AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene027909


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027909.t1 MTR_7g059070 100.000 136 0 0 1 136 1 136 4.79e-96 272
MS.gene027909.t1 MTR_5g029820 100.000 136 0 0 1 136 1 136 4.79e-96 272
MS.gene027909.t1 MTR_5g029770 100.000 136 0 0 1 136 1 136 4.79e-96 272
MS.gene027909.t1 MTR_4g065990 100.000 136 0 0 1 136 1 136 4.79e-96 272
MS.gene027909.t1 MTR_4g088150 100.000 136 0 0 1 136 1 136 4.79e-96 272
MS.gene027909.t1 MTR_2g035230 100.000 136 0 0 1 136 1 136 4.79e-96 272
MS.gene027909.t1 MTR_8g092720 100.000 136 0 0 1 136 1 136 4.79e-96 272
MS.gene027909.t1 MTR_8g063500 100.000 136 0 0 1 136 1 136 4.79e-96 272
MS.gene027909.t1 MTR_8g103245 100.000 136 0 0 1 136 1 136 4.79e-96 272
MS.gene027909.t1 MTR_8g092820 100.000 136 0 0 1 136 1 136 4.79e-96 272
MS.gene027909.t1 MTR_7g013610 100.000 136 0 0 1 136 100 235 1.10e-95 275
MS.gene027909.t1 MTR_4g097175 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene027909.t1 MTR_1g023630 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene027909.t1 MTR_8g061940 97.059 136 4 0 1 136 1 136 3.29e-93 265
MS.gene027909.t1 MTR_8g099430 96.324 136 5 0 1 136 1 136 1.38e-92 264
MS.gene027909.t1 MTR_4g097170 96.324 136 5 0 1 136 42 177 2.29e-91 262
MS.gene027909.t1 MTR_2g082310 89.706 136 14 0 1 136 1 136 1.38e-86 248
MS.gene027909.t1 MTR_2g082340 89.706 136 14 0 1 136 1 136 1.38e-86 248
MS.gene027909.t1 MTR_2g082370 85.616 146 11 1 1 136 1 146 1.74e-82 238
MS.gene027909.t1 MTR_2g082400 84.559 136 19 2 1 135 1 135 6.38e-75 219
MS.gene027909.t1 MTR_7g013600 86.607 112 15 0 25 136 2 113 1.01e-65 195
MS.gene027909.t1 MTR_7g023830 67.164 134 43 1 1 134 1 133 6.48e-56 171
MS.gene027909.t1 MTR_1g023630 73.504 117 15 3 1 111 1 107 3.81e-52 160
MS.gene027909.t1 MTR_5g024630 67.241 116 35 2 1 116 1 113 1.63e-45 144
MS.gene027909.t1 MTR_7g023880 58.647 133 41 3 3 134 18 137 5.46e-43 139
MS.gene027909.t1 MTR_5g024530 68.182 110 12 2 19 128 68 154 4.56e-42 137
MS.gene027909.t1 MTR_0197s0100 100.000 66 0 0 1 66 1 66 1.45e-40 132
MS.gene027909.t1 MTR_8g027840 55.102 98 43 1 37 133 28 125 4.83e-30 105
MS.gene027909.t1 MTR_8g105150 53.846 91 10 1 37 127 11 69 1.43e-25 92.4
MS.gene027909.t1 MTR_8g092740 97.368 38 1 0 99 136 118 155 4.60e-20 80.9
MS.gene027909.t1 MTR_5g089120 76.190 42 10 0 82 123 6 47 6.07e-18 73.6
MS.gene027909.t1 MTR_5g024600 62.963 54 20 0 1 54 1 54 1.76e-15 66.2
MS.gene027909.t1 MTR_4g128040 75.676 37 9 0 79 115 20 56 3.38e-15 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.gene027909.t1 AT5G65360 99.265 136 1 0 1 136 1 136 1.55e-95 271
MS.gene027909.t1 AT5G10390 99.265 136 1 0 1 136 1 136 1.55e-95 271
MS.gene027909.t1 AT5G10400 99.265 136 1 0 1 136 1 136 1.55e-95 271
MS.gene027909.t1 AT3G27360 99.265 136 1 0 1 136 1 136 1.55e-95 271
MS.gene027909.t1 AT1G09200 99.265 136 1 0 1 136 1 136 1.55e-95 271
MS.gene027909.t1 AT5G10980 97.059 136 4 0 1 136 1 136 3.44e-93 265
MS.gene027909.t1 AT4G40040 97.059 136 4 0 1 136 1 136 3.44e-93 265
MS.gene027909.t1 AT4G40040 97.059 136 4 0 1 136 1 136 3.44e-93 265
MS.gene027909.t1 AT4G40040 97.059 136 4 0 1 136 1 136 3.44e-93 265
MS.gene027909.t1 AT4G40030 97.059 136 4 0 1 136 1 136 3.44e-93 265
MS.gene027909.t1 AT4G40030 97.059 136 4 0 1 136 1 136 3.44e-93 265
MS.gene027909.t1 AT4G40030 97.059 136 4 0 1 136 1 136 3.44e-93 265
MS.gene027909.t1 AT4G40030 97.059 136 4 0 1 136 29 164 6.76e-93 266
MS.gene027909.t1 AT5G65350 94.853 136 7 0 1 136 1 136 5.09e-91 260
MS.gene027909.t1 AT1G75600 93.382 136 9 0 1 136 1 136 1.20e-89 256
MS.gene027909.t1 AT1G13370 93.382 136 9 0 1 136 1 136 5.32e-89 254
MS.gene027909.t1 AT1G19890 89.781 137 13 1 1 136 1 137 1.03e-83 241
MS.gene027909.t1 AT5G12910 71.111 135 34 2 1 135 1 130 9.51e-67 198
MS.gene027909.t1 AT1G01370 53.982 113 49 2 24 134 63 174 2.86e-31 110
MS.gene027909.t1 AT1G01370 53.982 113 49 2 24 134 63 174 2.86e-31 110
MS.gene027909.t1 AT1G01370 53.982 113 49 2 24 134 63 174 2.86e-31 110
MS.gene027909.t1 AT1G01370 53.982 113 49 2 24 134 63 174 2.86e-31 110

Find 37 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGGTTGCCGGAGCAGATTTC+CGG 0.243304 5.2:-18647320 None:intergenic
TTGGTGGCTAGCTGCTTTCT+TGG 0.277587 5.2:-18647291 None:intergenic
TCACGAAGTGCAACGGTTCC+TGG 0.291776 5.2:-18647372 None:intergenic
TTCTTGACTCCTCCGGTTGC+CGG 0.293014 5.2:-18647333 None:intergenic
TGAGAAGCTCAGTGCTCTTC+TGG 0.304985 5.2:-18647407 None:intergenic
GCTGCTGAAGCTTATCTTGT+TGG 0.357332 5.2:+18647528 MS.gene027909:CDS
AGCAGATTTCCGGGCAGCTT+TGG 0.390197 5.2:-18647310 None:intergenic
CGGAAATCTGCTCCGGCAAC+CGG 0.392471 5.2:+18647321 MS.gene027909:CDS
GGTTGCCGGAGCAGATTTCC+GGG 0.407337 5.2:-18647319 None:intergenic
CTTTCTTGGTGCCTTTCCTC+CGG 0.425692 5.2:-18647277 None:intergenic
TTATCTTGTTGGTTTGTTTG+AGG 0.428809 5.2:+18647539 MS.gene027909:CDS
CGATTTCACGAACAAGTCTC+TGG 0.432729 5.2:-18647446 None:intergenic
AAACAGCGCTGCTTTGAAAT+CGG 0.457546 5.2:-18647491 None:intergenic
AGATTTCCGGGCAGCTTTGG+TGG 0.468887 5.2:-18647307 None:intergenic
AGCTAGCCACCAAAGCTGCC+CGG 0.491500 5.2:+18647301 MS.gene027909:CDS
CGAGCAAGTTGAATATCCTT+AGG 0.499677 5.2:-18647606 None:intergenic
GTGTGGCTTCTTGACTCCTC+CGG 0.501667 5.2:-18647340 None:intergenic
AGCTGCCCGGAAATCTGCTC+CGG 0.505877 5.2:+18647314 MS.gene027909:CDS
AGTAACTCTCTTAGCATGAA+TGG 0.521941 5.2:-18647577 None:intergenic
AGAGCACTGAGCTTCTCATA+AGG 0.531497 5.2:+18647412 MS.gene027909:CDS
TCGCAAATCCACCGGAGGAA+AGG 0.532804 5.2:+18647266 MS.gene027909:CDS
TGTTTGCTTTGTACGAGCCA+TGG 0.537743 5.2:-18647241 None:intergenic
GAGAGTTACTATCATGCCTA+AGG 0.550012 5.2:+18647590 MS.gene027909:CDS
ACTTGTTCGTGAAATCGCTC+AGG 0.551065 5.2:+18647452 MS.gene027909:CDS
TCTTGGTGCCTTTCCTCCGG+TGG 0.556160 5.2:-18647274 None:intergenic
CAGTGCTCTTCTGGTACTTG+CGG 0.579006 5.2:-18647398 None:intergenic
CAAACAGCTCGCAAATCCAC+CGG 0.586123 5.2:+18647258 MS.gene027909:CDS
TCACGAACAAGTCTCTGGAA+TGG 0.590006 5.2:-18647441 None:intergenic
CAACTTGCTCGCAGAATCAG+AGG 0.592233 5.2:+18647618 MS.gene027909:CDS
AAATCTGCTCCGGCAACCGG+AGG 0.607496 5.2:+18647324 MS.gene027909:CDS
TCGCAGAATCAGAGGCGAGA+GGG 0.615698 5.2:+18647626 MS.gene027909:CDS
CTCGCAGAATCAGAGGCGAG+AGG 0.629911 5.2:+18647625 MS.gene027909:CDS
AAGCCACACAGATTCCGTCC+AGG 0.632383 5.2:+18647354 MS.gene027909:CDS
GCGGATCTCACGAAGTGCAA+CGG 0.633057 5.2:-18647379 None:intergenic
GAAGTGCAACGGTTCCTGGA+CGG 0.655834 5.2:-18647368 None:intergenic
GTTCCTGGACGGAATCTGTG+TGG 0.669194 5.2:-18647357 None:intergenic
ACAGCTCGCAAATCCACCGG+AGG 0.704783 5.2:+18647261 MS.gene027909:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATCTTGTTGGTTTGTTTG+AGG + chr5.2:18647539-18647558 MS.gene027909:CDS 30.0%
AGTAACTCTCTTAGCATGAA+TGG - chr5.2:18647580-18647599 None:intergenic 35.0%
GAGAGTTACTATCATGCCTA+AGG + chr5.2:18647590-18647609 MS.gene027909:CDS 40.0%
! CGAGCAAGTTGAATATCCTT+AGG - chr5.2:18647609-18647628 None:intergenic 40.0%
!! AAACAGCGCTGCTTTGAAAT+CGG - chr5.2:18647494-18647513 None:intergenic 40.0%
ACTTGTTCGTGAAATCGCTC+AGG + chr5.2:18647452-18647471 MS.gene027909:CDS 45.0%
CGATTTCACGAACAAGTCTC+TGG - chr5.2:18647449-18647468 None:intergenic 45.0%
GCTGCTGAAGCTTATCTTGT+TGG + chr5.2:18647528-18647547 MS.gene027909:CDS 45.0%
! TCACGAACAAGTCTCTGGAA+TGG - chr5.2:18647444-18647463 None:intergenic 45.0%
!! AGAGCACTGAGCTTCTCATA+AGG + chr5.2:18647412-18647431 MS.gene027909:CDS 45.0%
CAAACAGCTCGCAAATCCAC+CGG + chr5.2:18647258-18647277 MS.gene027909:CDS 50.0%
CAGTGCTCTTCTGGTACTTG+CGG - chr5.2:18647401-18647420 None:intergenic 50.0%
TGAGAAGCTCAGTGCTCTTC+TGG - chr5.2:18647410-18647429 None:intergenic 50.0%
! CAACTTGCTCGCAGAATCAG+AGG + chr5.2:18647618-18647637 MS.gene027909:CDS 50.0%
! TTGGTGGCTAGCTGCTTTCT+TGG - chr5.2:18647294-18647313 None:intergenic 50.0%
!! CTTTCTTGGTGCCTTTCCTC+CGG - chr5.2:18647280-18647299 None:intergenic 50.0%
AAGCCACACAGATTCCGTCC+AGG + chr5.2:18647354-18647373 MS.gene027909:CDS 55.0%
AGCAGATTTCCGGGCAGCTT+TGG - chr5.2:18647313-18647332 None:intergenic 55.0%
GAAGTGCAACGGTTCCTGGA+CGG - chr5.2:18647371-18647390 None:intergenic 55.0%
GCGGATCTCACGAAGTGCAA+CGG - chr5.2:18647382-18647401 None:intergenic 55.0%
GTGTGGCTTCTTGACTCCTC+CGG - chr5.2:18647343-18647362 None:intergenic 55.0%
GTTCCTGGACGGAATCTGTG+TGG - chr5.2:18647360-18647379 None:intergenic 55.0%
TCACGAAGTGCAACGGTTCC+TGG - chr5.2:18647375-18647394 None:intergenic 55.0%
TCGCAAATCCACCGGAGGAA+AGG + chr5.2:18647266-18647285 MS.gene027909:CDS 55.0%
TCGCAGAATCAGAGGCGAGA+GGG + chr5.2:18647626-18647645 MS.gene027909:CDS 55.0%
TTCTTGACTCCTCCGGTTGC+CGG - chr5.2:18647336-18647355 None:intergenic 55.0%
! AGATTTCCGGGCAGCTTTGG+TGG - chr5.2:18647310-18647329 None:intergenic 55.0%
AAATCTGCTCCGGCAACCGG+AGG + chr5.2:18647324-18647343 MS.gene027909:CDS 60.0%
ACAGCTCGCAAATCCACCGG+AGG + chr5.2:18647261-18647280 MS.gene027909:CDS 60.0%
AGCTAGCCACCAAAGCTGCC+CGG + chr5.2:18647301-18647320 MS.gene027909:CDS 60.0%
AGCTGCCCGGAAATCTGCTC+CGG + chr5.2:18647314-18647333 MS.gene027909:CDS 60.0%
CGGAAATCTGCTCCGGCAAC+CGG + chr5.2:18647321-18647340 MS.gene027909:CDS 60.0%
CGGTTGCCGGAGCAGATTTC+CGG - chr5.2:18647323-18647342 None:intergenic 60.0%
CTCGCAGAATCAGAGGCGAG+AGG + chr5.2:18647625-18647644 MS.gene027909:CDS 60.0%
GGTTGCCGGAGCAGATTTCC+GGG - chr5.2:18647322-18647341 None:intergenic 60.0%
!! TCTTGGTGCCTTTCCTCCGG+TGG - chr5.2:18647277-18647296 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 18647243 18647653 18647243 ID=MS.gene027909
chr5.2 mRNA 18647243 18647653 18647243 ID=MS.gene027909.t1;Parent=MS.gene027909
chr5.2 exon 18647243 18647653 18647243 ID=MS.gene027909.t1.exon1;Parent=MS.gene027909.t1
chr5.2 CDS 18647243 18647653 18647243 ID=cds.MS.gene027909.t1;Parent=MS.gene027909.t1
Gene Sequence

>MS.gene027909

ATGGCTCGTACAAAGCAAACAGCTCGCAAATCCACCGGAGGAAAGGCACCAAGAAAGCAGCTAGCCACCAAAGCTGCCCGGAAATCTGCTCCGGCAACCGGAGGAGTCAAGAAGCCACACAGATTCCGTCCAGGAACCGTTGCACTTCGTGAGATCCGCAAGTACCAGAAGAGCACTGAGCTTCTCATAAGGAAGCTTCCATTCCAGAGACTTGTTCGTGAAATCGCTCAGGATTTCAAAACAGATCTCCGATTTCAAAGCAGCGCTGTTTCTGCTCTTCAAGAAGCTGCTGAAGCTTATCTTGTTGGTTTGTTTGAGGATACTAATCTCTGTGCCATTCATGCTAAGAGAGTTACTATCATGCCTAAGGATATTCAACTTGCTCGCAGAATCAGAGGCGAGAGGGCTTAG

Protein sequence

>MS.gene027909.t1

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVSALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA