AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31477

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31477.t1 MTR_2g090295 96.761 247 8 0 1 247 1 247 0.0 506
MS.gene31477.t1 MTR_8g465910 57.255 255 90 7 1 247 1 244 4.49e-98 286
MS.gene31477.t1 MTR_2g013550 41.038 212 95 5 37 232 24 221 3.04e-44 149
MS.gene31477.t1 MTR_2g090330 64.545 110 29 2 37 146 30 129 9.54e-44 145
MS.gene31477.t1 MTR_2g090330 64.545 110 29 2 37 146 27 126 1.36e-43 145
MS.gene31477.t1 MTR_2g090325 60.630 127 35 4 29 153 7 120 3.34e-41 140
MS.gene31477.t1 MTR_4g088870 34.979 243 105 10 14 247 1 199 6.32e-33 119
MS.gene31477.t1 MTR_4g088875 39.706 204 98 6 38 232 29 216 1.10e-32 119
MS.gene31477.t1 MTR_1g021895 52.128 94 33 3 37 128 27 110 1.41e-26 103
MS.gene31477.t1 MTR_5g019300 50.562 89 36 2 40 128 35 115 9.18e-26 101
MS.gene31477.t1 MTR_7g093390 41.964 112 51 4 15 126 149 246 4.07e-23 97.4
MS.gene31477.t1 MTR_1g054260 30.921 152 97 4 3 152 55 200 1.55e-21 89.4
MS.gene31477.t1 MTR_4g029440 38.462 130 65 4 8 129 86 208 1.89e-21 92.4
MS.gene31477.t1 MTR_4g029440 38.462 130 65 4 8 129 92 214 2.00e-21 92.4
MS.gene31477.t1 MTR_1g054465 40.449 89 51 2 40 126 55 143 1.02e-20 87.0
MS.gene31477.t1 MTR_1g054280 38.889 108 58 3 19 126 56 155 1.16e-20 88.2
MS.gene31477.t1 MTR_1g054210 43.011 93 44 3 36 126 116 201 8.61e-19 82.4
MS.gene31477.t1 MTR_2g061230 36.667 90 50 1 40 129 107 189 7.40e-16 74.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31477.t1 AT4G03510 46.047 215 108 4 35 247 41 249 2.30e-63 198
MS.gene31477.t1 AT4G03510 46.047 215 108 4 35 247 41 249 2.30e-63 198
MS.gene31477.t1 AT4G03510 46.047 215 108 4 35 247 41 249 2.30e-63 198
MS.gene31477.t1 AT4G03510 46.047 215 108 4 35 247 41 249 2.30e-63 198
MS.gene31477.t1 AT4G28270 40.773 233 88 9 24 247 2 193 8.89e-47 154
MS.gene31477.t1 AT4G27470 42.647 204 89 10 40 232 42 228 1.29e-39 137
MS.gene31477.t1 AT2G23780 36.111 216 113 8 40 245 26 226 3.60e-27 104
MS.gene31477.t1 AT2G23780 36.111 216 113 8 40 245 26 226 3.60e-27 104
MS.gene31477.t1 AT2G23780 36.111 216 113 8 40 245 26 226 3.60e-27 104
MS.gene31477.t1 AT1G74990 44.545 110 49 3 30 137 7 106 1.52e-26 100
MS.gene31477.t1 AT1G19310 44.860 107 49 3 24 128 3 101 3.06e-25 99.8
MS.gene31477.t1 AT3G58030 32.759 232 119 10 27 235 122 339 1.01e-22 96.3
MS.gene31477.t1 AT3G58030 32.759 232 119 10 27 235 122 339 1.01e-22 96.3
MS.gene31477.t1 AT3G58030 32.759 232 119 10 27 235 122 339 1.01e-22 96.3
MS.gene31477.t1 AT3G58030 32.759 232 119 10 27 235 122 339 1.01e-22 96.3
MS.gene31477.t1 AT2G42030 33.880 183 91 6 36 213 133 290 2.00e-20 89.7
MS.gene31477.t1 AT2G44410 37.037 108 51 3 25 126 106 202 2.55e-17 80.9

Find 67 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTGTAAGATTGTATGAATT+TGG 0.196085 2.4:-10495552 None:intergenic
TTTCTTCCATGGAATCAATT+TGG 0.249281 2.4:-10494975 None:intergenic
AAAGGCAATGATCACCAATT+AGG 0.249482 2.4:+10495273 MS.gene31477:CDS
GTTGAGAATGATTCGGATAA+TGG 0.278191 2.4:-10495401 None:intergenic
CTTTGGAAGGCGGCGTAGTT+TGG 0.290827 2.4:-10495254 None:intergenic
ATGATATATGCAAGGATCTT+TGG 0.299279 2.4:+10495501 MS.gene31477:CDS
CCAAATTCATACAATCTTAC+AGG 0.303928 2.4:+10495552 MS.gene31477:CDS
GCAAGTGGTGAAGCAATTTC+TGG 0.315559 2.4:+10495024 MS.gene31477:CDS
GAGATTTCTGATTTGCATAC+TGG 0.331060 2.4:-10495198 None:intergenic
CTGTAAGATTGTATGAATTT+GGG 0.342103 2.4:-10495551 None:intergenic
GATACAAGTTATGGTGTCTT+TGG 0.352630 2.4:+10495474 MS.gene31477:CDS
TTGAGAATGATTCGGATAAT+GGG 0.356464 2.4:-10495400 None:intergenic
CTAGACCGCTTGGTCCTTCA+TGG 0.359817 2.4:+10495310 MS.gene31477:CDS
AAGGCAATGATCACCAATTA+GGG 0.391729 2.4:+10495274 MS.gene31477:CDS
GTGGTATGACACTCCCTAAT+TGG 0.404265 2.4:-10495287 None:intergenic
ATGTTTCACAACATAATTCT+CGG 0.420768 2.4:+10495367 MS.gene31477:CDS
CATGAAGGACCAAGCGGTCT+AGG 0.421483 2.4:-10495309 None:intergenic
TTTGCAGCGTCAAGTGATCT+TGG 0.423758 2.4:-10495345 None:intergenic
ATCAAATGCCTTCTGATCCT+TGG 0.432608 2.4:-10495585 None:intergenic
ATTAAGCCATTTGTAAATGC+AGG 0.444845 2.4:-10495130 None:intergenic
GATCCAGTGGTCACTCTTTG+TGG 0.447780 2.4:+10495090 MS.gene31477:CDS
TAATTGGTGATCATTGCCTT+TGG 0.448612 2.4:-10495271 None:intergenic
TATGGAATAGCATTCAAAAC+AGG 0.456218 2.4:-10495674 None:intergenic
GCTGGCCCTGCATTTACAAA+TGG 0.463384 2.4:+10495124 MS.gene31477:CDS
CTCCTCAAAATACTGATTGA+AGG 0.463468 2.4:-10494944 None:intergenic
TATGAACCAAATTGATTCCA+TGG 0.475517 2.4:+10494969 MS.gene31477:CDS
TTTGTGGTCATCTCTACTGC+TGG 0.480977 2.4:+10495106 MS.gene31477:CDS
AATCCATTGGATACAAGTTA+TGG 0.483929 2.4:+10495465 MS.gene31477:CDS
ATAACTTGTATCCAATGGAT+TGG 0.489925 2.4:-10495463 None:intergenic
ATGTATATATGTTTGTCACT+TGG 0.494265 2.4:-10495527 None:intergenic
TAACTTGTATCCAATGGATT+GGG 0.500116 2.4:-10495462 None:intergenic
CTTTGACTGCAACATATGCT+TGG 0.503274 2.4:+10495056 MS.gene31477:CDS
GTTTGGCCGCGGCCGTAGAG+TGG 0.505416 2.4:-10495237 None:intergenic
GAAGCAATTTCTGGTTCTAG+TGG 0.514216 2.4:+10495033 MS.gene31477:CDS
TGGTGATCATTGCCTTTGGA+AGG 0.521075 2.4:-10495267 None:intergenic
TGGTTCACTGCCCAATCCAT+TGG 0.524258 2.4:+10495452 MS.gene31477:CDS
TCATCCCTTGTTCCACTCTA+CGG 0.525770 2.4:+10495225 MS.gene31477:CDS
AAGGCGGCGTAGTTTGGCCG+CGG 0.530973 2.4:-10495248 None:intergenic
GACACAAAACTGTGCAGCAA+AGG 0.541056 2.4:-10495647 None:intergenic
CGCGGCCGTAGAGTGGAACA+AGG 0.543163 2.4:-10495230 None:intergenic
GTGTATCGTTGAGAATGATT+CGG 0.543480 2.4:-10495408 None:intergenic
CAAATTCATACAATCTTACA+GGG 0.556632 2.4:+10495553 MS.gene31477:CDS
GTCATACCACCTAGACCGCT+TGG 0.564556 2.4:+10495300 MS.gene31477:CDS
CAAACTACGCCGCCTTCCAA+AGG 0.572732 2.4:+10495255 MS.gene31477:CDS
GGTAAGTTCGTCATCCATGA+AGG 0.573904 2.4:-10495324 None:intergenic
ACACCATAACTTGTATCCAA+TGG 0.574386 2.4:-10495468 None:intergenic
ACAAAACTGTGCAGCAAAGG+AGG 0.577384 2.4:-10495644 None:intergenic
TGATCATTGCCTTTGGAAGG+CGG 0.577497 2.4:-10495264 None:intergenic
TCAGTAATCCAAGGATCAGA+AGG 0.591994 2.4:+10495577 MS.gene31477:CDS
TGACCACAAAGAGTGACCAC+TGG 0.593140 2.4:-10495093 None:intergenic
TTAAGCCATTTGTAAATGCA+GGG 0.593204 2.4:-10495129 None:intergenic
TCGCCAATGTTTAACACAGG+TGG 0.595550 2.4:+10495432 MS.gene31477:CDS
GATTTGCATACTGGACATTG+TGG 0.605821 2.4:-10495189 None:intergenic
AAATCAAGAGAAGCAGAAGG+AGG 0.609520 2.4:+10495164 MS.gene31477:CDS
GAACCACCTGTGTTAAACAT+TGG 0.613627 2.4:-10495435 None:intergenic
ATGCGAGCTGATAAGTCGCT+CGG 0.619945 2.4:+10495606 MS.gene31477:CDS
TTACAGGGATCAGTAATCCA+AGG 0.633705 2.4:+10495568 MS.gene31477:CDS
CGAAAATCAAGAGAAGCAGA+AGG 0.635468 2.4:+10495161 MS.gene31477:CDS
TGAGAATGATTCGGATAATG+GGG 0.646474 2.4:-10495399 None:intergenic
TTGGTGAGATGATATATGCA+AGG 0.649382 2.4:+10495493 MS.gene31477:CDS
GAAGGACCAAGCGGTCTAGG+TGG 0.660331 2.4:-10495306 None:intergenic
ACTTCGCCAATGTTTAACAC+AGG 0.666429 2.4:+10495429 MS.gene31477:CDS
GGAGTGTGTGCAAGATCCAG+TGG 0.671005 2.4:+10495077 MS.gene31477:CDS
CTTGTTCCACTCTACGGCCG+CGG 0.675004 2.4:+10495231 MS.gene31477:CDS
GTCATCCATGAAGGACCAAG+CGG 0.707584 2.4:-10495315 None:intergenic
GAAGTGTGGAAATGTGCAAG+TGG 0.714630 2.4:+10495009 MS.gene31477:CDS
GCGGCCGTAGAGTGGAACAA+GGG 0.719279 2.4:-10495229 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATGTATATATGTTTGTCACT+TGG - chr2.4:10495530-10495549 None:intergenic 25.0%
! ATGTTTCACAACATAATTCT+CGG + chr2.4:10495367-10495386 MS.gene31477:CDS 25.0%
! CAAATTCATACAATCTTACA+GGG + chr2.4:10495553-10495572 MS.gene31477:CDS 25.0%
! CTGTAAGATTGTATGAATTT+GGG - chr2.4:10495554-10495573 None:intergenic 25.0%
AAAAATCATCTCAAGAAGTG+TGG + chr2.4:10494995-10495014 MS.gene31477:CDS 30.0%
AATCCATTGGATACAAGTTA+TGG + chr2.4:10495465-10495484 MS.gene31477:CDS 30.0%
ATGATATATGCAAGGATCTT+TGG + chr2.4:10495501-10495520 MS.gene31477:CDS 30.0%
ATTAAGCCATTTGTAAATGC+AGG - chr2.4:10495133-10495152 None:intergenic 30.0%
CCAAATTCATACAATCTTAC+AGG + chr2.4:10495552-10495571 MS.gene31477:CDS 30.0%
CCTGTAAGATTGTATGAATT+TGG - chr2.4:10495555-10495574 None:intergenic 30.0%
TTAAGCCATTTGTAAATGCA+GGG - chr2.4:10495132-10495151 None:intergenic 30.0%
TTTCTTCCATGGAATCAATT+TGG - chr2.4:10494978-10494997 None:intergenic 30.0%
! ATAACTTGTATCCAATGGAT+TGG - chr2.4:10495466-10495485 None:intergenic 30.0%
! TAACTTGTATCCAATGGATT+GGG - chr2.4:10495465-10495484 None:intergenic 30.0%
! TATGAACCAAATTGATTCCA+TGG + chr2.4:10494969-10494988 MS.gene31477:CDS 30.0%
! TTGAGAATGATTCGGATAAT+GGG - chr2.4:10495403-10495422 None:intergenic 30.0%
! TTGAGATGATTTTTCTTCCA+TGG - chr2.4:10494989-10495008 None:intergenic 30.0%
!! TTCAATCAGTATTTTGAGGA+GGG + chr2.4:10494946-10494965 MS.gene31477:CDS 30.0%
AAAGGCAATGATCACCAATT+AGG + chr2.4:10495273-10495292 MS.gene31477:CDS 35.0%
AAGGCAATGATCACCAATTA+GGG + chr2.4:10495274-10495293 MS.gene31477:CDS 35.0%
GATACAAGTTATGGTGTCTT+TGG + chr2.4:10495474-10495493 MS.gene31477:CDS 35.0%
GTGTATCGTTGAGAATGATT+CGG - chr2.4:10495411-10495430 None:intergenic 35.0%
TTGGTGAGATGATATATGCA+AGG + chr2.4:10495493-10495512 MS.gene31477:CDS 35.0%
! ACACCATAACTTGTATCCAA+TGG - chr2.4:10495471-10495490 None:intergenic 35.0%
! CTCCTCAAAATACTGATTGA+AGG - chr2.4:10494947-10494966 None:intergenic 35.0%
! CTTCTGCTTCTCTTGATTTT+CGG - chr2.4:10495163-10495182 None:intergenic 35.0%
! GAGATTTCTGATTTGCATAC+TGG - chr2.4:10495201-10495220 None:intergenic 35.0%
! GTTGAGAATGATTCGGATAA+TGG - chr2.4:10495404-10495423 None:intergenic 35.0%
! TAATTGGTGATCATTGCCTT+TGG - chr2.4:10495274-10495293 None:intergenic 35.0%
! TGAGAATGATTCGGATAATG+GGG - chr2.4:10495402-10495421 None:intergenic 35.0%
!! CTTCAATCAGTATTTTGAGG+AGG + chr2.4:10494945-10494964 MS.gene31477:CDS 35.0%
AAATCAAGAGAAGCAGAAGG+AGG + chr2.4:10495164-10495183 MS.gene31477:CDS 40.0%
ACTTCGCCAATGTTTAACAC+AGG + chr2.4:10495429-10495448 MS.gene31477:CDS 40.0%
ATCAAATGCCTTCTGATCCT+TGG - chr2.4:10495588-10495607 None:intergenic 40.0%
CGAAAATCAAGAGAAGCAGA+AGG + chr2.4:10495161-10495180 MS.gene31477:CDS 40.0%
CTTTGACTGCAACATATGCT+TGG + chr2.4:10495056-10495075 MS.gene31477:CDS 40.0%
GAACCACCTGTGTTAAACAT+TGG - chr2.4:10495438-10495457 None:intergenic 40.0%
GATTTGCATACTGGACATTG+TGG - chr2.4:10495192-10495211 None:intergenic 40.0%
TCAGTAATCCAAGGATCAGA+AGG + chr2.4:10495577-10495596 MS.gene31477:CDS 40.0%
TTACAGGGATCAGTAATCCA+AGG + chr2.4:10495568-10495587 MS.gene31477:CDS 40.0%
! GGCCTTCAATCAGTATTTTG+AGG + chr2.4:10494942-10494961 MS.gene31477:CDS 40.0%
!! GAAGCAATTTCTGGTTCTAG+TGG + chr2.4:10495033-10495052 MS.gene31477:CDS 40.0%
ACAAAACTGTGCAGCAAAGG+AGG - chr2.4:10495647-10495666 None:intergenic 45.0%
GAAGTGTGGAAATGTGCAAG+TGG + chr2.4:10495009-10495028 MS.gene31477:CDS 45.0%
GACACAAAACTGTGCAGCAA+AGG - chr2.4:10495650-10495669 None:intergenic 45.0%
GCAAGTGGTGAAGCAATTTC+TGG + chr2.4:10495024-10495043 MS.gene31477:CDS 45.0%
GGTAAGTTCGTCATCCATGA+AGG - chr2.4:10495327-10495346 None:intergenic 45.0%
GTGGTATGACACTCCCTAAT+TGG - chr2.4:10495290-10495309 None:intergenic 45.0%
TCATCCCTTGTTCCACTCTA+CGG + chr2.4:10495225-10495244 MS.gene31477:CDS 45.0%
TCGCCAATGTTTAACACAGG+TGG + chr2.4:10495432-10495451 MS.gene31477:CDS 45.0%
TGGTGATCATTGCCTTTGGA+AGG - chr2.4:10495270-10495289 None:intergenic 45.0%
TTTGCAGCGTCAAGTGATCT+TGG - chr2.4:10495348-10495367 None:intergenic 45.0%
TTTGTGGTCATCTCTACTGC+TGG + chr2.4:10495106-10495125 MS.gene31477:CDS 45.0%
! GCTTCTCTTGATTTTCGGCA+TGG - chr2.4:10495158-10495177 None:intergenic 45.0%
! TGATCATTGCCTTTGGAAGG+CGG - chr2.4:10495267-10495286 None:intergenic 45.0%
ATGCGAGCTGATAAGTCGCT+CGG + chr2.4:10495606-10495625 MS.gene31477:CDS 50.0%
GATCCAGTGGTCACTCTTTG+TGG + chr2.4:10495090-10495109 MS.gene31477:CDS 50.0%
GCTGGCCCTGCATTTACAAA+TGG + chr2.4:10495124-10495143 MS.gene31477:CDS 50.0%
GTCATCCATGAAGGACCAAG+CGG - chr2.4:10495318-10495337 None:intergenic 50.0%
TGACCACAAAGAGTGACCAC+TGG - chr2.4:10495096-10495115 None:intergenic 50.0%
TGGTTCACTGCCCAATCCAT+TGG + chr2.4:10495452-10495471 MS.gene31477:CDS 50.0%
CAAACTACGCCGCCTTCCAA+AGG + chr2.4:10495255-10495274 MS.gene31477:CDS 55.0%
CATGAAGGACCAAGCGGTCT+AGG - chr2.4:10495312-10495331 None:intergenic 55.0%
CTAGACCGCTTGGTCCTTCA+TGG + chr2.4:10495310-10495329 MS.gene31477:CDS 55.0%
GGAGTGTGTGCAAGATCCAG+TGG + chr2.4:10495077-10495096 MS.gene31477:CDS 55.0%
GTCATACCACCTAGACCGCT+TGG + chr2.4:10495300-10495319 MS.gene31477:CDS 55.0%
! CTTTGGAAGGCGGCGTAGTT+TGG - chr2.4:10495257-10495276 None:intergenic 55.0%
CTTGTTCCACTCTACGGCCG+CGG + chr2.4:10495231-10495250 MS.gene31477:CDS 60.0%
GAAGGACCAAGCGGTCTAGG+TGG - chr2.4:10495309-10495328 None:intergenic 60.0%
GCGGCCGTAGAGTGGAACAA+GGG - chr2.4:10495232-10495251 None:intergenic 60.0%
AAGGCGGCGTAGTTTGGCCG+CGG - chr2.4:10495251-10495270 None:intergenic 65.0%
CGCGGCCGTAGAGTGGAACA+AGG - chr2.4:10495233-10495252 None:intergenic 65.0%
GTTTGGCCGCGGCCGTAGAG+TGG - chr2.4:10495240-10495259 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 10494940 10495683 10494940 ID=MS.gene31477
chr2.4 mRNA 10494940 10495683 10494940 ID=MS.gene31477.t1;Parent=MS.gene31477
chr2.4 exon 10494940 10495683 10494940 ID=MS.gene31477.t1.exon1;Parent=MS.gene31477.t1
chr2.4 CDS 10494940 10495683 10494940 ID=cds.MS.gene31477.t1;Parent=MS.gene31477.t1
Gene Sequence

>MS.gene31477

ATGGCCTTCAATCAGTATTTTGAGGAGGGTATGAACCAAATTGATTCCATGGAAGAAAAATCATCTCAAGAAGTGTGGAAATGTGCAAGTGGTGAAGCAATTTCTGGTTCTAGTGGCTTTGACTGCAACATATGCTTGGAGTGTGTGCAAGATCCAGTGGTCACTCTTTGTGGTCATCTCTACTGCTGGCCCTGCATTTACAAATGGCTTAATTTCCATGCCGAAAATCAAGAGAAGCAGAAGGAGGAGCCACAATGTCCAGTATGCAAATCAGAAATCTCAAAATCATCCCTTGTTCCACTCTACGGCCGCGGCCAAACTACGCCGCCTTCCAAAGGCAATGATCACCAATTAGGGAGTGTCATACCACCTAGACCGCTTGGTCCTTCATGGATGACGAACTTACCAAGATCACTTGACGCTGCAAATGTTTCACAACATAATTCTCGGTCTTATCATCCCCATTATCCGAATCATTCTCAACGATACACTTCGCCAATGTTTAACACAGGTGGTTCACTGCCCAATCCATTGGATACAAGTTATGGTGTCTTTGGTGAGATGATATATGCAAGGATCTTTGGAAACCAAGTGACAAACATATATACATACCCAAATTCATACAATCTTACAGGGATCAGTAATCCAAGGATCAGAAGGCATTTGATGCGAGCTGATAAGTCGCTCGGTAGAATCTGTTTCTTCCTCCTTTGCTGCACAGTTTTGTGTCTTCTCCTGTTTTGA
Protein sequence

>MS.gene31477.t1

MAFNQYFEEGMNQIDSMEEKSSQEVWKCASGEAISGSSGFDCNICLECVQDPVVTLCGHLYCWPCIYKWLNFHAENQEKQKEEPQCPVCKSEISKSSLVPLYGRGQTTPPSKGNDHQLGSVIPPRPLGPSWMTNLPRSLDAANVSQHNSRSYHPHYPNHSQRYTSPMFNTGGSLPNPLDTSYGVFGEMIYARIFGNQVTNIYTYPNSYNLTGISNPRIRRHLMRADKSLGRICFFLLCCTVLCLLLF