AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31879


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31879.t1 MTR_2g090735 94.144 222 1 2 1 211 40 260 8.02e-153 425
MS.gene31879.t1 MTR_4g078875 76.106 226 37 4 1 211 39 262 1.75e-117 335
MS.gene31879.t1 MTR_4g088245 69.058 223 50 3 2 210 60 277 7.25e-105 305
MS.gene31879.t1 MTR_2g014680 64.865 222 63 3 2 210 45 264 3.78e-98 287
MS.gene31879.t1 MTR_8g069160 81.098 164 20 1 2 154 60 223 1.52e-92 271
MS.gene31879.t1 MTR_8g102240 74.011 177 28 3 9 167 46 222 8.15e-86 262
MS.gene31879.t1 MTR_8g102240 74.011 177 28 3 9 167 46 222 8.37e-86 262
MS.gene31879.t1 MTR_5g053430 57.225 173 62 2 4 165 52 223 2.81e-61 197
MS.gene31879.t1 MTR_5g053430 57.225 173 62 2 4 165 52 223 3.81e-61 197
MS.gene31879.t1 MTR_1g093680 56.977 172 62 2 5 165 53 223 9.30e-61 197
MS.gene31879.t1 MTR_7g033320 55.152 165 62 2 6 158 51 215 3.36e-55 183
MS.gene31879.t1 MTR_1g093670 48.837 172 62 2 5 165 18 174 3.93e-44 150
MS.gene31879.t1 MTR_4g078895 82.353 51 9 0 1 51 28 78 3.50e-22 86.3
MS.gene31879.t1 MTR_2g014700 67.568 37 12 0 75 111 44 80 2.73e-11 58.2
MS.gene31879.t1 MTR_1g008740 29.353 201 100 9 10 190 13 191 8.46e-11 60.8
MS.gene31879.t1 MTR_1g008740 29.353 201 100 9 10 190 27 205 8.68e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31879.t1 AT4G28500 78.919 185 27 2 2 174 51 235 4.61e-103 300
MS.gene31879.t1 AT1G28470 77.143 175 29 1 2 165 69 243 2.06e-95 281
MS.gene31879.t1 AT4G29230 73.034 178 29 2 9 167 47 224 7.84e-87 263
MS.gene31879.t1 AT4G29230 73.034 178 29 2 9 167 46 223 4.62e-86 263
MS.gene31879.t1 AT4G29230 73.034 178 29 2 9 167 47 224 4.74e-86 263
MS.gene31879.t1 AT5G56620 70.225 178 31 4 9 164 42 219 3.32e-82 250
MS.gene31879.t1 AT5G56620 70.225 178 31 4 9 164 42 219 3.65e-82 250
MS.gene31879.t1 AT5G56620 70.225 178 31 4 9 164 42 219 4.41e-82 249
MS.gene31879.t1 AT1G25580 56.725 171 56 4 4 163 52 215 2.67e-57 187
MS.gene31879.t1 AT5G14490 51.786 168 67 4 8 163 53 218 6.60e-48 159
MS.gene31879.t1 AT5G14490 51.786 168 67 4 8 163 53 218 1.00e-47 160
MS.gene31879.t1 AT5G14490 51.786 168 67 4 8 163 56 221 1.11e-47 160
MS.gene31879.t1 AT5G14490 51.786 168 67 4 8 163 56 221 1.25e-47 160
MS.gene31879.t1 AT3G01600 50.909 165 68 3 8 160 53 216 2.80e-45 154
MS.gene31879.t1 AT5G18270 31.844 179 85 7 3 161 14 175 2.13e-11 62.4
MS.gene31879.t1 AT5G18270 31.844 179 85 7 3 161 14 175 3.57e-11 62.0

Find 44 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAGAGATTCTTGAACATT+TGG 0.312906 2.4:-9715518 MS.gene31879:CDS
GAAAGCCAGAGAAAACAAAT+TGG 0.314159 2.4:-9715012 MS.gene31879:CDS
CACATTGTCTAGGCTGTGTT+TGG 0.340883 2.4:+9714915 None:intergenic
AGAGGAGAAAGAAGGAGAAT+TGG 0.354646 2.4:-9714957 MS.gene31879:CDS
AATTGACCTGGTAACTTCTC+TGG 0.367159 2.4:+9715400 None:intergenic
CATTATTTCCAAGATGGTAT+TGG 0.373788 2.4:+9714981 None:intergenic
TATGCAGGTGTCGGCAAAGA+TGG 0.386728 2.4:-9715233 MS.gene31879:intron
GAGTTACCTGGATTACCTGC+TGG 0.403541 2.4:-9715562 MS.gene31879:CDS
GAAACAAGATGGCATAAAAC+AGG 0.423381 2.4:-9715119 MS.gene31879:CDS
GGGATGAACTCATCAATTAA+AGG 0.427373 2.4:+9715460 None:intergenic
CCTCTTCATTATTTCCAAGA+TGG 0.434430 2.4:+9714975 None:intergenic
GAGTTCATCCCTACTCTTGA+AGG 0.437508 2.4:-9715448 MS.gene31879:CDS
CTGTGTTTGGTAGAAAACTT+TGG 0.443831 2.4:+9714928 None:intergenic
CCTACTCTTGAAGGAGAGAA+TGG 0.452976 2.4:-9715439 MS.gene31879:CDS
AGAGATTCTTGAACATTTGG+AGG 0.472757 2.4:-9715515 MS.gene31879:CDS
CCATCGAAAGCATACACAAC+AGG 0.476509 2.4:-9715185 MS.gene31879:CDS
TTCACCCCAGCAGGTAATCC+AGG 0.479471 2.4:+9715556 None:intergenic
CCATTCTCTCCTTCAAGAGT+AGG 0.481831 2.4:+9715439 None:intergenic
GGATCAAACTTCACCCCAGC+AGG 0.493343 2.4:+9715547 None:intergenic
GTTATGCACCAATACCATCT+TGG 0.493624 2.4:-9714989 MS.gene31879:CDS
TGATCCGACATTTCTTTCAC+AGG 0.494146 2.4:-9715208 MS.gene31879:CDS
CATTCTCTCCTTCAAGAGTA+GGG 0.494352 2.4:+9715440 None:intergenic
AGTTACCTGGATTACCTGCT+GGG 0.500946 2.4:-9715561 MS.gene31879:CDS
AAAGCCAGAGAAAACAAATT+GGG 0.504516 2.4:-9715011 MS.gene31879:CDS
GTTAATGAATTATAGGGTGC+TGG 0.506242 2.4:-9715592 None:intergenic
CCTGTTGTGTATGCTTTCGA+TGG 0.507588 2.4:+9715185 None:intergenic
AATAATGAAGAGGAGAAAGA+AGG 0.526318 2.4:-9714965 MS.gene31879:CDS
ATGCAGGTGTCGGCAAAGAT+GGG 0.533540 2.4:-9715232 MS.gene31879:intron
TCAAGAATCTCTTGATCAGT+AGG 0.542994 2.4:+9715526 None:intergenic
GCTGGAATTCATGAGTTACC+TGG 0.547070 2.4:-9715574 MS.gene31879:CDS
ACTCATCCAGAGAAGTTACC+AGG 0.581252 2.4:-9715406 MS.gene31879:intron
AATGAACCACCACATTGTCT+AGG 0.596526 2.4:+9714905 None:intergenic
TGTAGTTAGTGTAAAGCACA+AGG 0.598633 2.4:+9715044 None:intergenic
CAGATGGAAGTGAAACAAGA+TGG 0.608219 2.4:-9715130 MS.gene31879:CDS
ATGGCCTGTGAAAGAAATGT+CGG 0.608865 2.4:+9715204 None:intergenic
AACATTTGGAGGCAAAAGTG+AGG 0.622163 2.4:-9715504 MS.gene31879:CDS
CCATCTTGGAAATAATGAAG+AGG 0.636615 2.4:-9714975 MS.gene31879:CDS
AAAGTGCACACAGATGCAGA+TGG 0.660294 2.4:-9715146 MS.gene31879:CDS
GGCATAAAACAGGTAAAACA+AGG 0.665333 2.4:-9715109 MS.gene31879:CDS
CAAACACAGCCTAGACAATG+TGG 0.666262 2.4:-9714914 MS.gene31879:CDS
ACACAGCCTAGACAATGTGG+TGG 0.735435 2.4:-9714911 MS.gene31879:CDS
TCAAGGTGTGAATCATGAGG+TGG 0.742861 2.4:-9714837 MS.gene31879:CDS
TGATCAAGGTGTGAATCATG+AGG 0.746754 2.4:-9714840 MS.gene31879:CDS
GTTACCTGGATTACCTGCTG+GGG 0.752999 2.4:-9715560 MS.gene31879:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATATATATATATATTTGG+TGG + chr2.4:9714981-9715000 None:intergenic 10.0%
!! GGCATATATATATATATATT+TGG + chr2.4:9714984-9715003 None:intergenic 15.0%
!!! TTTTCTGATAAAAAACTAAA+TGG - chr2.4:9715488-9715507 MS.gene31879:CDS 15.0%
!! CTATGAAAGAATAAAAGAAA+TGG + chr2.4:9715021-9715040 None:intergenic 20.0%
!! GAAATGGAAAGTAAATTATA+AGG + chr2.4:9715005-9715024 None:intergenic 20.0%
! AAAAAACTAAATGGTGATCA+AGG - chr2.4:9715497-9715516 MS.gene31879:CDS 25.0%
! CACAAAAACTGTCATTATAT+AGG + chr2.4:9715073-9715092 None:intergenic 25.0%
!! ATATTTTACGTCTAATATGC+AGG - chr2.4:9715103-9715122 MS.gene31879:intron 25.0%
!! CTTTCATATCTTTTGATCAA+GGG - chr2.4:9715579-9715598 MS.gene31879:CDS 25.0%
!! TCTTTCATATCTTTTGATCA+AGG - chr2.4:9715578-9715597 MS.gene31879:CDS 25.0%
AAAGCCAGAGAAAACAAATT+GGG - chr2.4:9715340-9715359 MS.gene31879:intron 30.0%
AATAATGAAGAGGAGAAAGA+AGG - chr2.4:9715386-9715405 MS.gene31879:intron 30.0%
CATTATTTCCAAGATGGTAT+TGG + chr2.4:9715373-9715392 None:intergenic 30.0%
GTGGTTAATCATAAAAACAG+TGG - chr2.4:9715533-9715552 MS.gene31879:CDS 30.0%
TCAAGAGATTCTTGAACATT+TGG - chr2.4:9714833-9714852 MS.gene31879:CDS 30.0%
!! ATAACCCAATTTGTTTTCTC+TGG + chr2.4:9715347-9715366 None:intergenic 30.0%
AGAGATTCTTGAACATTTGG+AGG - chr2.4:9714836-9714855 MS.gene31879:CDS 35.0%
CCATCTTGGAAATAATGAAG+AGG - chr2.4:9715376-9715395 MS.gene31879:intron 35.0%
CCTCTTCATTATTTCCAAGA+TGG + chr2.4:9715379-9715398 None:intergenic 35.0%
CTGTGTTTGGTAGAAAACTT+TGG + chr2.4:9715426-9715445 None:intergenic 35.0%
GAAACAAGATGGCATAAAAC+AGG - chr2.4:9715232-9715251 MS.gene31879:intron 35.0%
GAAAGCCAGAGAAAACAAAT+TGG - chr2.4:9715339-9715358 MS.gene31879:intron 35.0%
GGCATAAAACAGGTAAAACA+AGG - chr2.4:9715242-9715261 MS.gene31879:intron 35.0%
GGGATGAACTCATCAATTAA+AGG + chr2.4:9714894-9714913 None:intergenic 35.0%
TCAAGAATCTCTTGATCAGT+AGG + chr2.4:9714828-9714847 None:intergenic 35.0%
TGTAGTTAGTGTAAAGCACA+AGG + chr2.4:9715310-9715329 None:intergenic 35.0%
AACATTTGGAGGCAAAAGTG+AGG - chr2.4:9714847-9714866 MS.gene31879:CDS 40.0%
AATGAACCACCACATTGTCT+AGG + chr2.4:9715449-9715468 None:intergenic 40.0%
AATTGACCTGGTAACTTCTC+TGG + chr2.4:9714954-9714973 None:intergenic 40.0%
AGAGGAGAAAGAAGGAGAAT+TGG - chr2.4:9715394-9715413 MS.gene31879:intron 40.0%
ATGGCCTGTGAAAGAAATGT+CGG + chr2.4:9715150-9715169 None:intergenic 40.0%
CAGATGGAAGTGAAACAAGA+TGG - chr2.4:9715221-9715240 MS.gene31879:CDS 40.0%
CATTCTCTCCTTCAAGAGTA+GGG + chr2.4:9714914-9714933 None:intergenic 40.0%
GTTATGCACCAATACCATCT+TGG - chr2.4:9715362-9715381 MS.gene31879:intron 40.0%
TACGTCTAATATGCAGGTGT+CGG - chr2.4:9715109-9715128 MS.gene31879:CDS 40.0%
TCGTGAGTGGCAAGTTTAAA+AGG - chr2.4:9715272-9715291 MS.gene31879:intron 40.0%
TGATCAAGGTGTGAATCATG+AGG - chr2.4:9715511-9715530 MS.gene31879:CDS 40.0%
TGATCCGACATTTCTTTCAC+AGG - chr2.4:9715143-9715162 MS.gene31879:CDS 40.0%
! TTTGGTGGCTTAAATTGACC+TGG + chr2.4:9714966-9714985 None:intergenic 40.0%
AAAGTGCACACAGATGCAGA+TGG - chr2.4:9715205-9715224 MS.gene31879:CDS 45.0%
AACTTGCCACTCACGAAAAC+TGG + chr2.4:9715268-9715287 None:intergenic 45.0%
ACTCATCCAGAGAAGTTACC+AGG - chr2.4:9714945-9714964 MS.gene31879:CDS 45.0%
AGTTACCTGGATTACCTGCT+GGG - chr2.4:9714790-9714809 MS.gene31879:CDS 45.0%
CAAACACAGCCTAGACAATG+TGG - chr2.4:9715437-9715456 MS.gene31879:CDS 45.0%
CACATTGTCTAGGCTGTGTT+TGG + chr2.4:9715439-9715458 None:intergenic 45.0%
CCATTCTCTCCTTCAAGAGT+AGG + chr2.4:9714915-9714934 None:intergenic 45.0%
CCTACTCTTGAAGGAGAGAA+TGG - chr2.4:9714912-9714931 MS.gene31879:CDS 45.0%
CCTGTTGTGTATGCTTTCGA+TGG + chr2.4:9715169-9715188 None:intergenic 45.0%
GAGTTCATCCCTACTCTTGA+AGG - chr2.4:9714903-9714922 MS.gene31879:CDS 45.0%
GCTGGAATTCATGAGTTACC+TGG - chr2.4:9714777-9714796 MS.gene31879:CDS 45.0%
TCAAGGTGTGAATCATGAGG+TGG - chr2.4:9715514-9715533 MS.gene31879:CDS 45.0%
! CCATCGAAAGCATACACAAC+AGG - chr2.4:9715166-9715185 MS.gene31879:CDS 45.0%
ACACAGCCTAGACAATGTGG+TGG - chr2.4:9715440-9715459 MS.gene31879:CDS 50.0%
GAGTTACCTGGATTACCTGC+TGG - chr2.4:9714789-9714808 MS.gene31879:CDS 50.0%
GTTACCTGGATTACCTGCTG+GGG - chr2.4:9714791-9714810 MS.gene31879:CDS 50.0%
! ACAAGGCCAGTTTTCGTGAG+TGG - chr2.4:9715259-9715278 MS.gene31879:intron 50.0%
!! ATGCAGGTGTCGGCAAAGAT+GGG - chr2.4:9715119-9715138 MS.gene31879:CDS 50.0%
!! TATGCAGGTGTCGGCAAAGA+TGG - chr2.4:9715118-9715137 MS.gene31879:CDS 50.0%
GGATCAAACTTCACCCCAGC+AGG + chr2.4:9714807-9714826 None:intergenic 55.0%
TTCACCCCAGCAGGTAATCC+AGG + chr2.4:9714798-9714817 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 9714774 9715599 9714774 ID=MS.gene31879
chr2.4 mRNA 9714774 9715599 9714774 ID=MS.gene31879.t1;Parent=MS.gene31879
chr2.4 exon 9715407 9715599 9715407 ID=MS.gene31879.t1.exon1;Parent=MS.gene31879.t1
chr2.4 CDS 9715407 9715599 9715407 ID=cds.MS.gene31879.t1;Parent=MS.gene31879.t1
chr2.4 exon 9715106 9715248 9715106 ID=MS.gene31879.t1.exon2;Parent=MS.gene31879.t1
chr2.4 CDS 9715106 9715248 9715106 ID=cds.MS.gene31879.t1;Parent=MS.gene31879.t1
chr2.4 exon 9714774 9715071 9714774 ID=MS.gene31879.t1.exon3;Parent=MS.gene31879.t1
chr2.4 CDS 9714774 9715071 9714774 ID=cds.MS.gene31879.t1;Parent=MS.gene31879.t1
Gene Sequence

>MS.gene31879

GGTGCTGGAATTCATGAGTTACCTGGATTACCTGCTGGGGTGAAGTTTGATCCTACTGATCAAGAGATTCTTGAACATTTGGAGGCAAAAGTGAGGTCTGATATTCAAATGCTTCATCCTTTAATTGATGAGTTCATCCCTACTCTTGAAGGAGAGAATGGAATCTGCTGTACTCATCCAGAGAAGTTACCAGGTCAATTTAAGCCACCAAATATATATATATATATGCCTTATAATTTACTTTCCATTTCTTTTATTCTTTCATAGTTTCTAATAAAAAAAGTCTCATCTTATATCCTATATAATGACAGTTTTTGTGTGTTAATTTAATATTTTACGTCTAATATGCAGGTGTCGGCAAAGATGGGTTGATCCGACATTTCTTTCACAGGCCATCGAAAGCATACACAACAGGAACGAGAAAAAGAAGAAAAGTGCACACAGATGCAGATGGAAGTGAAACAAGATGGCATAAAACAGGTAAAACAAGGCCAGTTTTCGTGAGTGGCAAGTTTAAAAGGCTATAAGAAAATCCTTGTGCTTTACACTAACTACAGAAAGCAAAGAAAGCCAGAGAAAACAAATTGGGTTATGCACCAATACCATCTTGGAAATAATGAAGAGGAGAAAGAAGGAGAATTGGTAGTTTCCAAAGTTTTCTACCAAACACAGCCTAGACAATGTGGTGGTTCATTGATGAAAGACTCAGCATCATTTTCTGATAAAAAACTAAATGGTGATCAAGGTGTGAATCATGAGGTGGTTAATCATAAAAACAGTGGATTTGTTGAATACTATAGTACTTCTTTCATATCTTTTGATCAAG

Protein sequence

>MS.gene31879.t1

GAGIHELPGLPAGVKFDPTDQEILEHLEAKVRSDIQMLHPLIDEFIPTLEGENGICCTHPEKLPGVGKDGLIRHFFHRPSKAYTTGTRKRRKVHTDADGSETRWHKTGKTRPKILVLYTNYRKQRKPEKTNWVMHQYHLGNNEEEKEGELVVSKVFYQTQPRQCGGSLMKDSASFSDKKLNGDQGVNHEVVNHKNSGFVEYYSTSFISFDQ