AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene34531

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene34531.t1 MTR_4g083510 84.242 330 43 1 1 330 1 321 0.0 545
MS.gene34531.t1 MTR_0867s0010 76.900 329 66 2 1 329 1 319 4.85e-171 478
MS.gene34531.t1 MTR_4g063670 70.606 330 87 2 1 330 1 320 2.37e-160 451
MS.gene34531.t1 MTR_1g051185 61.462 301 81 3 1 301 1 266 7.70e-114 331
MS.gene34531.t1 MTR_8g015750 69.951 203 44 2 127 329 1 186 1.69e-85 256
MS.gene34531.t1 MTR_3g069460 61.202 183 62 1 1 183 1 174 5.71e-75 228
MS.gene34531.t1 MTR_7g088160 40.964 332 156 11 20 329 75 388 2.32e-60 198
MS.gene34531.t1 MTR_7g107340 40.385 260 124 10 78 329 98 334 6.56e-42 148
MS.gene34531.t1 MTR_8g015740 70.330 91 18 1 1 91 49 130 2.96e-33 120
MS.gene34531.t1 MTR_2g023560 77.419 62 14 0 55 116 57 118 6.02e-27 103
MS.gene34531.t1 MTR_7g114170 32.484 314 123 14 18 328 61 288 1.97e-21 92.8
MS.gene34531.t1 MTR_6g081150 37.179 156 56 5 79 232 40 155 1.62e-20 87.4
MS.gene34531.t1 MTR_5g044920 77.551 49 2 1 43 91 17 56 1.17e-15 72.0
MS.gene34531.t1 MTR_6g051405 25.767 163 114 3 19 181 96 251 3.88e-12 67.0
MS.gene34531.t1 MTR_3g067785 28.108 185 117 5 33 208 61 238 4.80e-12 66.2
MS.gene34531.t1 MTR_4g026120 28.108 185 117 5 33 208 61 238 5.13e-12 66.2
MS.gene34531.t1 MTR_4g036435 28.108 185 117 5 33 208 61 238 5.13e-12 66.2
MS.gene34531.t1 MTR_5g066280 28.108 185 117 5 33 208 61 238 5.27e-12 66.2
MS.gene34531.t1 MTR_2g022120 27.451 204 119 6 33 227 125 308 9.74e-12 65.9
MS.gene34531.t1 MTR_1g106885 27.451 204 119 6 33 227 122 305 9.83e-12 65.9
MS.gene34531.t1 MTR_5g077245 28.108 185 117 5 33 208 114 291 1.01e-11 65.9
MS.gene34531.t1 MTR_3g450670 25.309 162 114 3 20 181 93 247 1.03e-11 65.5
MS.gene34531.t1 MTR_1g471070 25.309 162 114 3 20 181 93 247 1.03e-11 65.5
MS.gene34531.t1 MTR_2g072860 26.250 160 111 3 22 181 31 183 1.06e-11 65.1
MS.gene34531.t1 MTR_6g092533 30.128 156 95 4 33 181 125 273 1.30e-11 65.5
MS.gene34531.t1 MTR_4g013220 27.568 185 118 5 33 208 61 238 1.52e-11 64.7
MS.gene34531.t1 MTR_7g461350 25.309 162 114 3 20 181 97 251 1.52e-11 65.1
MS.gene34531.t1 MTR_6g016670 25.309 162 114 3 20 181 97 251 1.52e-11 65.1
MS.gene34531.t1 MTR_3g464310 25.309 162 114 3 20 181 97 251 1.52e-11 65.1
MS.gene34531.t1 MTR_3g464170 25.309 162 114 3 20 181 97 251 1.60e-11 65.1
MS.gene34531.t1 MTR_1g100375 25.309 162 114 3 20 181 97 251 1.60e-11 65.1
MS.gene34531.t1 MTR_7g062380 29.104 134 88 3 48 181 18 144 1.76e-11 63.9
MS.gene34531.t1 MTR_7g083520 28.289 152 99 4 33 179 35 181 4.08e-11 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene34531.t1 AT5G41220 37.963 216 112 8 44 245 202 409 1.52e-32 127
MS.gene34531.t1 AT5G41220 37.963 216 112 8 44 245 210 417 2.08e-32 126
MS.gene34531.t1 AT5G41220 37.963 216 112 8 44 245 260 467 2.73e-32 127
MS.gene34531.t1 AT5G41240 37.297 185 103 6 60 232 272 455 7.35e-27 111
MS.gene34531.t1 AT3G47680 35.025 197 114 7 30 223 23 208 4.64e-25 103
MS.gene34531.t1 AT1G66235 26.378 254 164 7 61 299 7 252 9.67e-17 79.7

Find 58 sgRNAs with CRISPR-Local

Find 71 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTTCAAAGCATCAAATT+TGG 0.164119 6.3:-54315990 None:intergenic
CATTCTCTTGATCATTTAAT+TGG 0.185656 6.3:-54315304 None:intergenic
CCAACAAACTTTGAAATAGA+TGG 0.279570 6.3:-54315641 None:intergenic
CTTTGATCATTCCCAACAAT+TGG 0.310977 6.3:-54315506 None:intergenic
TTCAGCTTCTGGAGCATATT+CGG 0.312536 6.3:+54315856 MS.gene34531:CDS
AGAACAAAGAATTCAGCTTC+TGG 0.340604 6.3:+54315845 MS.gene34531:CDS
CATCTATTTCAAAGTTTGTT+GGG 0.369114 6.3:+54315642 MS.gene34531:CDS
GATGAACCGAAATGGCTTGC+AGG 0.369514 6.3:+54315797 MS.gene34531:CDS
TCTTTCAAAGCATCAAATTT+GGG 0.374468 6.3:-54315989 None:intergenic
AGAAAACCAGAGGCACTTAA+AGG 0.378046 6.3:+54315596 MS.gene34531:CDS
CATGCATTCTCAAGTGTGAA+TGG 0.388314 6.3:-54315761 None:intergenic
ACACAACCTGCAAGCCATTT+CGG 0.388495 6.3:-54315803 None:intergenic
CTCCGAGAGCGACAACATTT+CGG 0.391789 6.3:+54315703 MS.gene34531:CDS
TGCAAAGAGTTGAAAATGAT+AGG 0.394552 6.3:+54316116 MS.gene34531:CDS
ATTTCAAAGGATCCAATTGT+TGG 0.399370 6.3:+54315494 MS.gene34531:CDS
TCATAATCTTGTAGTTGTCT+TGG 0.400714 6.3:-54316196 None:intergenic
ATGAGAAGTTCATCCTCCTT+TGG 0.406782 6.3:-54315455 None:intergenic
GGTGGATTGTATTCGCTTGT+TGG 0.416563 6.3:-54315899 None:intergenic
GGCTTGGAAACAATTAATCT+TGG 0.423881 6.3:+54315353 MS.gene34531:CDS
CCATCTATTTCAAAGTTTGT+TGG 0.437206 6.3:+54315641 MS.gene34531:CDS
AATTGTTTCCAAGCCATCTT+GGG 0.439909 6.3:-54315345 None:intergenic
CATCGACCTTTAAGTGCCTC+TGG 0.445875 6.3:-54315602 None:intergenic
TCCAAGCCATCTTGGGTGCA+AGG 0.447157 6.3:-54315338 None:intergenic
TTTCAAAGGATCCAATTGTT+GGG 0.450141 6.3:+54315495 MS.gene34531:CDS
ATGGCTTGCAGGTTGTGTAT+TGG 0.465781 6.3:+54315808 MS.gene34531:CDS
TAATTGTTTCCAAGCCATCT+TGG 0.472415 6.3:-54315346 None:intergenic
TATTGAGAGATGAACCGAAA+TGG 0.474221 6.3:+54315789 MS.gene34531:CDS
AGCCGAAATGTTGTCGCTCT+CGG 0.477888 6.3:-54315705 None:intergenic
TATTCGCTTGTTGGTGTTGG+TGG 0.480363 6.3:-54315890 None:intergenic
CCATCTTGGGTGCAAGGTTG+TGG 0.481149 6.3:-54315332 None:intergenic
ACAACGTCCAATCGGTCAAA+AGG 0.486049 6.3:+54315922 MS.gene34531:CDS
TCGGTCAAAAGGCGGCAAAA+AGG 0.487566 6.3:+54315933 MS.gene34531:CDS
ACCTTGCACCCAAGATGGCT+TGG 0.489398 6.3:+54315337 MS.gene34531:CDS
ATGAACTTCTCATTCAATCA+TGG 0.496152 6.3:+54315465 MS.gene34531:CDS
CATTTGCACTTCATGAGACA+TGG 0.508686 6.3:-54315267 None:intergenic
TTGTATTCGCTTGTTGGTGT+TGG 0.511913 6.3:-54315893 None:intergenic
AATGGAGATAGAGAGAAAGA+AGG 0.517552 6.3:+54316081 MS.gene34531:CDS
GCAAAGAGTTGAAAATGATA+GGG 0.522318 6.3:+54316117 MS.gene34531:CDS
TGAATGGTTCACGTACATCT+TGG 0.533697 6.3:-54315745 None:intergenic
CTTGAAAATTCTCGTCGCGA+TGG 0.533833 6.3:-54315571 None:intergenic
AATCCACCACAACGTCCAAT+CGG 0.536837 6.3:+54315914 MS.gene34531:CDS
CATTCACACTTGAGAATGCA+TGG 0.543088 6.3:+54315762 MS.gene34531:CDS
ATCATGGCTCAATATTTCAA+AGG 0.547059 6.3:+54315481 MS.gene34531:CDS
CCACAACCTTGCACCCAAGA+TGG 0.549550 6.3:+54315332 MS.gene34531:CDS
GGCGTGATTAGAGATAAATA+TGG 0.559077 6.3:+54316229 MS.gene34531:CDS
ATTCGCTTGTTGGTGTTGGT+GGG 0.567081 6.3:-54315889 None:intergenic
CAAGATTATGAATTTCTATG+TGG 0.568516 6.3:+54316208 MS.gene34531:CDS
GTTGTCGCTCTAAAGAAAAG+TGG 0.594037 6.3:+54315677 MS.gene34531:CDS
AATAAGATTTAAACCAAAGG+AGG 0.598325 6.3:+54315442 MS.gene34531:CDS
TGACCGATTGGACGTTGTGG+TGG 0.605293 6.3:-54315917 None:intergenic
CAGAGGCACTTAAAGGTCGA+TGG 0.621203 6.3:+54315603 MS.gene34531:CDS
GAAAATAAGATTTAAACCAA+AGG 0.637971 6.3:+54315439 MS.gene34531:CDS
GAAGGGAAAAGAAAAGCTTG+TGG 0.644203 6.3:+54315955 MS.gene34531:CDS
CGAAATGTTGTCGCTCTCGG+AGG 0.658068 6.3:-54315702 None:intergenic
TGATTTAGAAATACTCACAA+AGG 0.661251 6.3:+54316156 MS.gene34531:CDS
ACGTCCAATCGGTCAAAAGG+CGG 0.661921 6.3:+54315925 MS.gene34531:CDS
ATTGTTGGGAATGATCAAAG+AGG 0.674803 6.3:+54315509 MS.gene34531:CDS
TGAAGAAGTCAGAGCTACGT+CGG 0.718655 6.3:+54315376 MS.gene34531:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAAATAAGATTTAAACCAA+AGG + chr6.3:54315439-54315458 MS.gene34531:CDS 20.0%
! AATAAGATTTAAACCAAAGG+AGG + chr6.3:54315442-54315461 MS.gene34531:CDS 25.0%
! CAAGATTATGAATTTCTATG+TGG + chr6.3:54316208-54316227 MS.gene34531:CDS 25.0%
! CATTCTCTTGATCATTTAAT+TGG - chr6.3:54315307-54315326 None:intergenic 25.0%
! GAAAAAAAGATTTCAACCAA+AGG + chr6.3:54315412-54315431 MS.gene34531:CDS 25.0%
! TGATTTAGAAATACTCACAA+AGG + chr6.3:54316156-54316175 MS.gene34531:CDS 25.0%
!! ATCTTTCAAAGCATCAAATT+TGG - chr6.3:54315993-54316012 None:intergenic 25.0%
!! CATCTATTTCAAAGTTTGTT+GGG + chr6.3:54315642-54315661 MS.gene34531:CDS 25.0%
!! TCTTTCAAAGCATCAAATTT+GGG - chr6.3:54315992-54316011 None:intergenic 25.0%
AAAAAGATTTCAACCAAAGG+AGG + chr6.3:54315415-54315434 MS.gene34531:CDS 30.0%
ATCATGGCTCAATATTTCAA+AGG + chr6.3:54315481-54315500 MS.gene34531:CDS 30.0%
ATGAACTTCTCATTCAATCA+TGG + chr6.3:54315465-54315484 MS.gene34531:CDS 30.0%
ATTTCAAAGGATCCAATTGT+TGG + chr6.3:54315494-54315513 MS.gene34531:CDS 30.0%
CCATCTATTTCAAAGTTTGT+TGG + chr6.3:54315641-54315660 MS.gene34531:CDS 30.0%
GCAAAGAGTTGAAAATGATA+GGG + chr6.3:54316117-54316136 MS.gene34531:CDS 30.0%
TCATAATCTTGTAGTTGTCT+TGG - chr6.3:54316199-54316218 None:intergenic 30.0%
TGCAAAGAGTTGAAAATGAT+AGG + chr6.3:54316116-54316135 MS.gene34531:CDS 30.0%
TTTCAAAGGATCCAATTGTT+GGG + chr6.3:54315495-54315514 MS.gene34531:CDS 30.0%
! ATCAAAGAGGAGATAGTTTT+TGG + chr6.3:54315522-54315541 MS.gene34531:CDS 30.0%
! ATTTTCAACTCTTTGCAACT+CGG - chr6.3:54316113-54316132 None:intergenic 30.0%
! TTCTTTGTTCTTTTTGCGAA+CGG - chr6.3:54315836-54315855 None:intergenic 30.0%
!! CCAACAAACTTTGAAATAGA+TGG - chr6.3:54315644-54315663 None:intergenic 30.0%
!!! ACGTTTTGAGAGTGAAAAAA+TGG + chr6.3:54316063-54316082 MS.gene34531:CDS 30.0%
AATGGAGATAGAGAGAAAGA+AGG + chr6.3:54316081-54316100 MS.gene34531:CDS 35.0%
AATTGTTTCCAAGCCATCTT+GGG - chr6.3:54315348-54315367 None:intergenic 35.0%
AGAACAAAGAATTCAGCTTC+TGG + chr6.3:54315845-54315864 MS.gene34531:CDS 35.0%
ATTGTTGGGAATGATCAAAG+AGG + chr6.3:54315509-54315528 MS.gene34531:CDS 35.0%
CTTTGATCATTCCCAACAAT+TGG - chr6.3:54315509-54315528 None:intergenic 35.0%
GGCGTGATTAGAGATAAATA+TGG + chr6.3:54316229-54316248 MS.gene34531:CDS 35.0%
GGCTTGGAAACAATTAATCT+TGG + chr6.3:54315353-54315372 MS.gene34531:CDS 35.0%
TAATTGTTTCCAAGCCATCT+TGG - chr6.3:54315349-54315368 None:intergenic 35.0%
TATTGAGAGATGAACCGAAA+TGG + chr6.3:54315789-54315808 MS.gene34531:CDS 35.0%
!! GATAGTTTTTGGAAGAGGAT+TGG + chr6.3:54315533-54315552 MS.gene34531:CDS 35.0%
!! TTTTCAAGAGAGAAAACCAG+AGG + chr6.3:54315586-54315605 MS.gene34531:CDS 35.0%
!!! AATCTTATTTTCGCCTCCTT+TGG - chr6.3:54315431-54315450 None:intergenic 35.0%
ATGAGAAGTTCATCCTCCTT+TGG - chr6.3:54315458-54315477 None:intergenic 40.0%
CATGCATTCTCAAGTGTGAA+TGG - chr6.3:54315764-54315783 None:intergenic 40.0%
CATTCACACTTGAGAATGCA+TGG + chr6.3:54315762-54315781 MS.gene34531:CDS 40.0%
GAAGGGAAAAGAAAAGCTTG+TGG + chr6.3:54315955-54315974 MS.gene34531:CDS 40.0%
TGAATGGTTCACGTACATCT+TGG - chr6.3:54315748-54315767 None:intergenic 40.0%
! TTGTATTCGCTTGTTGGTGT+TGG - chr6.3:54315896-54315915 None:intergenic 40.0%
!! AGAAAACCAGAGGCACTTAA+AGG + chr6.3:54315596-54315615 MS.gene34531:CDS 40.0%
!! GAGGAGATAGTTTTTGGAAG+AGG + chr6.3:54315528-54315547 MS.gene34531:CDS 40.0%
!! GTTGTCGCTCTAAAGAAAAG+TGG + chr6.3:54315677-54315696 MS.gene34531:CDS 40.0%
!! TTCAGCTTCTGGAGCATATT+CGG + chr6.3:54315856-54315875 MS.gene34531:CDS 40.0%
AATCCACCACAACGTCCAAT+CGG + chr6.3:54315914-54315933 MS.gene34531:CDS 45.0%
ACAACGTCCAATCGGTCAAA+AGG + chr6.3:54315922-54315941 MS.gene34531:CDS 45.0%
ACACAACCTGCAAGCCATTT+CGG - chr6.3:54315806-54315825 None:intergenic 45.0%
CAAAAGGCGGCAAAAAGGAA+GGG + chr6.3:54315938-54315957 MS.gene34531:CDS 45.0%
CTTGAAAATTCTCGTCGCGA+TGG - chr6.3:54315574-54315593 None:intergenic 45.0%
TCAAAAGGCGGCAAAAAGGA+AGG + chr6.3:54315937-54315956 MS.gene34531:CDS 45.0%
TGAAGAAGTCAGAGCTACGT+CGG + chr6.3:54315376-54315395 MS.gene34531:CDS 45.0%
! ATGGCTTGCAGGTTGTGTAT+TGG + chr6.3:54315808-54315827 MS.gene34531:CDS 45.0%
! TTTTGACCGATTGGACGTTG+TGG - chr6.3:54315923-54315942 None:intergenic 45.0%
!! ATTCGCTTGTTGGTGTTGGT+GGG - chr6.3:54315892-54315911 None:intergenic 45.0%
!! GGTGGATTGTATTCGCTTGT+TGG - chr6.3:54315902-54315921 None:intergenic 45.0%
!! TATTCGCTTGTTGGTGTTGG+TGG - chr6.3:54315893-54315912 None:intergenic 45.0%
ACGTCCAATCGGTCAAAAGG+CGG + chr6.3:54315925-54315944 MS.gene34531:CDS 50.0%
AGCCGAAATGTTGTCGCTCT+CGG - chr6.3:54315708-54315727 None:intergenic 50.0%
CATCGACCTTTAAGTGCCTC+TGG - chr6.3:54315605-54315624 None:intergenic 50.0%
CTCCGAGAGCGACAACATTT+CGG + chr6.3:54315703-54315722 MS.gene34531:CDS 50.0%
TCGGTCAAAAGGCGGCAAAA+AGG + chr6.3:54315933-54315952 MS.gene34531:CDS 50.0%
! GATGAACCGAAATGGCTTGC+AGG + chr6.3:54315797-54315816 MS.gene34531:CDS 50.0%
! TTTGCCGCCTTTTGACCGAT+TGG - chr6.3:54315932-54315951 None:intergenic 50.0%
!! CAGAGGCACTTAAAGGTCGA+TGG + chr6.3:54315603-54315622 MS.gene34531:CDS 50.0%
ACCTTGCACCCAAGATGGCT+TGG + chr6.3:54315337-54315356 MS.gene34531:CDS 55.0%
CCACAACCTTGCACCCAAGA+TGG + chr6.3:54315332-54315351 MS.gene34531:CDS 55.0%
CCATCTTGGGTGCAAGGTTG+TGG - chr6.3:54315335-54315354 None:intergenic 55.0%
CGAAATGTTGTCGCTCTCGG+AGG - chr6.3:54315705-54315724 None:intergenic 55.0%
TCCAAGCCATCTTGGGTGCA+AGG - chr6.3:54315341-54315360 None:intergenic 55.0%
TGACCGATTGGACGTTGTGG+TGG - chr6.3:54315920-54315939 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 54315269 54316261 54315269 ID=MS.gene34531
chr6.3 mRNA 54315269 54316261 54315269 ID=MS.gene34531.t1;Parent=MS.gene34531
chr6.3 exon 54315269 54316261 54315269 ID=MS.gene34531.t1.exon1;Parent=MS.gene34531.t1
chr6.3 CDS 54315269 54316261 54315269 ID=cds.MS.gene34531.t1;Parent=MS.gene34531.t1
Gene Sequence

>MS.gene34531

ATGTCTCATGAAGTGCAAATGAATAATAGTGATGTCCAATTAAATGATCAAGAGAATGAAACACCACAACCTTGCACCCAAGATGGCTTGGAAACAATTAATCTTGGTGAAGAAGTCAGAGCTACGTCGGTTGCGAATACTTCGAAAAAAAGATTTCAACCAAAGGAGGCGAAAATAAGATTTAAACCAAAGGAGGATGAACTTCTCATTCAATCATGGCTCAATATTTCAAAGGATCCAATTGTTGGGAATGATCAAAGAGGAGATAGTTTTTGGAAGAGGATTGGTGAAGCTTATAACAACCATCGCGACGAGAATTTTCAAGAGAGAAAACCAGAGGCACTTAAAGGTCGATGGCACAAAAAAATCAATCCATCTATTTCAAAGTTTGTTGGGTGCTACAAAGATGTTGTCGCTCTAAAGAAAAGTGGTGCCTCCGAGAGCGACAACATTTCGGCTGCAAAAGATATTTATTACCAAGATGTACGTGAACCATTCACACTTGAGAATGCATGGAAATTATTGAGAGATGAACCGAAATGGCTTGCAGGTTGTGTATTGGAACCGTTCGCAAAAAGAACAAAGAATTCAGCTTCTGGAGCATATTCGGCATCTTCTAACCCACCAACACCAACAAGCGAATACAATCCACCACAACGTCCAATCGGTCAAAAGGCGGCAAAAAGGAAGGGAAAAGAAAAGCTTGTGGAAATTTCTACTCCCAAATTTGATGCTTTGAAAGATGATTTCAACAAAAAATTTGAATTAATGTCAGAGTTTGCACGTGATTATGCACGTTTTGAGAGTGAAAAAATGGAGATAGAGAGAAAGAAGGTTGATGCCGAGTTGCAAAGAGTTGAAAATGATAGGGAAAGATCGAAGATCAATGATTTAGAAATACTCACAAAGGATACATCAAATATGAATCCAAGACAACTACAAGATTATGAATTTCTATGTGGCGTGATTAGAGATAAATATGGACTTAATTGA
Protein sequence

>MS.gene34531.t1

MSHEVQMNNSDVQLNDQENETPQPCTQDGLETINLGEEVRATSVANTSKKRFQPKEAKIRFKPKEDELLIQSWLNISKDPIVGNDQRGDSFWKRIGEAYNNHRDENFQERKPEALKGRWHKKINPSISKFVGCYKDVVALKKSGASESDNISAAKDIYYQDVREPFTLENAWKLLRDEPKWLAGCVLEPFAKRTKNSASGAYSASSNPPTPTSEYNPPQRPIGQKAAKRKGKEKLVEISTPKFDALKDDFNKKFELMSEFARDYARFESEKMEIERKKVDAELQRVENDRERSKINDLEILTKDTSNMNPRQLQDYEFLCGVIRDKYGLN