AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene02389

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene02389.t1 MTR_2g023340 84.825 257 23 4 1 254 1 244 3.33e-146 409
MS.gene02389.t1 MTR_7g113680 48.913 184 87 6 66 248 133 310 3.22e-51 169
MS.gene02389.t1 MTR_1g082660 51.205 166 66 6 66 227 82 236 6.89e-49 162
MS.gene02389.t1 MTR_3g099180 51.678 149 56 2 67 215 37 169 6.00e-44 148
MS.gene02389.t1 MTR_3g099180 51.678 149 56 2 67 215 37 169 6.16e-44 148
MS.gene02389.t1 MTR_2g081600 52.747 91 42 1 86 175 23 113 5.37e-24 93.6
MS.gene02389.t1 MTR_2g081630 59.740 77 30 1 86 161 23 99 1.31e-23 92.4
MS.gene02389.t1 MTR_3g012030 44.872 78 43 0 86 163 9 86 3.15e-13 68.2
MS.gene02389.t1 MTR_8g041420 42.308 78 45 0 86 163 9 86 1.26e-12 66.6
MS.gene02389.t1 MTR_5g088760 38.462 78 48 0 86 163 9 86 5.60e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene02389.t1 AT1G54830 53.750 160 68 3 66 221 51 208 2.25e-50 164
MS.gene02389.t1 AT1G54830 53.750 160 68 3 66 221 51 208 2.25e-50 164
MS.gene02389.t1 AT1G54830 53.750 160 68 3 66 221 51 208 2.25e-50 164
MS.gene02389.t1 AT1G08970 52.941 170 63 6 67 234 62 216 5.58e-49 161
MS.gene02389.t1 AT1G08970 52.941 170 63 6 67 234 62 216 5.58e-49 161
MS.gene02389.t1 AT1G08970 52.941 170 63 6 67 234 62 216 5.58e-49 161
MS.gene02389.t1 AT1G08970 52.941 170 63 6 67 234 62 216 5.58e-49 161
MS.gene02389.t1 AT1G56170 60.317 126 49 1 64 189 55 179 1.77e-48 159
MS.gene02389.t1 AT1G56170 60.317 126 49 1 64 189 55 179 1.77e-48 159
MS.gene02389.t1 AT3G48590 53.020 149 61 2 67 215 47 186 3.06e-47 157
MS.gene02389.t1 AT5G63470 57.812 128 51 1 67 191 60 187 4.35e-45 152
MS.gene02389.t1 AT5G63470 57.812 128 51 1 67 191 60 187 4.35e-45 152
MS.gene02389.t1 AT5G50480 48.125 160 66 5 63 220 35 179 2.42e-39 135
MS.gene02389.t1 AT5G27910 42.012 169 77 6 62 228 16 165 1.48e-31 115
MS.gene02389.t1 AT5G50490 46.154 104 53 1 62 165 16 116 4.30e-26 100
MS.gene02389.t1 AT5G50470 40.310 129 68 2 67 189 48 173 1.73e-24 97.4
MS.gene02389.t1 AT5G38140 40.777 103 59 1 60 162 44 144 2.52e-22 91.3

Find 53 sgRNAs with CRISPR-Local

Find 63 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTGCTTAATCTTCTGAATT+TGG 0.149271 2.2:-62321170 None:intergenic
ATTGGGACACTTTCTCTTCT+TGG 0.197098 2.2:-62320948 None:intergenic
AATGGAGCGTGACATATTTA+TGG 0.230451 2.2:+62320920 MS.gene02389:CDS
GGCGAGGCACTGATACTATT+TGG 0.252757 2.2:-62320482 None:intergenic
TGGTCCTCCAAGAATGCTTA+TGG 0.263320 2.2:+62321040 MS.gene02389:CDS
GGCATGTGAAATGTTTATTA+TGG 0.268895 2.2:+62320764 MS.gene02389:CDS
TGTCTTCCCATAAGCATTCT+TGG 0.296015 2.2:-62321047 None:intergenic
GTTGTCGGTGAGAGATTTCT+TGG 0.314048 2.2:-62320563 None:intergenic
TAATAAGGAACATTTCCTAT+TGG 0.359824 2.2:-62320966 None:intergenic
AATAAGGAACATTTCCTATT+GGG 0.360025 2.2:-62320965 None:intergenic
GAATTTGGCAAATCAGTAGA+AGG 0.372595 2.2:-62321155 None:intergenic
ATCTTCTTAATCCTTGCTAA+TGG 0.378288 2.2:-62320681 None:intergenic
GTGCCACCTCAGTATGTTGC+AGG 0.380885 2.2:+62321008 MS.gene02389:CDS
ACAGACATAGGCAGATAATA+AGG 0.391390 2.2:-62320981 None:intergenic
GGAAACATTTGATTTGCAAA+AGG 0.397276 2.2:-62321110 None:intergenic
CCCGTTGTAAGGAGGTTGAT+TGG 0.412220 2.2:-62321075 None:intergenic
GAAACATTTGATTTGCAAAA+GGG 0.424540 2.2:-62321109 None:intergenic
ACTGTTGATTTCAAAAGTAA+TGG 0.437192 2.2:+62320654 MS.gene02389:CDS
ATGGAGCGTGACATATTTAT+GGG 0.438860 2.2:+62320921 MS.gene02389:CDS
TCTACTCAGGTATGATGAAA+AGG 0.465576 2.2:-62320532 None:intergenic
GGTCCTCCAAGAATGCTTAT+GGG 0.469493 2.2:+62321041 MS.gene02389:CDS
CCGTTGTAAGGAGGTTGATT+GGG 0.477387 2.2:-62321074 None:intergenic
CCAATCAACCTCCTTACAAC+GGG 0.477395 2.2:+62321075 MS.gene02389:CDS
CATGCCTTAGCAAACAGAAT+AGG 0.486382 2.2:-62320747 None:intergenic
CCTAGTTGATATTGTCCCTA+GGG 0.487741 2.2:+62320890 MS.gene02389:CDS
AGAAGAGAAAGTGTCCCAAT+AGG 0.489439 2.2:+62320951 MS.gene02389:CDS
TGGAGCTAGCAACAAGGTCA+TGG 0.501489 2.2:+62320784 MS.gene02389:CDS
CCCTAGGGACAATATCAACT+AGG 0.511793 2.2:-62320890 None:intergenic
TGTGATGGATGCCCGTTGTA+AGG 0.514096 2.2:-62321086 None:intergenic
TATGTTGCAGGTCCATCATA+TGG 0.515120 2.2:+62321020 MS.gene02389:CDS
CTTGGAGTTGAACTCTACTC+AGG 0.515545 2.2:-62320545 None:intergenic
GGCACCTATTCTGTTTGCTA+AGG 0.530640 2.2:+62320743 MS.gene02389:CDS
AAGATCATGAAAGCTGATGA+AGG 0.545148 2.2:+62320699 MS.gene02389:CDS
TGATTTGCAAAAGGGTGTGA+TGG 0.553637 2.2:-62321101 None:intergenic
GCACTTGCAGTGTGAAACAA+AGG 0.556863 2.2:-62320504 None:intergenic
TCCTAGTTGATATTGTCCCT+AGG 0.558927 2.2:+62320889 MS.gene02389:CDS
CTTCCCATAAGCATTCTTGG+AGG 0.580142 2.2:-62321044 None:intergenic
GGAGCTAGCAACAAGGTCAT+GGG 0.582315 2.2:+62320785 MS.gene02389:CDS
CACTTGCAGTGTGAAACAAA+GGG 0.597437 2.2:-62320503 None:intergenic
GTAATGGCTTGCCATTAGCA+AGG 0.597965 2.2:+62320670 MS.gene02389:CDS
CCCAATCAACCTCCTTACAA+CGG 0.599569 2.2:+62321074 MS.gene02389:CDS
ATTCTTGGAGGACCATATGA+TGG 0.609961 2.2:-62321032 None:intergenic
GGTGGCACATGAACAGACAT+AGG 0.629233 2.2:-62320993 None:intergenic
AAAAGACACAAGAGGAACGA+AGG 0.630879 2.2:+62320430 MS.gene02389:CDS
AAGGTCATGGGCTAATACAG+AGG 0.637560 2.2:+62320797 MS.gene02389:CDS
GCAGTGTGAAACAAAGGGCG+AGG 0.647228 2.2:-62320498 None:intergenic
TATGGATCAAAAGACACAAG+AGG 0.647854 2.2:+62320422 None:intergenic
AATTTGGCAAATCAGTAGAA+GGG 0.648246 2.2:-62321154 None:intergenic
GATGGATGCCCGTTGTAAGG+AGG 0.657482 2.2:-62321083 None:intergenic
AGTGAGTATGATATCAGCTG+AGG 0.690629 2.2:+62320722 MS.gene02389:CDS
TTATTATGGAGCTAGCAACA+AGG 0.697305 2.2:+62320778 MS.gene02389:CDS
GGACCTGCAACATACTGAGG+TGG 0.712994 2.2:-62321011 None:intergenic
GATGGACCTGCAACATACTG+AGG 0.735823 2.2:-62321014 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATAAGGAACATTTCCTATT+GGG - chr2.2:62320968-62320987 None:intergenic 25.0%
! TAATAAGGAACATTTCCTAT+TGG - chr2.2:62320969-62320988 None:intergenic 25.0%
!!! ACTGTTGATTTCAAAAGTAA+TGG + chr2.2:62320654-62320673 MS.gene02389:CDS 25.0%
!!! ATTCTTGTTGTTTTTGTTGT+CGG - chr2.2:62320581-62320600 None:intergenic 25.0%
!!! GAAACATTTGATTTGCAAAA+GGG - chr2.2:62321112-62321131 None:intergenic 25.0%
AATTTGGCAAATCAGTAGAA+GGG - chr2.2:62321157-62321176 None:intergenic 30.0%
ATCTTCTTAATCCTTGCTAA+TGG - chr2.2:62320684-62320703 None:intergenic 30.0%
CAAGAATTGCAGAAAAAACT+TGG + chr2.2:62320594-62320613 MS.gene02389:CDS 30.0%
GGCATGTGAAATGTTTATTA+TGG + chr2.2:62320764-62320783 MS.gene02389:CDS 30.0%
!! GGAAACATTTGATTTGCAAA+AGG - chr2.2:62321113-62321132 None:intergenic 30.0%
!! TGGTTTGATTGATTTTGTGT+TGG - chr2.2:62320465-62320484 None:intergenic 30.0%
AAGATCATGAAAGCTGATGA+AGG + chr2.2:62320699-62320718 MS.gene02389:CDS 35.0%
AATGGAGCGTGACATATTTA+TGG + chr2.2:62320920-62320939 MS.gene02389:CDS 35.0%
ACAGACATAGGCAGATAATA+AGG - chr2.2:62320984-62321003 None:intergenic 35.0%
ATGGAGCGTGACATATTTAT+GGG + chr2.2:62320921-62320940 MS.gene02389:CDS 35.0%
GAATTTGGCAAATCAGTAGA+AGG - chr2.2:62321158-62321177 None:intergenic 35.0%
TCTACTCAGGTATGATGAAA+AGG - chr2.2:62320535-62320554 None:intergenic 35.0%
TTATTATGGAGCTAGCAACA+AGG + chr2.2:62320778-62320797 MS.gene02389:CDS 35.0%
!! AAGGGTCGTTTTCTTTCTTT+GGG - chr2.2:62321139-62321158 None:intergenic 35.0%
!!! TCGTTTTCTTTCTTTGGGAT+TGG - chr2.2:62321134-62321153 None:intergenic 35.0%
!!! TTCATTTTGTTTTGCCCAGA+AGG - chr2.2:62320622-62320641 None:intergenic 35.0%
AAAAGACACAAGAGGAACGA+AGG + chr2.2:62320430-62320449 MS.gene02389:CDS 40.0%
AGAAAAAACTTGGCACCTTC+TGG + chr2.2:62320604-62320623 MS.gene02389:CDS 40.0%
AGTGAGTATGATATCAGCTG+AGG + chr2.2:62320722-62320741 MS.gene02389:CDS 40.0%
ATTCTTGGAGGACCATATGA+TGG - chr2.2:62321035-62321054 None:intergenic 40.0%
ATTGGGACACTTTCTCTTCT+TGG - chr2.2:62320951-62320970 None:intergenic 40.0%
CACTTGCAGTGTGAAACAAA+GGG - chr2.2:62320506-62320525 None:intergenic 40.0%
CATGCCTTAGCAAACAGAAT+AGG - chr2.2:62320750-62320769 None:intergenic 40.0%
GAAAAAACTTGGCACCTTCT+GGG + chr2.2:62320605-62320624 MS.gene02389:CDS 40.0%
TATGTTGCAGGTCCATCATA+TGG + chr2.2:62321020-62321039 MS.gene02389:CDS 40.0%
TGTCCCTAGGGAAAAAACAA+TGG + chr2.2:62320902-62320921 MS.gene02389:CDS 40.0%
TGTCTTCCCATAAGCATTCT+TGG - chr2.2:62321050-62321069 None:intergenic 40.0%
! CCTAGTTGATATTGTCCCTA+GGG + chr2.2:62320890-62320909 MS.gene02389:CDS 40.0%
! TCCTAGTTGATATTGTCCCT+AGG + chr2.2:62320889-62320908 MS.gene02389:CDS 40.0%
! TGATTTGCAAAAGGGTGTGA+TGG - chr2.2:62321104-62321123 None:intergenic 40.0%
!! AGAAGAGAAAGTGTCCCAAT+AGG + chr2.2:62320951-62320970 MS.gene02389:CDS 40.0%
!! GAAGGGTCGTTTTCTTTCTT+TGG - chr2.2:62321140-62321159 None:intergenic 40.0%
!!! GCTCCATTGTTTTTTCCCTA+GGG - chr2.2:62320908-62320927 None:intergenic 40.0%
CCAATCAACCTCCTTACAAC+GGG + chr2.2:62321075-62321094 MS.gene02389:CDS 45.0%
CCCAATCAACCTCCTTACAA+CGG + chr2.2:62321074-62321093 MS.gene02389:CDS 45.0%
CCCTAGGGACAATATCAACT+AGG - chr2.2:62320893-62320912 None:intergenic 45.0%
CTTCCCATAAGCATTCTTGG+AGG - chr2.2:62321047-62321066 None:intergenic 45.0%
CTTGGAGTTGAACTCTACTC+AGG - chr2.2:62320548-62320567 None:intergenic 45.0%
GCACTTGCAGTGTGAAACAA+AGG - chr2.2:62320507-62320526 None:intergenic 45.0%
GGTCCTCCAAGAATGCTTAT+GGG + chr2.2:62321041-62321060 MS.gene02389:CDS 45.0%
GTTGTCGGTGAGAGATTTCT+TGG - chr2.2:62320566-62320585 None:intergenic 45.0%
TGGTCCTCCAAGAATGCTTA+TGG + chr2.2:62321040-62321059 MS.gene02389:CDS 45.0%
! AAGGTCATGGGCTAATACAG+AGG + chr2.2:62320797-62320816 MS.gene02389:CDS 45.0%
! CCGTTGTAAGGAGGTTGATT+GGG - chr2.2:62321077-62321096 None:intergenic 45.0%
! GGCACCTATTCTGTTTGCTA+AGG + chr2.2:62320743-62320762 MS.gene02389:CDS 45.0%
! GTAATGGCTTGCCATTAGCA+AGG + chr2.2:62320670-62320689 MS.gene02389:CDS 45.0%
!!! CGCTCCATTGTTTTTTCCCT+AGG - chr2.2:62320909-62320928 None:intergenic 45.0%
GATGGACCTGCAACATACTG+AGG - chr2.2:62321017-62321036 None:intergenic 50.0%
GGAGCTAGCAACAAGGTCAT+GGG + chr2.2:62320785-62320804 MS.gene02389:CDS 50.0%
GGTGGCACATGAACAGACAT+AGG - chr2.2:62320996-62321015 None:intergenic 50.0%
TGGAGCTAGCAACAAGGTCA+TGG + chr2.2:62320784-62320803 MS.gene02389:CDS 50.0%
! CCCGTTGTAAGGAGGTTGAT+TGG - chr2.2:62321078-62321097 None:intergenic 50.0%
!! GGCGAGGCACTGATACTATT+TGG - chr2.2:62320485-62320504 None:intergenic 50.0%
!! TGTGATGGATGCCCGTTGTA+AGG - chr2.2:62321089-62321108 None:intergenic 50.0%
GATGGATGCCCGTTGTAAGG+AGG - chr2.2:62321086-62321105 None:intergenic 55.0%
GCAGTGTGAAACAAAGGGCG+AGG - chr2.2:62320501-62320520 None:intergenic 55.0%
GGACCTGCAACATACTGAGG+TGG - chr2.2:62321014-62321033 None:intergenic 55.0%
GTGCCACCTCAGTATGTTGC+AGG + chr2.2:62321008-62321027 MS.gene02389:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 62320423 62321187 62320423 ID=MS.gene02389
chr2.2 mRNA 62320423 62321187 62320423 ID=MS.gene02389.t1;Parent=MS.gene02389
chr2.2 exon 62320423 62321187 62320423 ID=MS.gene02389.t1.exon1;Parent=MS.gene02389.t1
chr2.2 CDS 62320423 62321187 62320423 ID=cds.MS.gene02389.t1;Parent=MS.gene02389.t1
Gene Sequence

>MS.gene02389

ATGGATCAAAAGACACAAGAGGAACGAAGGAATGATACACCAACACAAAATCAATCAAACCAAATAGTATCAGTGCCTCGCCCTTTGTTTCACACTGCAAGTGCTTCTGCCTTTTCATCATACCTGAGTAGAGTTCAACTCCAAGAAATCTCTCACCGACAACAAAAACAACAAGAATTGCAGAAAAAACTTGGCACCTTCTGGGCAAAACAAAATGAAGAAGTTCAGAAGACTGTTGATTTCAAAAGTAATGGCTTGCCATTAGCAAGGATTAAGAAGATCATGAAAGCTGATGAAGGAGTGAGTATGATATCAGCTGAGGCACCTATTCTGTTTGCTAAGGCATGTGAAATGTTTATTATGGAGCTAGCAACAAGGTCATGGGCTAATACAGAGGTGAACAAAAGAAAGACACTTCAAAAGAGTGACATTGCATCTGCTGTCTCAAGTAATGAAGTGTTTGATTTCCTAGTTGATATTGTCCCTAGGGAAAAAACAATGGAGCGTGACATATTTATGGGTATGCCAAGAAGAGAAAGTGTCCCAATAGGAAATGTTCCTTATTATCTGCCTATGTCTGTTCATGTGCCACCTCAGTATGTTGCAGGTCCATCATATGGTCCTCCAAGAATGCTTATGGGAAGACATCTTCCCAATCAACCTCCTTACAACGGGCATCCATCACACCCTTTTGCAAATCAAATGTTTCCAATCCCAAAGAAAGAAAACGACCCTTCTACTGATTTGCCAAATTCAGAAGATTAA
Protein sequence

>MS.gene02389.t1

MDQKTQEERRNDTPTQNQSNQIVSVPRPLFHTASASAFSSYLSRVQLQEISHRQQKQQELQKKLGTFWAKQNEEVQKTVDFKSNGLPLARIKKIMKADEGVSMISAEAPILFAKACEMFIMELATRSWANTEVNKRKTLQKSDIASAVSSNEVFDFLVDIVPREKTMERDIFMGMPRRESVPIGNVPYYLPMSVHVPPQYVAGPSYGPPRMLMGRHLPNQPPYNGHPSHPFANQMFPIPKKENDPSTDLPNSED