AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene32116

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32116.t1 MTR_1g073380 82.400 250 16 1 1 222 343 592 2.17e-143 413
MS.gene32116.t1 MTR_1g073530 79.200 250 22 2 1 222 335 582 1.92e-130 379
MS.gene32116.t1 MTR_1g073590 78.800 250 23 2 1 222 332 579 1.70e-129 377
MS.gene32116.t1 MTR_8g098645 66.932 251 54 2 1 222 90 340 2.96e-115 333
MS.gene32116.t1 MTR_8g098605 62.800 250 41 2 1 222 365 590 5.93e-100 302
MS.gene32116.t1 MTR_8g098635 68.750 192 32 1 58 221 99 290 4.41e-88 262
MS.gene32116.t1 MTR_8g098635 68.750 192 32 1 58 221 182 373 8.05e-87 261
MS.gene32116.t1 MTR_0259s0060 49.727 183 17 3 49 203 12 147 7.76e-47 152
MS.gene32116.t1 MTR_7g078120 41.489 188 82 1 53 212 387 574 1.77e-43 154
MS.gene32116.t1 MTR_7g078120 41.489 188 82 1 53 212 387 574 2.64e-43 154
MS.gene32116.t1 MTR_1g073420 92.857 70 5 0 153 222 59 128 5.87e-43 141
MS.gene32116.t1 MTR_8g028905 39.429 175 74 3 53 195 408 582 5.55e-36 133
MS.gene32116.t1 MTR_6g071355 57.732 97 22 1 116 212 1 78 4.67e-28 102
MS.gene32116.t1 MTR_5g048010 60.000 85 21 1 56 127 205 289 6.57e-25 100
MS.gene32116.t1 MTR_3g023780 40.714 140 81 2 55 193 188 326 1.17e-24 101
MS.gene32116.t1 MTR_6g071350 52.941 102 20 2 54 127 273 374 8.30e-24 98.2
MS.gene32116.t1 MTR_7g066890 31.548 168 83 2 53 188 194 361 8.55e-21 89.4
MS.gene32116.t1 MTR_7g066890 31.548 168 83 2 53 188 296 463 2.15e-20 89.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene32116.t1 AT4G11400 50.000 156 73 2 67 222 418 568 5.93e-46 160
MS.gene32116.t1 AT4G11400 50.000 156 73 2 67 222 418 568 5.93e-46 160
MS.gene32116.t1 AT2G46040 34.254 181 87 2 45 194 352 531 8.65e-25 102
MS.gene32116.t1 AT2G46040 34.254 181 87 2 45 194 352 531 8.65e-25 102
MS.gene32116.t1 AT2G46040 34.254 181 87 2 45 194 366 545 1.04e-24 101
MS.gene32116.t1 AT1G13880 41.600 125 71 2 70 193 180 303 3.33e-21 91.3
MS.gene32116.t1 AT1G13880 41.600 125 71 2 70 193 179 302 3.44e-21 91.3
MS.gene32116.t1 AT1G13880 41.600 125 71 2 70 193 189 312 3.75e-21 91.3
MS.gene32116.t1 AT2G03470 40.146 137 78 3 67 199 167 303 3.77e-21 91.3
MS.gene32116.t1 AT2G03470 40.146 137 78 3 67 199 168 304 3.94e-21 91.3
MS.gene32116.t1 AT5G04110 29.375 160 75 2 53 174 361 520 6.00e-19 85.1
MS.gene32116.t1 AT5G04110 29.375 160 75 2 53 174 361 520 6.00e-19 85.1
MS.gene32116.t1 AT5G04110 29.375 160 75 2 53 174 362 521 6.06e-19 85.1
MS.gene32116.t1 AT1G26580 33.108 148 96 3 63 209 124 269 7.28e-19 84.7
MS.gene32116.t1 AT1G26580 33.108 148 96 3 63 209 190 335 8.48e-19 84.7
MS.gene32116.t1 AT1G26580 33.108 148 96 3 63 209 190 335 8.48e-19 84.7
MS.gene32116.t1 AT5G04110 27.083 144 67 2 53 158 361 504 2.92e-11 62.8

Find 33 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCATTGGGGATTTGATAAAA+TGG 0.180493 1.2:-56310785 MS.gene32116:CDS
TGACGAGAATCATCACTAAA+TGG 0.242832 1.2:+56311069 None:intergenic
GATGATGACGAAGTCGAATT+TGG 0.269756 1.2:-56310544 MS.gene32116:CDS
TGATGAAGAAAAGACATTTA+AGG 0.313271 1.2:-56310734 MS.gene32116:CDS
GATGAAGCTGAAGTTTGAAT+TGG 0.326776 1.2:-56310821 MS.gene32116:CDS
TTCTTCTTGATCACAACATC+TGG 0.358660 1.2:+56311174 None:intergenic
GAAGTCGAATTTGGATCTTT+TGG 0.361975 1.2:-56310535 MS.gene32116:CDS
CACTCCTTGAATTCAGTTGA+TGG 0.389473 1.2:+56310481 None:intergenic
CGTCATAAGTTTGTTTCTGT+TGG 0.390129 1.2:-56311051 MS.gene32116:CDS
CATTGGGGATTTGATAAAAT+GGG 0.415280 1.2:-56310784 MS.gene32116:CDS
AAACTACACCAGTCCATTGC+GGG 0.425596 1.2:+56311007 None:intergenic
CTCTTCAGTCACAGCTGCAT+TGG 0.432193 1.2:+56311104 None:intergenic
TTTCTTCATCACCAGTCCAT+TGG 0.435383 1.2:+56310746 None:intergenic
GCGTCCATCAACTGAATTCA+AGG 0.441722 1.2:-56310485 MS.gene32116:CDS
ACTACTTAAACAGATCTTGT+TGG 0.444458 1.2:-56310922 MS.gene32116:intron
CGTCCAGTTACTTTGAAAAG+AGG 0.446172 1.2:-56310660 MS.gene32116:CDS
ATGAAGCTGAAGTTTGAATT+GGG 0.447468 1.2:-56310820 MS.gene32116:CDS
GATTGCATATTGCTGCAAAC+AGG 0.460811 1.2:-56310843 MS.gene32116:CDS
AGTCCTATGGAGAAAACAAC+TGG 0.476468 1.2:-56311201 None:intergenic
TCCATTGCGGGACTTCCACT+TGG 0.490081 1.2:+56311019 None:intergenic
GGGACTTCCACTTGGAAAAG+AGG 0.495364 1.2:+56311027 None:intergenic
GACGAGAATCATCACTAAAT+GGG 0.495915 1.2:+56311070 None:intergenic
GTGGAAGTCCCGCAATGGAC+TGG 0.500938 1.2:-56311015 MS.gene32116:intron
TAAACAGATCTTGTTGGTAG+AGG 0.521966 1.2:-56310916 MS.gene32116:intron
CTATCAGAATCGAGTGACTT+CGG 0.542718 1.2:-56310581 MS.gene32116:CDS
GCGAGGAAGTTTCACTCCAA+TGG 0.542815 1.2:-56310762 MS.gene32116:CDS
GGGATTTGATAAAATGGGCG+AGG 0.561801 1.2:-56310779 MS.gene32116:CDS
TCCAAGTGGAAGTCCCGCAA+TGG 0.584534 1.2:-56311020 MS.gene32116:CDS
GAAGTTTCACTCCAATGGAC+TGG 0.584625 1.2:-56310757 MS.gene32116:CDS
AGTGTTCAGAGAACAAGTAA+TGG 0.612428 1.2:-56310462 None:intergenic
CTTGTTGGTAGAGGAAGACG+AGG 0.623018 1.2:-56310907 MS.gene32116:CDS
AAAGAGGACAAGAAAAGACA+TGG 0.650870 1.2:-56310644 MS.gene32116:CDS
TAAACTACACCAGTCCATTG+CGG 0.655876 1.2:+56311006 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGATGAAGAAAAGACATTTA+AGG - chr1.2:56310926-56310945 MS.gene32116:intron 25.0%
!! TGTTCCAAAAATACTTGTTT+TGG + chr1.2:56310977-56310996 None:intergenic 25.0%
!!! GTTCCAAAAATACTTGTTTT+GGG + chr1.2:56310976-56310995 None:intergenic 25.0%
ACAAGATCTGTTTAAGTAGT+AGG + chr1.2:56310738-56310757 None:intergenic 30.0%
ACTACTTAAACAGATCTTGT+TGG - chr1.2:56310738-56310757 MS.gene32116:CDS 30.0%
ATGAAGCTGAAGTTTGAATT+GGG - chr1.2:56310840-56310859 MS.gene32116:CDS 30.0%
CATTGGGGATTTGATAAAAT+GGG - chr1.2:56310876-56310895 MS.gene32116:CDS 30.0%
!!! AAAAATACTTGTTTTGGGAG+GGG + chr1.2:56310971-56310990 None:intergenic 30.0%
!!! CAAAAATACTTGTTTTGGGA+GGG + chr1.2:56310972-56310991 None:intergenic 30.0%
AAAGAGGACAAGAAAAGACA+TGG - chr1.2:56311016-56311035 MS.gene32116:CDS 35.0%
CCATTGGGGATTTGATAAAA+TGG - chr1.2:56310875-56310894 MS.gene32116:CDS 35.0%
GACGAGAATCATCACTAAAT+GGG + chr1.2:56310593-56310612 None:intergenic 35.0%
GATGAAGCTGAAGTTTGAAT+TGG - chr1.2:56310839-56310858 MS.gene32116:CDS 35.0%
GGTCTTGAATCATCTTTAAG+AGG + chr1.2:56310717-56310736 None:intergenic 35.0%
TGACGAGAATCATCACTAAA+TGG + chr1.2:56310594-56310613 None:intergenic 35.0%
TTCTTCTTGATCACAACATC+TGG + chr1.2:56310489-56310508 None:intergenic 35.0%
! CCATTTTATCAAATCCCCAA+TGG + chr1.2:56310878-56310897 None:intergenic 35.0%
! CCTCCCAAAACAAGTATTTT+TGG - chr1.2:56310970-56310989 MS.gene32116:intron 35.0%
! CTCTTTTCAAAGTAACTGGA+CGG + chr1.2:56311002-56311021 None:intergenic 35.0%
! GAAGTCGAATTTGGATCTTT+TGG - chr1.2:56311125-56311144 MS.gene32116:CDS 35.0%
! GAATTTGGATCTTTTGGTGA+TGG - chr1.2:56311131-56311150 MS.gene32116:CDS 35.0%
! TAAACAGATCTTGTTGGTAG+AGG - chr1.2:56310744-56310763 MS.gene32116:CDS 35.0%
! TGTCCTCTTTTCAAAGTAAC+TGG + chr1.2:56311006-56311025 None:intergenic 35.0%
!! AATGGACTGGTGTAGTTTAT+GGG - chr1.2:56310658-56310677 MS.gene32116:CDS 35.0%
!! CGTCATAAGTTTGTTTCTGT+TGG - chr1.2:56310609-56310628 MS.gene32116:CDS 35.0%
!!! CCAAAAATACTTGTTTTGGG+AGG + chr1.2:56310973-56310992 None:intergenic 35.0%
AATCGTTAGGCACACAAGTA+TGG - chr1.2:56310691-56310710 MS.gene32116:CDS 40.0%
CACTCCTTGAATTCAGTTGA+TGG + chr1.2:56311182-56311201 None:intergenic 40.0%
CTATCAGAATCGAGTGACTT+CGG - chr1.2:56311079-56311098 MS.gene32116:CDS 40.0%
GATTGCATATTGCTGCAAAC+AGG - chr1.2:56310817-56310836 MS.gene32116:CDS 40.0%
TAAACTACACCAGTCCATTG+CGG + chr1.2:56310657-56310676 None:intergenic 40.0%
TTTCTTCATCACCAGTCCAT+TGG + chr1.2:56310917-56310936 None:intergenic 40.0%
! CGTCCAGTTACTTTGAAAAG+AGG - chr1.2:56311000-56311019 MS.gene32116:intron 40.0%
! GATGATGACGAAGTCGAATT+TGG - chr1.2:56311116-56311135 MS.gene32116:CDS 40.0%
! GGGTTCTGCATTTTACCATT+GGG - chr1.2:56310860-56310879 MS.gene32116:CDS 40.0%
! GGTTCTGCATTTTACCATTG+GGG - chr1.2:56310861-56310880 MS.gene32116:CDS 40.0%
! TGGGTTCTGCATTTTACCAT+TGG - chr1.2:56310859-56310878 MS.gene32116:CDS 40.0%
!! CAATGGACTGGTGTAGTTTA+TGG - chr1.2:56310657-56310676 MS.gene32116:CDS 40.0%
!!! CTTTTTTCTCACAGCTGCTT+TGG + chr1.2:56310523-56310542 None:intergenic 40.0%
!!! GATCTTTTGGTGATGGTTTC+GGG - chr1.2:56311138-56311157 MS.gene32116:CDS 40.0%
!!! GGATCTTTTGGTGATGGTTT+CGG - chr1.2:56311137-56311156 MS.gene32116:CDS 40.0%
AAACTACACCAGTCCATTGC+GGG + chr1.2:56310656-56310675 None:intergenic 45.0%
GAAGTTTCACTCCAATGGAC+TGG - chr1.2:56310903-56310922 MS.gene32116:CDS 45.0%
GCGTCCATCAACTGAATTCA+AGG - chr1.2:56311175-56311194 MS.gene32116:CDS 45.0%
GGGAGTGACTCTAAATCGTT+AGG - chr1.2:56310678-56310697 MS.gene32116:CDS 45.0%
GGGATTTGATAAAATGGGCG+AGG - chr1.2:56310881-56310900 MS.gene32116:CDS 45.0%
! TGTTGGTCCTCTTTTCCAAG+TGG - chr1.2:56310626-56310645 MS.gene32116:CDS 45.0%
CTCTTCAGTCACAGCTGCAT+TGG + chr1.2:56310559-56310578 None:intergenic 50.0%
GCGAGGAAGTTTCACTCCAA+TGG - chr1.2:56310898-56310917 MS.gene32116:CDS 50.0%
GGGACTTCCACTTGGAAAAG+AGG + chr1.2:56310636-56310655 None:intergenic 50.0%
! CTTGTTGGTAGAGGAAGACG+AGG - chr1.2:56310753-56310772 MS.gene32116:CDS 50.0%
TCCAAGTGGAAGTCCCGCAA+TGG - chr1.2:56310640-56310659 MS.gene32116:CDS 55.0%
TCCATTGCGGGACTTCCACT+TGG + chr1.2:56310644-56310663 None:intergenic 55.0%
GTGGAAGTCCCGCAATGGAC+TGG - chr1.2:56310645-56310664 MS.gene32116:CDS 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 56310465 56311217 56310465 ID=MS.gene32116
chr1.2 mRNA 56310465 56311217 56310465 ID=MS.gene32116.t1;Parent=MS.gene32116
chr1.2 exon 56311016 56311217 56311016 ID=MS.gene32116.t1.exon1;Parent=MS.gene32116.t1
chr1.2 CDS 56311016 56311217 56311016 ID=cds.MS.gene32116.t1;Parent=MS.gene32116.t1
chr1.2 exon 56310465 56310931 56310465 ID=MS.gene32116.t1.exon2;Parent=MS.gene32116.t1
chr1.2 CDS 56310465 56310931 56310465 ID=cds.MS.gene32116.t1;Parent=MS.gene32116.t1
Gene Sequence

>MS.gene32116

ATGGAGAAAACAACTGGCAAACCAGATGTTGTGATCAAGAAGAAAAAATCAATTGCCAAAGCAGCTGTGAGAAAAAAGAAAAAATCAACTGCCAATGCAGCTGTGACTGAAGAGAAAAAATATGACCCATTTAGTGATGATTCTCGTCATAAGTTTGTTTCTGTTGGTCCTCTTTTCCAAGTGGAAGTCCCGCAATGGACTGGTGTAGTTTATGGGAGTGACTCTAAATCGTTAGGCACACAAGTATGGCCTCTTAAAGATGATTCAAGACCTACTACTTAAACAGATCTTGTTGGTAGAGGAAGACGAGGAAAGTGTAGCTGCAATGTTCAATGTTCAGTTGACTGTGTAAGATTGCATATTGCTGCAAACAGGATGAAGCTGAAGTTTGAATTGGGTTCTGCATTTTACCATTGGGGATTTGATAAAATGGGCGAGGAAGTTTCACTCCAATGGACTGGTGATGAAGAAAAGACATTTAAGGATATAATGAGTTTAAAAATCCCCTCCCAAAACAAGTATTTTTGGAACAATCCGTCCAGTTACTTTGAAAAGAGGACAAGAAAAGACATGGTGAGATATTACTTCAATGTATATCTTATTCAACTAAGAAGCTATCAGAATCGAGTGACTTCGGAGACTGTTGACAGTGATGATGACGAAGTCGAATTTGGATCTTTTGGTGATGGTTTCGGGAGAAAAGCTATCAAGCGTCCATCAACTGAATTCAAGGAGTGTTCAGAGAACAAGTAA
Protein sequence

>MS.gene32116.t1

MEKTTGKPDVVIKKKKSIAKAAVRKKKKSTANAAVTEEKKYDPFSDDSRHKFVSVGPLFQVEVPQWTDLVGRGRRGKCSCNVQCSVDCVRLHIAANRMKLKFELGSAFYHWGFDKMGEEVSLQWTGDEEKTFKDIMSLKIPSQNKYFWNNPSSYFEKRTRKDMVRYYFNVYLIQLRSYQNRVTSETVDSDDDEVEFGSFGDGFGRKAIKRPSTEFKECSENK