AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29316


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29316.t1 MTR_7g113830 87.385 325 12 4 1 318 14 316 0.0 565
MS.gene29316.t1 MTR_1g082480 57.941 340 102 13 1 315 14 337 5.68e-109 320
MS.gene29316.t1 MTR_3g099620 50.613 326 135 6 1 311 1 315 1.18e-100 299
MS.gene29316.t1 MTR_1g082480 56.452 310 94 13 1 285 14 307 1.09e-89 271
MS.gene29316.t1 MTR_5g064950 46.037 328 131 13 1 313 1 297 1.05e-81 249
MS.gene29316.t1 MTR_8g066770 56.338 213 74 4 114 314 104 309 1.01e-72 227
MS.gene29316.t1 MTR_5g064950 45.667 300 117 13 1 285 1 269 1.74e-70 221
MS.gene29316.t1 MTR_8g024210 53.846 195 86 2 114 308 171 361 7.47e-57 188
MS.gene29316.t1 MTR_0194s0050 44.298 228 102 7 106 314 166 387 2.13e-49 169
MS.gene29316.t1 MTR_2g022280 40.761 184 104 3 124 303 1 183 1.02e-34 125
MS.gene29316.t1 MTR_1g028470 35.088 228 120 5 101 303 66 290 1.36e-31 120
MS.gene29316.t1 MTR_3g090850 30.769 260 126 7 96 303 69 326 6.68e-24 100
MS.gene29316.t1 MTR_5g014600 24.775 222 143 7 98 305 122 333 6.63e-13 68.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29316.t1 AT1G72210 47.904 334 141 7 1 315 1 320 2.67e-82 252
MS.gene29316.t1 AT1G22490 44.615 325 146 8 1 312 1 304 1.81e-73 229
MS.gene29316.t1 AT1G72210 47.682 302 129 6 1 285 1 290 4.32e-71 223
MS.gene29316.t1 AT1G22490 45.000 300 127 8 1 285 1 277 1.01e-62 202
MS.gene29316.t1 AT4G01460 48.309 207 93 3 114 311 105 306 5.77e-56 184
MS.gene29316.t1 AT4G01460 48.309 207 93 3 114 311 105 306 5.77e-56 184
MS.gene29316.t1 AT5G65320 47.980 198 97 3 120 311 98 295 1.28e-52 175
MS.gene29316.t1 AT2G46810 47.150 193 95 3 115 306 112 298 2.08e-51 172
MS.gene29316.t1 AT2G46810 47.150 193 95 3 115 306 172 358 1.18e-50 172
MS.gene29316.t1 AT2G46810 47.150 193 95 3 115 306 184 370 1.63e-50 172
MS.gene29316.t1 AT5G46690 44.828 232 87 5 114 311 78 302 1.15e-49 168
MS.gene29316.t1 AT3G24140 41.410 227 116 3 104 314 177 402 5.31e-48 166
MS.gene29316.t1 AT3G24140 40.969 227 117 3 104 314 177 402 1.49e-47 165
MS.gene29316.t1 AT3G61950 45.876 194 97 2 114 306 117 303 3.73e-47 161
MS.gene29316.t1 AT3G61950 45.876 194 97 2 114 306 168 354 3.22e-46 160
MS.gene29316.t1 AT2G46810 41.629 221 94 4 115 306 112 326 8.67e-46 158
MS.gene29316.t1 AT5G65320 49.708 171 81 2 120 285 98 268 1.11e-45 156
MS.gene29316.t1 AT3G61950 46.541 159 78 1 114 272 117 268 1.56e-39 141
MS.gene29316.t1 AT3G61950 46.541 159 78 1 114 272 168 319 1.00e-38 140
MS.gene29316.t1 AT5G46690 43.689 206 75 5 114 285 78 276 1.64e-38 138
MS.gene29316.t1 AT3G06120 38.095 189 105 3 124 301 1 188 4.52e-32 119
MS.gene29316.t1 AT5G53210 48.485 99 34 2 104 186 67 164 1.01e-20 91.7
MS.gene29316.t1 AT5G53210 48.485 99 34 2 104 186 67 164 1.23e-20 91.7
MS.gene29316.t1 AT3G61950 71.429 42 12 0 114 155 168 209 1.44e-13 69.3
MS.gene29316.t1 AT3G61950 71.429 42 12 0 114 155 168 209 1.44e-13 69.3

Find 43 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAATTATGCTTATGGAAAT+TGG 0.223168 7.2:-3507963 MS.gene29316:CDS
ACCATCTTCAAGAGCTGTTT+TGG 0.261447 7.2:+3507236 None:intergenic
GGTGATCAAGCATCAATTAT+TGG 0.265730 7.2:-3507512 MS.gene29316:CDS
GTTGAATTCTTTCCAACATT+TGG 0.301786 7.2:+3506909 None:intergenic
GAGCAGAAGCTACAATTTCT+TGG 0.311027 7.2:-3507461 MS.gene29316:CDS
GTGATCAAGCATCAATTATT+GGG 0.314095 7.2:-3507511 MS.gene29316:CDS
CATCAGCTGTAGTGACATTA+AGG 0.320979 7.2:+3507177 None:intergenic
ACCCTTTGGACGTAAGATTC+AGG 0.337296 7.2:+3507700 None:intergenic
TTGCTTCAGAATCTGTTAAC+AGG 0.346873 7.2:+3508067 None:intergenic
CAAACAGAGAATTATGCTTA+TGG 0.362320 7.2:-3507970 MS.gene29316:CDS
CTTCTATTCTATCAGCGTTA+AGG 0.373348 7.2:-3507147 MS.gene29316:intron
AAGCATAATTCTCTGTTTGT+TGG 0.375728 7.2:+3507974 None:intergenic
GTTGAAGATGATTGCAAGCT+TGG 0.385709 7.2:-3506962 MS.gene29316:CDS
ACAATCATTGTTGCCACAAA+TGG 0.405629 7.2:-3507905 MS.gene29316:CDS
CCACAAGACCCTTTCACCTA+TGG 0.431613 7.2:-3508117 MS.gene29316:CDS
TTAACAGGTTGTAATTGTAA+TGG 0.451750 7.2:+3508082 None:intergenic
ACCAAAACAGCTCTTGAAGA+TGG 0.460812 7.2:-3507237 MS.gene29316:CDS
ACATTGCTGTAGAACGCAAC+AGG 0.469202 7.2:-3507768 MS.gene29316:CDS
TTCTTACTTTGAGATTTGCA+TGG 0.473698 7.2:+3507270 None:intergenic
TGTTGAATCCATAGGTGAAA+GGG 0.493303 7.2:+3508109 None:intergenic
AAGATGGTTTCTAGTTTGCA+TGG 0.504712 7.2:-3507221 MS.gene29316:CDS
GGCAACAATGATTGTGGTGG+TGG 0.505665 7.2:+3507913 None:intergenic
TTTGACACTTCATCCATTTG+TGG 0.511454 7.2:+3507892 None:intergenic
TGCCTGAATCTTACGTCCAA+AGG 0.512531 7.2:-3507702 MS.gene29316:CDS
GCCTGAATCTTACGTCCAAA+GGG 0.523230 7.2:-3507701 MS.gene29316:intron
TCTTGTGGATATAGTAGAGT+TGG 0.525531 7.2:+3508132 None:intergenic
AACAATGATTGTGGTGGTGG+TGG 0.531255 7.2:+3507916 None:intergenic
CTGTCACTTGTTGAGTATTG+TGG 0.536473 7.2:+3507377 None:intergenic
TTGTTGAATCCATAGGTGAA+AGG 0.539793 7.2:+3508108 None:intergenic
CCATAGGTGAAAGGGTCTTG+TGG 0.567251 7.2:+3508117 None:intergenic
GAAATTGAACTATCTAAAGA+CGG 0.572375 7.2:+3507868 None:intergenic
ATGGTCTTTGTTGAATCCAT+AGG 0.572517 7.2:+3508101 None:intergenic
TAGAGTTGGTTCTAGTGCCA+TGG 0.572651 7.2:+3508146 None:intergenic
TGCAGCTGTATACCAAATGT+TGG 0.583918 7.2:-3506921 MS.gene29316:CDS
TGATTGCAAGCTTGGATCAG+TGG 0.587540 7.2:-3506954 MS.gene29316:CDS
CAGAAGCTACAATTTCTTGG+TGG 0.593039 7.2:-3507458 MS.gene29316:CDS
TGATCAAGCATCAATTATTG+GGG 0.599410 7.2:-3507510 MS.gene29316:CDS
AACCTTCAAAATCAAGAACA+AGG 0.614022 7.2:-3508024 MS.gene29316:CDS
TGCTGATATTGAAGTGACAA+TGG 0.646131 7.2:-3507300 MS.gene29316:CDS
ATTTGTGGCAACAATGATTG+TGG 0.649128 7.2:+3507907 None:intergenic
ACTTGTTGAGTATTGTGGAA+AGG 0.653314 7.2:+3507382 None:intergenic
TGTGGCAACAATGATTGTGG+TGG 0.680500 7.2:+3507910 None:intergenic
GATCAAGCATCAATTATTGG+GGG 0.757063 7.2:-3507509 MS.gene29316:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTATTTTGTAATTTGT+AGG - chr7.2:3508040-3508059 MS.gene29316:CDS 10.0%
!!! TCATTTTTAAATTGAAATTG+CGG + chr7.2:3507462-3507481 None:intergenic 15.0%
!! AAGAAAAAAAAAAACATGAC+AGG + chr7.2:3507918-3507937 None:intergenic 20.0%
!! AGAAAAAAAAAAACATGACA+GGG + chr7.2:3507917-3507936 None:intergenic 20.0%
!! TTAAGTGCTTACAATAATTT+AGG + chr7.2:3507993-3508012 None:intergenic 20.0%
!!! CTTCTATTACTTTTAAATTG+TGG - chr7.2:3507348-3507367 MS.gene29316:CDS 20.0%
!!! TTTGATTGATGAATTTTTCA+GGG - chr7.2:3507491-3507510 MS.gene29316:CDS 20.0%
!!! TTTTGATTGATGAATTTTTC+AGG - chr7.2:3507490-3507509 MS.gene29316:CDS 20.0%
! AAAGGTGAAAAATTCAGAAA+AGG + chr7.2:3507627-3507646 None:intergenic 25.0%
! AAGGTGAAAAATTCAGAAAA+GGG + chr7.2:3507626-3507645 None:intergenic 25.0%
! AGAATTATGCTTATGGAAAT+TGG - chr7.2:3507061-3507080 MS.gene29316:intron 25.0%
! GAAATTGAACTATCTAAAGA+CGG + chr7.2:3507159-3507178 None:intergenic 25.0%
! TTAACAGGTTGTAATTGTAA+TGG + chr7.2:3506945-3506964 None:intergenic 25.0%
AACCTTCAAAATCAAGAACA+AGG - chr7.2:3507000-3507019 MS.gene29316:intron 30.0%
AAGCATAATTCTCTGTTTGT+TGG + chr7.2:3507053-3507072 None:intergenic 30.0%
CAAACAGAGAATTATGCTTA+TGG - chr7.2:3507054-3507073 MS.gene29316:intron 30.0%
GCTAAAAAGTGGTTAGAATT+TGG + chr7.2:3507948-3507967 None:intergenic 30.0%
GTGATCAAGCATCAATTATT+GGG - chr7.2:3507513-3507532 MS.gene29316:CDS 30.0%
GTTGAATTCTTTCCAACATT+TGG + chr7.2:3508118-3508137 None:intergenic 30.0%
TGATCAAGCATCAATTATTG+GGG - chr7.2:3507514-3507533 MS.gene29316:CDS 30.0%
TTCAAGAGAAAGCTAAAAAG+TGG + chr7.2:3507959-3507978 None:intergenic 30.0%
! AACCTTGTTCTTGATTTTGA+AGG + chr7.2:3507005-3507024 None:intergenic 30.0%
! TGCATTTTGCCTCAATATAA+AGG + chr7.2:3507396-3507415 None:intergenic 30.0%
!! AAAGTAATAGAAGTACCCTT+TGG + chr7.2:3507341-3507360 None:intergenic 30.0%
!! TTCTTACTTTGAGATTTGCA+TGG + chr7.2:3507757-3507776 None:intergenic 30.0%
!! TTGATTTTGAAGGTTGAAGT+TGG + chr7.2:3506995-3507014 None:intergenic 30.0%
ACAATCATTGTTGCCACAAA+TGG - chr7.2:3507119-3507138 MS.gene29316:intron 35.0%
AGTGGTTAGAATTTGGAAAG+TGG + chr7.2:3507941-3507960 None:intergenic 35.0%
ATGGTCTTTGTTGAATCCAT+AGG + chr7.2:3506926-3506945 None:intergenic 35.0%
ATTTGTGGCAACAATGATTG+TGG + chr7.2:3507120-3507139 None:intergenic 35.0%
CTTCTATTCTATCAGCGTTA+AGG - chr7.2:3507877-3507896 MS.gene29316:CDS 35.0%
GATCAAGCATCAATTATTGG+GGG - chr7.2:3507515-3507534 MS.gene29316:CDS 35.0%
GGTGATCAAGCATCAATTAT+TGG - chr7.2:3507512-3507531 MS.gene29316:CDS 35.0%
TCTTGTGGATATAGTAGAGT+TGG + chr7.2:3506895-3506914 None:intergenic 35.0%
TGCTGATATTGAAGTGACAA+TGG - chr7.2:3507724-3507743 MS.gene29316:CDS 35.0%
TGCTGCAAACCTTTATATTG+AGG - chr7.2:3507384-3507403 MS.gene29316:CDS 35.0%
TGGTGTTCAGAAACAAAAAG+AGG - chr7.2:3507586-3507605 MS.gene29316:intron 35.0%
TGTTGAATCCATAGGTGAAA+GGG + chr7.2:3506918-3506937 None:intergenic 35.0%
TTGCTTCAGAATCTGTTAAC+AGG + chr7.2:3506960-3506979 None:intergenic 35.0%
TTGTTGAATCCATAGGTGAA+AGG + chr7.2:3506919-3506938 None:intergenic 35.0%
TTTGACACTTCATCCATTTG+TGG + chr7.2:3507135-3507154 None:intergenic 35.0%
! ACTTGTTGAGTATTGTGGAA+AGG + chr7.2:3507645-3507664 None:intergenic 35.0%
!! AAGATGGTTTCTAGTTTGCA+TGG - chr7.2:3507803-3507822 MS.gene29316:CDS 35.0%
!! GAGAGTTCTGAGACAAAAAT+GGG - chr7.2:3507677-3507696 MS.gene29316:intron 35.0%
!! TGAGAGTTCTGAGACAAAAA+TGG - chr7.2:3507676-3507695 MS.gene29316:intron 35.0%
ACCAAAACAGCTCTTGAAGA+TGG - chr7.2:3507787-3507806 MS.gene29316:CDS 40.0%
AGCGTTAAGGTAATTGTCTG+TGG - chr7.2:3507890-3507909 MS.gene29316:CDS 40.0%
CAGAAGCTACAATTTCTTGG+TGG - chr7.2:3507566-3507585 MS.gene29316:intron 40.0%
CATCAGCTGTAGTGACATTA+AGG + chr7.2:3507850-3507869 None:intergenic 40.0%
CTGCAAGAGAAACGATTCTA+AGG + chr7.2:3507439-3507458 None:intergenic 40.0%
GAGCAGAAGCTACAATTTCT+TGG - chr7.2:3507563-3507582 MS.gene29316:intron 40.0%
GAGGCAAAATGCAGAAATTG+CGG - chr7.2:3507403-3507422 MS.gene29316:CDS 40.0%
GTTGAAGATGATTGCAAGCT+TGG - chr7.2:3508062-3508081 MS.gene29316:CDS 40.0%
TGCAGCTGTATACCAAATGT+TGG - chr7.2:3508103-3508122 MS.gene29316:CDS 40.0%
! ACCATCTTCAAGAGCTGTTT+TGG + chr7.2:3507791-3507810 None:intergenic 40.0%
! CTGTCACTTGTTGAGTATTG+TGG + chr7.2:3507650-3507669 None:intergenic 40.0%
!! AGTTCTGAGACAAAAATGGG+TGG - chr7.2:3507680-3507699 MS.gene29316:intron 40.0%
!!! TGTTTTGACTCTGCGTTTCT+TGG + chr7.2:3507196-3507215 None:intergenic 40.0%
ACATTGCTGTAGAACGCAAC+AGG - chr7.2:3507256-3507275 MS.gene29316:CDS 45.0%
ACCCTTTGGACGTAAGATTC+AGG + chr7.2:3507327-3507346 None:intergenic 45.0%
GCCTGAATCTTACGTCCAAA+GGG - chr7.2:3507323-3507342 MS.gene29316:CDS 45.0%
TGAGACAAAAATGGGTGGTG+AGG - chr7.2:3507685-3507704 MS.gene29316:intron 45.0%
TGATTGCAAGCTTGGATCAG+TGG - chr7.2:3508070-3508089 MS.gene29316:CDS 45.0%
TGCCTGAATCTTACGTCCAA+AGG - chr7.2:3507322-3507341 MS.gene29316:CDS 45.0%
TGTGGCAACAATGATTGTGG+TGG + chr7.2:3507117-3507136 None:intergenic 45.0%
!! AACAATGATTGTGGTGGTGG+TGG + chr7.2:3507111-3507130 None:intergenic 45.0%
CCACAAGACCCTTTCACCTA+TGG - chr7.2:3506907-3506926 MS.gene29316:CDS 50.0%
CCATAGGTGAAAGGGTCTTG+TGG + chr7.2:3506910-3506929 None:intergenic 50.0%
GGCAACAATGATTGTGGTGG+TGG + chr7.2:3507114-3507133 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr7.2 gene 3506880 3508166 3506880 ID=MS.gene29316
chr7.2 mRNA 3506880 3508166 3506880 ID=MS.gene29316.t1;Parent=MS.gene29316
chr7.2 exon 3507702 3508166 3507702 ID=MS.gene29316.t1.exon1;Parent=MS.gene29316.t1
chr7.2 CDS 3507702 3508166 3507702 ID=cds.MS.gene29316.t1;Parent=MS.gene29316.t1
chr7.2 exon 3507148 3507534 3507148 ID=MS.gene29316.t1.exon2;Parent=MS.gene29316.t1
chr7.2 CDS 3507148 3507534 3507148 ID=cds.MS.gene29316.t1;Parent=MS.gene29316.t1
chr7.2 exon 3506880 3506984 3506880 ID=MS.gene29316.t1.exon3;Parent=MS.gene29316.t1
chr7.2 CDS 3506880 3506984 3506880 ID=cds.MS.gene29316.t1;Parent=MS.gene29316.t1
Gene Sequence

>MS.gene29316

ATGGCACTAGAACCAACTCTACTATATCCACAAGACCCTTTCACCTATGGATTCAACAAAGACCATTACAATTACAACCTGTTAACAGATTCTGAAGCAAACTTTGACTACACCAACTTCAACCTTCAAAATCAAGAACAAGGTTCTATTTCTACTTTTCTCATCAAGAACCAACAAACAGAGAATTATGCTTATGGAAATTGGAGTAACAATTGTTCATCTTCTTCACCACCACCACCACAATCATTGTTGCCACAAATGGATGAAGTGTCAAATCCGTCTTTAGATAGTTCAATTTCAACTCGTTCTCGTTCCAAGAAACGCAGAGTCAAAACACGTAAGAATAAAGAAGAAATTGAGAATCAGAGAATGACTCACATTGCTGTAGAACGCAACAGGAGAAAACAAATGAATGAGTATCTCTCTGTTCTTAGATCTCTCATGCCTGAATCTTACGTCCAAAGGGTACTTCTATTACTTTTAAATTGTGGTTAATCACATTTTTGCTGCAAACCTTTATATTGAGGCAAAATGCAGAAATTGCGGTTGCAAGAGACCTTAGAATCGTTTCTCTTGCAGCCGCAATTTCAATTTAAAAATGAGTTTTGTGTTTTGATTGATGAATTTTTCAGGGTGATCAAGCATCAATTATTGGGGGTGCTATTAACTTTGTTAAGAAGCTTGAGCAGAAGCTACAATTTCTTGGTGGTGTTCAGAAACAAAAAGAGGAAAATAAAAACAAGCCCTTTTCTGAATTTTTCACCTTTCCACAATACTCAACAAGTGACAGTGTGTGTGAGAGTTCTGAGACAAAAATGGGTGGTGAGGTTCAATCTCGCAATATTGCTGATATTGAAGTGACAATGGTTGAAAGCCATGCAAATCTCAAAGTAAGAACAAAGAAAAGACCAAAACAGCTCTTGAAGATGGTTTCTAGTTTGCATGGATTGTGTCTCACAATCTTGCACCTTAATGTCACTACAGCTGATGAATTTGTCTTCTATTCTATCAGCGTTAAGGTAATTGTCTGTGGTCCCTGTCATGTTTTTTTTTTTCTTCCACTTTCCAAATTCTAACCACTTTTTAGCTTTCTCTTGAATTTCTTTGCTTCCTAAATTATTGTAAGCACTTAAAGTGAAATTAATGAATGTGTGTTGTTGAATTTTATTTTGTAATTTGTAGGTTGAAGATGATTGCAAGCTTGGATCAGTGGATGAGATAGCTGCAGCTGTATACCAAATGTTGGAAAGAATTCAACAAGAGTCATCAATCAATATATTGAATTAA

Protein sequence

>MS.gene29316.t1

MALEPTLLYPQDPFTYGFNKDHYNYNLLTDSEANFDYTNFNLQNQEQGSISTFLIKNQQTENYAYGNWSNNCSSSSPPPPQSLLPQMDEVSNPSLDSSISTRSRSKKRRVKTRKNKEEIENQRMTHIAVERNRRKQMNEYLSVLRSLMPESYVQRGDQASIIGGAINFVKKLEQKLQFLGGVQKQKEENKNKPFSEFFTFPQYSTSDSVCESSETKMGGEVQSRNIADIEVTMVESHANLKVRTKKRPKQLLKMVSSLHGLCLTILHLNVTTADEFVFYSISVKVEDDCKLGSVDEIAAAVYQMLERIQQESSINILN