AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene02448

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene02448.t1 MTR_5g020510 97.872 188 4 0 1 188 110 297 3.15e-138 387
MS.gene02448.t1 MTR_4g134580 40.000 225 98 6 1 188 124 348 3.85e-45 152
MS.gene02448.t1 MTR_1g077020 39.267 191 91 4 1 188 20 188 2.33e-43 143
MS.gene02448.t1 MTR_3g100650 40.609 197 92 4 1 186 91 273 3.02e-40 137
MS.gene02448.t1 MTR_5g032600 39.500 200 90 4 1 186 89 271 6.57e-40 137
MS.gene02448.t1 MTR_7g010300 37.688 199 98 7 1 187 99 283 3.71e-38 134
MS.gene02448.t1 MTR_5g065440 37.811 201 108 5 1 186 69 267 3.11e-36 127
MS.gene02448.t1 MTR_2g076780 37.186 199 96 5 1 183 48 233 2.45e-35 124
MS.gene02448.t1 MTR_8g069080 37.245 196 97 5 1 182 80 263 4.21e-34 122
MS.gene02448.t1 MTR_6g012280 37.056 197 99 5 1 186 102 284 4.13e-33 120
MS.gene02448.t1 MTR_8g442330 28.571 161 78 3 1 161 16 139 2.22e-19 80.5
MS.gene02448.t1 MTR_8g467340 60.345 58 23 0 124 181 271 328 2.24e-19 84.7
MS.gene02448.t1 MTR_8g467340 50.943 53 17 2 1 51 75 120 6.40e-11 60.5
MS.gene02448.t1 MTR_6g073013 55.000 60 26 1 124 182 101 160 7.28e-19 80.1
MS.gene02448.t1 MTR_8g051480 51.786 56 26 1 125 180 68 122 5.59e-16 71.2
MS.gene02448.t1 MTR_8g069380 46.032 63 34 0 124 186 52 114 1.61e-15 69.7
MS.gene02448.t1 MTR_3g039810 55.814 43 19 0 1 43 31 73 1.71e-12 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.gene02448.t1 AT2G18350 49.231 195 65 7 2 188 94 262 7.02e-51 165
MS.gene02448.t1 AT1G75240 40.455 220 91 4 1 185 87 301 1.14e-44 150
MS.gene02448.t1 AT2G02540 37.321 209 86 6 1 186 98 284 6.98e-41 140
MS.gene02448.t1 AT2G02540 37.321 209 86 6 1 186 98 284 6.98e-41 140
MS.gene02448.t1 AT3G50890 43.243 185 90 4 2 185 72 242 1.21e-40 138
MS.gene02448.t1 AT4G24660 40.107 187 84 6 1 186 60 219 2.65e-40 136
MS.gene02448.t1 AT4G24660 39.683 189 86 6 1 188 60 221 3.38e-40 136
MS.gene02448.t1 AT1G14440 39.153 189 91 5 1 180 101 274 1.10e-37 132
MS.gene02448.t1 AT1G14440 39.153 189 91 5 1 180 101 274 1.10e-37 132
MS.gene02448.t1 AT5G65410 38.624 189 90 4 1 185 86 252 1.40e-37 131
MS.gene02448.t1 AT1G69600 37.838 185 102 4 1 183 42 215 4.64e-36 126
MS.gene02448.t1 AT3G28920 35.938 192 113 3 1 184 63 252 5.53e-34 122
MS.gene02448.t1 AT5G15210 36.264 182 101 4 1 180 67 235 8.44e-31 113
MS.gene02448.t1 AT5G60480 35.450 189 80 6 1 180 48 203 1.72e-29 108
MS.gene02448.t1 AT5G39760 37.374 198 114 3 1 188 67 264 4.46e-28 107
MS.gene02448.t1 AT5G42780 28.649 185 109 5 1 183 75 238 1.38e-21 88.6
MS.gene02448.t1 AT1G74660 55.814 43 19 0 1 43 50 92 2.90e-13 63.2
MS.gene02448.t1 AT1G74660 55.814 43 19 0 1 43 50 92 4.79e-13 62.8
MS.gene02448.t1 AT1G14687 23.913 184 101 6 1 181 18 165 2.92e-12 62.4
MS.gene02448.t1 AT3G28917 56.818 44 18 1 1 43 44 87 1.08e-11 59.3

Find 34 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTGCTATGATGATAATT+AGG 0.318608 5.3:-11832764 None:intergenic
CCGTCCATGATGATGACTTT+TGG 0.355768 5.3:+11832863 MS.gene02448:CDS
AGAGTTTCACAACCTAGTTC+TGG 0.368324 5.3:+11832830 MS.gene02448:CDS
AAGATGGTGTTGGAAGATTA+AGG 0.396177 5.3:-11832796 None:intergenic
CTTACCCTCTTCTTCAAAAC+CGG 0.408989 5.3:-11832962 None:intergenic
CGGTTGCTGCGGCGTTTGTA+TGG 0.409265 5.3:-11832942 None:intergenic
ATGGAGTTTGCTGAAAAGAT+TGG 0.437625 5.3:+11833019 MS.gene02448:CDS
CATACAAACGCCGCAGCAAC+CGG 0.441402 5.3:+11832943 MS.gene02448:CDS
GAGGAATACTATGTTGTTGT+TGG 0.445811 5.3:-11832721 None:intergenic
AGTGAAGATCTCAACATGTT+TGG 0.446843 5.3:+11832908 MS.gene02448:CDS
ATGGGAAGCCACGTGGTAGA+TGG 0.447420 5.3:+11832602 MS.gene02448:CDS
TCAAGTTGGTATCAAGAGAC+AGG 0.468371 5.3:+11833090 MS.gene02448:CDS
GGGGTACCTTCTTCACCGCT+TGG 0.472411 5.3:-11832641 None:intergenic
CAGCACATTTGAAATATTGT+GGG 0.475954 5.3:-11832661 None:intergenic
GCAGCACATTTGAAATATTG+TGG 0.476946 5.3:-11832662 None:intergenic
TCTTCACTTGATGATTCAGC+TGG 0.479858 5.3:-11832893 None:intergenic
TTCACAACCTAGTTCTGGAC+AGG 0.499932 5.3:+11832835 MS.gene02448:CDS
TTCATGCCAAGCGGTGAAGA+AGG 0.514566 5.3:+11832635 MS.gene02448:CDS
TGGAGTTTGCTGAAAAGATT+GGG 0.549528 5.3:+11833020 MS.gene02448:CDS
GGTGGAACCTGTCCAGAACT+AGG 0.552234 5.3:-11832842 None:intergenic
TGATCCAAAAGTCATCATCA+TGG 0.575663 5.3:-11832867 None:intergenic
TTCTTCAAAACCGGTTGCTG+CGG 0.576173 5.3:-11832953 None:intergenic
TGAGATGACGAAGATGGTGT+TGG 0.582966 5.3:-11832806 None:intergenic
CCAAAAGTCATCATCATGGA+CGG 0.622115 5.3:-11832863 None:intergenic
AGCCACGTGGTAGATGGATG+TGG 0.625991 5.3:+11832608 MS.gene02448:CDS
ACTCTTTGAGATGACGAAGA+TGG 0.644785 5.3:-11832812 None:intergenic
AGCACATTTGAAATATTGTG+GGG 0.654466 5.3:-11832660 None:intergenic
ACATGCTGAACATGTTGTTG+AGG 0.672696 5.3:-11832740 None:intergenic
AGTTTGCTGAAAAGATTGGG+TGG 0.678186 5.3:+11833023 MS.gene02448:CDS
AAAGTCATCATCATGGACGG+TGG 0.680716 5.3:-11832860 None:intergenic
GGCAAGCATGGGAAGCCACG+TGG 0.697743 5.3:+11832595 None:intergenic
CACCACATCCATCTACCACG+TGG 0.722647 5.3:-11832610 None:intergenic
TATCATCATAGCAACAACAA+CGG 0.730770 5.3:+11832770 MS.gene02448:CDS
TGTGGTGAATTCATGCCAAG+CGG 0.769326 5.3:+11832626 MS.gene02448:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTGTTGCTATGATGATAATT+AGG - chr5.3:11832767-11832786 None:intergenic 25.0%
!! TATGTTTTCGATGGAAATTA+CGG - chr5.3:11832700-11832719 None:intergenic 25.0%
TATCATCATAGCAACAACAA+CGG + chr5.3:11832770-11832789 MS.gene02448:CDS 30.0%
! AGCACATTTGAAATATTGTG+GGG - chr5.3:11832663-11832682 None:intergenic 30.0%
! CAGCACATTTGAAATATTGT+GGG - chr5.3:11832664-11832683 None:intergenic 30.0%
AGTGAAGATCTCAACATGTT+TGG + chr5.3:11832908-11832927 MS.gene02448:CDS 35.0%
GAGGAATACTATGTTGTTGT+TGG - chr5.3:11832724-11832743 None:intergenic 35.0%
GCAACAAAAAGATAGGATGA+TGG + chr5.3:11833000-11833019 MS.gene02448:CDS 35.0%
TCTCACAGCAACAAAAAGAT+AGG + chr5.3:11832993-11833012 MS.gene02448:CDS 35.0%
TGATCCAAAAGTCATCATCA+TGG - chr5.3:11832870-11832889 None:intergenic 35.0%
! AAGATGGTGTTGGAAGATTA+AGG - chr5.3:11832799-11832818 None:intergenic 35.0%
! GCAGCACATTTGAAATATTG+TGG - chr5.3:11832665-11832684 None:intergenic 35.0%
! GTTGTTGGATATGTTTTCGA+TGG - chr5.3:11832709-11832728 None:intergenic 35.0%
!! ATGGAGTTTGCTGAAAAGAT+TGG + chr5.3:11833019-11833038 MS.gene02448:CDS 35.0%
!! TGGAGTTTGCTGAAAAGATT+GGG + chr5.3:11833020-11833039 MS.gene02448:CDS 35.0%
!!! CAACAGTTTTGTTCTCAAGT+TGG + chr5.3:11833076-11833095 MS.gene02448:CDS 35.0%
ACATGCTGAACATGTTGTTG+AGG - chr5.3:11832743-11832762 None:intergenic 40.0%
AGAGTTTCACAACCTAGTTC+TGG + chr5.3:11832830-11832849 MS.gene02448:CDS 40.0%
CCAAAAGTCATCATCATGGA+CGG - chr5.3:11832866-11832885 None:intergenic 40.0%
CTTACCCTCTTCTTCAAAAC+CGG - chr5.3:11832965-11832984 None:intergenic 40.0%
! TCTTCACTTGATGATTCAGC+TGG - chr5.3:11832896-11832915 None:intergenic 40.0%
!! ACTCTTTGAGATGACGAAGA+TGG - chr5.3:11832815-11832834 None:intergenic 40.0%
!! AGTTTGCTGAAAAGATTGGG+TGG + chr5.3:11833023-11833042 MS.gene02448:CDS 40.0%
!! TCAAGTTGGTATCAAGAGAC+AGG + chr5.3:11833090-11833109 MS.gene02448:CDS 40.0%
AAAGTCATCATCATGGACGG+TGG - chr5.3:11832863-11832882 None:intergenic 45.0%
TGAGATGACGAAGATGGTGT+TGG - chr5.3:11832809-11832828 None:intergenic 45.0%
TGTGGTGAATTCATGCCAAG+CGG + chr5.3:11832626-11832645 MS.gene02448:CDS 45.0%
TTCTTCAAAACCGGTTGCTG+CGG - chr5.3:11832956-11832975 None:intergenic 45.0%
!! CCGTCCATGATGATGACTTT+TGG + chr5.3:11832863-11832882 MS.gene02448:CDS 45.0%
!! TTCACAACCTAGTTCTGGAC+AGG + chr5.3:11832835-11832854 MS.gene02448:CDS 45.0%
!!! AGCAACCGGTTTTGAAGAAG+AGG + chr5.3:11832957-11832976 MS.gene02448:CDS 45.0%
!!! CGGTTTTGAAGAAGAGGGTA+AGG + chr5.3:11832963-11832982 MS.gene02448:CDS 45.0%
!!! GCAACCGGTTTTGAAGAAGA+GGG + chr5.3:11832958-11832977 MS.gene02448:CDS 45.0%
TTCATGCCAAGCGGTGAAGA+AGG + chr5.3:11832635-11832654 MS.gene02448:CDS 50.0%
AGCCACGTGGTAGATGGATG+TGG + chr5.3:11832608-11832627 MS.gene02448:CDS 55.0%
ATGGGAAGCCACGTGGTAGA+TGG + chr5.3:11832602-11832621 MS.gene02448:CDS 55.0%
CACCACATCCATCTACCACG+TGG - chr5.3:11832613-11832632 None:intergenic 55.0%
CATACAAACGCCGCAGCAAC+CGG + chr5.3:11832943-11832962 MS.gene02448:CDS 55.0%
GGTGGAACCTGTCCAGAACT+AGG - chr5.3:11832845-11832864 None:intergenic 55.0%
CGGTTGCTGCGGCGTTTGTA+TGG - chr5.3:11832945-11832964 None:intergenic 60.0%
! GGGGTACCTTCTTCACCGCT+TGG - chr5.3:11832644-11832663 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 11832602 11833168 11832602 ID=MS.gene02448
chr5.3 mRNA 11832602 11833168 11832602 ID=MS.gene02448.t1;Parent=MS.gene02448
chr5.3 exon 11832602 11833168 11832602 ID=MS.gene02448.t1.exon1;Parent=MS.gene02448.t1
chr5.3 CDS 11832602 11833168 11832602 ID=cds.MS.gene02448.t1;Parent=MS.gene02448.t1
Gene Sequence

>MS.gene02448

ATGGGAAGCCACGTGGTAGATGGATGTGGTGAATTCATGCCAAGCGGTGAAGAAGGTACCCCACAATATTTCAAATGTGCTGCTTGTGATTGTCACCGTAATTTCCATCGAAAACATATCCAACAACAACATAGTATTCCTCAACAACATGTTCAGCATGTTCCTAATTATCATCATAGCAACAACAACGGTCACCTTAATCTTCCAACACCATCTTCGTCATCTCAAAGAGTTTCACAACCTAGTTCTGGACAGGTTCCACCGTCCATGATGATGACTTTTGGATCAGTTCCAGCTGAATCATCAAGTGAAGATCTCAACATGTTTGGTGCACAATTTTCCATACAAACGCCGCAGCAACCGGTTTTGAAGAAGAGGGTAAGGACGAAATTCTCACAGCAACAAAAAGATAGGATGATGGAGTTTGCTGAAAAGATTGGGTGGAAGATTCAGAAACATGATGAACAAGAAGTGCAACAGTTTTGTTCTCAAGTTGGTATCAAGAGACAGGTTTTTAAAGTTTTTATGCATAATAACAAACAAGCTATGAAGAAACAGCAAATGTAA
Protein sequence

>MS.gene02448.t1

MGSHVVDGCGEFMPSGEEGTPQYFKCAACDCHRNFHRKHIQQQHSIPQQHVQHVPNYHHSNNNGHLNLPTPSSSSQRVSQPSSGQVPPSMMMTFGSVPAESSSEDLNMFGAQFSIQTPQQPVLKKRVRTKFSQQQKDRMMEFAEKIGWKIQKHDEQEVQQFCSQVGIKRQVFKVFMHNNKQAMKKQQM