AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene46290

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene46290.t1 MTR_8g069080 93.810 210 13 0 12 221 33 242 4.25e-140 392
MS.gene46290.t1 MTR_2g076780 90.995 211 18 1 12 221 1 211 1.69e-132 372
MS.gene46290.t1 MTR_5g032600 44.751 181 91 2 43 221 73 246 1.08e-40 140
MS.gene46290.t1 MTR_3g100650 42.697 178 91 3 47 221 79 248 8.72e-32 117
MS.gene46290.t1 MTR_1g077020 37.912 182 78 4 47 221 8 161 2.31e-31 114
MS.gene46290.t1 MTR_5g020510 37.705 183 94 4 48 221 99 270 1.24e-30 114
MS.gene46290.t1 MTR_4g134580 35.211 213 97 6 47 221 112 321 3.36e-30 115
MS.gene46290.t1 MTR_8g442330 39.412 170 54 4 57 221 14 139 1.94e-28 104
MS.gene46290.t1 MTR_5g065440 33.043 230 118 7 18 221 23 242 3.15e-27 105
MS.gene46290.t1 MTR_7g010300 36.158 177 103 4 48 221 88 257 1.56e-24 99.4
MS.gene46290.t1 MTR_6g012280 37.853 177 99 5 48 221 91 259 4.56e-23 95.1
MS.gene46290.t1 MTR_3g039810 62.745 51 19 0 47 97 19 69 3.80e-18 76.3
MS.gene46290.t1 MTR_8g069380 56.944 72 22 3 154 221 23 89 1.14e-15 70.9
MS.gene46290.t1 MTR_8g467340 61.538 52 18 1 48 97 64 115 4.65e-15 73.6
MS.gene46290.t1 MTR_6g012220 58.000 50 17 1 47 96 20 65 8.97e-15 67.4
MS.gene46290.t1 MTR_6g073013 40.909 66 38 1 48 112 19 84 2.40e-13 66.2
MS.gene46290.t1 MTR_8g051480 54.286 70 24 4 155 219 36 102 1.79e-12 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene46290.t1 AT2G02540 40.000 180 97 4 47 221 86 259 2.91e-35 127
MS.gene46290.t1 AT2G02540 40.000 180 97 4 47 221 86 259 2.91e-35 127
MS.gene46290.t1 AT4G24660 34.978 223 114 5 1 221 1 194 6.00e-35 124
MS.gene46290.t1 AT4G24660 39.429 175 78 3 47 221 48 194 6.09e-35 124
MS.gene46290.t1 AT5G65410 34.632 231 121 5 1 221 18 228 3.31e-32 118
MS.gene46290.t1 AT1G14440 35.979 189 85 5 47 221 89 255 2.34e-29 111
MS.gene46290.t1 AT1G14440 35.979 189 85 5 47 221 89 255 2.34e-29 111
MS.gene46290.t1 AT1G69600 38.333 180 88 6 48 221 31 193 1.53e-26 102
MS.gene46290.t1 AT2G18350 36.464 181 87 7 45 221 79 235 4.79e-26 102
MS.gene46290.t1 AT5G15210 34.409 186 85 5 48 221 56 216 4.92e-25 99.4
MS.gene46290.t1 AT3G50890 31.050 219 106 7 15 221 33 218 5.23e-22 90.9
MS.gene46290.t1 AT1G74660 64.706 51 18 0 47 97 38 88 9.64e-22 86.3
MS.gene46290.t1 AT1G74660 64.706 51 18 0 47 97 38 88 1.57e-21 85.9
MS.gene46290.t1 AT1G75240 61.290 62 23 1 47 107 75 136 1.41e-20 88.2
MS.gene46290.t1 AT3G28917 50.000 68 29 2 47 113 32 95 1.28e-17 75.5
MS.gene46290.t1 AT5G42780 30.622 209 115 5 18 221 33 216 1.30e-17 79.0
MS.gene46290.t1 AT5G60480 34.091 176 86 5 48 221 37 184 1.84e-17 78.2
MS.gene46290.t1 AT3G28920 33.333 195 92 8 48 221 52 229 2.02e-17 79.7
MS.gene46290.t1 AT1G18835 58.824 51 18 1 47 97 25 72 9.93e-16 70.1
MS.gene46290.t1 AT5G39760 59.615 52 19 1 48 97 56 107 2.21e-13 68.6

Find 50 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGAGTCGGCTGAGGGAAAC+GGG 0.315201 8.1:-36080473 None:intergenic
CACTTTCCAAGGGGTGATCT+TGG 0.335585 8.1:+36080598 MS.gene46290:CDS
TTTCTCTCCGATGAAAATTT+CGG 0.335714 8.1:-36080405 None:intergenic
AGCATGTGACTGGGACTTCT+AGG 0.339165 8.1:+36080530 MS.gene46290:CDS
AGGGAGTCGGCTGAGGGAAA+CGG 0.388732 8.1:-36080474 None:intergenic
ATTGTTTCAACGTAACTAGT+TGG 0.415917 8.1:-36080187 None:intergenic
ACCGGTTACCAGCATGTGAC+TGG 0.421058 8.1:+36080520 MS.gene46290:CDS
CCCAGTCACATGCTGGTAAC+CGG 0.435647 8.1:-36080521 None:intergenic
TTCTTCATCATGATGATTCG+AGG 0.450499 8.1:-36080215 None:intergenic
TAAGTATCACCATGATAGAT+TGG 0.451827 8.1:-36080637 None:intergenic
GTCGAGAAGGGAGTCGGCTG+AGG 0.453909 8.1:-36080481 None:intergenic
ATTGGAGGCTACGCTCTTGA+TGG 0.454275 8.1:+36080310 MS.gene46290:CDS
GGAGTCGGCTGAGGGAAACG+GGG 0.458116 8.1:-36080472 None:intergenic
TATCAAAAGGAAAGGATGCT+TGG 0.463362 8.1:+36080715 MS.gene46290:CDS
AAGAATCACGCTTCCAGCAT+TGG 0.464419 8.1:+36080292 MS.gene46290:CDS
CAAGTTCACTCATTATCAAA+AGG 0.480127 8.1:+36080702 MS.gene46290:CDS
ATGATGAGGCCCACTTTCCA+AGG 0.481132 8.1:+36080587 MS.gene46290:CDS
TATCATGGTGATACTTATAG+TGG 0.482130 8.1:+36080643 MS.gene46290:CDS
TTCTTCAGTTGTTCATGATG+AGG 0.486893 8.1:+36080573 MS.gene46290:CDS
AAGAGCGTAGCCTCCAATGC+TGG 0.502391 8.1:-36080305 None:intergenic
GCATGTGACTGGGACTTCTA+GGG 0.505358 8.1:+36080531 MS.gene46290:CDS
CAAGATCACCCCTTGGAAAG+TGG 0.509725 8.1:-36080597 None:intergenic
AATGGAAACAAAAGAAAATG+AGG 0.526367 8.1:+36080135 None:intergenic
AATCACGCTTCCAGCATTGG+AGG 0.528529 8.1:+36080295 MS.gene46290:CDS
TCATCATGAACAACTGAAGA+AGG 0.530900 8.1:-36080571 None:intergenic
AAGATCACCCCTTGGAAAGT+GGG 0.533623 8.1:-36080596 None:intergenic
GGCTACGCTCTTGATGGCTG+TGG 0.535093 8.1:+36080316 MS.gene46290:CDS
GAGTCGGCTGAGGGAAACGG+GGG 0.542032 8.1:-36080471 None:intergenic
CCAAGGGGTGATCTTGGAGA+AGG 0.555872 8.1:+36080604 MS.gene46290:CDS
GATACTTATAGTGGTGGAGA+AGG 0.556865 8.1:+36080652 MS.gene46290:CDS
TGATGAGGCCCACTTTCCAA+GGG 0.559791 8.1:+36080588 MS.gene46290:CDS
TAGAAGTCCCAGTCACATGC+TGG 0.560832 8.1:-36080528 None:intergenic
TCACTCATTATCAAAAGGAA+AGG 0.573122 8.1:+36080707 MS.gene46290:CDS
TCTCAAAGCAATAACTTCGA+AGG 0.575954 8.1:+36080250 MS.gene46290:CDS
CCGGTTACCAGCATGTGACT+GGG 0.576238 8.1:+36080521 MS.gene46290:CDS
TCGAGAAGGGAGTCGGCTGA+GGG 0.581880 8.1:-36080480 None:intergenic
ATGGTTCCTTCAATTCCAGC+GGG 0.587215 8.1:-36080349 None:intergenic
AAATGAGGAAGACGTAGTGA+TGG 0.593757 8.1:+36080150 MS.gene46290:CDS
CATGGTGATACTTATAGTGG+TGG 0.595025 8.1:+36080646 MS.gene46290:CDS
GTTGTTGAGCCAATCTATCA+TGG 0.597526 8.1:+36080628 MS.gene46290:CDS
TCAGCCGACTCCCTTCTCGA+CGG 0.603425 8.1:+36080483 MS.gene46290:CDS
CCTTCTCCAAGATCACCCCT+TGG 0.609902 8.1:-36080604 None:intergenic
AAAACCGTCGAGAAGGGAGT+CGG 0.612389 8.1:-36080487 None:intergenic
CATGTGACTGGGACTTCTAG+GGG 0.623678 8.1:+36080532 MS.gene46290:CDS
ATACTTATAGTGGTGGAGAA+GGG 0.640736 8.1:+36080653 MS.gene46290:CDS
GTCACATGCTGGTAACCGGT+CGG 0.647933 8.1:-36080517 None:intergenic
GATGGTTCCTTCAATTCCAG+CGG 0.666037 8.1:-36080350 None:intergenic
AAGGGTCGTCAAAATCAAAG+AGG 0.684157 8.1:+36080671 MS.gene46290:CDS
ATGTGACTGGGACTTCTAGG+GGG 0.700324 8.1:+36080533 MS.gene46290:CDS
GATGAGGCCCACTTTCCAAG+GGG 0.725349 8.1:+36080589 MS.gene46290:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AGCACAATTGAAAAATTCGA+TGG - chr8.1:36080371-36080390 None:intergenic 30.0%
ATTGTTTCAACGTAACTAGT+TGG - chr8.1:36080190-36080209 None:intergenic 30.0%
CAAGTTCACTCATTATCAAA+AGG + chr8.1:36080702-36080721 MS.gene46290:CDS 30.0%
TAAGTATCACCATGATAGAT+TGG - chr8.1:36080640-36080659 None:intergenic 30.0%
TATCATGGTGATACTTATAG+TGG + chr8.1:36080643-36080662 MS.gene46290:CDS 30.0%
TCACTCATTATCAAAAGGAA+AGG + chr8.1:36080707-36080726 MS.gene46290:CDS 30.0%
TTTCTCTCCGATGAAAATTT+CGG - chr8.1:36080408-36080427 None:intergenic 30.0%
! AATTTTCATCGGAGAGAAAA+TGG + chr8.1:36080409-36080428 MS.gene46290:CDS 30.0%
! ACTACATTTTCATCTTGCTT+AGG - chr8.1:36080769-36080788 None:intergenic 30.0%
!!! CTTTTGATAATGAGTGAACT+TGG - chr8.1:36080704-36080723 None:intergenic 30.0%
TATCAAAAGGAAAGGATGCT+TGG + chr8.1:36080715-36080734 MS.gene46290:CDS 35.0%
TCATCATGAACAACTGAAGA+AGG - chr8.1:36080574-36080593 None:intergenic 35.0%
TCTCAAAGCAATAACTTCGA+AGG + chr8.1:36080250-36080269 MS.gene46290:CDS 35.0%
TTCTTCAGTTGTTCATGATG+AGG + chr8.1:36080573-36080592 MS.gene46290:CDS 35.0%
TTCTTCATCATGATGATTCG+AGG - chr8.1:36080218-36080237 None:intergenic 35.0%
! ACTGTCACCGAAATTTTCAT+CGG + chr8.1:36080398-36080417 MS.gene46290:CDS 35.0%
! ATACTTATAGTGGTGGAGAA+GGG + chr8.1:36080653-36080672 MS.gene46290:CDS 35.0%
!!! CTTGGTTTTGCTATGAAATC+GGG + chr8.1:36080733-36080752 MS.gene46290:CDS 35.0%
!!! GCTTGGTTTTGCTATGAAAT+CGG + chr8.1:36080732-36080751 MS.gene46290:CDS 35.0%
AAATGAGGAAGACGTAGTGA+TGG + chr8.1:36080150-36080169 MS.gene46290:CDS 40.0%
AAGGGTCGTCAAAATCAAAG+AGG + chr8.1:36080671-36080690 MS.gene46290:CDS 40.0%
AGTTTGAAAAACCGTCGAGA+AGG - chr8.1:36080497-36080516 None:intergenic 40.0%
CATGGTGATACTTATAGTGG+TGG + chr8.1:36080646-36080665 MS.gene46290:CDS 40.0%
GTTGTTGAGCCAATCTATCA+TGG + chr8.1:36080628-36080647 MS.gene46290:CDS 40.0%
GTTTGAAAAACCGTCGAGAA+GGG - chr8.1:36080496-36080515 None:intergenic 40.0%
! GATACTTATAGTGGTGGAGA+AGG + chr8.1:36080652-36080671 MS.gene46290:CDS 40.0%
! TTTTTACCCGCTGGAATTGA+AGG + chr8.1:36080343-36080362 MS.gene46290:CDS 40.0%
!! GTTTTGCTATGAAATCGGGT+TGG + chr8.1:36080737-36080756 MS.gene46290:CDS 40.0%
AACGGGGGTTGTTAAAAGGA+AGG - chr8.1:36080459-36080478 None:intergenic 45.0%
AAGAATCACGCTTCCAGCAT+TGG + chr8.1:36080292-36080311 MS.gene46290:CDS 45.0%
AAGATCACCCCTTGGAAAGT+GGG - chr8.1:36080599-36080618 None:intergenic 45.0%
ACGGGGGTTGTTAAAAGGAA+GGG - chr8.1:36080458-36080477 None:intergenic 45.0%
ATGGTTCCTTCAATTCCAGC+GGG - chr8.1:36080352-36080371 None:intergenic 45.0%
GATGGTTCCTTCAATTCCAG+CGG - chr8.1:36080353-36080372 None:intergenic 45.0%
!! ACGGTTTTTCAAACTCCGAC+CGG + chr8.1:36080502-36080521 MS.gene46290:CDS 45.0%
AAAACCGTCGAGAAGGGAGT+CGG - chr8.1:36080490-36080509 None:intergenic 50.0%
AGCATGTGACTGGGACTTCT+AGG + chr8.1:36080530-36080549 MS.gene46290:CDS 50.0%
ATGATGAGGCCCACTTTCCA+AGG + chr8.1:36080587-36080606 MS.gene46290:CDS 50.0%
ATGTGACTGGGACTTCTAGG+GGG + chr8.1:36080533-36080552 MS.gene46290:CDS 50.0%
ATTGGAGGCTACGCTCTTGA+TGG + chr8.1:36080310-36080329 MS.gene46290:CDS 50.0%
CAAGATCACCCCTTGGAAAG+TGG - chr8.1:36080600-36080619 None:intergenic 50.0%
CACTTTCCAAGGGGTGATCT+TGG + chr8.1:36080598-36080617 MS.gene46290:CDS 50.0%
CATGTGACTGGGACTTCTAG+GGG + chr8.1:36080532-36080551 MS.gene46290:CDS 50.0%
GCATGTGACTGGGACTTCTA+GGG + chr8.1:36080531-36080550 MS.gene46290:CDS 50.0%
GGGAAACGGGGGTTGTTAAA+AGG - chr8.1:36080463-36080482 None:intergenic 50.0%
TAGAAGTCCCAGTCACATGC+TGG - chr8.1:36080531-36080550 None:intergenic 50.0%
TGATGAGGCCCACTTTCCAA+GGG + chr8.1:36080588-36080607 MS.gene46290:CDS 50.0%
! AATCACGCTTCCAGCATTGG+AGG + chr8.1:36080295-36080314 MS.gene46290:CDS 50.0%
ACCGGTTACCAGCATGTGAC+TGG + chr8.1:36080520-36080539 MS.gene46290:CDS 55.0%
CCAAGGGGTGATCTTGGAGA+AGG + chr8.1:36080604-36080623 MS.gene46290:CDS 55.0%
CCCAGTCACATGCTGGTAAC+CGG - chr8.1:36080524-36080543 None:intergenic 55.0%
CCGGTTACCAGCATGTGACT+GGG + chr8.1:36080521-36080540 MS.gene46290:CDS 55.0%
CCTTCTCCAAGATCACCCCT+TGG - chr8.1:36080607-36080626 None:intergenic 55.0%
GATGAGGCCCACTTTCCAAG+GGG + chr8.1:36080589-36080608 MS.gene46290:CDS 55.0%
GTCACATGCTGGTAACCGGT+CGG - chr8.1:36080520-36080539 None:intergenic 55.0%
! AAGAGCGTAGCCTCCAATGC+TGG - chr8.1:36080308-36080327 None:intergenic 55.0%
! TGTGGCGAGTTTTTACCCGC+TGG + chr8.1:36080334-36080353 MS.gene46290:CDS 55.0%
AGGGAGTCGGCTGAGGGAAA+CGG - chr8.1:36080477-36080496 None:intergenic 60.0%
TCGAGAAGGGAGTCGGCTGA+GGG - chr8.1:36080483-36080502 None:intergenic 60.0%
! GGCTACGCTCTTGATGGCTG+TGG + chr8.1:36080316-36080335 MS.gene46290:CDS 60.0%
! TCAGCCGACTCCCTTCTCGA+CGG + chr8.1:36080483-36080502 MS.gene46290:CDS 60.0%
GAGTCGGCTGAGGGAAACGG+GGG - chr8.1:36080474-36080493 None:intergenic 65.0%
GGAGTCGGCTGAGGGAAACG+GGG - chr8.1:36080475-36080494 None:intergenic 65.0%
GGGAGTCGGCTGAGGGAAAC+GGG - chr8.1:36080476-36080495 None:intergenic 65.0%
GTCGAGAAGGGAGTCGGCTG+AGG - chr8.1:36080484-36080503 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr8.1 gene 36080136 36080799 36080136 ID=MS.gene46290
chr8.1 mRNA 36080136 36080799 36080136 ID=MS.gene46290.t1;Parent=MS.gene46290
chr8.1 exon 36080136 36080799 36080136 ID=MS.gene46290.t1.exon1;Parent=MS.gene46290.t1
chr8.1 CDS 36080136 36080799 36080136 ID=cds.MS.gene46290.t1;Parent=MS.gene46290.t1
Gene Sequence

>MS.gene46290

ATGGAAACAAAAGAAAATGAGGAAGACGTAGTGATGGCTAATGACAGTGATCCAACTAGTTACGTTGAAACAATTAAAACCTCGAATCATCATGATGAAGAAACTCTAATGAATTCTCAAAGCAATAACTTCGAAGGAAAGTTCAAAGAGTGTAGAAAGAATCACGCTTCCAGCATTGGAGGCTACGCTCTTGATGGCTGTGGCGAGTTTTTACCCGCTGGAATTGAAGGAACCATCGAATTTTTCAATTGTGCTGCGTGTAACTGTCACCGAAATTTTCATCGGAGAGAAAATGGTGTTGTTAATGAAGAGAATATTTCCCTTCCTTTTAACAACCCCCGTTTCCCTCAGCCGACTCCCTTCTCGACGGTTTTTCAAACTCCGACCGGTTACCAGCATGTGACTGGGACTTCTAGGGGGACAACTACTTCTATTCCTTCTTCAGTTGTTCATGATGAGGCCCACTTTCCAAGGGGTGATCTTGGAGAAGGTGTTGTTGAGCCAATCTATCATGGTGATACTTATAGTGGTGGAGAAGGGTCGTCAAAATCAAAGAGGTTCAGATCCAAGTTCACTCATTATCAAAAGGAAAGGATGCTTGGTTTTGCTATGAAATCGGGTTGGAAGATTCCTAAGCAAGATGAAAATGTAGTTGAACAATTTT
Protein sequence

>MS.gene46290.t1

METKENEEDVVMANDSDPTSYVETIKTSNHHDEETLMNSQSNNFEGKFKECRKNHASSIGGYALDGCGEFLPAGIEGTIEFFNCAACNCHRNFHRRENGVVNEENISLPFNNPRFPQPTPFSTVFQTPTGYQHVTGTSRGTTTSIPSSVVHDEAHFPRGDLGEGVVEPIYHGDTYSGGEGSSKSKRFRSKFTHYQKERMLGFAMKSGWKIPKQDENVVEQF