AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene002504

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002504.t1 MTR_2g014550 97.630 211 4 1 1 211 1 210 1.00e-151 419
MS.gene002504.t1 MTR_2g014520 87.923 207 25 0 5 211 1 207 8.15e-135 376
MS.gene002504.t1 MTR_4g088335 73.604 197 52 0 15 211 10 206 1.24e-109 313
MS.gene002504.t1 MTR_4g078870 54.922 193 81 3 20 209 14 203 1.44e-75 226
MS.gene002504.t1 MTR_5g044580 43.094 181 101 2 26 205 35 214 5.19e-49 159
MS.gene002504.t1 MTR_2g020850 38.947 190 109 2 25 210 2 188 2.56e-46 152
MS.gene002504.t1 MTR_7g010890 41.436 181 104 2 26 205 35 214 4.74e-46 152
MS.gene002504.t1 MTR_4g118470 41.361 191 98 3 24 210 18 198 5.82e-43 144
MS.gene002504.t1 MTR_4g118480 42.045 176 92 2 39 210 27 196 9.21e-41 138
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002504.t1 AT5G46090 61.682 214 75 3 1 209 1 212 2.01e-97 282
MS.gene002504.t1 AT4G18425 59.434 212 82 3 3 210 1 212 4.42e-92 269
MS.gene002504.t1 AT4G28485 50.254 197 96 2 15 209 2 198 7.52e-67 204
MS.gene002504.t1 AT3G02430 47.396 192 95 2 24 211 26 215 1.88e-64 199
MS.gene002504.t1 AT4G24310 50.000 192 89 3 23 209 18 207 5.76e-61 190
MS.gene002504.t1 AT1G09157 38.587 184 101 1 34 205 56 239 1.70e-42 143
MS.gene002504.t1 AT3G21550 43.605 172 91 2 37 207 6 172 5.16e-42 140
MS.gene002504.t1 AT5G39650 38.172 186 99 2 34 205 57 240 6.10e-42 142
MS.gene002504.t1 AT3G21520 40.000 160 89 2 49 206 33 187 5.67e-36 125
MS.gene002504.t1 AT4G28485 56.566 99 43 0 111 209 65 163 1.55e-33 118
MS.gene002504.t1 AT5G27370 35.227 176 99 3 45 205 11 186 2.58e-30 110

Find 43 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTCAGAGCACGGCGCATT+TGG 0.350269 2.1:+70560894 MS.gene002504:CDS
AGCAAGGGGAATATTTGTTA+TGG 0.356880 2.1:+70561081 MS.gene002504:CDS
AAAGGTTTGTGGGTCATTGA+TGG 0.367892 2.1:+70561117 MS.gene002504:CDS
GCAAGGGGAATATTTGTTAT+GGG 0.374957 2.1:+70561082 MS.gene002504:CDS
ATTAACTAACTTGTTGAAAG+AGG 0.380446 2.1:-70561387 None:intergenic
ACGGCGTTGCCTGTGGCAAT+TGG 0.380489 2.1:+70561306 MS.gene002504:CDS
CCTACTGAGAGACATGGAAT+TGG 0.411080 2.1:+70561360 MS.gene002504:CDS
ACCAGGCTCCTCTCTGCCTC+TGG 0.411547 2.1:-70560850 None:intergenic
TATGGGTTTGCCACCTTCAA+AGG 0.413754 2.1:+70561099 MS.gene002504:CDS
TGCCACCTTCAAAGGTTTGT+GGG 0.416898 2.1:+70561107 MS.gene002504:CDS
AGCAACTTGAGGTGGAAGTT+TGG 0.423290 2.1:-70561145 None:intergenic
AACTTATAGCTTTCTGTACC+AGG 0.430636 2.1:-70560867 None:intergenic
GCATGCGGTGATGTCAATTC+TGG 0.434994 2.1:+70561200 MS.gene002504:CDS
GAACAGTGCCTGTAGGTAGA+AGG 0.449758 2.1:-70560921 None:intergenic
AATGACCCACAAACCTTTGA+AGG 0.450179 2.1:-70561112 None:intergenic
TTGCCACCTTCAAAGGTTTG+TGG 0.452480 2.1:+70561106 MS.gene002504:CDS
TGCTATCAGTAAAGTTTAGC+AGG 0.458079 2.1:-70561050 None:intergenic
TAGGAATGACGATGAACAAA+AGG 0.495588 2.1:+70560801 MS.gene002504:CDS
TTAACTAACTTGTTGAAAGA+GGG 0.526967 2.1:-70561386 None:intergenic
TTGGCAAACCTTCTACCTAC+AGG 0.528525 2.1:+70560913 MS.gene002504:CDS
TCTGTACTTGTGACTCTATG+TGG 0.546587 2.1:+70561015 MS.gene002504:CDS
TCCAGAGGCAGAGAGGAGCC+TGG 0.549208 2.1:+70560849 MS.gene002504:CDS
CCAATTCCATGTCTCTCAGT+AGG 0.555703 2.1:-70561360 None:intergenic
TAGAAATCGATGATGACTCT+AGG 0.560367 2.1:+70560782 MS.gene002504:CDS
AGTCACAAGTACAGAAGTCA+TGG 0.564650 2.1:-70561007 None:intergenic
TCCACTTCTGCGGAATGCGG+AGG 0.572373 2.1:+70560825 MS.gene002504:CDS
ACCTCCGCATTCCGCAGAAG+TGG 0.578568 2.1:-70560826 None:intergenic
TGATAGCATTAGAGACAGCA+AGG 0.586072 2.1:+70561065 MS.gene002504:CDS
GTTTATAGATTTCATGCATG+CGG 0.586781 2.1:+70561185 MS.gene002504:CDS
AACAAAAGGTTCCACTTCTG+CGG 0.591604 2.1:+70560815 MS.gene002504:CDS
AAGTTCGACATTTCAGAGCA+CGG 0.595642 2.1:+70560885 MS.gene002504:CDS
AATCCTCACGGCGTTGCCTG+TGG 0.613810 2.1:+70561299 MS.gene002504:CDS
TTGCCACAGGCAACGCCGTG+AGG 0.614771 2.1:-70561302 None:intergenic
GCGGAATGCGGAGGTTCCAG+AGG 0.622187 2.1:+70560834 MS.gene002504:CDS
TGCATTGTTTGATCAGAATG+TGG 0.627363 2.1:+70561236 MS.gene002504:CDS
GGTTCCACTTCTGCGGAATG+CGG 0.628493 2.1:+70560822 MS.gene002504:CDS
CGGAGGTTCCAGAGGCAGAG+AGG 0.628788 2.1:+70560842 MS.gene002504:CDS
GCATTTCCTACTGAGAGACA+TGG 0.635534 2.1:+70561354 MS.gene002504:CDS
GATAGCATTAGAGACAGCAA+GGG 0.637719 2.1:+70561066 MS.gene002504:CDS
GACCCACAAACCTTTGAAGG+TGG 0.639111 2.1:-70561109 None:intergenic
AATGCAAGAACAGTGCCTGT+AGG 0.674988 2.1:-70560928 None:intergenic
AGAGATACAAGAAATCCTCA+CGG 0.689697 2.1:+70561287 MS.gene002504:CDS
ATAGCATTAGAGACAGCAAG+GGG 0.732552 2.1:+70561067 MS.gene002504:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTGCCAACATTTGTAAAAAT+TGG - chr2.1:70560967-70560986 None:intergenic 25.0%
!! ATTTCTTGTATCTCTTTTGA+TGG - chr2.1:70561282-70561301 None:intergenic 25.0%
!! TAAAAATTGGTGACAAAAGT+TGG - chr2.1:70560954-70560973 None:intergenic 25.0%
!! TCACCAATTTTTACAAATGT+TGG + chr2.1:70560961-70560980 MS.gene002504:CDS 25.0%
GTTTATAGATTTCATGCATG+CGG + chr2.1:70561185-70561204 MS.gene002504:CDS 30.0%
AACTTATAGCTTTCTGTACC+AGG - chr2.1:70560870-70560889 None:intergenic 35.0%
AGAGATACAAGAAATCCTCA+CGG + chr2.1:70561287-70561306 MS.gene002504:CDS 35.0%
TAGAAATCGATGATGACTCT+AGG + chr2.1:70560782-70560801 MS.gene002504:CDS 35.0%
TAGGAATGACGATGAACAAA+AGG + chr2.1:70560801-70560820 MS.gene002504:CDS 35.0%
TGCATTGTTTGATCAGAATG+TGG + chr2.1:70561236-70561255 MS.gene002504:CDS 35.0%
TGCTATCAGTAAAGTTTAGC+AGG - chr2.1:70561053-70561072 None:intergenic 35.0%
! AGCAAGGGGAATATTTGTTA+TGG + chr2.1:70561081-70561100 MS.gene002504:CDS 35.0%
!! GCAAGGGGAATATTTGTTAT+GGG + chr2.1:70561082-70561101 MS.gene002504:CDS 35.0%
!! TGTATCTCTTTTGATGGTTC+TGG - chr2.1:70561276-70561295 None:intergenic 35.0%
AAAGGTTTGTGGGTCATTGA+TGG + chr2.1:70561117-70561136 MS.gene002504:CDS 40.0%
AACAAAAGGTTCCACTTCTG+CGG + chr2.1:70560815-70560834 MS.gene002504:CDS 40.0%
AAGTTCGACATTTCAGAGCA+CGG + chr2.1:70560885-70560904 MS.gene002504:CDS 40.0%
AATGACCCACAAACCTTTGA+AGG - chr2.1:70561115-70561134 None:intergenic 40.0%
AGTCACAAGTACAGAAGTCA+TGG - chr2.1:70561010-70561029 None:intergenic 40.0%
ATAGCATTAGAGACAGCAAG+GGG + chr2.1:70561067-70561086 MS.gene002504:CDS 40.0%
GATAGCATTAGAGACAGCAA+GGG + chr2.1:70561066-70561085 MS.gene002504:CDS 40.0%
TCTGTACTTGTGACTCTATG+TGG + chr2.1:70561015-70561034 MS.gene002504:CDS 40.0%
TGATAGCATTAGAGACAGCA+AGG + chr2.1:70561065-70561084 MS.gene002504:CDS 40.0%
! CGATATTTTGCAGCAACTTG+AGG - chr2.1:70561159-70561178 None:intergenic 40.0%
! TATTTTGCAGCAACTTGAGG+TGG - chr2.1:70561156-70561175 None:intergenic 40.0%
AATGCAAGAACAGTGCCTGT+AGG - chr2.1:70560931-70560950 None:intergenic 45.0%
AGCAACTTGAGGTGGAAGTT+TGG - chr2.1:70561148-70561167 None:intergenic 45.0%
CAAAAAACGCCAATTGCCAC+AGG - chr2.1:70561318-70561337 None:intergenic 45.0%
CCAATTCCATGTCTCTCAGT+AGG - chr2.1:70561363-70561382 None:intergenic 45.0%
CCTACTGAGAGACATGGAAT+TGG + chr2.1:70561360-70561379 MS.gene002504:CDS 45.0%
GCATTTCCTACTGAGAGACA+TGG + chr2.1:70561354-70561373 MS.gene002504:CDS 45.0%
TATGGGTTTGCCACCTTCAA+AGG + chr2.1:70561099-70561118 MS.gene002504:CDS 45.0%
TGCCACCTTCAAAGGTTTGT+GGG + chr2.1:70561107-70561126 MS.gene002504:CDS 45.0%
TTGCCACCTTCAAAGGTTTG+TGG + chr2.1:70561106-70561125 MS.gene002504:CDS 45.0%
TTGGCAAACCTTCTACCTAC+AGG + chr2.1:70560913-70560932 MS.gene002504:CDS 45.0%
ATTTCAGAGCACGGCGCATT+TGG + chr2.1:70560894-70560913 MS.gene002504:CDS 50.0%
GAACAGTGCCTGTAGGTAGA+AGG - chr2.1:70560924-70560943 None:intergenic 50.0%
GCATGCGGTGATGTCAATTC+TGG + chr2.1:70561200-70561219 MS.gene002504:CDS 50.0%
! GACCCACAAACCTTTGAAGG+TGG - chr2.1:70561112-70561131 None:intergenic 50.0%
GGTTCCACTTCTGCGGAATG+CGG + chr2.1:70560822-70560841 MS.gene002504:CDS 55.0%
AATCCTCACGGCGTTGCCTG+TGG + chr2.1:70561299-70561318 MS.gene002504:CDS 60.0%
ACCTCCGCATTCCGCAGAAG+TGG - chr2.1:70560829-70560848 None:intergenic 60.0%
ACGGCGTTGCCTGTGGCAAT+TGG + chr2.1:70561306-70561325 MS.gene002504:CDS 60.0%
TCCACTTCTGCGGAATGCGG+AGG + chr2.1:70560825-70560844 MS.gene002504:CDS 60.0%
ACCAGGCTCCTCTCTGCCTC+TGG - chr2.1:70560853-70560872 None:intergenic 65.0%
CGGAGGTTCCAGAGGCAGAG+AGG + chr2.1:70560842-70560861 MS.gene002504:CDS 65.0%
GCGGAATGCGGAGGTTCCAG+AGG + chr2.1:70560834-70560853 MS.gene002504:CDS 65.0%
TCCAGAGGCAGAGAGGAGCC+TGG + chr2.1:70560849-70560868 MS.gene002504:CDS 65.0%
TTGCCACAGGCAACGCCGTG+AGG - chr2.1:70561305-70561324 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 70560769 70561404 70560769 ID=MS.gene002504
chr2.1 mRNA 70560769 70561404 70560769 ID=MS.gene002504.t1;Parent=MS.gene002504
chr2.1 exon 70560769 70561404 70560769 ID=MS.gene002504.t1.exon1;Parent=MS.gene002504.t1
chr2.1 CDS 70560769 70561404 70560769 ID=cds.MS.gene002504.t1;Parent=MS.gene002504.t1
Gene Sequence

>MS.gene002504

ATGGACATCAATTTAGAAATCGATGATGACTCTAGGAATGACGATGAACAAAAGGTTCCACTTCTGCGGAATGCGGAGGTTCCAGAGGCAGAGAGGAGCCTGGTACAGAAAGCTATAAGTTCGACATTTCAGAGCACGGCGCATTTGGCAAACCTTCTACCTACAGGCACTGTTCTTGCATTCCAACTTTTGTCACCAATTTTTACAAATGTTGGCAACTGTGACTCTGTCAGCAAGTCCATGACTTCTGTACTTGTGACTCTATGTGGTGCATCATGCTTCCTGCTAAACTTTACTGATAGCATTAGAGACAGCAAGGGGAATATTTGTTATGGGTTTGCCACCTTCAAAGGTTTGTGGGTCATTGATGGATCAACCAAACTTCCACCTCAAGTTGCTGCAAAATATCGCATACAGTTTATAGATTTCATGCATGCGGTGATGTCAATTCTGGTGTTTGCAGCAATTGCATTGTTTGATCAGAATGTGGTGAATTGCTTTTTTCCAGAACCATCAAAAGAGATACAAGAAATCCTCACGGCGTTGCCTGTGGCAATTGGCGTTTTTTGCAGCATGCTTTTTGTTGCATTTCCTACTGAGAGACATGGAATTGGCTTCCCTCTTTCAACAAGTTAG
Protein sequence

>MS.gene002504.t1

MDINLEIDDDSRNDDEQKVPLLRNAEVPEAERSLVQKAISSTFQSTAHLANLLPTGTVLAFQLLSPIFTNVGNCDSVSKSMTSVLVTLCGASCFLLNFTDSIRDSKGNICYGFATFKGLWVIDGSTKLPPQVAAKYRIQFIDFMHAVMSILVFAAIALFDQNVVNCFFPEPSKEIQEILTALPVAIGVFCSMLFVAFPTERHGIGFPLSTS