AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene79416

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene79416.t1 MTR_3g025380 78.571 140 30 0 3 142 2 141 5.28e-68 202
MS.gene79416.t1 MTR_3g025510 52.349 149 61 4 1 139 1 149 2.87e-42 137
MS.gene79416.t1 MTR_3g025550 88.136 59 7 0 84 142 6 64 6.86e-35 115
MS.gene79416.t1 MTR_3g025620 59.259 54 22 0 89 142 2 55 1.58e-18 74.3
MS.gene79416.t1 MTR_2g058360 48.052 77 35 3 66 139 66 140 4.02e-16 70.5
MS.gene79416.t1 MTR_7g074170 43.750 64 35 1 78 140 327 390 1.17e-15 72.8
MS.gene79416.t1 MTR_3g088080 37.209 86 47 2 56 141 6 84 8.18e-15 65.5
MS.gene79416.t1 MTR_3g072630 40.323 62 37 0 79 140 205 266 5.66e-14 67.8
MS.gene79416.t1 MTR_3g072630 40.323 62 37 0 79 140 205 266 6.60e-14 67.4
MS.gene79416.t1 MTR_1g114320 35.135 74 47 1 68 140 166 239 2.45e-13 65.9
MS.gene79416.t1 MTR_1g114620 38.667 75 44 1 66 140 237 309 2.57e-13 65.9
MS.gene79416.t1 MTR_5g041310 36.471 85 50 2 57 140 79 160 2.88e-13 64.7
MS.gene79416.t1 MTR_4g110100 44.615 65 35 1 77 140 341 405 2.91e-13 65.9
MS.gene79416.t1 MTR_6g079660 36.842 76 47 1 66 140 205 280 3.04e-13 65.9
MS.gene79416.t1 MTR_2g097620 33.846 65 43 0 77 141 171 235 3.39e-13 65.5
MS.gene79416.t1 MTR_5g041330 41.176 68 37 1 73 140 86 150 5.13e-13 63.9
MS.gene79416.t1 MTR_1g051105 34.667 75 49 0 66 140 130 204 3.68e-12 62.0
MS.gene79416.t1 MTR_4g108830 34.259 108 56 2 47 139 112 219 4.70e-12 61.2
MS.gene79416.t1 MTR_5g088720 34.667 75 49 0 66 140 217 291 5.90e-12 62.0
MS.gene79416.t1 MTR_2g007340 44.828 58 32 0 79 136 185 242 6.68e-12 61.6
MS.gene79416.t1 MTR_5g088720 34.667 75 49 0 66 140 176 250 7.47e-12 61.6
MS.gene79416.t1 MTR_5g088720 34.667 75 49 0 66 140 171 245 8.11e-12 61.6
MS.gene79416.t1 MTR_3g083480 32.877 73 44 1 67 139 214 281 1.06e-11 61.2
MS.gene79416.t1 MTR_6g016350 45.833 48 26 0 93 140 309 356 2.01e-11 60.5
MS.gene79416.t1 MTR_4g108830 36.364 77 48 1 64 139 115 191 2.57e-11 58.9
MS.gene79416.t1 MTR_8g056930 38.667 75 42 2 68 139 90 163 2.94e-11 58.2
MS.gene79416.t1 MTR_0186s0090 51.020 49 21 1 94 139 115 163 3.66e-11 58.2
MS.gene79416.t1 MTR_4g064570 37.500 64 40 0 78 141 164 227 6.60e-11 58.9
MS.gene79416.t1 MTR_5g080350 37.097 62 39 0 79 140 177 238 8.21e-11 58.9
MS.gene79416.t1 MTR_5g058530 52.381 42 20 0 95 136 224 265 9.30e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene79416.t1 AT1G14200 44.444 63 35 0 78 140 92 154 2.77e-16 72.0
MS.gene79416.t1 AT3G02340 29.371 143 83 5 1 140 253 380 1.57e-14 69.7
MS.gene79416.t1 AT3G02340 29.371 143 83 5 1 140 253 380 1.57e-14 69.7
MS.gene79416.t1 AT1G60360 40.625 64 37 1 78 140 206 269 2.97e-14 68.6
MS.gene79416.t1 AT5G08139 42.188 64 36 1 78 140 291 354 3.27e-14 68.6
MS.gene79416.t1 AT5G01980 40.625 64 38 0 77 140 332 395 5.99e-14 68.2
MS.gene79416.t1 AT3G60080 39.286 56 34 0 85 140 159 214 1.30e-13 66.6
MS.gene79416.t1 AT5G60820 45.283 53 29 0 89 141 366 418 1.63e-13 66.6
MS.gene79416.t1 AT4G05350 43.939 66 32 2 79 139 139 204 3.82e-13 63.9
MS.gene79416.t1 AT5G15820 37.662 77 47 1 65 140 260 336 4.44e-13 65.1
MS.gene79416.t1 AT4G12190 47.619 63 28 2 79 136 4 66 5.15e-13 60.5
MS.gene79416.t1 AT2G40830 36.709 79 49 1 64 141 158 236 9.75e-13 64.3
MS.gene79416.t1 AT2G40830 36.709 79 49 1 64 141 158 236 9.75e-13 64.3
MS.gene79416.t1 AT2G40830 36.709 79 49 1 64 141 158 236 9.75e-13 64.3
MS.gene79416.t1 AT2G40830 36.709 79 49 1 64 141 158 236 9.75e-13 64.3
MS.gene79416.t1 AT2G44330 52.174 46 22 0 95 140 96 141 1.00e-12 62.4
MS.gene79416.t1 AT4G26400 41.270 63 32 1 78 140 229 286 1.79e-12 63.5
MS.gene79416.t1 AT4G26400 41.270 63 32 1 78 140 229 286 1.79e-12 63.5
MS.gene79416.t1 AT3G10815 38.095 63 39 0 78 140 104 166 1.82e-12 62.0
MS.gene79416.t1 AT4G12150 50.909 55 25 1 82 134 140 194 3.01e-12 62.8
MS.gene79416.t1 AT4G12210 46.032 63 29 2 79 136 135 197 4.64e-12 61.2
MS.gene79416.t1 AT4G12140 46.774 62 29 2 79 136 135 196 6.24e-12 60.8
MS.gene79416.t1 AT3G30460 28.571 133 76 4 13 139 22 141 1.17e-11 58.9
MS.gene79416.t1 AT3G19950 36.508 63 39 1 79 140 257 319 1.39e-11 61.2
MS.gene79416.t1 AT3G19950 36.508 63 39 1 79 140 257 319 1.39e-11 61.2
MS.gene79416.t1 AT3G19950 36.508 63 39 1 79 140 199 261 1.47e-11 60.8
MS.gene79416.t1 AT3G30460 28.571 133 76 4 13 139 58 177 1.58e-11 59.3
MS.gene79416.t1 AT3G14320 36.250 80 50 1 61 139 54 133 3.01e-11 58.9
MS.gene79416.t1 AT5G54990 51.111 45 22 0 92 136 171 215 3.56e-11 58.9
MS.gene79416.t1 AT1G55530 30.137 73 46 1 68 140 201 268 4.47e-11 59.7
MS.gene79416.t1 AT1G55530 30.137 73 46 1 68 140 201 268 4.47e-11 59.7
MS.gene79416.t1 AT1G21960 43.137 51 29 0 90 140 153 203 4.49e-11 58.5
MS.gene79416.t1 AT1G55530 29.730 74 47 1 67 140 167 235 4.58e-11 59.3
MS.gene79416.t1 AT5G64920 37.931 58 36 0 79 136 241 298 4.98e-11 59.3
MS.gene79416.t1 AT3G56580 38.095 63 38 1 79 140 169 231 7.10e-11 58.9
MS.gene79416.t1 AT3G56580 38.095 63 38 1 79 140 169 231 7.10e-11 58.9
MS.gene79416.t1 AT3G56580 38.095 63 38 1 79 140 169 231 7.10e-11 58.9
MS.gene79416.t1 AT5G43200 42.373 59 32 2 83 139 144 202 8.70e-11 57.8
MS.gene79416.t1 AT3G13430 36.538 52 33 0 89 140 219 270 9.75e-11 58.5
MS.gene79416.t1 AT3G13430 36.538 52 33 0 89 140 219 270 9.75e-11 58.5
MS.gene79416.t1 AT3G13430 36.538 52 33 0 89 140 219 270 9.75e-11 58.5
MS.gene79416.t1 AT3G13430 36.538 52 33 0 89 140 219 270 9.75e-11 58.5

Find 23 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATCACTTTCTACATTTAT+AGG 0.123833 3.1:-16541050 None:intergenic
TATCTGTTTGGCGGAGCTTT+TGG 0.296874 3.1:+16541307 MS.gene79416:CDS
CATAAACAAACTCAGATATT+AGG 0.326615 3.1:-16541437 None:intergenic
GATTACGATTAGAATGCCTT+TGG 0.413240 3.1:-16541232 None:intergenic
ACGAAGGATGTATTATGAAA+TGG 0.423422 3.1:+16541372 MS.gene79416:CDS
GAACCTCGTTGATGAGGTTA+TGG 0.437573 3.1:-16541181 None:intergenic
TTATGGTGGCGAACAATAGA+AGG 0.439093 3.1:-16541164 None:intergenic
AATGATGTGTTCTATCTGTT+TGG 0.466778 3.1:+16541295 MS.gene79416:CDS
AATTAGAGTTGAAGAAGGAA+AGG 0.503387 3.1:+16541262 MS.gene79416:CDS
ATAACCTCATCAACGAGGTT+CGG 0.516089 3.1:+16541183 MS.gene79416:CDS
GATGTGTTCTATCTGTTTGG+CGG 0.555139 3.1:+16541298 MS.gene79416:CDS
GGAACAGTCTGACGACACAT+AGG 0.570479 3.1:-16541416 None:intergenic
GAACAGTCTGACGACACATA+GGG 0.586165 3.1:-16541415 None:intergenic
GGATGTATTATGAAATGGCT+AGG 0.587358 3.1:+16541377 MS.gene79416:CDS
TGGTTGGATCGCAAGCAACT+CGG 0.597083 3.1:+16541327 MS.gene79416:CDS
CCTCGTTGATGAGGTTATGG+TGG 0.604309 3.1:-16541178 None:intergenic
TAATCCGAACCTCGTTGATG+AGG 0.608297 3.1:-16541187 None:intergenic
GAAATACTGAAACTATCCAA+AGG 0.644867 3.1:+16541216 MS.gene79416:CDS
TCGTGATACAAATGTGAACA+CGG 0.667380 3.1:-16541353 None:intergenic
TGTTCACATTTGTATCACGA+AGG 0.683248 3.1:+16541356 MS.gene79416:CDS
GCTCATCGTCGTCATACACA+TGG 0.711088 3.1:+16541107 MS.gene79416:CDS
ATGGTACAAATCGATCAACA+AGG 0.728585 3.1:+16541126 MS.gene79416:CDS
CCACCATAACCTCATCAACG+AGG 0.765219 3.1:+16541178 MS.gene79416:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATCACTTTCTACATTTAT+AGG - chr3.1:16541053-16541072 None:intergenic 20.0%
AATGATGTGTTCTATCTGTT+TGG + chr3.1:16541295-16541314 MS.gene79416:CDS 30.0%
AATTAGAGTTGAAGAAGGAA+AGG + chr3.1:16541262-16541281 MS.gene79416:CDS 30.0%
ACGAAGGATGTATTATGAAA+TGG + chr3.1:16541372-16541391 MS.gene79416:CDS 30.0%
CCAAAAATTAGAGTTGAAGA+AGG + chr3.1:16541257-16541276 MS.gene79416:CDS 30.0%
GAAATACTGAAACTATCCAA+AGG + chr3.1:16541216-16541235 MS.gene79416:CDS 30.0%
! CCTTCTTCAACTCTAATTTT+TGG - chr3.1:16541260-16541279 None:intergenic 30.0%
ATGGTACAAATCGATCAACA+AGG + chr3.1:16541126-16541145 MS.gene79416:CDS 35.0%
GATTACGATTAGAATGCCTT+TGG - chr3.1:16541235-16541254 None:intergenic 35.0%
GGATGTATTATGAAATGGCT+AGG + chr3.1:16541377-16541396 MS.gene79416:CDS 35.0%
TCGTGATACAAATGTGAACA+CGG - chr3.1:16541356-16541375 None:intergenic 35.0%
TGTTCACATTTGTATCACGA+AGG + chr3.1:16541356-16541375 MS.gene79416:CDS 35.0%
ATAACCTCATCAACGAGGTT+CGG + chr3.1:16541183-16541202 MS.gene79416:CDS 40.0%
GATGTGTTCTATCTGTTTGG+CGG + chr3.1:16541298-16541317 MS.gene79416:CDS 40.0%
! TTATGGTGGCGAACAATAGA+AGG - chr3.1:16541167-16541186 None:intergenic 40.0%
GAACAGTCTGACGACACATA+GGG - chr3.1:16541418-16541437 None:intergenic 45.0%
TAATCCGAACCTCGTTGATG+AGG - chr3.1:16541190-16541209 None:intergenic 45.0%
! GAACCTCGTTGATGAGGTTA+TGG - chr3.1:16541184-16541203 None:intergenic 45.0%
! TATCTGTTTGGCGGAGCTTT+TGG + chr3.1:16541307-16541326 MS.gene79416:CDS 45.0%
CCACCATAACCTCATCAACG+AGG + chr3.1:16541178-16541197 MS.gene79416:CDS 50.0%
GCTCATCGTCGTCATACACA+TGG + chr3.1:16541107-16541126 MS.gene79416:CDS 50.0%
GGAACAGTCTGACGACACAT+AGG - chr3.1:16541419-16541438 None:intergenic 50.0%
TGGTTGGATCGCAAGCAACT+CGG + chr3.1:16541327-16541346 MS.gene79416:CDS 50.0%
! CCTCGTTGATGAGGTTATGG+TGG - chr3.1:16541181-16541200 None:intergenic 50.0%
! TGTTTGGCGGAGCTTTTGGT+TGG + chr3.1:16541311-16541330 MS.gene79416:CDS 50.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 16541020 16541448 16541020 ID=MS.gene79416
chr3.1 mRNA 16541020 16541448 16541020 ID=MS.gene79416.t1;Parent=MS.gene79416
chr3.1 exon 16541020 16541448 16541020 ID=MS.gene79416.t1.exon1;Parent=MS.gene79416.t1
chr3.1 CDS 16541020 16541448 16541020 ID=cds.MS.gene79416.t1;Parent=MS.gene79416.t1
Gene Sequence

>MS.gene79416

ATGGAGCAACAACAACGTAATATAAGAAGTCCTATAAATGTAGAAAGTGATTATGTAATGATTCTTGATGCTGTTGATCTAAATCTCGCTCATCGTCGTCATACACATGGTACAAATCGATCAACAAGGTTCACTCTCTTGCGTCCTTCTATTGTTCGCCACCATAACCTCATCAACGAGGTTCGGATTACTATAAGAAATACTGAAACTATCCAAAGGCATTCTAATCGTAATCTTCCAAAAATTAGAGTTGAAGAAGGAAAGGAGTCTGAAGCAATGATGTGTTCTATCTGTTTGGCGGAGCTTTTGGTTGGATCGCAAGCAACTCGGTTGCCGTGTTCACATTTGTATCACGAAGGATGTATTATGAAATGGCTAGGTAGATCAAACACTTGCCCTATGTGTCGTCAGACTGTTCCTAATATCTGA
Protein sequence

>MS.gene79416.t1

MEQQQRNIRSPINVESDYVMILDAVDLNLAHRRHTHGTNRSTRFTLLRPSIVRHHNLINEVRITIRNTETIQRHSNRNLPKIRVEEGKESEAMMCSICLAELLVGSQATRLPCSHLYHEGCIMKWLGRSNTCPMCRQTVPNI