AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene003923

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003923.t1 MTR_4g051538 54.980 251 92 5 1 248 1 233 2.63e-81 244
MS.gene003923.t1 MTR_3g104630 56.757 148 57 5 94 238 3 146 4.55e-42 140
MS.gene003923.t1 MTR_3g052920 36.527 167 89 5 1 150 1 167 7.16e-22 90.9
MS.gene003923.t1 MTR_2g030740 37.126 167 88 4 1 150 1 167 1.04e-21 90.5
MS.gene003923.t1 MTR_1g105910 36.646 161 85 4 1 144 1 161 1.14e-21 90.5
MS.gene003923.t1 MTR_1g012570 37.356 174 87 8 1 156 1 170 1.25e-21 90.5
MS.gene003923.t1 MTR_8g043650 36.424 151 81 3 1 136 1 151 3.11e-21 89.4
MS.gene003923.t1 MTR_1g077360 30.457 197 113 5 1 187 1 183 3.98e-21 89.0
MS.gene003923.t1 MTR_5g053390 32.075 212 116 8 1 201 1 195 6.40e-21 88.6
MS.gene003923.t1 MTR_1g106070 36.646 161 85 5 1 144 1 161 1.34e-20 86.3
MS.gene003923.t1 MTR_1g108510 32.530 166 99 3 1 156 1 163 1.89e-20 87.0
MS.gene003923.t1 MTR_3g030770 32.530 166 99 3 1 156 1 163 3.13e-20 86.3
MS.gene003923.t1 MTR_3g080940 33.133 166 96 4 1 155 1 162 1.72e-19 84.0
MS.gene003923.t1 MTR_1g105920 35.762 151 82 3 1 136 1 151 2.93e-19 84.0
MS.gene003923.t1 MTR_2g085280 30.625 160 100 3 1 151 1 158 4.89e-19 83.6
MS.gene003923.t1 MTR_2g085250 30.625 160 100 3 1 151 1 158 5.31e-19 83.2
MS.gene003923.t1 MTR_8g086290 31.579 171 84 4 4 156 7 162 1.23e-18 80.9
MS.gene003923.t1 MTR_1g075600 30.682 176 106 4 1 163 1 173 1.52e-18 82.0
MS.gene003923.t1 MTR_3g052870 51.389 72 35 0 1 72 1 72 2.62e-18 80.9
MS.gene003923.t1 MTR_5g045560 33.577 137 81 3 1 127 1 137 2.65e-18 81.3
MS.gene003923.t1 MTR_1g108580 34.132 167 81 6 1 144 1 161 2.98e-18 81.3
MS.gene003923.t1 MTR_2g105290 30.818 159 101 3 4 156 7 162 1.66e-17 77.8
MS.gene003923.t1 MTR_5g055100 29.536 237 127 10 1 202 1 232 2.06e-17 79.0
MS.gene003923.t1 MTR_2g093190 31.677 161 93 4 1 144 1 161 1.05e-16 77.0
MS.gene003923.t1 MTR_0121s0100 42.857 77 44 0 1 77 1 77 7.05e-16 72.4
MS.gene003923.t1 MTR_3g030780 39.252 107 62 2 1 104 1 107 2.63e-15 70.9
MS.gene003923.t1 MTR_4g094638 49.275 69 35 0 9 77 2 70 2.82e-15 72.0
MS.gene003923.t1 MTR_4g094632 34.028 144 83 4 9 151 2 134 2.74e-14 68.9
MS.gene003923.t1 MTR_1g047550 36.885 122 61 3 9 118 2 119 2.98e-14 69.3
MS.gene003923.t1 MTR_1g105905 29.189 185 112 6 18 185 1 183 7.43e-14 68.9
MS.gene003923.t1 MTR_8g046350 41.667 72 42 0 9 80 2 73 8.01e-14 67.8
MS.gene003923.t1 MTR_8g051580 32.143 140 71 4 9 126 2 139 9.28e-14 67.8
MS.gene003923.t1 MTR_8g079502 41.250 80 46 1 9 87 2 81 1.57e-13 67.4
MS.gene003923.t1 MTR_0121s0080 30.120 166 99 4 1 149 1 166 1.75e-13 68.2
MS.gene003923.t1 MTR_3g067875 49.091 55 28 0 18 72 1 55 3.70e-13 63.2
MS.gene003923.t1 MTR_8g022970 32.515 163 94 4 8 159 17 174 4.50e-13 66.2
MS.gene003923.t1 MTR_1g063160 36.134 119 66 3 9 118 2 119 1.76e-12 64.3
MS.gene003923.t1 MTR_1g054265 40.000 70 42 0 9 78 2 71 6.28e-12 62.8
MS.gene003923.t1 MTR_4g131030 38.889 72 44 0 9 80 2 73 9.67e-12 63.2
MS.gene003923.t1 MTR_1g029670 48.438 64 33 0 9 72 2 65 2.72e-11 61.2
MS.gene003923.t1 MTR_7g028448 29.921 127 83 4 26 148 29 153 5.82e-11 60.1
MS.gene003923.t1 MTR_4g036915 29.921 127 83 4 26 148 29 153 5.82e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003923.t1 AT4G36590 34.132 167 93 3 5 156 3 167 2.36e-21 90.1
MS.gene003923.t1 AT1G29962 35.227 176 96 4 1 161 1 173 2.56e-21 88.2
MS.gene003923.t1 AT2G24840 32.474 194 109 6 7 187 61 245 1.49e-20 88.2
MS.gene003923.t1 AT1G28460 35.260 173 97 4 1 161 1 170 1.98e-19 83.2
MS.gene003923.t1 AT5G60440 32.547 212 115 7 5 205 3 197 8.52e-18 81.3
MS.gene003923.t1 AT1G01530 37.288 118 68 2 5 117 3 119 1.11e-17 80.1
MS.gene003923.t1 AT2G34440 32.203 177 97 7 9 174 2 166 5.75e-17 76.3
MS.gene003923.t1 AT1G28450 32.759 174 99 4 1 159 1 171 1.79e-16 75.5
MS.gene003923.t1 AT3G04100 41.573 89 49 1 2 90 7 92 1.97e-15 73.2
MS.gene003923.t1 AT1G65360 33.019 106 67 1 5 106 3 108 8.89e-15 71.6
MS.gene003923.t1 AT3G66656 47.692 65 34 0 9 73 2 66 1.83e-13 67.0
MS.gene003923.t1 AT1G47760 39.759 83 47 1 9 91 2 81 3.79e-13 66.2
MS.gene003923.t1 AT4G11880 49.254 67 32 1 10 76 3 67 8.30e-11 59.7
MS.gene003923.t1 AT4G11880 49.254 67 32 1 10 76 3 67 8.30e-11 59.7

Find 46 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAGCATATCATTCATCTTT+AGG 0.191781 4.2:-39619671 None:intergenic
ACAAATCCTCCTTATGTCTT+TGG 0.244037 4.2:+39619254 MS.gene003923:CDS
AACAACAACGGTTATGAAAT+TGG 0.254239 4.2:+39619281 MS.gene003923:CDS
TCAGGAAAGTTTGAAGGCTT+TGG 0.277217 4.2:+39618927 MS.gene003923:CDS
CAAATCCTCCTTATGTCTTT+GGG 0.283816 4.2:+39619255 MS.gene003923:CDS
GAAGGTTCTCCATAACAATA+TGG 0.353627 4.2:-39618769 None:intergenic
CTTTGGAAAGTTATGGCTAT+TGG 0.358280 4.2:+39618944 MS.gene003923:CDS
AAAATTGGACACATCTTTAG+TGG 0.370003 4.2:+39619014 MS.gene003923:CDS
GATGTTATTGCTTCTCTTGA+AGG 0.392101 4.2:+39619575 MS.gene003923:CDS
TCTGAATTATCAACACTTTG+TGG 0.392582 4.2:+39618706 MS.gene003923:CDS
TTGAAGGCTTTGGAAAGTTA+TGG 0.393387 4.2:+39618937 MS.gene003923:CDS
GCATGTTGCGGAAGCTCATC+AGG 0.403902 4.2:+39618909 MS.gene003923:CDS
CTTGCTATGGATTGAGAAGA+AGG 0.408194 4.2:-39618787 None:intergenic
GCAGGAAAACCATATTGTTA+TGG 0.420932 4.2:+39618760 MS.gene003923:CDS
TCACTTGCACGGTCAAGGTT+TGG 0.423194 4.2:-39619617 None:intergenic
CTGAATTATCAACACTTTGT+GGG 0.424852 4.2:+39618707 MS.gene003923:CDS
CTACCTCTTGATGTCCTCTT+CGG 0.429458 4.2:-39618595 None:intergenic
CTTCAAAATTGTTCTTGCTA+TGG 0.431100 4.2:-39618800 None:intergenic
CATTTCCACTTTCACTTGCA+CGG 0.448306 4.2:-39619628 None:intergenic
ATTCTTATTATTTCTCCAGC+AGG 0.453510 4.2:+39618742 MS.gene003923:CDS
CACTTTCACTTGCACGGTCA+AGG 0.460125 4.2:-39619622 None:intergenic
AATTTCATAACCGTTGTTGT+TGG 0.462889 4.2:-39619279 None:intergenic
AGACATAAGGAGGATTTGTC+TGG 0.473975 4.2:-39619250 None:intergenic
CTTGACCGTGCAAGTGAAAG+TGG 0.475104 4.2:+39619623 MS.gene003923:CDS
TTGTTGGCCCCAAAGACATA+AGG 0.478695 4.2:-39619263 None:intergenic
TTTAATTCTTCTTCTACCGA+AGG 0.479866 4.2:-39618832 None:intergenic
AGCTCATCAGGAAAGTTTGA+AGG 0.487303 4.2:+39618921 MS.gene003923:CDS
CGTGCAAGTGAAAGTGGAAA+TGG 0.489776 4.2:+39619629 MS.gene003923:CDS
ATTTATGATCCAAAAGGAAA+AGG 0.506756 4.2:+39619548 MS.gene003923:CDS
TCCCAGATTTATGATCCAAA+AGG 0.515467 4.2:+39619542 MS.gene003923:CDS
TTTGAAGAATGAAAACCCTT+CGG 0.527588 4.2:+39618816 MS.gene003923:CDS
TCTTGCATAGATGAACTGAA+TGG 0.533604 4.2:+39619224 MS.gene003923:CDS
TTAATTCTTCTTCTACCGAA+GGG 0.546382 4.2:-39618831 None:intergenic
ATAAGTAGTGTCTTAAGCAA+TGG 0.548667 4.2:+39619054 MS.gene003923:CDS
TGAATTATCAACACTTTGTG+GGG 0.569118 4.2:+39618708 MS.gene003923:CDS
GTCTTTGGGGCCAACAACAA+CGG 0.574083 4.2:+39619269 MS.gene003923:CDS
GGAGGAGAGATTAATCCTCA+TGG 0.604055 4.2:+39619075 MS.gene003923:CDS
AAATCCTCCTTATGTCTTTG+GGG 0.607760 4.2:+39619256 MS.gene003923:CDS
AGTAGTGTCTTAAGCAATGG+AGG 0.611596 4.2:+39619057 MS.gene003923:CDS
TTGGCCCCAAAGACATAAGG+AGG 0.611952 4.2:-39619260 None:intergenic
ACAAAGTGTTGATAATTCAG+AGG 0.616841 4.2:-39618704 None:intergenic
TGATCCAAAAGGAAAAGGCA+AGG 0.624272 4.2:+39619553 MS.gene003923:CDS
TTTGGATGAAAAGCATGTTG+CGG 0.629913 4.2:+39618897 MS.gene003923:CDS
TGGTTAAGATGGCTCCGAAG+AGG 0.660173 4.2:+39618581 None:intergenic
GCTCCGAAGAGGACATCAAG+AGG 0.673948 4.2:+39618592 MS.gene003923:CDS
GAAGGTAGAAATAAAACACA+AGG 0.705496 4.2:+39619593 MS.gene003923:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CTAATTTATTTATGAAAAAG+TGG + chr4.2:39619178-39619197 MS.gene003923:intron 15.0%
!! GAAATTATACAATATGTGTT+AGG - chr4.2:39619502-39619521 None:intergenic 20.0%
!! TTATGACCAGTTAAAAAAAT+TGG + chr4.2:39618999-39619018 MS.gene003923:CDS 20.0%
!!! AATGTCTTCATATCTTTTTT+TGG - chr4.2:39619454-39619473 None:intergenic 20.0%
!!! ATGTCTTCATATCTTTTTTT+GGG - chr4.2:39619453-39619472 None:intergenic 20.0%
!!! TACTCTTGTTTATATGAATT+TGG - chr4.2:39619327-39619346 None:intergenic 20.0%
! AGTATAGATATTTGATGTGT+TGG - chr4.2:39619368-39619387 None:intergenic 25.0%
! ATTTATGATCCAAAAGGAAA+AGG + chr4.2:39619548-39619567 MS.gene003923:CDS 25.0%
! GCATTAAAAATGGTTAAAGT+TGG - chr4.2:39619392-39619411 None:intergenic 25.0%
! TCTCATAAGTGCATTAAAAA+TGG - chr4.2:39619402-39619421 None:intergenic 25.0%
!!! ATGTGTCCAATTTTTTTAAC+TGG - chr4.2:39619008-39619027 None:intergenic 25.0%
AAAATTGGACACATCTTTAG+TGG + chr4.2:39619014-39619033 MS.gene003923:CDS 30.0%
AACAACAACGGTTATGAAAT+TGG + chr4.2:39619281-39619300 MS.gene003923:CDS 30.0%
AATTTCATAACCGTTGTTGT+TGG - chr4.2:39619282-39619301 None:intergenic 30.0%
ATAAGTAGTGTCTTAAGCAA+TGG + chr4.2:39619054-39619073 MS.gene003923:CDS 30.0%
CTGAATTATCAACACTTTGT+GGG + chr4.2:39618707-39618726 MS.gene003923:CDS 30.0%
CTTCAAAATTGTTCTTGCTA+TGG - chr4.2:39618803-39618822 None:intergenic 30.0%
GAAGGTAGAAATAAAACACA+AGG + chr4.2:39619593-39619612 MS.gene003923:CDS 30.0%
TCTGAATTATCAACACTTTG+TGG + chr4.2:39618706-39618725 MS.gene003923:CDS 30.0%
TGAATTATCAACACTTTGTG+GGG + chr4.2:39618708-39618727 MS.gene003923:CDS 30.0%
TGTACATCTTCTAATCAACT+TGG + chr4.2:39619102-39619121 MS.gene003923:intron 30.0%
TTAATTCTTCTTCTACCGAA+GGG - chr4.2:39618834-39618853 None:intergenic 30.0%
TTTAATTCTTCTTCTACCGA+AGG - chr4.2:39618835-39618854 None:intergenic 30.0%
TTTGAAGAATGAAAACCCTT+CGG + chr4.2:39618816-39618835 MS.gene003923:CDS 30.0%
! ATTCTTATTATTTCTCCAGC+AGG + chr4.2:39618742-39618761 MS.gene003923:CDS 30.0%
! CACAAAAAATGATGAGCTTT+TGG + chr4.2:39618879-39618898 MS.gene003923:CDS 30.0%
! GCATTTTCAAAAAGAAAGTC+TGG + chr4.2:39618667-39618686 MS.gene003923:CDS 30.0%
! TCCTTTTGGATCATAAATCT+GGG - chr4.2:39619546-39619565 None:intergenic 30.0%
! TTCCTTTTGGATCATAAATC+TGG - chr4.2:39619547-39619566 None:intergenic 30.0%
!! ACAAAGTGTTGATAATTCAG+AGG - chr4.2:39618707-39618726 None:intergenic 30.0%
AAATCCTCCTTATGTCTTTG+GGG + chr4.2:39619256-39619275 MS.gene003923:CDS 35.0%
ACAAATCCTCCTTATGTCTT+TGG + chr4.2:39619254-39619273 MS.gene003923:CDS 35.0%
CAAATCCTCCTTATGTCTTT+GGG + chr4.2:39619255-39619274 MS.gene003923:CDS 35.0%
GAAGGTTCTCCATAACAATA+TGG - chr4.2:39618772-39618791 None:intergenic 35.0%
GATGTTATTGCTTCTCTTGA+AGG + chr4.2:39619575-39619594 MS.gene003923:CDS 35.0%
GCAGGAAAACCATATTGTTA+TGG + chr4.2:39618760-39618779 MS.gene003923:CDS 35.0%
TATGTGTTAGGTTTATCGCA+TGG - chr4.2:39619490-39619509 None:intergenic 35.0%
TCCCAGATTTATGATCCAAA+AGG + chr4.2:39619542-39619561 MS.gene003923:CDS 35.0%
TCTTGCATAGATGAACTGAA+TGG + chr4.2:39619224-39619243 MS.gene003923:CDS 35.0%
TTTCTTGTCATTGAAGCTCA+TGG + chr4.2:39619518-39619537 MS.gene003923:intron 35.0%
! CTTTGGAAAGTTATGGCTAT+TGG + chr4.2:39618944-39618963 MS.gene003923:CDS 35.0%
! TAACAATATGGTTTTCCTGC+TGG - chr4.2:39618760-39618779 None:intergenic 35.0%
! TTTGGATGAAAAGCATGTTG+CGG + chr4.2:39618897-39618916 MS.gene003923:CDS 35.0%
!! TTGAAGGCTTTGGAAAGTTA+TGG + chr4.2:39618937-39618956 MS.gene003923:CDS 35.0%
AGACATAAGGAGGATTTGTC+TGG - chr4.2:39619253-39619272 None:intergenic 40.0%
AGCTCATCAGGAAAGTTTGA+AGG + chr4.2:39618921-39618940 MS.gene003923:CDS 40.0%
AGTAGTGTCTTAAGCAATGG+AGG + chr4.2:39619057-39619076 MS.gene003923:CDS 40.0%
CATTTCCACTTTCACTTGCA+CGG - chr4.2:39619631-39619650 None:intergenic 40.0%
TCAGGAAAGTTTGAAGGCTT+TGG + chr4.2:39618927-39618946 MS.gene003923:CDS 40.0%
TGATCCAAAAGGAAAAGGCA+AGG + chr4.2:39619553-39619572 MS.gene003923:CDS 40.0%
! ACATCCTTGCCTTTTCCTTT+TGG - chr4.2:39619560-39619579 None:intergenic 40.0%
! CTTGCTATGGATTGAGAAGA+AGG - chr4.2:39618790-39618809 None:intergenic 40.0%
CGTGCAAGTGAAAGTGGAAA+TGG + chr4.2:39619629-39619648 MS.gene003923:CDS 45.0%
CTACCTCTTGATGTCCTCTT+CGG - chr4.2:39618598-39618617 None:intergenic 45.0%
GAAGATGTACACGTACCATG+AGG - chr4.2:39619093-39619112 None:intergenic 45.0%
GGAGGAGAGATTAATCCTCA+TGG + chr4.2:39619075-39619094 MS.gene003923:CDS 45.0%
TTGTTGGCCCCAAAGACATA+AGG - chr4.2:39619266-39619285 None:intergenic 45.0%
CACTTTCACTTGCACGGTCA+AGG - chr4.2:39619625-39619644 None:intergenic 50.0%
CTTGACCGTGCAAGTGAAAG+TGG + chr4.2:39619623-39619642 MS.gene003923:CDS 50.0%
TCACTTGCACGGTCAAGGTT+TGG - chr4.2:39619620-39619639 None:intergenic 50.0%
TTGGCCCCAAAGACATAAGG+AGG - chr4.2:39619263-39619282 None:intergenic 50.0%
!! GTCTTTGGGGCCAACAACAA+CGG + chr4.2:39619269-39619288 MS.gene003923:CDS 50.0%
GCATGTTGCGGAAGCTCATC+AGG + chr4.2:39618909-39618928 MS.gene003923:CDS 55.0%
GCTCCGAAGAGGACATCAAG+AGG + chr4.2:39618592-39618611 MS.gene003923:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 39618589 39619685 39618589 ID=MS.gene003923
chr4.2 mRNA 39618589 39619685 39618589 ID=MS.gene003923.t1;Parent=MS.gene003923
chr4.2 exon 39618589 39619096 39618589 ID=MS.gene003923.t1.exon1;Parent=MS.gene003923.t1
chr4.2 CDS 39618589 39619096 39618589 ID=cds.MS.gene003923.t1;Parent=MS.gene003923.t1
chr4.2 exon 39619219 39619308 39619219 ID=MS.gene003923.t1.exon2;Parent=MS.gene003923.t1
chr4.2 CDS 39619219 39619308 39619219 ID=cds.MS.gene003923.t1;Parent=MS.gene003923.t1
chr4.2 exon 39619534 39619685 39619534 ID=MS.gene003923.t1.exon3;Parent=MS.gene003923.t1
chr4.2 CDS 39619534 39619685 39619534 ID=cds.MS.gene003923.t1;Parent=MS.gene003923.t1
Gene Sequence

>MS.gene003923

ATGGCTCCGAAGAGGACATCAAGAGGTAGACAAAAAAGAGAAATGAAGAAGATTGAGAGAGAATGCGATCTTTTAGTAGCATTTTCAAAAAGAAAGTCTGGCATTTACAACAAAGCCTCTGAATTATCAACACTTTGTGGGGCTTTAGTTGATATTCTTATTATTTCTCCAGCAGGAAAACCATATTGTTATGGAGAACCTTCTTCTCAATCCATAGCAAGAACAATTTTGAAGAATGAAAACCCTTCGGTAGAAGAAGAATTAAAGCAACTAAAGATTAACAAAGTTAACACAAAAAATGATGAGCTTTTGGATGAAAAGCATGTTGCGGAAGCTCATCAGGAAAGTTTGAAGGCTTTGGAAAGTTATGGCTATTGGTCGATCAATGAGAAAGATGTTGAAAGCTTTGATTATGACCAGTTAAAAAAATTGGACACATCTTTAGTGGACATTGCAAATAAATTGATAAGTAGTGTCTTAAGCAATGGAGGAGAGATTAATCCTCATGGTACGTGTACATCTTCTAATCAACTTGGTCTTATATTTGATATATTAATGATGTCAAATGATTTCATTTCATGTTTTCTGTCTAATTTATTTATGAAAAAGTGGTTATAATTTTATTTGCAGCAATTTCTTGCATAGATGAACTGAATGGAGTCCAGACAAATCCTCCTTATGTCTTTGGGGCCAACAACAACGGTTATGAAATTGGTGCAAGTAAGAAATCTCATTCCAAATTCATATAAACAAGAGTAATACATATTACTCGCACTCCAACACATCAAATATCTATACTGCCAACTTTAACCATTTTTAATGCACTTATGAGATAAATCTTGTTTATTTTTTCATTTTGATCCCAAAAAAAGATATGAAGACATTAAATTTTAATATTCCATGCGATAAACCTAACACATATTGTATAATTTCTTGTCATTGAAGCTCATGGATCCCAGATTTATGATCCAAAAGGAAAAGGCAAGGATGTTATTGCTTCTCTTGAAGGTAGAAATAAAACACAAGGACCAAACCTTGACCGTGCAAGTGAAAGTGGAAATGGAAGTGATGTTGATCATTCTCCTAAAGATGAATGA
Protein sequence

>MS.gene003923.t1

MAPKRTSRGRQKREMKKIERECDLLVAFSKRKSGIYNKASELSTLCGALVDILIISPAGKPYCYGEPSSQSIARTILKNENPSVEEELKQLKINKVNTKNDELLDEKHVAEAHQESLKALESYGYWSINEKDVESFDYDQLKKLDTSLVDIANKLISSVLSNGGEINPHAISCIDELNGVQTNPPYVFGANNNGYEIGATHGSQIYDPKGKGKDVIASLEGRNKTQGPNLDRASESGNGSDVDHSPKDE