AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene01477

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01477.t1 MTR_2g014550 97.630 211 4 1 1 211 1 210 1.00e-151 419
MS.gene01477.t1 MTR_2g014520 87.923 207 25 0 5 211 1 207 8.15e-135 376
MS.gene01477.t1 MTR_4g088335 73.604 197 52 0 15 211 10 206 1.24e-109 313
MS.gene01477.t1 MTR_4g078870 54.922 193 81 3 20 209 14 203 1.44e-75 226
MS.gene01477.t1 MTR_5g044580 43.094 181 101 2 26 205 35 214 5.19e-49 159
MS.gene01477.t1 MTR_2g020850 38.947 190 109 2 25 210 2 188 2.56e-46 152
MS.gene01477.t1 MTR_7g010890 41.436 181 104 2 26 205 35 214 4.74e-46 152
MS.gene01477.t1 MTR_4g118470 41.361 191 98 3 24 210 18 198 5.82e-43 144
MS.gene01477.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.gene01477.t1 AT5G46090 61.682 214 75 3 1 209 1 212 2.01e-97 282
MS.gene01477.t1 AT4G18425 59.434 212 82 3 3 210 1 212 4.42e-92 269
MS.gene01477.t1 AT4G28485 50.254 197 96 2 15 209 2 198 7.52e-67 204
MS.gene01477.t1 AT3G02430 47.396 192 95 2 24 211 26 215 1.88e-64 199
MS.gene01477.t1 AT4G24310 50.000 192 89 3 23 209 18 207 5.76e-61 190
MS.gene01477.t1 AT1G09157 38.587 184 101 1 34 205 56 239 1.70e-42 143
MS.gene01477.t1 AT3G21550 43.605 172 91 2 37 207 6 172 5.16e-42 140
MS.gene01477.t1 AT5G39650 38.172 186 99 2 34 205 57 240 6.10e-42 142
MS.gene01477.t1 AT3G21520 40.000 160 89 2 49 206 33 187 5.67e-36 125
MS.gene01477.t1 AT4G28485 56.566 99 43 0 111 209 65 163 1.55e-33 118
MS.gene01477.t1 AT5G27370 35.227 176 99 3 45 205 11 186 2.58e-30 110

Find 42 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTAATTAACTTGTTGAAAG+AGG 0.329827 2.2:-68390237 None:intergenic
ATTTCAGAGCACGGCGCATT+TGG 0.350269 2.2:+68389744 MS.gene01477:CDS
AGCAAGGGGAATATTTGTTA+TGG 0.356880 2.2:+68389931 MS.gene01477:CDS
AAAGGTTTGTGGGTCATTGA+TGG 0.367892 2.2:+68389967 MS.gene01477:CDS
GCAAGGGGAATATTTGTTAT+GGG 0.374957 2.2:+68389932 MS.gene01477:CDS
ACGGCGTTGCCTGTGGCAAT+TGG 0.380489 2.2:+68390156 MS.gene01477:CDS
CCTACTGAGAGACATGGAAT+TGG 0.411080 2.2:+68390210 MS.gene01477:CDS
ACCAGGCTCCTCTCTGCCTC+TGG 0.411547 2.2:-68389700 None:intergenic
TATGGGTTTGCCACCTTCAA+AGG 0.413754 2.2:+68389949 MS.gene01477:CDS
TGCCACCTTCAAAGGTTTGT+GGG 0.416898 2.2:+68389957 MS.gene01477:CDS
AGCAACTTGAGGTGGAAGTT+TGG 0.423290 2.2:-68389995 None:intergenic
AACTTATAGCTTTCTGTACC+AGG 0.430636 2.2:-68389717 None:intergenic
GAACAGTGCCTGTAGGTAGA+AGG 0.449758 2.2:-68389771 None:intergenic
AATGACCCACAAACCTTTGA+AGG 0.450179 2.2:-68389962 None:intergenic
TTGCCACCTTCAAAGGTTTG+TGG 0.452480 2.2:+68389956 MS.gene01477:CDS
TGCTATCAGTAAAGTTTAGC+AGG 0.458079 2.2:-68389900 None:intergenic
TTAATTAACTTGTTGAAAGA+GGG 0.489952 2.2:-68390236 None:intergenic
TAGGAATGACGATGAACAAA+AGG 0.495588 2.2:+68389651 MS.gene01477:CDS
TTGGCAAACCTTCTACCTAC+AGG 0.528525 2.2:+68389763 MS.gene01477:CDS
TCTGTACTTGTGACTCTATG+TGG 0.546587 2.2:+68389865 MS.gene01477:CDS
TCCAGAGGCAGAGAGGAGCC+TGG 0.549208 2.2:+68389699 MS.gene01477:CDS
CCAATTCCATGTCTCTCAGT+AGG 0.555703 2.2:-68390210 None:intergenic
TAGAAATCGATGATGACTCT+AGG 0.560367 2.2:+68389632 MS.gene01477:CDS
AGTCACAAGTACAGAAGTCA+TGG 0.564650 2.2:-68389857 None:intergenic
TCCACTTCTGCGGAATGCGG+AGG 0.572373 2.2:+68389675 MS.gene01477:CDS
ACCTCCGCATTCCGCAGAAG+TGG 0.578568 2.2:-68389676 None:intergenic
TGATAGCATTAGAGACAGCA+AGG 0.586072 2.2:+68389915 MS.gene01477:CDS
GTTTATAGATTTCATGCATG+CGG 0.586781 2.2:+68390035 MS.gene01477:CDS
AACAAAAGGTTCCACTTCTG+CGG 0.591604 2.2:+68389665 MS.gene01477:CDS
AAGTTCGACATTTCAGAGCA+CGG 0.595642 2.2:+68389735 MS.gene01477:CDS
AATCCTCACGGCGTTGCCTG+TGG 0.613810 2.2:+68390149 MS.gene01477:CDS
TTGCCACAGGCAACGCCGTG+AGG 0.614771 2.2:-68390152 None:intergenic
GCGGAATGCGGAGGTTCCAG+AGG 0.622187 2.2:+68389684 MS.gene01477:CDS
TGCATTGTTTGATCAGAATG+TGG 0.627363 2.2:+68390086 MS.gene01477:CDS
GGTTCCACTTCTGCGGAATG+CGG 0.628493 2.2:+68389672 MS.gene01477:CDS
CGGAGGTTCCAGAGGCAGAG+AGG 0.628788 2.2:+68389692 MS.gene01477:CDS
GCATTTCCTACTGAGAGACA+TGG 0.635534 2.2:+68390204 MS.gene01477:CDS
GATAGCATTAGAGACAGCAA+GGG 0.637719 2.2:+68389916 MS.gene01477:CDS
GACCCACAAACCTTTGAAGG+TGG 0.639111 2.2:-68389959 None:intergenic
AATGCAAGAACAGTGCCTGT+AGG 0.674988 2.2:-68389778 None:intergenic
AGAGATACAAGAAATCCTCA+CGG 0.689697 2.2:+68390137 MS.gene01477:CDS
ATAGCATTAGAGACAGCAAG+GGG 0.732552 2.2:+68389917 MS.gene01477:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTGCCAACATTTGTAAAAAT+TGG - chr2.2:68389817-68389836 None:intergenic 25.0%
!! ATTTCTTGTATCTCTTTTGA+TGG - chr2.2:68390132-68390151 None:intergenic 25.0%
!! TAAAAATTGGTGACAAAAGT+TGG - chr2.2:68389804-68389823 None:intergenic 25.0%
!! TCACCAATTTTTACAAATGT+TGG + chr2.2:68389811-68389830 MS.gene01477:CDS 25.0%
GTTTATAGATTTCATGCATG+CGG + chr2.2:68390035-68390054 MS.gene01477:CDS 30.0%
AACTTATAGCTTTCTGTACC+AGG - chr2.2:68389720-68389739 None:intergenic 35.0%
AGAGATACAAGAAATCCTCA+CGG + chr2.2:68390137-68390156 MS.gene01477:CDS 35.0%
TAGAAATCGATGATGACTCT+AGG + chr2.2:68389632-68389651 MS.gene01477:CDS 35.0%
TAGGAATGACGATGAACAAA+AGG + chr2.2:68389651-68389670 MS.gene01477:CDS 35.0%
TGCATTGTTTGATCAGAATG+TGG + chr2.2:68390086-68390105 MS.gene01477:CDS 35.0%
TGCTATCAGTAAAGTTTAGC+AGG - chr2.2:68389903-68389922 None:intergenic 35.0%
! AGCAAGGGGAATATTTGTTA+TGG + chr2.2:68389931-68389950 MS.gene01477:CDS 35.0%
!! GCAAGGGGAATATTTGTTAT+GGG + chr2.2:68389932-68389951 MS.gene01477:CDS 35.0%
!! TGTATCTCTTTTGATGGTTC+TGG - chr2.2:68390126-68390145 None:intergenic 35.0%
AAAGGTTTGTGGGTCATTGA+TGG + chr2.2:68389967-68389986 MS.gene01477:CDS 40.0%
AACAAAAGGTTCCACTTCTG+CGG + chr2.2:68389665-68389684 MS.gene01477:CDS 40.0%
AAGTTCGACATTTCAGAGCA+CGG + chr2.2:68389735-68389754 MS.gene01477:CDS 40.0%
AATGACCCACAAACCTTTGA+AGG - chr2.2:68389965-68389984 None:intergenic 40.0%
AGTCACAAGTACAGAAGTCA+TGG - chr2.2:68389860-68389879 None:intergenic 40.0%
ATAGCATTAGAGACAGCAAG+GGG + chr2.2:68389917-68389936 MS.gene01477:CDS 40.0%
GATAGCATTAGAGACAGCAA+GGG + chr2.2:68389916-68389935 MS.gene01477:CDS 40.0%
TCTGTACTTGTGACTCTATG+TGG + chr2.2:68389865-68389884 MS.gene01477:CDS 40.0%
TGATAGCATTAGAGACAGCA+AGG + chr2.2:68389915-68389934 MS.gene01477:CDS 40.0%
! CGATATTTTGCAGCAACTTG+AGG - chr2.2:68390009-68390028 None:intergenic 40.0%
! TATTTTGCAGCAACTTGAGG+TGG - chr2.2:68390006-68390025 None:intergenic 40.0%
AATGCAAGAACAGTGCCTGT+AGG - chr2.2:68389781-68389800 None:intergenic 45.0%
AGCAACTTGAGGTGGAAGTT+TGG - chr2.2:68389998-68390017 None:intergenic 45.0%
CAAAAAACGCCAATTGCCAC+AGG - chr2.2:68390168-68390187 None:intergenic 45.0%
CCAATTCCATGTCTCTCAGT+AGG - chr2.2:68390213-68390232 None:intergenic 45.0%
CCTACTGAGAGACATGGAAT+TGG + chr2.2:68390210-68390229 MS.gene01477:CDS 45.0%
GCATTTCCTACTGAGAGACA+TGG + chr2.2:68390204-68390223 MS.gene01477:CDS 45.0%
TATGGGTTTGCCACCTTCAA+AGG + chr2.2:68389949-68389968 MS.gene01477:CDS 45.0%
TGCCACCTTCAAAGGTTTGT+GGG + chr2.2:68389957-68389976 MS.gene01477:CDS 45.0%
TTGCCACCTTCAAAGGTTTG+TGG + chr2.2:68389956-68389975 MS.gene01477:CDS 45.0%
TTGGCAAACCTTCTACCTAC+AGG + chr2.2:68389763-68389782 MS.gene01477:CDS 45.0%
ATTTCAGAGCACGGCGCATT+TGG + chr2.2:68389744-68389763 MS.gene01477:CDS 50.0%
GAACAGTGCCTGTAGGTAGA+AGG - chr2.2:68389774-68389793 None:intergenic 50.0%
! GACCCACAAACCTTTGAAGG+TGG - chr2.2:68389962-68389981 None:intergenic 50.0%
GGTTCCACTTCTGCGGAATG+CGG + chr2.2:68389672-68389691 MS.gene01477:CDS 55.0%
AATCCTCACGGCGTTGCCTG+TGG + chr2.2:68390149-68390168 MS.gene01477:CDS 60.0%
ACCTCCGCATTCCGCAGAAG+TGG - chr2.2:68389679-68389698 None:intergenic 60.0%
ACGGCGTTGCCTGTGGCAAT+TGG + chr2.2:68390156-68390175 MS.gene01477:CDS 60.0%
TCCACTTCTGCGGAATGCGG+AGG + chr2.2:68389675-68389694 MS.gene01477:CDS 60.0%
ACCAGGCTCCTCTCTGCCTC+TGG - chr2.2:68389703-68389722 None:intergenic 65.0%
CGGAGGTTCCAGAGGCAGAG+AGG + chr2.2:68389692-68389711 MS.gene01477:CDS 65.0%
GCGGAATGCGGAGGTTCCAG+AGG + chr2.2:68389684-68389703 MS.gene01477:CDS 65.0%
TCCAGAGGCAGAGAGGAGCC+TGG + chr2.2:68389699-68389718 MS.gene01477:CDS 65.0%
TTGCCACAGGCAACGCCGTG+AGG - chr2.2:68390155-68390174 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 68389619 68390254 68389619 ID=MS.gene01477
chr2.2 mRNA 68389619 68390254 68389619 ID=MS.gene01477.t1;Parent=MS.gene01477
chr2.2 exon 68389619 68390254 68389619 ID=MS.gene01477.t1.exon1;Parent=MS.gene01477.t1
chr2.2 CDS 68389619 68390254 68389619 ID=cds.MS.gene01477.t1;Parent=MS.gene01477.t1
Gene Sequence

>MS.gene01477

ATGGACATCAATTTAGAAATCGATGATGACTCTAGGAATGACGATGAACAAAAGGTTCCACTTCTGCGGAATGCGGAGGTTCCAGAGGCAGAGAGGAGCCTGGTACAGAAAGCTATAAGTTCGACATTTCAGAGCACGGCGCATTTGGCAAACCTTCTACCTACAGGCACTGTTCTTGCATTCCAACTTTTGTCACCAATTTTTACAAATGTTGGCAACTGTGACTCTGTCAGCAAGTCCATGACTTCTGTACTTGTGACTCTATGTGGTGCATCATGCTTCCTGCTAAACTTTACTGATAGCATTAGAGACAGCAAGGGGAATATTTGTTATGGGTTTGCCACCTTCAAAGGTTTGTGGGTCATTGATGGATCAACCAAACTTCCACCTCAAGTTGCTGCAAAATATCGCATACAGTTTATAGATTTCATGCATGCGGTGATGTCAATTCTTGTGTTTGCAGCAATTGCATTGTTTGATCAGAATGTGGTGAATTGCTTTTTTCCAGAACCATCAAAAGAGATACAAGAAATCCTCACGGCGTTGCCTGTGGCAATTGGCGTTTTTTGCAGCATGCTTTTTGTTGCATTTCCTACTGAGAGACATGGAATTGGCTTCCCTCTTTCAACAAGTTAA
Protein sequence

>MS.gene01477.t1

MDINLEIDDDSRNDDEQKVPLLRNAEVPEAERSLVQKAISSTFQSTAHLANLLPTGTVLAFQLLSPIFTNVGNCDSVSKSMTSVLVTLCGASCFLLNFTDSIRDSKGNICYGFATFKGLWVIDGSTKLPPQVAAKYRIQFIDFMHAVMSILVFAAIALFDQNVVNCFFPEPSKEIQEILTALPVAIGVFCSMLFVAFPTERHGIGFPLSTS