AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004174

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004174.t1 MTR_2g014550 97.156 211 5 1 1 211 1 210 3.59e-151 418
MS.gene004174.t1 MTR_2g014520 87.440 207 26 0 5 211 1 207 2.97e-134 375
MS.gene004174.t1 MTR_4g088335 73.604 197 52 0 15 211 10 206 1.49e-109 313
MS.gene004174.t1 MTR_4g078870 55.440 193 80 3 20 209 14 203 5.17e-76 228
MS.gene004174.t1 MTR_5g044580 43.094 181 101 2 26 205 35 214 5.42e-49 159
MS.gene004174.t1 MTR_2g020850 39.474 190 108 2 25 210 2 188 1.17e-46 152
MS.gene004174.t1 MTR_7g010890 41.436 181 104 2 26 205 35 214 5.28e-46 152
MS.gene004174.t1 MTR_4g118470 41.361 191 98 3 24 210 18 198 4.12e-43 144
MS.gene004174.t1 MTR_4g118480 42.045 176 92 2 39 210 27 196 1.15e-40 138
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004174.t1 AT5G46090 61.682 214 75 3 1 209 1 212 1.39e-97 283
MS.gene004174.t1 AT4G18425 59.434 212 82 3 3 210 1 212 3.71e-92 269
MS.gene004174.t1 AT4G28485 52.459 183 86 1 28 209 16 198 8.30e-67 204
MS.gene004174.t1 AT3G02430 47.917 192 94 2 24 211 26 215 5.73e-65 200
MS.gene004174.t1 AT4G24310 50.000 192 89 3 23 209 18 207 5.00e-61 190
MS.gene004174.t1 AT1G09157 38.587 184 101 1 34 205 56 239 1.61e-42 144
MS.gene004174.t1 AT3G21550 43.605 172 91 2 37 207 6 172 5.05e-42 140
MS.gene004174.t1 AT5G39650 38.172 186 99 2 34 205 57 240 6.10e-42 142
MS.gene004174.t1 AT3G21520 40.000 160 89 2 49 206 33 187 5.85e-36 125
MS.gene004174.t1 AT4G28485 56.566 99 43 0 111 209 65 163 1.62e-33 118
MS.gene004174.t1 AT5G27370 35.227 176 99 3 45 205 11 186 2.55e-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
ATTTCAGAGTACGGCGCATT+TGG 0.299298 2.4:+70306045 MS.gene004174:CDS
AGCAAGGGGAATATTTGTTA+TGG 0.356880 2.4:+70306232 MS.gene004174:CDS
AAAGGTTTGTGGGTCATTGA+TGG 0.367892 2.4:+70306268 MS.gene004174:CDS
GCAAGGGGAATATTTGTTAT+GGG 0.374957 2.4:+70306233 MS.gene004174:CDS
ATTAACTAACTTGTTGAAAG+AGG 0.380446 2.4:-70306538 None:intergenic
ACGGCGTTGCCTGTGGCAAT+TGG 0.380489 2.4:+70306457 MS.gene004174:CDS
GGTTCCACTTCTGCGGAATT+CGG 0.390562 2.4:+70305973 MS.gene004174:CDS
CCTACTGAGAGACATGGAAT+TGG 0.411080 2.4:+70306511 MS.gene004174:CDS
ACCAGGCTCCTCTCTGCCTC+TGG 0.411547 2.4:-70306001 None:intergenic
TATGGGTTTGCCACCTTCAA+AGG 0.413754 2.4:+70306250 MS.gene004174:CDS
TGCCACCTTCAAAGGTTTGT+GGG 0.416898 2.4:+70306258 MS.gene004174:CDS
AGCAACTTGAGGTGGAAGTT+TGG 0.423290 2.4:-70306296 None:intergenic
AACTTATAGCTTTCTGTACC+AGG 0.430636 2.4:-70306018 None:intergenic
GCATGCGGTGATGTCAATTC+TGG 0.434994 2.4:+70306351 MS.gene004174:CDS
GAACAGTGCCTGTAGGTAGA+AGG 0.449758 2.4:-70306072 None:intergenic
AATGACCCACAAACCTTTGA+AGG 0.450179 2.4:-70306263 None:intergenic
TTGCCACCTTCAAAGGTTTG+TGG 0.452480 2.4:+70306257 MS.gene004174:CDS
TGCTATCAGTAAAGTTTAGC+AGG 0.458079 2.4:-70306201 None:intergenic
TAGGAATGACGATGAACAAA+AGG 0.495588 2.4:+70305952 MS.gene004174:CDS
TTAACTAACTTGTTGAAAGA+GGG 0.526967 2.4:-70306537 None:intergenic
TTGGCAAACCTTCTACCTAC+AGG 0.528525 2.4:+70306064 MS.gene004174:CDS
AAGTTCGACATTTCAGAGTA+CGG 0.528727 2.4:+70306036 MS.gene004174:CDS
TCTGTACTTGTGACTCTATG+TGG 0.546587 2.4:+70306166 MS.gene004174:CDS
TCCAGAGGCAGAGAGGAGCC+TGG 0.549208 2.4:+70306000 MS.gene004174:CDS
CCAATTCCATGTCTCTCAGT+AGG 0.555703 2.4:-70306511 None:intergenic
TAGAAATCGATGATGACTCT+AGG 0.560367 2.4:+70305933 MS.gene004174:CDS
AGTCACAAGTACAGAAGTCA+TGG 0.564650 2.4:-70306158 None:intergenic
ACCTCCGAATTCCGCAGAAG+TGG 0.566239 2.4:-70305977 None:intergenic
TCCACTTCTGCGGAATTCGG+AGG 0.571752 2.4:+70305976 MS.gene004174:CDS
TGATAGCATTAGAGACAGCA+AGG 0.586072 2.4:+70306216 MS.gene004174:CDS
GTTTATAGATTTCATGCATG+CGG 0.586781 2.4:+70306336 MS.gene004174:CDS
AACAAAAGGTTCCACTTCTG+CGG 0.591604 2.4:+70305966 MS.gene004174:CDS
AATCCTCACGGCGTTGCCTG+TGG 0.613810 2.4:+70306450 MS.gene004174:CDS
TTGCCACAGGCAACGCCGTG+AGG 0.614771 2.4:-70306453 None:intergenic
GCGGAATTCGGAGGTTCCAG+AGG 0.623166 2.4:+70305985 MS.gene004174:CDS
TGCATTGTTTGATCAGAATG+TGG 0.627363 2.4:+70306387 MS.gene004174:CDS
CGGAGGTTCCAGAGGCAGAG+AGG 0.628788 2.4:+70305993 MS.gene004174:CDS
GCATTTCCTACTGAGAGACA+TGG 0.635534 2.4:+70306505 MS.gene004174:CDS
GATAGCATTAGAGACAGCAA+GGG 0.637719 2.4:+70306217 MS.gene004174:CDS
GACCCACAAACCTTTGAAGG+TGG 0.639111 2.4:-70306260 None:intergenic
AATGCAAGAACAGTGCCTGT+AGG 0.674988 2.4:-70306079 None:intergenic
AGAGATACAAGAAATCCTCA+CGG 0.689697 2.4:+70306438 MS.gene004174:CDS
ATAGCATTAGAGACAGCAAG+GGG 0.732552 2.4:+70306218 MS.gene004174:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTGCCAACATTTGTAAAAAT+TGG - chr2.4:70306118-70306137 None:intergenic 25.0%
!! ATTTCTTGTATCTCTTTTGA+TGG - chr2.4:70306433-70306452 None:intergenic 25.0%
!! TAAAAATTGGTGACAAAAGT+TGG - chr2.4:70306105-70306124 None:intergenic 25.0%
!! TCACCAATTTTTACAAATGT+TGG + chr2.4:70306112-70306131 MS.gene004174:CDS 25.0%
GTTTATAGATTTCATGCATG+CGG + chr2.4:70306336-70306355 MS.gene004174:CDS 30.0%
AACTTATAGCTTTCTGTACC+AGG - chr2.4:70306021-70306040 None:intergenic 35.0%
AAGTTCGACATTTCAGAGTA+CGG + chr2.4:70306036-70306055 MS.gene004174:CDS 35.0%
AGAGATACAAGAAATCCTCA+CGG + chr2.4:70306438-70306457 MS.gene004174:CDS 35.0%
TAGAAATCGATGATGACTCT+AGG + chr2.4:70305933-70305952 MS.gene004174:CDS 35.0%
TAGGAATGACGATGAACAAA+AGG + chr2.4:70305952-70305971 MS.gene004174:CDS 35.0%
TGCATTGTTTGATCAGAATG+TGG + chr2.4:70306387-70306406 MS.gene004174:CDS 35.0%
TGCTATCAGTAAAGTTTAGC+AGG - chr2.4:70306204-70306223 None:intergenic 35.0%
! AGCAAGGGGAATATTTGTTA+TGG + chr2.4:70306232-70306251 MS.gene004174:CDS 35.0%
!! GCAAGGGGAATATTTGTTAT+GGG + chr2.4:70306233-70306252 MS.gene004174:CDS 35.0%
!! TGTATCTCTTTTGATGGTTC+TGG - chr2.4:70306427-70306446 None:intergenic 35.0%
AAAGGTTTGTGGGTCATTGA+TGG + chr2.4:70306268-70306287 MS.gene004174:CDS 40.0%
AACAAAAGGTTCCACTTCTG+CGG + chr2.4:70305966-70305985 MS.gene004174:CDS 40.0%
AATGACCCACAAACCTTTGA+AGG - chr2.4:70306266-70306285 None:intergenic 40.0%
AGTCACAAGTACAGAAGTCA+TGG - chr2.4:70306161-70306180 None:intergenic 40.0%
ATAGCATTAGAGACAGCAAG+GGG + chr2.4:70306218-70306237 MS.gene004174:CDS 40.0%
GATAGCATTAGAGACAGCAA+GGG + chr2.4:70306217-70306236 MS.gene004174:CDS 40.0%
TCTGTACTTGTGACTCTATG+TGG + chr2.4:70306166-70306185 MS.gene004174:CDS 40.0%
TGATAGCATTAGAGACAGCA+AGG + chr2.4:70306216-70306235 MS.gene004174:CDS 40.0%
! CGATATTTTGCAGCAACTTG+AGG - chr2.4:70306310-70306329 None:intergenic 40.0%
! TATTTTGCAGCAACTTGAGG+TGG - chr2.4:70306307-70306326 None:intergenic 40.0%
AATGCAAGAACAGTGCCTGT+AGG - chr2.4:70306082-70306101 None:intergenic 45.0%
AGCAACTTGAGGTGGAAGTT+TGG - chr2.4:70306299-70306318 None:intergenic 45.0%
ATTTCAGAGTACGGCGCATT+TGG + chr2.4:70306045-70306064 MS.gene004174:CDS 45.0%
CAAAAAACGCCAATTGCCAC+AGG - chr2.4:70306469-70306488 None:intergenic 45.0%
CCAATTCCATGTCTCTCAGT+AGG - chr2.4:70306514-70306533 None:intergenic 45.0%
CCTACTGAGAGACATGGAAT+TGG + chr2.4:70306511-70306530 MS.gene004174:CDS 45.0%
GCATTTCCTACTGAGAGACA+TGG + chr2.4:70306505-70306524 MS.gene004174:CDS 45.0%
TATGGGTTTGCCACCTTCAA+AGG + chr2.4:70306250-70306269 MS.gene004174:CDS 45.0%
TGCCACCTTCAAAGGTTTGT+GGG + chr2.4:70306258-70306277 MS.gene004174:CDS 45.0%
TTGCCACCTTCAAAGGTTTG+TGG + chr2.4:70306257-70306276 MS.gene004174:CDS 45.0%
TTGGCAAACCTTCTACCTAC+AGG + chr2.4:70306064-70306083 MS.gene004174:CDS 45.0%
GAACAGTGCCTGTAGGTAGA+AGG - chr2.4:70306075-70306094 None:intergenic 50.0%
GCATGCGGTGATGTCAATTC+TGG + chr2.4:70306351-70306370 MS.gene004174:CDS 50.0%
GGTTCCACTTCTGCGGAATT+CGG + chr2.4:70305973-70305992 MS.gene004174:CDS 50.0%
! GACCCACAAACCTTTGAAGG+TGG - chr2.4:70306263-70306282 None:intergenic 50.0%
ACCTCCGAATTCCGCAGAAG+TGG - chr2.4:70305980-70305999 None:intergenic 55.0%
TCCACTTCTGCGGAATTCGG+AGG + chr2.4:70305976-70305995 MS.gene004174:CDS 55.0%
AATCCTCACGGCGTTGCCTG+TGG + chr2.4:70306450-70306469 MS.gene004174:CDS 60.0%
ACGGCGTTGCCTGTGGCAAT+TGG + chr2.4:70306457-70306476 MS.gene004174:CDS 60.0%
GCGGAATTCGGAGGTTCCAG+AGG + chr2.4:70305985-70306004 MS.gene004174:CDS 60.0%
ACCAGGCTCCTCTCTGCCTC+TGG - chr2.4:70306004-70306023 None:intergenic 65.0%
CGGAGGTTCCAGAGGCAGAG+AGG + chr2.4:70305993-70306012 MS.gene004174:CDS 65.0%
TCCAGAGGCAGAGAGGAGCC+TGG + chr2.4:70306000-70306019 MS.gene004174:CDS 65.0%
TTGCCACAGGCAACGCCGTG+AGG - chr2.4:70306456-70306475 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 70305920 70306555 70305920 ID=MS.gene004174
chr2.4 mRNA 70305920 70306555 70305920 ID=MS.gene004174.t1;Parent=MS.gene004174
chr2.4 exon 70305920 70306555 70305920 ID=MS.gene004174.t1.exon1;Parent=MS.gene004174.t1
chr2.4 CDS 70305920 70306555 70305920 ID=cds.MS.gene004174.t1;Parent=MS.gene004174.t1
Gene Sequence

>MS.gene004174

ATGGACATCAATTTAGAAATCGATGATGACTCTAGGAATGACGATGAACAAAAGGTTCCACTTCTGCGGAATTCGGAGGTTCCAGAGGCAGAGAGGAGCCTGGTACAGAAAGCTATAAGTTCGACATTTCAGAGTACGGCGCATTTGGCAAACCTTCTACCTACAGGCACTGTTCTTGCATTCCAACTTTTGTCACCAATTTTTACAAATGTTGGCAACTGTGACTCTGTCAGCAAGTCCATGACTTCTGTACTTGTGACTCTATGTGGTGCATCATGCTTCCTGCTAAACTTTACTGATAGCATTAGAGACAGCAAGGGGAATATTTGTTATGGGTTTGCCACCTTCAAAGGTTTGTGGGTCATTGATGGATCAACCAAACTTCCACCTCAAGTTGCTGCAAAATATCGCATACAGTTTATAGATTTCATGCATGCGGTGATGTCAATTCTGGTGTTTGCAGCAATTGCATTGTTTGATCAGAATGTGGTGAATTGCTTTTTTCCAGAACCATCAAAAGAGATACAAGAAATCCTCACGGCGTTGCCTGTGGCAATTGGCGTTTTTTGCAGCATGCTTTTTGTTGCATTTCCTACTGAGAGACATGGAATTGGCTTCCCTCTTTCAACAAGTTAG
Protein sequence

>MS.gene004174.t1

MDINLEIDDDSRNDDEQKVPLLRNSEVPEAERSLVQKAISSTFQSTAHLANLLPTGTVLAFQLLSPIFTNVGNCDSVSKSMTSVLVTLCGASCFLLNFTDSIRDSKGNICYGFATFKGLWVIDGSTKLPPQVAAKYRIQFIDFMHAVMSILVFAAIALFDQNVVNCFFPEPSKEIQEILTALPVAIGVFCSMLFVAFPTERHGIGFPLSTS