTA+GGG + chr4.3:13409529-13409548 None:intergenic 40.0%
!!! TTTGTAGGTGCTGGTTTTTC+TGG + chr4.3:13409500-13409519 None:intergenic 40.0%
AGCAGGTTACTTCAACTCCT+TGG - chr4.3:13409793-13409812 MS.gene53262:CDS 45.0%
AGCGTAAACGATTCCAGTGA+TGG + chr4.3:13410002-13410021 None:intergenic 45.0%
AGCTGGTGATTGAGCTAAAG+TGG + chr4.3:13409462-13409481 None:intergenic 45.0%
CACTAGCTAGTGTCAACACA+GGG + chr4.3:13409901-13409920 None:intergenic 45.0%
CTGCAAGCAGAGAAATTCCA+AGG + chr4.3:13410240-13410259 None:intergenic 45.0%
GCAGGTTACTTCAACTCCTT+GGG - chr4.3:13409794-13409813 MS.gene53262:CDS 45.0%
TCACTAGCTAGTGTCAACAC+AGG + chr4.3:13409902-13409921 None:intergenic 45.0%
TCTTGGTTTCCTGACGAATC+AGG + chr4.3:13409614-13409633 None:intergenic 45.0%
! GCCTTTTCAGAACTCAAAGC+AGG - chr4.3:13409776-13409795 MS.gene53262:CDS 45.0%
! GTAGGTGATTGTGGTAATGC+TGG + chr4.3:13409584-13409603 None:intergenic 45.0%
! TGTGGTAATGCTGGGACTAA+TGG + chr4.3:13409575-13409594 None:intergenic 45.0%
!! ACTAATGGTTTTGCTGGTGC+TGG + chr4.3:13409560-13409579 None:intergenic 45.0%
!! GTTGAAGGGGTAGGTTTTGT+AGG + chr4.3:13409530-13409549 None:intergenic 45.0%
!! TCTGAAAAGGCACCATCATC+TGG + chr4.3:13409767-13409786 None:intergenic 45.0%
!! TGAAGGGGTAGGTTTTGTAG+GGG + chr4.3:13409528-13409547 None:intergenic 45.0%
!!! GCTGGTTTTTCTGGTGCTTT+TGG + chr4.3:13409491-13409510 None:intergenic 45.0%
!!! TTTGTAGGGGCTGGTTTTGT+AGG + chr4.3:13409515-13409534 None:intergenic 45.0%
CTAGCTAGTGATAGCCCACA+AGG - chr4.3:13409911-13409930 MS.gene53262:CDS 50.0%
TGATCAGACTCAGGCACACA+AGG - chr4.3:13410159-13410178 MS.gene53262:CDS 50.0%
TTAGGTGCCTTAGCAAGAGC+TGG + chr4.3:13410106-13410125 None:intergenic 50.0%
!! GCTGGGACTAATGGTTTTGC+TGG + chr4.3:13409566-13409585 None:intergenic 50.0%
!! GGTGCTGGAGCTTTAGCTTT+AGG + chr4.3:13410085-13410104 None:intergenic 50.0%
TCCAGCACCAGCTCTTGCTA+AGG - chr4.3:13410096-13410115 MS.gene53262:CDS 55.0%
!! GTGCTGGAGCAGGTGTTGAA+GGG + chr4.3:13409544-13409563 None:intergenic 55.0%
!! TGCTGGAGCAGGTGTTGAAG+GGG + chr4.3:13409543-13409562 None:intergenic 55.0%
GCCTTAGCAAGAGCTGGTGC+TGG + chr4.3:13410100-13410119 None:intergenic 60.0%
!! GGAGCAGGTGTTGAAGGGGT+AGG + chr4.3:13409539-13409558 None:intergenic 60.0%
!! GGGGTAGGTTTTGTAGGGGC+TGG + chr4.3:13409524-13409543 None:intergenic 60.0%
!! GGTGCTGGAGCAGGTGTTGA+AGG + chr4.3:13409545-13409564 None:intergenic 60.0%
!! GGTTTTGCTGGTGCTGGAGC+AGG + chr4.3:13409554-13409573 None:intergenic 60.0%
!!! GGGGCTGGTTTTGTAGGTGC+TGG + chr4.3:13409509-13409528 None:intergenic 60.0%
!!! GGTGCTTTTGGTGCTGCAGC+TGG + chr4.3:13409479-13409498 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 13409404 13410282 13409404 ID=MS.gene53262
chr4.3 mRNA 13409404 13410282 13409404 ID=MS.gene53262.t1;Parent=MS.gene53262
chr4.3 exon 13409404 13410282 13409404 ID=MS.gene53262.t1.exon1;Parent=MS.gene53262.t1
chr4.3 CDS 13409404 13410282 13409404 ID=cds.MS.gene53262.t1;Parent=MS.gene53262.t1
Gene Sequence

>MS.gene53262

ATGAATCAAATTTTCTTGTTCTCACTCCTACTACTTGCCTCTATCTTCTCAATCACCACTTTAGCTCAATCACCAGCTGCAGCACCAAAAGCACCAGAAAAACCAGCACCTACAAAACCAGCCCCTACAAAACCTACCCCTTCAACACCTGCTCCAGCACCAGCAAAACCATTAGTCCCAGCATTACCACAATCACCTACAACAAATCCTGATTCGTCAGGAAACCAAGACATAATCAAGATTCTAAGAAAAGCCAAATCATTCAACACACTAATCCGTTTGCTCAAGACAACACAAATCATCAACCAAGTCAATGCACAGCTTGTAACTACAAAAAATGGAGGCTTGACAATTCTTGCACCAGATGATGGTGCCTTTTCAGAACTCAAAGCAGGTTACTTCAACTCCTTGGGAGAAAGACAACAAAAAGAATTGATTCAGTATCATGTTCTTCCTGAATATGTATCAAGTTCGAACTTTGATTCTCTCAGCAACCCTGTGTTGACACTAGCTAGTGATAGCCCACAAGGATTTCAGATTAATGTGACTGCATATGGAAACAGTGTGAATATTTCAACTGGCGTTGTTGATACAACCATCACTGGAATCGTTTACGCTGATAAAACACTTGCTATATATCATGTGAATAAGGTTCTTATTCCTTTGGATTTTGTTAAGCCTAAAGCTAAAGCTCCAGCACCAGCTCTTGCTAAGGCACCTAAAGCTGAGAAAGAGAATTCATCTGCAGATGATGATGATCAGACTCAGGCACACAAGGATAGTTCTGATGCCATTAGCTTGAATAACATGCATGGAATATCAGTGTTGGTTTCCCTTGGAATTTCTCTGCTTGCAGTTGCAGTAACAACTATGTTGTGA
Protein sequence

>MS.gene53262.t1

MNQIFLFSLLLLASIFSITTLAQSPAAAPKAPEKPAPTKPAPTKPTPSTPAPAPAKPLVPALPQSPTTNPDSSGNQDIIKILRKAKSFNTLIRLLKTTQIINQVNAQLVTTKNGGLTILAPDDGAFSELKAGYFNSLGERQQKELIQYHVLPEYVSSSNFDSLSNPVLTLASDSPQGFQINVTAYGNSVNISTGVVDTTITGIVYADKTLAIYHVNKVLIPLDFVKPKAKAPAPALAKAPKAEKENSSADDDDQTQAHKDSSDAISLNNMHGISVLVSLGISLLAVAVTTML