AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene01947

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01947.t1 MTR_2g027100 98.795 166 2 0 1 166 1 166 2.86e-117 328
MS.gene01947.t1 MTR_8g088320 46.626 163 74 2 1 157 161 316 4.80e-41 140
MS.gene01947.t1 MTR_2g011590 43.791 153 84 1 5 157 4 154 1.51e-39 132
MS.gene01947.t1 MTR_3g067585 43.312 157 87 1 1 157 1 155 6.32e-39 130
MS.gene01947.t1 MTR_2g030230 45.223 157 85 1 1 157 168 323 1.74e-37 131
MS.gene01947.t1 MTR_8g107340 42.038 157 89 1 1 157 17 171 2.39e-36 124
MS.gene01947.t1 MTR_6g069470 40.127 157 92 2 1 157 13 167 3.17e-36 124
MS.gene01947.t1 MTR_3g017500 45.860 157 84 1 1 157 209 364 8.07e-35 125
MS.gene01947.t1 MTR_3g017500 45.860 157 84 1 1 157 239 394 1.95e-34 124
MS.gene01947.t1 MTR_8g038400 43.312 157 88 1 1 157 206 361 2.80e-32 118
MS.gene01947.t1 MTR_4g084280 39.474 152 90 1 1 152 1 150 2.92e-30 108
MS.gene01947.t1 MTR_1g031650 42.282 149 83 2 5 152 6 152 7.46e-30 107
MS.gene01947.t1 MTR_1g031650 40.517 116 67 1 37 152 2 115 3.03e-20 81.6
MS.gene01947.t1 MTR_8g032320 37.500 96 58 2 6 99 4 99 1.69e-12 62.0
MS.gene01947.t1 MTR_1g008950 35.417 96 60 2 6 99 4 99 1.73e-12 61.2
MS.gene01947.t1 MTR_8g032300 37.363 91 55 2 6 94 4 94 1.54e-11 59.3
MS.gene01947.t1 MTR_6g084400 38.053 113 61 5 7 113 484 593 3.61e-11 60.8
MS.gene01947.t1 MTR_1g045930 35.556 90 56 2 6 93 127 216 5.85e-11 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.gene01947.t1 AT5G47710 69.880 166 50 0 1 166 1 166 3.90e-84 245
MS.gene01947.t1 AT5G47710 69.880 166 50 0 1 166 1 166 3.90e-84 245
MS.gene01947.t1 AT5G47710 69.880 166 50 0 1 166 1 166 3.90e-84 245
MS.gene01947.t1 AT5G47710 69.880 166 50 0 1 166 1 166 3.90e-84 245
MS.gene01947.t1 AT1G70790 45.513 156 83 2 5 159 6 160 1.76e-39 132
MS.gene01947.t1 AT1G70790 45.513 156 83 2 5 159 6 160 1.76e-39 132
MS.gene01947.t1 AT1G70790 45.513 156 83 2 5 159 6 160 1.76e-39 132
MS.gene01947.t1 AT1G73580 45.223 157 84 1 1 157 4 158 2.60e-39 131
MS.gene01947.t1 AT2G01540 44.156 154 84 2 5 157 6 158 1.62e-37 127
MS.gene01947.t1 AT4G05330 44.586 157 86 1 1 157 140 295 2.91e-37 130
MS.gene01947.t1 AT4G05330 44.586 157 86 1 1 157 175 330 9.30e-37 129
MS.gene01947.t1 AT4G05330 44.586 157 86 1 1 157 175 330 9.30e-37 129
MS.gene01947.t1 AT3G17980 41.401 157 90 2 1 157 13 167 1.29e-36 125
MS.gene01947.t1 AT4G21160 43.312 157 88 1 1 157 176 331 1.32e-36 129
MS.gene01947.t1 AT4G21160 43.312 157 88 1 1 157 176 331 1.32e-36 129
MS.gene01947.t1 AT4G21160 43.312 157 88 1 1 157 176 331 1.32e-36 129
MS.gene01947.t1 AT4G21160 43.312 157 88 1 1 157 176 331 1.32e-36 129
MS.gene01947.t1 AT5G37740 40.506 158 93 1 1 157 1 158 1.69e-36 124
MS.gene01947.t1 AT1G66360 38.854 157 96 0 1 157 1 157 4.66e-36 123
MS.gene01947.t1 AT1G70810 41.401 157 90 2 1 157 1 155 8.98e-36 122
MS.gene01947.t1 AT3G07940 45.223 157 85 1 1 157 224 379 9.37e-35 125
MS.gene01947.t1 AT1G23140 37.576 165 101 2 1 165 1 163 5.60e-34 117
MS.gene01947.t1 AT1G48590 39.490 157 93 2 1 157 6 160 7.06e-34 117
MS.gene01947.t1 AT1G48590 39.490 157 93 2 1 157 6 160 7.06e-34 117
MS.gene01947.t1 AT1G48590 39.490 157 93 2 1 157 37 191 1.21e-33 118
MS.gene01947.t1 AT5G37740 38.095 168 93 2 1 157 1 168 4.12e-33 116
MS.gene01947.t1 AT1G70800 36.943 157 97 1 1 157 10 164 2.57e-31 111
MS.gene01947.t1 AT1G70790 42.149 121 68 2 40 159 4 123 1.84e-26 98.2
MS.gene01947.t1 AT1G48590 32.484 157 72 3 1 157 37 159 8.72e-20 81.6

Find 34 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCCTTGGGAGTTCTCAATT+TGG 0.326299 2.2:-60072720 MS.gene01947:intron
CCTTATGTTGTTCTCAAACT+AGG 0.327913 2.2:-60073270 MS.gene01947:CDS
AGCATAATGAGTGAACAATT+AGG 0.351310 2.2:-60073357 None:intergenic
CTTCCGGTGAGCAAACATTA+AGG 0.379148 2.2:-60072200 MS.gene01947:CDS
ATAGCTGTTTGAATCCTGTT+TGG 0.381671 2.2:-60072772 MS.gene01947:CDS
TGTTCTCAAACTAGGGAATC+AGG 0.396033 2.2:-60073262 MS.gene01947:intron
GCATAATGAGTGAACAATTA+GGG 0.402497 2.2:-60073356 None:intergenic
GCGCGGTTGTGCAGAATGTT+TGG 0.408048 2.2:-60072116 MS.gene01947:CDS
TTCAGCTCTTCATTCCAAAC+AGG 0.413548 2.2:+60072758 None:intergenic
AGCAGTATCAATTGTGTTAA+CGG 0.427721 2.2:-60072138 MS.gene01947:CDS
TTGTGCAGAATGTTTGGTTA+AGG 0.448350 2.2:-60072110 MS.gene01947:CDS
AATCTAGCTGCAGAGACTAA+TGG 0.452322 2.2:+60072243 None:intergenic
CTTATGTTGTTCTCAAACTA+GGG 0.459241 2.2:-60073269 MS.gene01947:CDS
CCTAGTTTGAGAACAACATA+AGG 0.471060 2.2:+60073270 None:intergenic
AAGGGAAAAGGTTAGTGATC+CGG 0.474630 2.2:-60073311 MS.gene01947:CDS
CTGCAGAGACTAATGGTTGA+AGG 0.477932 2.2:+60072250 None:intergenic
TTTCACATTGACAGAACCCT+TGG 0.483462 2.2:-60072735 MS.gene01947:CDS
TCATAGTTGTGCAAGGGAAA+AGG 0.483953 2.2:-60073323 MS.gene01947:CDS
GAGTGTCAATTCTATCTCTC+CGG 0.491542 2.2:+60072071 None:intergenic
TTTGAAAGCTGACGACAAGA+TGG 0.511147 2.2:-60072289 MS.gene01947:CDS
AGGGAAAAGGTTAGTGATCC+GGG 0.515305 2.2:-60073310 MS.gene01947:CDS
GATCACTGGTCTTGAAATCC+CGG 0.525136 2.2:+60073292 None:intergenic
CTTCCTTAATGTTTGCTCAC+CGG 0.528914 2.2:+60072197 None:intergenic
TTGAAAGCTGACGACAAGAT+GGG 0.533213 2.2:-60072288 MS.gene01947:CDS
TTCACATTGACAGAACCCTT+GGG 0.549458 2.2:-60072734 MS.gene01947:CDS
GAGAACAACATAAGGATCAC+TGG 0.556443 2.2:+60073278 None:intergenic
TGAACAATTAGGGCAACTAA+AGG 0.562294 2.2:-60073346 MS.gene01947:CDS
AGGCTTCGCGAAGTAGAATC+CGG 0.566418 2.2:-60072090 MS.gene01947:CDS
CTAAAGGTCATAGTTGTGCA+AGG 0.584222 2.2:-60073330 MS.gene01947:CDS
CGGTGAGCAAACATTAAGGA+AGG 0.588349 2.2:-60072196 MS.gene01947:CDS
CACCAAATTGAGAACTCCCA+AGG 0.596444 2.2:+60072718 None:intergenic
TAAAGGTCATAGTTGTGCAA+GGG 0.611606 2.2:-60073329 MS.gene01947:CDS
ACCAAATTGAGAACTCCCAA+GGG 0.650902 2.2:+60072719 None:intergenic
TATCAATTGTGTTAACGGCG+CGG 0.708048 2.2:-60072133 MS.gene01947:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTAACTTCAAAATATTAA+AGG - chr2.2:60072549-60072568 MS.gene01947:intron 10.0%
!!! TTAGGTATAAGTTTTTTTTA+AGG + chr2.2:60072964-60072983 None:intergenic 15.0%
!! ATACTACTGAATAATGTTAA+GGG + chr2.2:60072528-60072547 None:intergenic 20.0%
!! ATTTACAATGCCTTATATAT+TGG - chr2.2:60072705-60072724 MS.gene01947:intron 20.0%
!! TATACTACTGAATAATGTTA+AGG + chr2.2:60072529-60072548 None:intergenic 20.0%
!!! CTACAATTTTTTTGACATTA+AGG - chr2.2:60072290-60072309 MS.gene01947:CDS 20.0%
! AGTTGAACAAATAAGTGTTT+AGG + chr2.2:60072982-60073001 None:intergenic 25.0%
! TACTACTGAATAATGTTAAG+GGG + chr2.2:60072527-60072546 None:intergenic 25.0%
! TATGTTATACGTGCATAATT+AGG - chr2.2:60073004-60073023 MS.gene01947:intron 25.0%
! TGCAACTCAGTTATAAATAT+AGG + chr2.2:60073048-60073067 None:intergenic 25.0%
! TTTGACATTAAGGACATATA+TGG - chr2.2:60072300-60072319 MS.gene01947:CDS 25.0%
!! GATTATCAAATGAGCTATTT+TGG - chr2.2:60072342-60072361 MS.gene01947:intron 25.0%
!! TAATTTCTGAAAACAGTTGT+GGG - chr2.2:60072405-60072424 MS.gene01947:intron 25.0%
!!! ATTAGGTTTTTTATCTGAAG+AGG - chr2.2:60073021-60073040 MS.gene01947:intron 25.0%
!!! TATAAGGCATTGTAAATATC+AGG + chr2.2:60072702-60072721 None:intergenic 25.0%
!!! TTAGGTTTTTTATCTGAAGA+GGG - chr2.2:60073022-60073041 MS.gene01947:intron 25.0%
AGCAAAGAGACCAATATATA+AGG + chr2.2:60072718-60072737 None:intergenic 30.0%
AGCAGTATCAATTGTGTTAA+CGG - chr2.2:60073251-60073270 MS.gene01947:intron 30.0%
ATGCATCTTCAAAGTTTATC+TGG + chr2.2:60072491-60072510 None:intergenic 30.0%
ATGTTGTATATAGGACTGTT+TGG - chr2.2:60072753-60072772 MS.gene01947:CDS 30.0%
CTTATGTTGTTCTCAAACTA+GGG - chr2.2:60072120-60072139 MS.gene01947:CDS 30.0%
TAAACTCTTCCAAGTCTATT+AGG + chr2.2:60072798-60072817 None:intergenic 30.0%
! ATTGACTTACTGCTTCATAT+AGG + chr2.2:60072200-60072219 None:intergenic 30.0%
! CTAATTTCTGAAAACAGTTG+TGG - chr2.2:60072404-60072423 MS.gene01947:intron 30.0%
! CTGAGTTGCATTTTGAATAT+AGG - chr2.2:60073058-60073077 MS.gene01947:intron 30.0%
! TACAAGACAATTTTCAGAGT+CGG + chr2.2:60073225-60073244 None:intergenic 30.0%
! TATATATTGGTCTCTTTGCT+TGG - chr2.2:60072718-60072737 MS.gene01947:intron 30.0%
!! ATCAAATGAGCTATTTTGGA+GGG - chr2.2:60072346-60072365 MS.gene01947:intron 30.0%
!! TATCAAATGAGCTATTTTGG+AGG - chr2.2:60072345-60072364 MS.gene01947:intron 30.0%
!! TTATGATCAGAAGCTGTTTT+TGG - chr2.2:60072378-60072397 MS.gene01947:intron 30.0%
ATAGCTGTTTGAATCCTGTT+TGG - chr2.2:60072617-60072636 MS.gene01947:intron 35.0%
CCTAGTTTGAGAACAACATA+AGG + chr2.2:60072122-60072141 None:intergenic 35.0%
CCTTATGTTGTTCTCAAACT+AGG - chr2.2:60072119-60072138 MS.gene01947:CDS 35.0%
GTACTCTGCATGTTGTATAT+AGG - chr2.2:60072744-60072763 MS.gene01947:CDS 35.0%
GTATATAGGACTGTTTGGAA+TGG - chr2.2:60072758-60072777 MS.gene01947:CDS 35.0%
TAAAGGTCATAGTTGTGCAA+GGG - chr2.2:60072060-60072079 MS.gene01947:CDS 35.0%
TGAACAATTAGGGCAACTAA+AGG - chr2.2:60072043-60072062 MS.gene01947:CDS 35.0%
TTGAGCTTACCTAATAGACT+TGG - chr2.2:60072786-60072805 MS.gene01947:CDS 35.0%
TTGTGCAGAATGTTTGGTTA+AGG - chr2.2:60073279-60073298 MS.gene01947:CDS 35.0%
! ACAAGACAATTTTCAGAGTC+GGG + chr2.2:60073224-60073243 None:intergenic 35.0%
! TGAATAATGTTAAGGGGCAT+TGG + chr2.2:60072521-60072540 None:intergenic 35.0%
!! GACATTTTAAGAGTCTCTTC+CGG - chr2.2:60073173-60073192 MS.gene01947:intron 35.0%
AAGGGAAAAGGTTAGTGATC+CGG - chr2.2:60072078-60072097 MS.gene01947:CDS 40.0%
AATCTAGCTGCAGAGACTAA+TGG + chr2.2:60073149-60073168 None:intergenic 40.0%
ACCAAATTGAGAACTCCCAA+GGG + chr2.2:60072673-60072692 None:intergenic 40.0%
ACGCCTTCAATGTGAATTGT+TGG - chr2.2:60072265-60072284 MS.gene01947:CDS 40.0%
CTAAAGGTCATAGTTGTGCA+AGG - chr2.2:60072059-60072078 MS.gene01947:CDS 40.0%
CTTCCTTAATGTTTGCTCAC+CGG + chr2.2:60073195-60073214 None:intergenic 40.0%
GAGAACAACATAAGGATCAC+TGG + chr2.2:60072114-60072133 None:intergenic 40.0%
GAGTGTCAATTCTATCTCTC+CGG + chr2.2:60073321-60073340 None:intergenic 40.0%
GCACCAACAATTCACATTGA+AGG + chr2.2:60072271-60072290 None:intergenic 40.0%
GCTGTTGACAAAAGCTATCA+TGG + chr2.2:60072877-60072896 None:intergenic 40.0%
TATCAATTGTGTTAACGGCG+CGG - chr2.2:60073256-60073275 MS.gene01947:intron 40.0%
TCATAGTTGTGCAAGGGAAA+AGG - chr2.2:60072066-60072085 MS.gene01947:CDS 40.0%
TGTTCTCAAACTAGGGAATC+AGG - chr2.2:60072127-60072146 MS.gene01947:CDS 40.0%
TTCACATTGACAGAACCCTT+GGG - chr2.2:60072655-60072674 MS.gene01947:intron 40.0%
TTCAGCTCTTCATTCCAAAC+AGG + chr2.2:60072634-60072653 None:intergenic 40.0%
TTGAAAGCTGACGACAAGAT+GGG - chr2.2:60073101-60073120 MS.gene01947:intron 40.0%
TTTCACATTGACAGAACCCT+TGG - chr2.2:60072654-60072673 MS.gene01947:intron 40.0%
TTTGAAAGCTGACGACAAGA+TGG - chr2.2:60073100-60073119 MS.gene01947:intron 40.0%
! GCTTTTGTCAACAGCTTGTA+TGG - chr2.2:60072882-60072901 MS.gene01947:intron 40.0%
! TATTGGTCTCTTTGCTTGGA+AGG - chr2.2:60072722-60072741 MS.gene01947:CDS 40.0%
ACCCTTGGGAGTTCTCAATT+TGG - chr2.2:60072669-60072688 MS.gene01947:intron 45.0%
AGGGAAAAGGTTAGTGATCC+GGG - chr2.2:60072079-60072098 MS.gene01947:CDS 45.0%
CACCAAATTGAGAACTCCCA+AGG + chr2.2:60072674-60072693 None:intergenic 45.0%
CGGTGAGCAAACATTAAGGA+AGG - chr2.2:60073193-60073212 MS.gene01947:intron 45.0%
CTGCAGAGACTAATGGTTGA+AGG + chr2.2:60073142-60073161 None:intergenic 45.0%
CTTCCGGTGAGCAAACATTA+AGG - chr2.2:60073189-60073208 MS.gene01947:intron 45.0%
!! GATCACTGGTCTTGAAATCC+CGG + chr2.2:60072100-60072119 None:intergenic 45.0%
!!! TTTTGAAGCAGCAACAGGTG+TGG + chr2.2:60073351-60073370 None:intergenic 45.0%
AGGCTTCGCGAAGTAGAATC+CGG - chr2.2:60073299-60073318 MS.gene01947:CDS 50.0%
TGACTTTCGTCTTCGCAGTC+TGG + chr2.2:60072594-60072613 None:intergenic 50.0%
GCGCGGTTGTGCAGAATGTT+TGG - chr2.2:60073273-60073292 MS.gene01947:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 60072038 60073373 60072038 ID=MS.gene01947
chr2.2 mRNA 60072038 60073373 60072038 ID=MS.gene01947.t1;Parent=MS.gene01947
chr2.2 exon 60073263 60073373 60073263 ID=MS.gene01947.t1.exon1;Parent=MS.gene01947.t1
chr2.2 CDS 60073263 60073373 60073263 ID=cds.MS.gene01947.t1;Parent=MS.gene01947.t1
chr2.2 exon 60072721 60072816 60072721 ID=MS.gene01947.t1.exon2;Parent=MS.gene01947.t1
chr2.2 CDS 60072721 60072816 60072721 ID=cds.MS.gene01947.t1;Parent=MS.gene01947.t1
chr2.2 exon 60072038 60072331 60072038 ID=MS.gene01947.t1.exon3;Parent=MS.gene01947.t1
chr2.2 CDS 60072038 60072331 60072038 ID=cds.MS.gene01947.t1;Parent=MS.gene01947.t1
Gene Sequence

>MS.gene01947

ATGAGTGAACAATTAGGGCAACTAAAGGTCATAGTTGTGCAAGGGAAAAGGTTAGTGATCCGGGATTTCAAGACCAGTGATCCTTATGTTGTTCTCAAACTAGGGAATCAGGTAACTAACATTTATATTGCATATTCATCTTTCGTTTCTTTTTCTTGACCTATATGAAGCAGTAAGTCAATAATTTAAGAAAATAGACGTGATTGAATGTAACTTGAACACGAGACACGCCTTCAATGTGAATTGTTGGTGCTACAATTTTTTTGACATTAAGGACATATATGGATAAGCATTTTAAGTAATTGATTATCAAATGAGCTATTTTGGAGGGCTTAAACGCTTATGATCAGAAGCTGTTTTTGGCAGCTAATTTCTGAAAACAGTTGTGGGAATGTTATGATTTTTACAAGTGTATTAAAATATGTAAGTACTTGTGTCATGAGATATAATCCAGATAAACTTTGAAGATGCATGCTCTTTCCAATGCCCCTTAACATTATTCAGTAGTATATTTTAACTTCAAAATATTAAAGGATTCATTCATTAAACTGTACCAGACTGCGAAGACGAAAGTCATTAATAGCTGTTTGAATCCTGTTTGGAATGAAGAGCTGAATTTCACATTGACAGAACCCTTGGGAGTTCTCAATTTGGTGAGTTTCCTGATATTTACAATGCCTTATATATTGGTCTCTTTGCTTGGAAGGTACTCTGCATGTTGTATATAGGACTGTTTGGAATGGCATATTTGAGCTTACCTAATAGACTTGGAAGAGTTTATGAAAATGACATATGACACATTCATAAGCTGTTTTCAGCTTATTTGAACAAGCTCTCCATGATAGCTTTTGTCAACAGCTTGTATGGAAACAATTCACTTTATTTATTCTTTTGCTATAGAAATAACTTATACATAAGCATCGCCTTAAAAAAAACTTATACCTAAACACTTATTTGTTCAACTTTTATGTTATACGTGCATAATTAGGTTTTTTATCTGAAGAGGGCCTATATTTATAACTGAGTTGCATTTTGAATATAGGAAGTATTTGATAAAGATCTTTTGAAAGCTGACGACAAGATGGGAAATGCATTTATCAACCTTCAACCATTAGTCTCTGCAGCTAGATTAAGAGACATTTTAAGAGTCTCTTCCGGTGAGCAAACATTAAGGAAGGTTATACCCGACTCTGAAAATTGTCTTGTACGCGAAAGCAGTATCAATTGTGTTAACGGCGCGGTTGTGCAGAATGTTTGGTTAAGGCTTCGCGAAGTAGAATCCGGAGAGATAGAATTGACACTCAAGTTAACCACACCTGTTGCTGCTTCAAAATAG
Protein sequence

>MS.gene01947.t1

MSEQLGQLKVIVVQGKRLVIRDFKTSDPYVVLKLGNQTAKTKVINSCLNPVWNEELNFTLTEPLGVLNLEVFDKDLLKADDKMGNAFINLQPLVSAARLRDILRVSSGEQTLRKVIPDSENCLVRESSINCVNGAVVQNVWLRLREVESGEIELTLKLTTPVAASK