AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31312

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31312.t1 MTR_2g093990 95.600 250 11 0 1 250 1 250 1.45e-144 404
MS.gene31312.t1 MTR_4g059720 69.636 247 72 2 1 245 1 246 2.68e-110 318
MS.gene31312.t1 MTR_2g017950 44.828 290 115 7 1 245 1 290 8.64e-68 211
MS.gene31312.t1 MTR_2g017970 50.698 215 99 3 41 250 68 280 8.83e-63 198
MS.gene31312.t1 MTR_2g017960 50.237 211 100 3 41 248 68 276 7.32e-61 193
MS.gene31312.t1 MTR_4g059840 51.174 213 90 6 29 227 59 271 8.46e-60 191
MS.gene31312.t1 MTR_8g087460 50.000 226 94 6 32 239 79 303 2.51e-59 190
MS.gene31312.t1 MTR_8g087470 59.412 170 63 4 23 187 74 242 6.14e-59 189
MS.gene31312.t1 MTR_2g093980 48.319 238 112 4 21 249 49 284 8.73e-59 188
MS.gene31312.t1 MTR_4g059790 51.724 203 90 6 29 225 59 259 2.40e-58 187
MS.gene31312.t1 MTR_8g087450 46.903 226 107 4 29 245 64 285 3.40e-56 181
MS.gene31312.t1 MTR_4g053380 51.852 189 85 4 29 211 63 251 7.50e-56 181
MS.gene31312.t1 MTR_7g101080 51.412 177 81 3 13 188 16 188 2.85e-55 178
MS.gene31312.t1 MTR_4g059780 57.317 164 68 2 29 191 79 241 2.50e-53 174
MS.gene31312.t1 MTR_2g093970 44.498 209 87 3 8 187 8 216 4.60e-53 174
MS.gene31312.t1 MTR_2g090765 37.398 246 141 3 11 248 9 249 1.99e-39 137
MS.gene31312.t1 MTR_5g098060 38.788 165 93 3 41 200 48 209 2.56e-25 100
MS.gene31312.t1 MTR_7g075453 31.915 188 112 5 32 214 176 352 2.01e-18 84.0
MS.gene31312.t1 MTR_5g098420 26.339 224 136 7 32 233 185 401 4.29e-13 68.6
MS.gene31312.t1 MTR_2g437700 28.947 152 102 3 41 188 195 344 2.33e-12 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31312.t1 AT5G03170 56.219 201 82 5 9 207 7 203 6.81e-65 202
MS.gene31312.t1 AT5G60490 61.333 150 57 1 40 188 38 187 1.30e-58 186
MS.gene31312.t1 AT2G20520 42.739 241 130 5 4 239 1 238 3.55e-48 159
MS.gene31312.t1 AT5G44130 43.750 192 98 5 41 224 36 225 2.97e-41 142
MS.gene31312.t1 AT1G03870 41.546 207 116 4 45 248 43 247 3.85e-39 136
MS.gene31312.t1 AT2G04780 30.660 212 140 3 41 250 46 252 3.41e-18 81.6
MS.gene31312.t1 AT2G04780 30.660 212 140 3 41 250 46 252 3.41e-18 81.6
MS.gene31312.t1 AT3G60900 31.953 169 111 2 32 200 180 344 3.24e-15 74.7
MS.gene31312.t1 AT3G46550 32.370 173 110 5 34 201 200 370 6.21e-15 73.9
MS.gene31312.t1 AT4G12730 28.780 205 136 6 32 232 179 377 3.00e-14 72.0
MS.gene31312.t1 AT2G45470 29.299 157 107 2 32 188 180 332 1.82e-12 66.6
MS.gene31312.t1 AT5G55730 29.464 112 78 1 77 188 219 329 3.14e-11 63.2
MS.gene31312.t1 AT5G55730 29.464 112 78 1 77 188 219 329 3.14e-11 63.2

Find 53 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGTTCAATGCTAACCTTTC+AGG 0.147272 2.3:-7722116 None:intergenic
TGGTTTGGAGGAGGCGGATA+AGG 0.325830 2.3:-7721866 None:intergenic
TCACCAGCTTGTGTTCTAAC+TGG 0.342486 2.3:-7722089 None:intergenic
TGGGATAGAAGAGGACTATT+AGG 0.347658 2.3:-7721746 None:intergenic
TTAGTCCATTGTTTGAGTTT+AGG 0.358844 2.3:-7721920 None:intergenic
GCATTGAACATAACAAGTTC+AGG 0.362726 2.3:+7722128 MS.gene31312:CDS
GGATTCTGATAACGTCTGTT+GGG 0.385165 2.3:-7721818 None:intergenic
CGGAGCCGGTGGAGGAGACT+TGG 0.401331 2.3:-7722273 None:intergenic
GTTGAAAAGGAATTGTCATT+TGG 0.402638 2.3:-7721954 None:intergenic
TGATTCAACTGCTGAATTTG+TGG 0.418383 2.3:-7721772 None:intergenic
ATTGAGAAAACCAGGTTTGA+GGG 0.422399 2.3:-7721976 None:intergenic
ATCTTCTGCTATGAGTTTGA+AGG 0.426864 2.3:+7722367 MS.gene31312:CDS
TCTGGAGCCGGAGCCGGTGG+AGG 0.427935 2.3:-7722281 None:intergenic
ACCAGGTTTGAGGGTTGAAA+AGG 0.429920 2.3:-7721967 None:intergenic
GGTTTGGAGGAGGCGGATAA+GGG 0.431410 2.3:-7721865 None:intergenic
GCTGATGATGGTGATGGTGC+TGG 0.431800 2.3:-7721795 None:intergenic
CAAGTCTCCTCCACCGGCTC+CGG 0.455878 2.3:+7722274 MS.gene31312:CDS
GTGTGGCTACTTGAGTGGTT+TGG 0.457924 2.3:-7721881 None:intergenic
AACTGCTGAATTTGTGGTGG+TGG 0.462937 2.3:-7721766 None:intergenic
TGATAAAGTTCTTCTTCCTA+AGG 0.474783 2.3:+7722238 MS.gene31312:CDS
AGAAGTGAGAGTGTGAAGAG+AGG 0.477000 2.3:-7721723 None:intergenic
AGGATTCTGATAACGTCTGT+TGG 0.481414 2.3:-7721819 None:intergenic
ACTCAAGTGAATTTAACAAC+TGG 0.489837 2.3:+7722152 MS.gene31312:CDS
TTGGGAATGAAGAAATCCTT+AGG 0.492755 2.3:-7722254 None:intergenic
CTACTTGAGTGGTTTGGAGG+AGG 0.504028 2.3:-7721875 None:intergenic
TGGCTACTTGAGTGGTTTGG+AGG 0.514366 2.3:-7721878 None:intergenic
TCACTATCATCTGCAGAAGC+AGG 0.522638 2.3:-7722341 None:intergenic
CTTGAGTGGTTTGGAGGAGG+CGG 0.526143 2.3:-7721872 None:intergenic
AATTGAGAAAACCAGGTTTG+AGG 0.530468 2.3:-7721977 None:intergenic
TGAATCCGCCGGCTTTCTTG+AGG 0.536798 2.3:-7721839 None:intergenic
ACGTCTGTTGGGGCTGATGA+TGG 0.537504 2.3:-7721807 None:intergenic
GTTGTTAATGCTACTGTTGG+TGG 0.549812 2.3:+7722176 MS.gene31312:CDS
CATTGAACATAACAAGTTCA+GGG 0.550919 2.3:+7722129 MS.gene31312:CDS
ATTTGAGAGTGAAACAAATG+AGG 0.552176 2.3:-7722048 None:intergenic
GGTGTTGTTAATGCTACTGT+TGG 0.552358 2.3:+7722173 MS.gene31312:CDS
TTTGAGAGTGAAACAAATGA+GGG 0.553534 2.3:-7722047 None:intergenic
TTAAGGGAATTGAGAAAACC+AGG 0.557823 2.3:-7721984 None:intergenic
GGAGCCGGTGGAGGAGACTT+GGG 0.560404 2.3:-7722272 None:intergenic
ATCAGAATCCTCAAGAAAGC+CGG 0.560627 2.3:+7721831 MS.gene31312:CDS
GATTTGTGTGGCTACTTGAG+TGG 0.563809 2.3:-7721886 None:intergenic
TTGGAGGAGGCGGATAAGGG+TGG 0.565992 2.3:-7721862 None:intergenic
GTTGGGGCTGATGATGGTGA+TGG 0.565993 2.3:-7721801 None:intergenic
CAACTCCTAAACTCAAACAA+TGG 0.569617 2.3:+7721915 MS.gene31312:CDS
ACTGCTGAATTTGTGGTGGT+GGG 0.587110 2.3:-7721765 None:intergenic
CATTCCCAAGTCTCCTCCAC+CGG 0.590749 2.3:+7722268 MS.gene31312:CDS
AATCCAGTTAGAACACAAGC+TGG 0.595225 2.3:+7722086 MS.gene31312:CDS
TTGTGGTGGTGGGATAGAAG+AGG 0.596092 2.3:-7721755 None:intergenic
TTCAACTGCTGAATTTGTGG+TGG 0.608674 2.3:-7721769 None:intergenic
GATAAGGGTGGTGAATCCGC+CGG 0.611907 2.3:-7721850 None:intergenic
GAGTTGTGCATTGATTTGTG+TGG 0.650430 2.3:-7721898 None:intergenic
AAGCTGGTGATGATCCTGAA+AGG 0.650768 2.3:+7722102 MS.gene31312:CDS
GATTCTGATAACGTCTGTTG+GGG 0.654912 2.3:-7721817 None:intergenic
AGAATCCTCAAGAAAGCCGG+CGG 0.693831 2.3:+7721834 MS.gene31312:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTCTTTTGTTGATCATTAA+GGG - chr2.3:7722003-7722022 None:intergenic 20.0%
!! CATTCTTTTGTTGATCATTA+AGG - chr2.3:7722004-7722023 None:intergenic 25.0%
!! TTAGAATCTTTACTCTTTTC+TGG - chr2.3:7722302-7722321 None:intergenic 25.0%
ACTCAAGTGAATTTAACAAC+TGG + chr2.3:7722152-7722171 MS.gene31312:CDS 30.0%
ATGAGTTTGAAGGACAAAAA+TGG + chr2.3:7722377-7722396 MS.gene31312:CDS 30.0%
ATTTGAGAGTGAAACAAATG+AGG - chr2.3:7722051-7722070 None:intergenic 30.0%
CATTGAACATAACAAGTTCA+GGG + chr2.3:7722129-7722148 MS.gene31312:CDS 30.0%
GTTGAAAAGGAATTGTCATT+TGG - chr2.3:7721957-7721976 None:intergenic 30.0%
TCTAAGAAAAAATCTGCAGA+GGG + chr2.3:7722317-7722336 MS.gene31312:CDS 30.0%
TGATAAAGTTCTTCTTCCTA+AGG + chr2.3:7722238-7722257 MS.gene31312:CDS 30.0%
TTTGAGAGTGAAACAAATGA+GGG - chr2.3:7722050-7722069 None:intergenic 30.0%
! TTAGTCCATTGTTTGAGTTT+AGG - chr2.3:7721923-7721942 None:intergenic 30.0%
! TTCTAAGAAAAAATCTGCAG+AGG + chr2.3:7722316-7722335 MS.gene31312:CDS 30.0%
AATTGAGAAAACCAGGTTTG+AGG - chr2.3:7721980-7721999 None:intergenic 35.0%
ATCTTCTGCTATGAGTTTGA+AGG + chr2.3:7722367-7722386 MS.gene31312:CDS 35.0%
ATGTTCAATGCTAACCTTTC+AGG - chr2.3:7722119-7722138 None:intergenic 35.0%
ATTGAGAAAACCAGGTTTGA+GGG - chr2.3:7721979-7721998 None:intergenic 35.0%
CAACTCCTAAACTCAAACAA+TGG + chr2.3:7721915-7721934 MS.gene31312:CDS 35.0%
GCATTGAACATAACAAGTTC+AGG + chr2.3:7722128-7722147 MS.gene31312:CDS 35.0%
TGATTCAACTGCTGAATTTG+TGG - chr2.3:7721775-7721794 None:intergenic 35.0%
TTAAGGGAATTGAGAAAACC+AGG - chr2.3:7721987-7722006 None:intergenic 35.0%
TTGGGAATGAAGAAATCCTT+AGG - chr2.3:7722257-7722276 None:intergenic 35.0%
AATCCAGTTAGAACACAAGC+TGG + chr2.3:7722086-7722105 MS.gene31312:CDS 40.0%
ATCAGAATCCTCAAGAAAGC+CGG + chr2.3:7721831-7721850 MS.gene31312:CDS 40.0%
GTTGTTAATGCTACTGTTGG+TGG + chr2.3:7722176-7722195 MS.gene31312:CDS 40.0%
TGGGATAGAAGAGGACTATT+AGG - chr2.3:7721749-7721768 None:intergenic 40.0%
TTCAACTGCTGAATTTGTGG+TGG - chr2.3:7721772-7721791 None:intergenic 40.0%
! AGGATTCTGATAACGTCTGT+TGG - chr2.3:7721822-7721841 None:intergenic 40.0%
! GATTCTGATAACGTCTGTTG+GGG - chr2.3:7721820-7721839 None:intergenic 40.0%
! GGATTCTGATAACGTCTGTT+GGG - chr2.3:7721821-7721840 None:intergenic 40.0%
!! GAGTTGTGCATTGATTTGTG+TGG - chr2.3:7721901-7721920 None:intergenic 40.0%
!! GGTGTTGTTAATGCTACTGT+TGG + chr2.3:7722173-7722192 MS.gene31312:CDS 40.0%
!!! TCTTTACTCTTTTCTGGAGC+CGG - chr2.3:7722296-7722315 None:intergenic 40.0%
AACTGCTGAATTTGTGGTGG+TGG - chr2.3:7721769-7721788 None:intergenic 45.0%
ACCAGGTTTGAGGGTTGAAA+AGG - chr2.3:7721970-7721989 None:intergenic 45.0%
ACTGCTGAATTTGTGGTGGT+GGG - chr2.3:7721768-7721787 None:intergenic 45.0%
GATTTGTGTGGCTACTTGAG+TGG - chr2.3:7721889-7721908 None:intergenic 45.0%
TCACCAGCTTGTGTTCTAAC+TGG - chr2.3:7722092-7722111 None:intergenic 45.0%
TCACTATCATCTGCAGAAGC+AGG - chr2.3:7722344-7722363 None:intergenic 45.0%
! AAGCTGGTGATGATCCTGAA+AGG + chr2.3:7722102-7722121 MS.gene31312:CDS 45.0%
! AGAAGTGAGAGTGTGAAGAG+AGG - chr2.3:7721726-7721745 None:intergenic 45.0%
! TCCTTTTCAACCCTCAAACC+TGG + chr2.3:7721966-7721985 MS.gene31312:CDS 45.0%
AGAATCCTCAAGAAAGCCGG+CGG + chr2.3:7721834-7721853 MS.gene31312:CDS 50.0%
GTGTGGCTACTTGAGTGGTT+TGG - chr2.3:7721884-7721903 None:intergenic 50.0%
! CTACTTGAGTGGTTTGGAGG+AGG - chr2.3:7721878-7721897 None:intergenic 50.0%
! TGGCTACTTGAGTGGTTTGG+AGG - chr2.3:7721881-7721900 None:intergenic 50.0%
!! TTGTGGTGGTGGGATAGAAG+AGG - chr2.3:7721758-7721777 None:intergenic 50.0%
ACGTCTGTTGGGGCTGATGA+TGG - chr2.3:7721810-7721829 None:intergenic 55.0%
CATTCCCAAGTCTCCTCCAC+CGG + chr2.3:7722268-7722287 MS.gene31312:CDS 55.0%
GATAAGGGTGGTGAATCCGC+CGG - chr2.3:7721853-7721872 None:intergenic 55.0%
GGTTTGGAGGAGGCGGATAA+GGG - chr2.3:7721868-7721887 None:intergenic 55.0%
! CTTGAGTGGTTTGGAGGAGG+CGG - chr2.3:7721875-7721894 None:intergenic 55.0%
! TGGTTTGGAGGAGGCGGATA+AGG - chr2.3:7721869-7721888 None:intergenic 55.0%
!! GCTGATGATGGTGATGGTGC+TGG - chr2.3:7721798-7721817 None:intergenic 55.0%
!! GTTGGGGCTGATGATGGTGA+TGG - chr2.3:7721804-7721823 None:intergenic 55.0%
!! TGAATCCGCCGGCTTTCTTG+AGG - chr2.3:7721842-7721861 None:intergenic 55.0%
TTGGAGGAGGCGGATAAGGG+TGG - chr2.3:7721865-7721884 None:intergenic 60.0%
!!! CTCTTTTCTGGAGCCGGAGC+CGG - chr2.3:7722290-7722309 None:intergenic 60.0%
GGAGCCGGTGGAGGAGACTT+GGG - chr2.3:7722275-7722294 None:intergenic 65.0%
!! CAAGTCTCCTCCACCGGCTC+CGG + chr2.3:7722274-7722293 MS.gene31312:CDS 65.0%
!!! TTTTCTGGAGCCGGAGCCGG+TGG - chr2.3:7722287-7722306 None:intergenic 65.0%
CGGAGCCGGTGGAGGAGACT+TGG - chr2.3:7722276-7722295 None:intergenic 70.0%
! TCTGGAGCCGGAGCCGGTGG+AGG - chr2.3:7722284-7722303 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 7721705 7722457 7721705 ID=MS.gene31312
chr2.3 mRNA 7721705 7722457 7721705 ID=MS.gene31312.t1;Parent=MS.gene31312
chr2.3 exon 7721705 7722457 7721705 ID=MS.gene31312.t1.exon1;Parent=MS.gene31312.t1
chr2.3 CDS 7721705 7722457 7721705 ID=cds.MS.gene31312.t1;Parent=MS.gene31312.t1
Gene Sequence

>MS.gene31312

ATGGTGAAGATGAACTATCCTCTCTTCACACTCTCACTTCTCCTAATAGTCCTCTTCTATCCCACCACCACAAATTCAGCAGTTGAATCACCAGCACCATCACCATCATCAGCCCCAACAGACGTTATCAGAATCCTCAAGAAAGCCGGCGGATTCACCACCCTTATCCGCCTCCTCCAAACCACTCAAGTAGCCACACAAATCAATGCACAACTCCTAAACTCAAACAATGGACTAACACTCTTTGCACCAAATGACAATTCCTTTTCAACCCTCAAACCTGGTTTTCTCAATTCCCTTAATGATCAACAAAAGAATGAACTCATTCAATTTCATGAACTACCCTCATTTGTTTCACTCTCAAATTTTGATACTTTAAGTAATCCAGTTAGAACACAAGCTGGTGATGATCCTGAAAGGTTAGCATTGAACATAACAAGTTCAGGGACTCAAGTGAATTTAACAACTGGTGTTGTTAATGCTACTGTTGGTGGTAGTGTTTTTTCTGATCATCAACTTGCTATTTATCAAGTTGATAAAGTTCTTCTTCCTAAGGATTTCTTCATTCCCAAGTCTCCTCCACCGGCTCCGGCTCCAGAAAAGAGTAAAGATTCTAAGAAAAAATCTGCAGAGGGTCCTGCTTCTGCAGATGATAGTGATAAATCTTCTGCTATGAGTTTGAAGGACAAAAATGGAATGATGTTCATATTTGCAGTTGCTACAGTTGTTGCTGCAACTTTATTTTCATTGTGA
Protein sequence

>MS.gene31312.t1

MVKMNYPLFTLSLLLIVLFYPTTTNSAVESPAPSPSSAPTDVIRILKKAGGFTTLIRLLQTTQVATQINAQLLNSNNGLTLFAPNDNSFSTLKPGFLNSLNDQQKNELIQFHELPSFVSLSNFDTLSNPVRTQAGDDPERLALNITSSGTQVNLTTGVVNATVGGSVFSDHQLAIYQVDKVLLPKDFFIPKSPPPAPAPEKSKDSKKKSAEGPASADDSDKSSAMSLKDKNGMMFIFAVATVVAATLFSL