AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene39181

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39181.t1 MTR_1g054550 82.857 175 24 1 3 171 55 229 2.13e-102 293
MS.gene39181.t1 MTR_1g054540 82.840 169 23 1 1 163 94 262 4.41e-95 281
MS.gene39181.t1 MTR_1g054620 81.657 169 25 1 1 163 72 240 5.79e-94 278
MS.gene39181.t1 MTR_1g054620 81.657 169 25 1 1 163 72 240 7.35e-94 277
MS.gene39181.t1 MTR_3g113040 70.192 104 31 0 1 104 117 220 1.57e-44 150
MS.gene39181.t1 MTR_3g009280 64.423 104 37 0 1 104 121 224 2.07e-39 137
MS.gene39181.t1 MTR_3g115660 47.742 155 32 3 15 169 1 106 4.56e-38 126
MS.gene39181.t1 MTR_3g114110 70.930 86 24 1 8 93 111 195 4.00e-35 125
MS.gene39181.t1 MTR_3g114110 70.930 86 24 1 8 93 111 195 9.95e-35 125
MS.gene39181.t1 MTR_3g114110 70.930 86 24 1 8 93 111 195 1.06e-34 125
MS.gene39181.t1 MTR_1g054600 78.667 75 12 1 1 75 140 210 1.70e-34 120
MS.gene39181.t1 MTR_6g034405 58.095 105 29 2 8 112 116 205 2.39e-29 111
MS.gene39181.t1 MTR_6g034405 58.095 105 29 2 8 112 116 205 2.63e-29 111
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39181.t1 AT4G35450 44.872 78 43 0 1 78 118 195 1.57e-17 78.6
MS.gene39181.t1 AT4G35450 44.872 78 43 0 1 78 118 195 1.57e-17 78.6
MS.gene39181.t1 AT4G35450 44.872 78 43 0 1 78 118 195 1.57e-17 78.6
MS.gene39181.t1 AT4G35450 44.872 78 43 0 1 78 80 157 2.01e-17 77.8
MS.gene39181.t1 AT2G17390 46.154 78 42 0 1 78 122 199 4.01e-17 77.4
MS.gene39181.t1 AT4G35450 41.860 86 42 1 1 78 118 203 2.92e-15 72.4

Find 31 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAACTGATCGTTCTTATTC+TGG 0.187548 1.2:+42108272 MS.gene39181:CDS
GCCAGATGAGACAGGAGATA+TGG 0.344451 1.2:+42108187 MS.gene39181:CDS
GCAACTGCATCTGCAAAGTA+TGG 0.383529 1.2:-42108146 None:intergenic
CCCATATCTCCTGTCTCATC+TGG 0.397637 1.2:-42108188 None:intergenic
ACAACAACAATATGATGAAC+AGG 0.433934 1.2:-42108356 None:intergenic
CAACTGATCGTTCTTATTCT+GGG 0.434034 1.2:+42108273 MS.gene39181:CDS
GTCAGATGTGACAGAAGATA+TGG 0.442147 1.2:+42108235 MS.gene39181:CDS
CCTGCATCAAAGCACAAATC+AGG 0.453364 1.2:-42107726 None:intergenic
CCAGATGAGACAGGAGATAT+GGG 0.454049 1.2:+42108188 MS.gene39181:CDS
CCTGATTTGTGCTTTGATGC+AGG 0.456372 1.2:+42107726 MS.gene39181:CDS
CCCATCACTGTCTTCCATGC+TGG 0.469108 1.2:+42107829 MS.gene39181:CDS
GTATGTAACAGAAGAAGATA+TGG 0.471000 1.2:+42108295 MS.gene39181:CDS
GACGTTGAGGTATGTCATAA+TGG 0.477890 1.2:+42108383 MS.gene39181:CDS
TATACCGATCCATCACTTGA+AGG 0.482452 1.2:+42107857 MS.gene39181:CDS
GAAGATGTTTGGACTAGTCA+TGG 0.493835 1.2:+42108115 MS.gene39181:CDS
TTATGCTGGCCTTCAAGTGA+TGG 0.497197 1.2:-42107866 None:intergenic
GTGCCGTTCTACGTTTATGC+TGG 0.500883 1.2:-42107880 None:intergenic
AATTATGGGCCAGATGAGAC+AGG 0.529046 1.2:+42108179 MS.gene39181:CDS
AAGATGTTTGGACTAGTCAT+GGG 0.545322 1.2:+42108116 MS.gene39181:CDS
TTAAACCTCATCATTACTGC+AGG 0.553808 1.2:-42107959 None:intergenic
TCCAGCATGGAAGACAGTGA+TGG 0.583598 1.2:-42107830 None:intergenic
CTGGCCTTCAAGTGATGGAT+CGG 0.584169 1.2:-42107861 None:intergenic
CCAGCATGGAAGACAGTGAT+GGG 0.588307 1.2:-42107829 None:intergenic
ACAAATCAGGTGCCTGACCA+TGG 0.597723 1.2:-42107713 None:intergenic
ATCGGTATAAATTTCCAGCA+TGG 0.605131 1.2:-42107843 None:intergenic
CAGATACTGGAATAATGAGA+AGG 0.605660 1.2:+42108088 MS.gene39181:intron
TCTAAAATAAGTTTCAAACA+TGG 0.632145 1.2:-42107917 None:intergenic
TGTTGTTGTTGACGACGTTG+AGG 0.636788 1.2:+42108370 MS.gene39181:CDS
AGGCCAGCATAAACGTAGAA+CGG 0.646888 1.2:+42107877 MS.gene39181:CDS
TTAGATGAGATAGAGAATGG+TGG 0.705619 1.2:+42107935 MS.gene39181:CDS
GTGGTCCTGCAGTAATGATG+AGG 0.713822 1.2:+42107954 MS.gene39181:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAATTCTATTTTATTGTTT+TGG + chr1.2:42107993-42108012 MS.gene39181:intron 10.0%
!!! AATGAAGATTCTAAAAATTC+TGG + chr1.2:42108212-42108231 MS.gene39181:CDS 20.0%
!!! ATGAAGATTCTAAAAATTCT+GGG + chr1.2:42108213-42108232 MS.gene39181:CDS 20.0%
!!! TCTAAAATAAGTTTCAAACA+TGG - chr1.2:42107920-42107939 None:intergenic 20.0%
!!! TTGCTTCTTTTGAAAATTAT+GGG + chr1.2:42108165-42108184 MS.gene39181:CDS 20.0%
! ATTTACACCACAACAATTTA+TGG - chr1.2:42108035-42108054 None:intergenic 25.0%
! TAAATTGTTGTGGTGTAAAT+TGG + chr1.2:42108035-42108054 MS.gene39181:intron 25.0%
!! AACAATTTATGGTGGAAATA+TGG - chr1.2:42108024-42108043 None:intergenic 25.0%
!! ATTTTAGATGAGATAGAGAA+TGG + chr1.2:42107932-42107951 MS.gene39181:CDS 25.0%
!!! GTTGCTTCTTTTGAAAATTA+TGG + chr1.2:42108164-42108183 MS.gene39181:CDS 25.0%
ACAACAACAATATGATGAAC+AGG - chr1.2:42108359-42108378 None:intergenic 30.0%
ATTTCCACCATAAATTGTTG+TGG + chr1.2:42108025-42108044 MS.gene39181:intron 30.0%
GTATGTAACAGAAGAAGATA+TGG + chr1.2:42108295-42108314 MS.gene39181:CDS 30.0%
ATCGGTATAAATTTCCAGCA+TGG - chr1.2:42107846-42107865 None:intergenic 35.0%
CAACTGATCGTTCTTATTCT+GGG + chr1.2:42108273-42108292 MS.gene39181:CDS 35.0%
CAGATACTGGAATAATGAGA+AGG + chr1.2:42108088-42108107 MS.gene39181:intron 35.0%
TACACCACAACAATTTATGG+TGG - chr1.2:42108032-42108051 None:intergenic 35.0%
TCAACTGATCGTTCTTATTC+TGG + chr1.2:42108272-42108291 MS.gene39181:CDS 35.0%
TCATTATTCCAGTATCTGCA+TGG - chr1.2:42108086-42108105 None:intergenic 35.0%
TTAAACCTCATCATTACTGC+AGG - chr1.2:42107962-42107981 None:intergenic 35.0%
TTAGATGAGATAGAGAATGG+TGG + chr1.2:42107935-42107954 MS.gene39181:CDS 35.0%
! TATGTTTCTAACACTTCTGC+TGG + chr1.2:42107769-42107788 MS.gene39181:intron 35.0%
!! AAGATGTTTGGACTAGTCAT+GGG + chr1.2:42108116-42108135 MS.gene39181:CDS 35.0%
!!! GAGAAGGTTTTGAAGATGTT+TGG + chr1.2:42108104-42108123 MS.gene39181:CDS 35.0%
GACGTTGAGGTATGTCATAA+TGG + chr1.2:42108383-42108402 MS.gene39181:CDS 40.0%
GATTCTTTCCATGCAGATAC+TGG + chr1.2:42108075-42108094 MS.gene39181:intron 40.0%
GTCAGATGTGACAGAAGATA+TGG + chr1.2:42108235-42108254 MS.gene39181:CDS 40.0%
TATACCGATCCATCACTTGA+AGG + chr1.2:42107857-42107876 MS.gene39181:CDS 40.0%
!! GAAGATGTTTGGACTAGTCA+TGG + chr1.2:42108115-42108134 MS.gene39181:CDS 40.0%
AATTATGGGCCAGATGAGAC+AGG + chr1.2:42108179-42108198 MS.gene39181:CDS 45.0%
AGGCCAGCATAAACGTAGAA+CGG + chr1.2:42107877-42107896 MS.gene39181:CDS 45.0%
ATGCATGTGCTGTCTATCAC+AGG + chr1.2:42107805-42107824 MS.gene39181:intron 45.0%
CCAGATGAGACAGGAGATAT+GGG + chr1.2:42108188-42108207 MS.gene39181:CDS 45.0%
CCTGCATCAAAGCACAAATC+AGG - chr1.2:42107729-42107748 None:intergenic 45.0%
GCAACTGCATCTGCAAAGTA+TGG - chr1.2:42108149-42108168 None:intergenic 45.0%
! CCTGATTTGTGCTTTGATGC+AGG + chr1.2:42107726-42107745 MS.gene39181:CDS 45.0%
! TGTTGTTGTTGACGACGTTG+AGG + chr1.2:42108370-42108389 MS.gene39181:CDS 45.0%
!! TTATGCTGGCCTTCAAGTGA+TGG - chr1.2:42107869-42107888 None:intergenic 45.0%
!! ATAAAATAGAATTTAAAAAA+TGG - chr1.2:42107988-42108007 None:intergenic 5.0%
CCAGCATGGAAGACAGTGAT+GGG - chr1.2:42107832-42107851 None:intergenic 50.0%
CCCATATCTCCTGTCTCATC+TGG - chr1.2:42108191-42108210 None:intergenic 50.0%
GCCAGATGAGACAGGAGATA+TGG + chr1.2:42108187-42108206 MS.gene39181:CDS 50.0%
GTGGTCCTGCAGTAATGATG+AGG + chr1.2:42107954-42107973 MS.gene39181:CDS 50.0%
TCCAGCATGGAAGACAGTGA+TGG - chr1.2:42107833-42107852 None:intergenic 50.0%
! GTGCCGTTCTACGTTTATGC+TGG - chr1.2:42107883-42107902 None:intergenic 50.0%
!! CTGGCCTTCAAGTGATGGAT+CGG - chr1.2:42107864-42107883 None:intergenic 50.0%
CCCATCACTGTCTTCCATGC+TGG + chr1.2:42107829-42107848 MS.gene39181:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 42107715 42108424 42107715 ID=MS.gene39181
chr1.2 mRNA 42107715 42108424 42107715 ID=MS.gene39181.t1;Parent=MS.gene39181
chr1.2 exon 42107715 42107747 42107715 ID=MS.gene39181.t1.exon1;Parent=MS.gene39181.t1
chr1.2 CDS 42107715 42107747 42107715 ID=cds.MS.gene39181.t1;Parent=MS.gene39181.t1
chr1.2 exon 42107827 42107975 42107827 ID=MS.gene39181.t1.exon2;Parent=MS.gene39181.t1
chr1.2 CDS 42107827 42107975 42107827 ID=cds.MS.gene39181.t1;Parent=MS.gene39181.t1
chr1.2 exon 42108091 42108424 42108091 ID=MS.gene39181.t1.exon3;Parent=MS.gene39181.t1
chr1.2 CDS 42108091 42108424 42108091 ID=cds.MS.gene39181.t1;Parent=MS.gene39181.t1
Gene Sequence

>MS.gene39181

ATGGTCAGGCACCTGATTTGTGCTTTGATGCAGGTATTTTTAAAATTTCTTCGTTATGTTTCTAACACTTCTGCTGGTTGTTAGAGTAAAATGCATGTGCTGTCTATCACAGGACCCATCACTGTCTTCCATGCTGGAAATTTATACCGATCCATCACTTGAAGGCCAGCATAAACGTAGAACGGCACACTTGAACAAAGATCCATGTTTGAAACTTATTTTAGATGAGATAGAGAATGGTGGTCCTGCAGTAATGATGAGGTTTAAACACCATTTTTTAAATTCTATTTTATTGTTTTGGCATTTCCATATTTCCACCATAAATTGTTGTGGTGTAAATTGGTAAATAATTTCTGAAGCGATTCTTTCCATGCAGATACTGGAATAATGAGAAGGTTTTGAAGATGTTTGGACTAGTCATGGGCATTCGTCCATACTTTGCAGATGCAGTTGCTTCTTTTGAAAATTATGGGCCAGATGAGACAGGAGATATGGGAAATGAAGATTCTAAAAATTCTGGGTCAGATGTGACAGAAGATATGGAAAGTGAAGATGAATCAACTGATCGTTCTTATTCTGGGTATGTAACAGAAGAAGATATGGAAAATGAAGATGAATCAACTGTGCATCATATTGAATCACCTGTTCATCATATTGTTGTTGTTGACGACGTTGAGGTATGTCATAATGGCTATTCACTCTGTCATTGA
Protein sequence

>MS.gene39181.t1

MVRHLICALMQDPSLSSMLEIYTDPSLEGQHKRRTAHLNKDPCLKLILDEIENGGPAVMMRYWNNEKVLKMFGLVMGIRPYFADAVASFENYGPDETGDMGNEDSKNSGSDVTEDMESEDESTDRSYSGYVTEEDMENEDESTVHHIESPVHHIVVVDDVEVCHNGYSLCH