AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene02810

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene02810.t1 MTR_2g014550 94.231 208 11 1 23 230 4 210 4.45e-144 401
MS.gene02810.t1 MTR_2g014520 84.541 207 32 0 24 230 1 207 2.22e-130 366
MS.gene02810.t1 MTR_4g088335 69.543 197 60 0 34 230 10 206 1.39e-104 301
MS.gene02810.t1 MTR_4g078870 52.356 191 89 2 39 228 14 203 1.80e-72 219
MS.gene02810.t1 MTR_5g044580 41.848 184 102 3 45 224 32 214 3.51e-46 153
MS.gene02810.t1 MTR_2g020850 41.420 169 96 1 61 229 23 188 7.26e-46 151
MS.gene02810.t1 MTR_7g010890 40.000 185 106 3 44 224 31 214 2.32e-43 145
MS.gene02810.t1 MTR_4g118470 40.314 191 100 3 43 229 18 198 2.05e-41 140
MS.gene02810.t1 MTR_4g118480 38.537 205 112 3 29 229 2 196 9.47e-40 136
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene02810.t1 AT5G46090 60.190 211 79 2 23 228 2 212 9.56e-96 279
MS.gene02810.t1 AT4G18425 57.820 211 85 3 23 229 2 212 7.18e-90 264
MS.gene02810.t1 AT4G28485 48.731 197 99 2 34 228 2 198 1.02e-63 197
MS.gene02810.t1 AT3G02430 44.340 212 94 3 41 230 6 215 2.60e-62 194
MS.gene02810.t1 AT4G24310 48.438 192 92 3 42 228 18 207 6.67e-59 185
MS.gene02810.t1 AT3G21550 43.605 172 91 2 56 226 6 172 4.41e-43 144
MS.gene02810.t1 AT1G09157 36.957 184 104 1 53 224 56 239 5.20e-40 138
MS.gene02810.t1 AT5G39650 36.559 186 102 2 53 224 57 240 6.65e-39 135
MS.gene02810.t1 AT3G21520 40.000 160 89 2 68 225 33 187 5.06e-37 129
MS.gene02810.t1 AT4G28485 54.545 99 45 0 130 228 65 163 1.41e-31 114
MS.gene02810.t1 AT5G27370 36.932 176 96 4 64 224 11 186 1.93e-30 111

Find 51 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCAGGCTCCTCTCAGCTTC+TGG 0.270180 2.3:+60795906 None:intergenic
AGCAAGGGGAATATTTGTTA+TGG 0.356880 2.3:-60795675 MS.gene02810:CDS
GCAAGGGGAATATTTGTTAT+GGG 0.374957 2.3:-60795674 MS.gene02810:CDS
AAGGGCATGTGGGTTATTGA+TGG 0.393194 2.3:-60795639 MS.gene02810:CDS
ATTTCAGAGCACCGGACATT+TGG 0.394083 2.3:-60795862 MS.gene02810:CDS
TTATGGGTTTGCCACCTTCA+AGG 0.406503 2.3:-60795658 MS.gene02810:CDS
TGCAACTTGAGGTGGAAGTT+TGG 0.409649 2.3:+60795611 None:intergenic
CAATTATTAACTTGTTGAAA+GGG 0.415154 2.3:+60795368 None:intergenic
ATGGCGATGCCTGTGGCAAT+TGG 0.419997 2.3:-60795450 MS.gene02810:CDS
TATGGGTTTGCCACCTTCAA+GGG 0.422703 2.3:-60795657 MS.gene02810:CDS
CCTACTGAGAGACATGGAAT+AGG 0.427667 2.3:-60795396 MS.gene02810:CDS
AACTTATAGCTTTCTGTACC+AGG 0.430636 2.3:+60795889 None:intergenic
GCATGCGGTGATGTCAATTC+TGG 0.434994 2.3:-60795556 MS.gene02810:CDS
AGAACCATCAAAAGAGATAC+AGG 0.448641 2.3:-60795481 MS.gene02810:CDS
GAACAGTGCCTGTAGGTAGA+AGG 0.449758 2.3:+60795835 None:intergenic
TCAATTATTAACTTGTTGAA+AGG 0.463534 2.3:+60795367 None:intergenic
AGATAAGATAAACTGAATCA+TGG 0.464629 2.3:+60796319 None:intergenic
TGCTATCAGTAAAGTTTAGC+AGG 0.467137 2.3:+60795706 None:intergenic
TTGCCACCTTCAAGGGCATG+TGG 0.474826 2.3:-60795650 MS.gene02810:CDS
TAAGAATAACGATGAACAAA+AGG 0.479910 2.3:-60795955 MS.gene02810:CDS
AATAACCCACATGCCCTTGA+AGG 0.501829 2.3:+60795644 None:intergenic
TAGAAGGTTTGCCAAATGTC+CGG 0.511649 2.3:+60795851 None:intergenic
TTGGCAAACCTTCTACCTAC+AGG 0.528525 2.3:-60795843 MS.gene02810:CDS
GATAAGATAAACTGAATCAT+GGG 0.529876 2.3:+60796320 None:intergenic
CTGGAACATCCGCATTCCGC+AGG 0.537897 2.3:+60795925 None:intergenic
TCTGTACTTGTGTCTCTATG+TGG 0.542497 2.3:-60795741 MS.gene02810:CDS
AATTATTAACTTGTTGAAAG+GGG 0.546060 2.3:+60795369 None:intergenic
AGACACAAGTACAGAAGTCA+TGG 0.561323 2.3:+60795749 None:intergenic
TCCAGAAGCTGAGAGGAGCC+TGG 0.563140 2.3:-60795907 MS.gene02810:CDS
CCTATTCCATGTCTCTCAGT+AGG 0.565915 2.3:+60795396 None:intergenic
TGCCACCTTCAAGGGCATGT+GGG 0.570413 2.3:-60795649 MS.gene02810:CDS
AGTTCGACATTTCAGAGCAC+CGG 0.577759 2.3:-60795870 MS.gene02810:CDS
TGATAGCATTAGAGACAGCA+AGG 0.586072 2.3:-60795691 MS.gene02810:CDS
GTTTATAGATTTCATGCATG+CGG 0.586781 2.3:-60795571 MS.gene02810:CDS
AGAGATACAGGAAATTCTCA+TGG 0.587742 2.3:-60795469 MS.gene02810:CDS
TAACATTAAAGGAACGTGAA+AGG 0.590123 2.3:-60796023 MS.gene02810:intron
ATTATTAACTTGTTGAAAGG+GGG 0.590301 2.3:+60795370 None:intergenic
AATTCTCATGGCGATGCCTG+TGG 0.604206 2.3:-60795457 MS.gene02810:CDS
AACCCACATGCCCTTGAAGG+TGG 0.607741 2.3:+60795647 None:intergenic
AACAAAAGGTTCCACTCCTG+CGG 0.611057 2.3:-60795941 MS.gene02810:CDS
ACATCCGCATTCCGCAGGAG+TGG 0.617607 2.3:+60795930 None:intergenic
GGTTCCACTCCTGCGGAATG+CGG 0.617826 2.3:-60795934 MS.gene02810:CDS
AAAGGAGGTTGTATACGCGA+TGG 0.625075 2.3:-60796005 MS.gene02810:CDS
TGCATTGTTTGATCAGAATG+TGG 0.627363 2.3:-60795520 MS.gene02810:CDS
GATAGCATTAGAGACAGCAA+GGG 0.637719 2.3:-60795690 MS.gene02810:CDS
GCATTTCCTACTGAGAGACA+TGG 0.643869 2.3:-60795402 MS.gene02810:CDS
CATTAAAGGAACGTGAAAGG+AGG 0.648083 2.3:-60796020 MS.gene02810:intron
CGGATGTTCCAGAAGCTGAG+AGG 0.669051 2.3:-60795914 MS.gene02810:CDS
AATGCAAGAACAGTGCCTGT+AGG 0.674988 2.3:+60795828 None:intergenic
TATCAGTAAAGTTTAGCAGG+AGG 0.692885 2.3:+60795709 None:intergenic
ATAGCATTAGAGACAGCAAG+GGG 0.732552 2.3:-60795689 MS.gene02810:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAACAAAACATAACATTAA+AGG - chr2.3:60795657-60795676 MS.gene02810:CDS 15.0%
!!! GTTTTAAAAATCATAAATGA+TGG + chr2.3:60795429-60795448 None:intergenic 15.0%
!! TTCAAACTAACTACTATTTA+AGG - chr2.3:60795476-60795495 MS.gene02810:CDS 20.0%
!!! CATATGTTTTTTTGTTGATA+AGG + chr2.3:60795617-60795636 None:intergenic 20.0%
! GATATGAATCTAAATGCTTA+CGG + chr2.3:60795407-60795426 None:intergenic 25.0%
! TAAGAATAACGATGAACAAA+AGG - chr2.3:60795736-60795755 MS.gene02810:CDS 25.0%
! TTGCCAACATTTGTAAAAAT+CGG + chr2.3:60795902-60795921 None:intergenic 25.0%
!! ATAGTAGTTAGTTTGAAGAA+AGG + chr2.3:60795473-60795492 None:intergenic 25.0%
GTTTATAGATTTCATGCATG+CGG - chr2.3:60796120-60796139 MS.gene02810:intron 30.0%
TAAAAATCGGTGACAAAAGT+TGG + chr2.3:60795889-60795908 None:intergenic 30.0%
TAACATTAAAGGAACGTGAA+AGG - chr2.3:60795668-60795687 MS.gene02810:CDS 30.0%
! ATTTCCTGTATCTCTTTTGA+TGG + chr2.3:60796217-60796236 None:intergenic 30.0%
!!! TCACCGATTTTTACAAATGT+TGG - chr2.3:60795896-60795915 MS.gene02810:CDS 30.0%
AACTTATAGCTTTCTGTACC+AGG + chr2.3:60795805-60795824 None:intergenic 35.0%
AGAACCATCAAAAGAGATAC+AGG - chr2.3:60796210-60796229 MS.gene02810:intron 35.0%
AGAGATACAGGAAATTCTCA+TGG - chr2.3:60796222-60796241 MS.gene02810:intron 35.0%
ATGAATCTAAATGCTTACGG+TGG + chr2.3:60795404-60795423 None:intergenic 35.0%
GTTTGAAGAAAGGTTGTAAG+AGG + chr2.3:60795463-60795482 None:intergenic 35.0%
TATCAGTAAAGTTTAGCAGG+AGG + chr2.3:60795985-60796004 None:intergenic 35.0%
TGCATTGTTTGATCAGAATG+TGG - chr2.3:60796171-60796190 MS.gene02810:intron 35.0%
TGCTATCAGTAAAGTTTAGC+AGG + chr2.3:60795988-60796007 None:intergenic 35.0%
! AGCAAGGGGAATATTTGTTA+TGG - chr2.3:60796016-60796035 MS.gene02810:intron 35.0%
! ATAATTTTGAGCGAAGGGAA+GGG + chr2.3:60795566-60795585 None:intergenic 35.0%
! TCAGCATAATTTTGAGCGAA+GGG + chr2.3:60795571-60795590 None:intergenic 35.0%
!! GCAAGGGGAATATTTGTTAT+GGG - chr2.3:60796017-60796036 MS.gene02810:intron 35.0%
!! TGTATCTCTTTTGATGGTTC+TGG + chr2.3:60796211-60796230 None:intergenic 35.0%
AGACACAAGTACAGAAGTCA+TGG + chr2.3:60795945-60795964 None:intergenic 40.0%
ATAGCATTAGAGACAGCAAG+GGG - chr2.3:60796002-60796021 MS.gene02810:CDS 40.0%
CATTAAAGGAACGTGAAAGG+AGG - chr2.3:60795671-60795690 MS.gene02810:CDS 40.0%
GATAGCATTAGAGACAGCAA+GGG - chr2.3:60796001-60796020 MS.gene02810:CDS 40.0%
TAGAAGGTTTGCCAAATGTC+CGG + chr2.3:60795843-60795862 None:intergenic 40.0%
TCTGTACTTGTGTCTCTATG+TGG - chr2.3:60795950-60795969 MS.gene02810:CDS 40.0%
TGATAGCATTAGAGACAGCA+AGG - chr2.3:60796000-60796019 MS.gene02810:CDS 40.0%
! CATAATTTTGAGCGAAGGGA+AGG + chr2.3:60795567-60795586 None:intergenic 40.0%
! CGATATTTTGCTGCAACTTG+AGG + chr2.3:60796094-60796113 None:intergenic 40.0%
! GTCAGCATAATTTTGAGCGA+AGG + chr2.3:60795572-60795591 None:intergenic 40.0%
! TATTTTGCTGCAACTTGAGG+TGG + chr2.3:60796091-60796110 None:intergenic 40.0%
AAAGGAGGTTGTATACGCGA+TGG - chr2.3:60795686-60795705 MS.gene02810:CDS 45.0%
AACAAAAGGTTCCACTCCTG+CGG - chr2.3:60795750-60795769 MS.gene02810:CDS 45.0%
AATAACCCACATGCCCTTGA+AGG + chr2.3:60796050-60796069 None:intergenic 45.0%
AATGCAAGAACAGTGCCTGT+AGG + chr2.3:60795866-60795885 None:intergenic 45.0%
AGTTCGACATTTCAGAGCAC+CGG - chr2.3:60795821-60795840 MS.gene02810:CDS 45.0%
CAAAAAACGCCAATTGCCAC+AGG + chr2.3:60796253-60796272 None:intergenic 45.0%
CCTACTGAGAGACATGGAAT+AGG - chr2.3:60796295-60796314 MS.gene02810:intron 45.0%
CCTATTCCATGTCTCTCAGT+AGG + chr2.3:60796298-60796317 None:intergenic 45.0%
GCATTTCCTACTGAGAGACA+TGG - chr2.3:60796289-60796308 MS.gene02810:intron 45.0%
TATGGGTTTGCCACCTTCAA+GGG - chr2.3:60796034-60796053 MS.gene02810:intron 45.0%
TGCAACTTGAGGTGGAAGTT+TGG + chr2.3:60796083-60796102 None:intergenic 45.0%
TTATGGGTTTGCCACCTTCA+AGG - chr2.3:60796033-60796052 MS.gene02810:intron 45.0%
TTGGCAAACCTTCTACCTAC+AGG - chr2.3:60795848-60795867 MS.gene02810:CDS 45.0%
! AAGGGCATGTGGGTTATTGA+TGG - chr2.3:60796052-60796071 MS.gene02810:intron 45.0%
!! ATTTCAGAGCACCGGACATT+TGG - chr2.3:60795829-60795848 MS.gene02810:CDS 45.0%
!! TATATCTATATATAATATAT+AGG + chr2.3:60795594-60795613 None:intergenic 5.0%
AATTCTCATGGCGATGCCTG+TGG - chr2.3:60796234-60796253 MS.gene02810:intron 50.0%
GAACAGTGCCTGTAGGTAGA+AGG + chr2.3:60795859-60795878 None:intergenic 50.0%
GCATGCGGTGATGTCAATTC+TGG - chr2.3:60796135-60796154 MS.gene02810:intron 50.0%
! ATTTTGAGCGAAGGGAAGGG+AGG + chr2.3:60795563-60795582 None:intergenic 50.0%
! TTTTGAGCGAAGGGAAGGGA+GGG + chr2.3:60795562-60795581 None:intergenic 50.0%
AACCCACATGCCCTTGAAGG+TGG + chr2.3:60796047-60796066 None:intergenic 55.0%
ATGGCGATGCCTGTGGCAAT+TGG - chr2.3:60796241-60796260 MS.gene02810:intron 55.0%
CGGATGTTCCAGAAGCTGAG+AGG - chr2.3:60795777-60795796 MS.gene02810:CDS 55.0%
! TGCCACCTTCAAGGGCATGT+GGG - chr2.3:60796042-60796061 MS.gene02810:intron 55.0%
! TTGCCACCTTCAAGGGCATG+TGG - chr2.3:60796041-60796060 MS.gene02810:intron 55.0%
ACATCCGCATTCCGCAGGAG+TGG + chr2.3:60795764-60795783 None:intergenic 60.0%
ACCAGGCTCCTCTCAGCTTC+TGG + chr2.3:60795788-60795807 None:intergenic 60.0%
CTGGAACATCCGCATTCCGC+AGG + chr2.3:60795769-60795788 None:intergenic 60.0%
GGTTCCACTCCTGCGGAATG+CGG - chr2.3:60795757-60795776 MS.gene02810:CDS 60.0%
TCCAGAAGCTGAGAGGAGCC+TGG - chr2.3:60795784-60795803 MS.gene02810:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 60795374 60796339 60795374 ID=MS.gene02810
chr2.3 mRNA 60795374 60796339 60795374 ID=MS.gene02810.t1;Parent=MS.gene02810
chr2.3 exon 60796308 60796339 60796308 ID=MS.gene02810.t1.exon1;Parent=MS.gene02810.t1
chr2.3 CDS 60796308 60796339 60796308 ID=cds.MS.gene02810.t1;Parent=MS.gene02810.t1
chr2.3 exon 60795374 60796034 60795374 ID=MS.gene02810.t1.exon2;Parent=MS.gene02810.t1
chr2.3 CDS 60795374 60796034 60795374 ID=cds.MS.gene02810.t1;Parent=MS.gene02810.t1
Gene Sequence

>MS.gene02810

ATGATTCAGTTTATCTTATCTTACTTTCCACCGTAAGCATTTAGATTCATATCCATCATTTATGATTTTTAAAACAAAAAAACACACCTCTTACAACCTTTCTTCAAACTAACTACTATTTAAGGAATATATTGAAAGCTGTTTTATCAAGTTTTATGTTTGTGTTTCTTGCAAGCAATGTTTAACCCTCCCTTCCCTTCGCTCAAAATTATGCTGACCTATATATTATATATAGATATACCTTATCAACAAAAAAACATATGCTGCATATACAAAAGTGATCAAAACAAAACATAACATTAAAGGAACGTGAAAGGAGGTTGTATACGCGATGGACATCAATTAGAAATCGACGATGACTCTAAGAATAACGATGAACAAAAGGTTCCACTCCTGCGGAATGCGGATGTTCCAGAAGCTGAGAGGAGCCTGGTACAGAAAGCTATAAGTTCGACATTTCAGAGCACCGGACATTTGGCAAACCTTCTACCTACAGGCACTGTTCTTGCATTCCAACTTTTGTCACCGATTTTTACAAATGTTGGCAACTGTGACTCTGTCAGCAAGTCCATGACTTCTGTACTTGTGTCTCTATGTGGTGCATCATGCCTCCTGCTAAACTTTACTGATAGCATTAGAGACAGCAAGGGGAATATTTGTTATGGGTTTGCCACCTTCAAGGGCATGTGGGTTATTGATGGATCAACCAAACTTCCACCTCAAGTTGCAGCAAAATATCGCATAAAGTTTATAGATTTCATGCATGCGGTGATGTCAATTCTGGTGTTTGCAGCAATTGCATTGTTTGATCAGAATGTGGTGAATTGTTTTTTTCCAGAACCATCAAAAGAGATACAGGAAATTCTCATGGCGATGCCTGTGGCAATTGGCGTTTTTTGCAGCATGATTTTCGTTGCATTTCCTACTGAGAGACATGGAATAGGCTTCCCCCTTTCAACAAGTTAA
Protein sequence

>MS.gene02810.t1

MIQFILSYFPPNVKGGCIRDGHQLEIDDDSKNNDEQKVPLLRNADVPEAERSLVQKAISSTFQSTGHLANLLPTGTVLAFQLLSPIFTNVGNCDSVSKSMTSVLVSLCGASCLLLNFTDSIRDSKGNICYGFATFKGMWVIDGSTKLPPQVAAKYRIKFIDFMHAVMSILVFAAIALFDQNVVNCFFPEPSKEIQEILMAMPVAIGVFCSMIFVAFPTERHGIGFPLSTS