AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene35417

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35417.t1 MTR_2g086510 96.129 155 6 0 1 155 1 155 9.10e-110 308
MS.gene35417.t1 MTR_4g053120 73.548 155 41 0 1 155 1 155 3.65e-83 241
MS.gene35417.t1 MTR_1g112030 71.970 132 36 1 24 155 26 156 1.20e-66 200
MS.gene35417.t1 MTR_1g112030 71.970 132 36 1 24 155 30 160 1.21e-66 200
MS.gene35417.t1 MTR_1g112050 71.756 131 36 1 24 154 24 153 3.46e-64 193
MS.gene35417.t1 MTR_8g088720 60.976 123 46 2 33 154 25 146 2.21e-48 153
MS.gene35417.t1 MTR_2g006290 59.504 121 45 2 37 154 29 148 1.15e-47 151
MS.gene35417.t1 MTR_5g006320 40.404 99 57 2 56 154 47 143 1.80e-21 85.1
MS.gene35417.t1 MTR_4g098490 28.571 147 100 3 13 155 14 159 4.15e-16 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35417.t1 AT2G27510 73.171 123 32 1 34 155 33 155 1.01e-63 192
MS.gene35417.t1 AT1G60950 66.667 117 36 2 40 154 32 147 2.16e-50 158
MS.gene35417.t1 AT1G10960 67.544 114 34 2 40 151 32 144 9.90e-48 152
MS.gene35417.t1 AT5G10000 57.143 112 46 1 45 154 36 147 6.71e-44 142
MS.gene35417.t1 AT4G14890 45.263 95 50 2 60 154 52 144 2.45e-22 87.4
MS.gene35417.t1 AT1G32550 39.535 86 52 0 70 155 69 154 6.11e-18 76.6
MS.gene35417.t1 AT1G32550 37.255 102 45 3 70 155 69 167 2.97e-13 64.7

Find 32 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGCTGGGAAGGTTGTTTC+TGG 0.160515 2.1:-15603128 MS.gene35417:CDS
TCTCGATGACAATCAATTAA+AGG 0.218310 2.1:-15603078 MS.gene35417:CDS
CGGCAGTAGTGAATTGATTT+TGG 0.237516 2.1:+15603387 None:intergenic
AAGAATGTTTCACGATCTTT+TGG 0.297059 2.1:-15603329 MS.gene35417:CDS
GGAGCATGCTCTACCTGTGC+TGG 0.371691 2.1:-15603143 MS.gene35417:CDS
TAGATGAAGCAGATGACTTC+AGG 0.402843 2.1:+15603306 None:intergenic
CAAAATTAAGCTGATTGGTC+CGG 0.411846 2.1:-15603261 MS.gene35417:CDS
TGAAGTCATCTGCTTCATCT+AGG 0.420369 2.1:-15603304 MS.gene35417:CDS
GCTTACAAAATTAAGCTGAT+TGG 0.422819 2.1:-15603266 MS.gene35417:CDS
CTTCCGTATTCATGCCGTGC+TGG 0.464676 2.1:-15603164 MS.gene35417:CDS
TGAATAACACAGTCTGAAGT+TGG 0.477269 2.1:+15603026 None:intergenic
GCTCCAGCACGGCATGAATA+CGG 0.486288 2.1:+15603161 None:intergenic
GTAAACCTTCACAGTTGATA+AGG 0.489067 2.1:+15603436 None:intergenic
GTCAAGTGCCCTTCCACTCT+AGG 0.511274 2.1:-15603359 MS.gene35417:CDS
ATGCTCTACCTGTGCTGGGA+AGG 0.518844 2.1:-15603138 MS.gene35417:CDS
GAGCATGCTCTACCTGTGCT+GGG 0.533531 2.1:-15603142 MS.gene35417:CDS
GAAGTCATCTGCTTCATCTA+GGG 0.543475 2.1:-15603303 MS.gene35417:CDS
TTCGCAGATCCTAGAGTGGA+AGG 0.547384 2.1:+15603350 None:intergenic
TTCATCTAGGGTTACTGCAG+TGG 0.553859 2.1:-15603291 MS.gene35417:CDS
GGTTCTGTCGATCAGTCAGA+TGG 0.558348 2.1:-15603107 MS.gene35417:CDS
ATTAAGCTGATTGGTCCGGA+TGG 0.560404 2.1:-15603257 MS.gene35417:CDS
GTCAGCCTTATCAACTGTGA+AGG 0.577652 2.1:-15603441 MS.gene35417:CDS
AGAAACAACCTTCCCAGCAC+AGG 0.578473 2.1:+15603130 None:intergenic
TTAGATGCAGCAGAGAATGC+CGG 0.589828 2.1:-15603194 MS.gene35417:CDS
GTTATTCATACACACAAAGA+AGG 0.595409 2.1:-15603011 MS.gene35417:CDS
GATGACAATCAATTAAAGGA+AGG 0.602977 2.1:-15603074 MS.gene35417:CDS
GGAAGGGCACTTGACTGTTG+CGG 0.612607 2.1:+15603367 None:intergenic
AGGTAGAGCATGCTCCAGCA+CGG 0.616285 2.1:+15603150 None:intergenic
TGAAGTTGGATAAGCTACAC+AGG 0.630428 2.1:+15603040 None:intergenic
TGAATACGGAAGTTCAACTC+CGG 0.648667 2.1:+15603175 None:intergenic
TCGCAGATCCTAGAGTGGAA+GGG 0.653095 2.1:+15603351 None:intergenic
ATTCTTCGCAGATCCTAGAG+TGG 0.678656 2.1:+15603346 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTCATTTTCTTTTCCATC+CGG + chr2.1:15603202-15603221 None:intergenic 25.0%
GATGACAATCAATTAAAGGA+AGG - chr2.1:15603367-15603386 MS.gene35417:CDS 30.0%
GCTTACAAAATTAAGCTGAT+TGG - chr2.1:15603175-15603194 MS.gene35417:CDS 30.0%
GTTATTCATACACACAAAGA+AGG - chr2.1:15603430-15603449 MS.gene35417:CDS 30.0%
TCTCGATGACAATCAATTAA+AGG - chr2.1:15603363-15603382 MS.gene35417:CDS 30.0%
! AAGAATGTTTCACGATCTTT+TGG - chr2.1:15603112-15603131 MS.gene35417:CDS 30.0%
! CAAAATTAAGCTGATTGGTC+CGG - chr2.1:15603180-15603199 MS.gene35417:CDS 35.0%
! GTAAACCTTCACAGTTGATA+AGG + chr2.1:15603008-15603027 None:intergenic 35.0%
! TGAATAACACAGTCTGAAGT+TGG + chr2.1:15603418-15603437 None:intergenic 35.0%
GAAGTCATCTGCTTCATCTA+GGG - chr2.1:15603138-15603157 MS.gene35417:CDS 40.0%
TAGATGAAGCAGATGACTTC+AGG + chr2.1:15603138-15603157 None:intergenic 40.0%
TGAAGTCATCTGCTTCATCT+AGG - chr2.1:15603137-15603156 MS.gene35417:CDS 40.0%
TGAAGTTGGATAAGCTACAC+AGG + chr2.1:15603404-15603423 None:intergenic 40.0%
TGAATACGGAAGTTCAACTC+CGG + chr2.1:15603269-15603288 None:intergenic 40.0%
!! CGGCAGTAGTGAATTGATTT+TGG + chr2.1:15603057-15603076 None:intergenic 40.0%
!!! CAGTTTTAAGCGTGCAATAG+CGG + chr2.1:15603030-15603049 None:intergenic 40.0%
ATTCTTCGCAGATCCTAGAG+TGG + chr2.1:15603098-15603117 None:intergenic 45.0%
TTAGATGCAGCAGAGAATGC+CGG - chr2.1:15603247-15603266 MS.gene35417:CDS 45.0%
! ATTAAGCTGATTGGTCCGGA+TGG - chr2.1:15603184-15603203 MS.gene35417:CDS 45.0%
! GTCAGCCTTATCAACTGTGA+AGG - chr2.1:15603000-15603019 MS.gene35417:CDS 45.0%
! TTCATCTAGGGTTACTGCAG+TGG - chr2.1:15603150-15603169 MS.gene35417:CDS 45.0%
AGAAACAACCTTCCCAGCAC+AGG + chr2.1:15603314-15603333 None:intergenic 50.0%
GGTTCTGTCGATCAGTCAGA+TGG - chr2.1:15603334-15603353 MS.gene35417:CDS 50.0%
TCGCAGATCCTAGAGTGGAA+GGG + chr2.1:15603093-15603112 None:intergenic 50.0%
TTCGCAGATCCTAGAGTGGA+AGG + chr2.1:15603094-15603113 None:intergenic 50.0%
! TGTGCTGGGAAGGTTGTTTC+TGG - chr2.1:15603313-15603332 MS.gene35417:CDS 50.0%
AGGTAGAGCATGCTCCAGCA+CGG + chr2.1:15603294-15603313 None:intergenic 55.0%
ATGCTCTACCTGTGCTGGGA+AGG - chr2.1:15603303-15603322 MS.gene35417:CDS 55.0%
CTTCCGTATTCATGCCGTGC+TGG - chr2.1:15603277-15603296 MS.gene35417:CDS 55.0%
GAGCATGCTCTACCTGTGCT+GGG - chr2.1:15603299-15603318 MS.gene35417:CDS 55.0%
GCTCCAGCACGGCATGAATA+CGG + chr2.1:15603283-15603302 None:intergenic 55.0%
GTCAAGTGCCCTTCCACTCT+AGG - chr2.1:15603082-15603101 MS.gene35417:CDS 55.0%
!! GGAAGGGCACTTGACTGTTG+CGG + chr2.1:15603077-15603096 None:intergenic 55.0%
GGAGCATGCTCTACCTGTGC+TGG - chr2.1:15603298-15603317 MS.gene35417:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 15602998 15603465 15602998 ID=MS.gene35417
chr2.1 mRNA 15602998 15603465 15602998 ID=MS.gene35417.t1;Parent=MS.gene35417
chr2.1 exon 15602998 15603465 15602998 ID=MS.gene35417.t1.exon1;Parent=MS.gene35417.t1
chr2.1 CDS 15602998 15603465 15602998 ID=cds.MS.gene35417.t1;Parent=MS.gene35417.t1
Gene Sequence

>MS.gene35417

ATGTCAGCCTTATCAACTGTGAAGGTTTACCGCTATTGCACGCTTAAAACTGCTAACCAAAATCAATTCACTACTGCCGCAACAGTCAAGTGCCCTTCCACTCTAGGATCTGCGAAGAATGTTTCACGATCTTTTGGCCTGAAGTCATCTGCTTCATCTAGGGTTACTGCAGTGGCTGCTTACAAAATTAAGCTGATTGGTCCGGATGGAAAAGAAAATGAATTTGAAGCAACTGATGACACTTACATCTTAGATGCAGCAGAGAATGCCGGAGTTGAACTTCCGTATTCATGCCGTGCTGGAGCATGCTCTACCTGTGCTGGGAAGGTTGTTTCTGGTTCTGTCGATCAGTCAGATGGCTCATTTCTCGATGACAATCAATTAAAGGAAGGTTATGTTCTAACCTGTGTAGCTTATCCAACTTCAGACTGTGTTATTCATACACACAAAGAAGGTGACCTCTATTGA
Protein sequence

>MS.gene35417.t1

MSALSTVKVYRYCTLKTANQNQFTTAATVKCPSTLGSAKNVSRSFGLKSSASSRVTAVAAYKIKLIGPDGKENEFEATDDTYILDAAENAGVELPYSCRAGACSTCAGKVVSGSVDQSDGSFLDDNQLKEGYVLTCVAYPTSDCVIHTHKEGDLY