AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene35397

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35397.t1 MTR_2g086270 98.844 173 2 0 1 173 1 173 7.73e-128 356
MS.gene35397.t1 MTR_7g104460 76.023 171 41 0 3 173 4 174 2.92e-101 289
MS.gene35397.t1 MTR_0020s0120 66.474 173 57 1 1 173 1 172 5.52e-86 250
MS.gene35397.t1 MTR_1g060190 66.871 163 53 1 2 163 3 165 1.56e-81 239
MS.gene35397.t1 MTR_0020s0120 63.584 173 55 2 1 173 1 165 3.61e-79 233
MS.gene35397.t1 MTR_7g084970 54.118 170 77 1 4 173 5 173 7.59e-67 202
MS.gene35397.t1 MTR_6g033040 52.941 170 79 1 4 173 5 173 1.47e-62 191
MS.gene35397.t1 MTR_7g085020 55.357 168 74 1 6 173 8 174 2.00e-61 188
MS.gene35397.t1 MTR_7g006690 49.708 171 84 2 4 173 5 174 5.32e-59 182
MS.gene35397.t1 MTR_8g106840 49.711 173 86 1 1 173 2 173 3.14e-58 180
MS.gene35397.t1 MTR_7g006630 49.704 169 83 2 6 173 2 169 2.15e-57 177
MS.gene35397.t1 MTR_7g085040 49.405 168 80 3 6 173 7 169 2.31e-53 167
MS.gene35397.t1 MTR_5g078320 38.356 73 45 0 100 172 16 88 2.21e-13 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene35397.t1 AT2G27550 76.744 172 39 1 3 173 4 175 5.37e-100 286
MS.gene35397.t1 AT5G03840 73.214 168 45 0 6 173 10 177 1.54e-93 269
MS.gene35397.t1 AT5G62040 58.046 174 72 1 1 173 1 174 3.66e-74 220
MS.gene35397.t1 AT1G65480 54.598 174 77 2 1 173 1 173 7.35e-65 197
MS.gene35397.t1 AT1G65480 54.598 174 77 2 1 173 45 217 1.38e-64 197
MS.gene35397.t1 AT4G20370 53.448 174 79 2 1 173 1 173 4.93e-61 187
MS.gene35397.t1 AT1G18100 50.575 174 84 2 1 173 1 173 1.11e-57 178

Find 40 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCACCATGAATCTGAACTTT+AGG 0.259268 2.1:-15786785 None:intergenic
GCAACAGATCCTCTTGCTAT+TGG 0.264347 2.1:+15786644 MS.gene35397:CDS
AATCTGAACTTTAGGTTTAG+TGG 0.315784 2.1:-15786777 None:intergenic
CAACAGATCCTCTTGCTATT+GGG 0.339091 2.1:+15786645 MS.gene35397:CDS
CTTGCTATTGGGAGAGTGAT+TGG 0.342940 2.1:+15786656 MS.gene35397:CDS
AACCTATGGATTCCTATGTT+TGG 0.370955 2.1:-15788017 None:intergenic
TCACTAGGGCCAGGGACATC+TGG 0.386750 2.1:-15786999 None:intergenic
AAACCTAAAGTTCAGATTCA+TGG 0.412345 2.1:+15786782 MS.gene35397:CDS
TATGAGATCTTTCTTCACTT+TGG 0.453943 2.1:+15786811 MS.gene35397:CDS
GGCACAACTGATGCTACATT+TGG 0.461577 2.1:+15787855 MS.gene35397:CDS
GGTTTAGTGGTAACTGAGGA+AGG 0.482769 2.1:-15786764 None:intergenic
TGCGCTTCTGCTTGTAAAGA+AGG 0.483125 2.1:-15788046 None:intergenic
TCCCTCAGGTACGGATCACT+AGG 0.483821 2.1:-15787014 None:intergenic
AAAGAAGGAACACAAACCTA+TGG 0.532641 2.1:-15788031 None:intergenic
TGATGAAAATACCAACATCA+AGG 0.533106 2.1:+15788078 MS.gene35397:CDS
AGGTACGGATCACTAGGGCC+AGG 0.555831 2.1:-15787008 None:intergenic
GAAATGCCACGTCCAAACAT+AGG 0.556488 2.1:+15788005 MS.gene35397:CDS
ACCAGTGCAAGTGTTCCCTC+AGG 0.564091 2.1:-15787028 None:intergenic
TGGATTCCTATGTTTGGACG+TGG 0.564287 2.1:-15788011 None:intergenic
TGCAAGTGTTCCCTCAGGTA+CGG 0.564666 2.1:-15787023 None:intergenic
AATGTAGCATCAGTTGTGCC+TGG 0.566122 2.1:-15787852 None:intergenic
ACCTGAGGGAACACTTGCAC+TGG 0.569843 2.1:+15787027 MS.gene35397:CDS
CAATGACCTCGGGCCTCCTG+TGG 0.580778 2.1:+15788133 MS.gene35397:CDS
AGGATCTGTTGCAATACTCA+TGG 0.588182 2.1:-15786633 None:intergenic
CCCTAGTGATCCGTACCTGA+GGG 0.588627 2.1:+15787013 MS.gene35397:CDS
ATGACAGATCCAGATGTCCC+TGG 0.589097 2.1:+15786990 MS.gene35397:CDS
GATGAAAATACCAACATCAA+GGG 0.592305 2.1:+15788079 MS.gene35397:CDS
TTGCACAAGACAATGACCTC+GGG 0.602430 2.1:+15788123 MS.gene35397:CDS
AACACTAAGCAAGTTTACAA+TGG 0.606083 2.1:+15786728 MS.gene35397:CDS
ATCACTCTCCCAATAGCAAG+AGG 0.607444 2.1:-15786653 None:intergenic
CAGCAGCCACAGGAGGCCCG+AGG 0.611106 2.1:-15788139 None:intergenic
GCCCTAGTGATCCGTACCTG+AGG 0.613608 2.1:+15787012 MS.gene35397:CDS
TTAAAGAGATCCCTTGATGT+TGG 0.626156 2.1:-15788089 None:intergenic
GGTACGGATCACTAGGGCCA+GGG 0.631293 2.1:-15787007 None:intergenic
TTTAGGTTTAGTGGTAACTG+AGG 0.644885 2.1:-15786768 None:intergenic
TTTGCACAAGACAATGACCT+CGG 0.646965 2.1:+15788122 MS.gene35397:CDS
CCCTCAGGTACGGATCACTA+GGG 0.654397 2.1:-15787013 None:intergenic
GTCCAAACATAGGAATCCAT+AGG 0.668902 2.1:+15788015 MS.gene35397:CDS
AGGATAGTCACAGATATACC+AGG 0.670510 2.1:+15787834 MS.gene35397:intron
CCTAAAGTTCAGATTCATGG+TGG 0.696957 2.1:+15786785 MS.gene35397:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATTAGAAAAGAATTAA+AGG + chr2.1:15787353-15787372 MS.gene35397:intron 10.0%
!! ATAATTTAAGTAATATAGAT+AGG + chr2.1:15787272-15787291 MS.gene35397:intron 10.0%
!! ATTCAAATTTACTAAAAATA+AGG + chr2.1:15787554-15787573 MS.gene35397:intron 10.0%
!! TTCAAATTTACTAAAAATAA+GGG + chr2.1:15787555-15787574 MS.gene35397:intron 10.0%
!!! ATTTTTTATTTATATTAAGC+TGG + chr2.1:15787771-15787790 MS.gene35397:intron 10.0%
!!! TTCAACTTTTTATTAAAAAA+TGG - chr2.1:15787492-15787511 None:intergenic 10.0%
!! AAATAGAATATATTGAAGTA+AGG - chr2.1:15786932-15786951 None:intergenic 15.0%
!! ATCAAAAAAGAATTTCAAAA+AGG - chr2.1:15787727-15787746 None:intergenic 15.0%
!! TAATAACAAATGCTTATTAT+AGG - chr2.1:15787233-15787252 None:intergenic 15.0%
!! TAATTAATTGAAAATGAACA+GGG + chr2.1:15787964-15787983 MS.gene35397:intron 15.0%
!! TTAATTAATTGAAAATGAAC+AGG + chr2.1:15787963-15787982 MS.gene35397:intron 15.0%
!!! AGCATTTGTTATTAAATATA+AGG + chr2.1:15787239-15787258 MS.gene35397:intron 15.0%
!!! TCTTTTTTGATTACTTTAAA+TGG + chr2.1:15787736-15787755 MS.gene35397:intron 15.0%
!! AAATATGGATTTGTCTAATA+TGG + chr2.1:15787447-15787466 MS.gene35397:intron 20.0%
!! GAAATAAAGAAGTAATGATT+TGG - chr2.1:15786850-15786869 None:intergenic 20.0%
!!! AAACAATGAACAAACTTTTT+TGG + chr2.1:15787417-15787436 MS.gene35397:intron 20.0%
!!! AATTCTAATTTTCTTTCCTT+TGG - chr2.1:15787324-15787343 None:intergenic 20.0%
!!! TTCAATAACTCATATTTTCA+AGG + chr2.1:15787663-15787682 MS.gene35397:intron 20.0%
!!! TTTTTCTTGAATTTTCTTTC+AGG + chr2.1:15786965-15786984 MS.gene35397:intron 20.0%
!!! TTTTTTGGTGATCTAAAATA+TGG + chr2.1:15787432-15787451 MS.gene35397:intron 20.0%
!! AAAAAATGGTAGACTCTTTT+TGG - chr2.1:15787478-15787497 None:intergenic 25.0%
!! AAAAATGGTAGACTCTTTTT+GGG - chr2.1:15787477-15787496 None:intergenic 25.0%
!! AGCATTGAACATGATAAAAA+AGG - chr2.1:15787585-15787604 None:intergenic 25.0%
!! TCATTGTTTATATTTGAGAC+TGG - chr2.1:15787406-15787425 None:intergenic 25.0%
AAACCTAAAGTTCAGATTCA+TGG + chr2.1:15786782-15786801 MS.gene35397:CDS 30.0%
AACACTAAGCAAGTTTACAA+TGG + chr2.1:15786728-15786747 MS.gene35397:CDS 30.0%
AATTGATGTGACCATATTAG+AGG - chr2.1:15787891-15787910 None:intergenic 30.0%
ATATTGAAGTAAGGAACTCA+AGG - chr2.1:15786923-15786942 None:intergenic 30.0%
ATGCATGAATAAAGAACCAA+AGG + chr2.1:15787305-15787324 MS.gene35397:intron 30.0%
CTGTGATGCACAATTAAAAT+AGG - chr2.1:15787816-15787835 None:intergenic 30.0%
GATGAAAATACCAACATCAA+GGG + chr2.1:15788079-15788098 MS.gene35397:CDS 30.0%
GTAATCAAAGTCCTCTAATA+TGG + chr2.1:15787877-15787896 MS.gene35397:intron 30.0%
TATGAGATCTTTCTTCACTT+TGG + chr2.1:15786811-15786830 MS.gene35397:CDS 30.0%
TGATGAAAATACCAACATCA+AGG + chr2.1:15788078-15788097 MS.gene35397:CDS 30.0%
! AATCTGAACTTTAGGTTTAG+TGG - chr2.1:15786780-15786799 None:intergenic 30.0%
!!! CTATTTTAATTGTGCATCAC+AGG + chr2.1:15787814-15787833 MS.gene35397:intron 30.0%
AAAGAAGGAACACAAACCTA+TGG - chr2.1:15788034-15788053 None:intergenic 35.0%
AACCTATGGATTCCTATGTT+TGG - chr2.1:15788020-15788039 None:intergenic 35.0%
ATATACTTTGCATGCATCAG+AGG - chr2.1:15787210-15787229 None:intergenic 35.0%
TTAAAGAGATCCCTTGATGT+TGG - chr2.1:15788092-15788111 None:intergenic 35.0%
! GTTTATATTTGAGACTGGAG+TGG - chr2.1:15787401-15787420 None:intergenic 35.0%
! TTTAGGTTTAGTGGTAACTG+AGG - chr2.1:15786771-15786790 None:intergenic 35.0%
!! TCAAATCTGTGTGTTTTGAG+TGG + chr2.1:15787113-15787132 MS.gene35397:intron 35.0%
AAGTAAGGAACTCAAGGACA+AGG - chr2.1:15786917-15786936 None:intergenic 40.0%
AGGATAGTCACAGATATACC+AGG + chr2.1:15787834-15787853 MS.gene35397:intron 40.0%
CCACCATGAATCTGAACTTT+AGG - chr2.1:15786788-15786807 None:intergenic 40.0%
CCTAAAGTTCAGATTCATGG+TGG + chr2.1:15786785-15786804 MS.gene35397:CDS 40.0%
GTCCAAACATAGGAATCCAT+AGG + chr2.1:15788015-15788034 MS.gene35397:CDS 40.0%
TTGAAAAAAACAGCAGCCAC+AGG - chr2.1:15788152-15788171 None:intergenic 40.0%
TTTGCACAAGACAATGACCT+CGG + chr2.1:15788122-15788141 MS.gene35397:CDS 40.0%
!! CAACAGATCCTCTTGCTATT+GGG + chr2.1:15786645-15786664 MS.gene35397:CDS 40.0%
AAAAAAACAGCAGCCACAGG+AGG - chr2.1:15788149-15788168 None:intergenic 45.0%
AATGTAGCATCAGTTGTGCC+TGG - chr2.1:15787855-15787874 None:intergenic 45.0%
ATCACTCTCCCAATAGCAAG+AGG - chr2.1:15786656-15786675 None:intergenic 45.0%
GAAATGCCACGTCCAAACAT+AGG + chr2.1:15788005-15788024 MS.gene35397:CDS 45.0%
GGCACAACTGATGCTACATT+TGG + chr2.1:15787855-15787874 MS.gene35397:CDS 45.0%
GGTTTAGTGGTAACTGAGGA+AGG - chr2.1:15786767-15786786 None:intergenic 45.0%
TGCGCTTCTGCTTGTAAAGA+AGG - chr2.1:15788049-15788068 None:intergenic 45.0%
TGGATTCCTATGTTTGGACG+TGG - chr2.1:15788014-15788033 None:intergenic 45.0%
TTGCACAAGACAATGACCTC+GGG + chr2.1:15788123-15788142 MS.gene35397:CDS 45.0%
! GCAACAGATCCTCTTGCTAT+TGG + chr2.1:15786644-15786663 MS.gene35397:CDS 45.0%
!! CTTGCTATTGGGAGAGTGAT+TGG + chr2.1:15786656-15786675 MS.gene35397:CDS 45.0%
ATGACAGATCCAGATGTCCC+TGG + chr2.1:15786990-15787009 MS.gene35397:CDS 50.0%
TGCAAGTGTTCCCTCAGGTA+CGG - chr2.1:15787026-15787045 None:intergenic 50.0%
ACCAGTGCAAGTGTTCCCTC+AGG - chr2.1:15787031-15787050 None:intergenic 55.0%
ACCTGAGGGAACACTTGCAC+TGG + chr2.1:15787027-15787046 MS.gene35397:CDS 55.0%
CCCTAGTGATCCGTACCTGA+GGG + chr2.1:15787013-15787032 MS.gene35397:CDS 55.0%
CCCTCAGGTACGGATCACTA+GGG - chr2.1:15787016-15787035 None:intergenic 55.0%
TCCCTCAGGTACGGATCACT+AGG - chr2.1:15787017-15787036 None:intergenic 55.0%
AGGTACGGATCACTAGGGCC+AGG - chr2.1:15787011-15787030 None:intergenic 60.0%
GCCCTAGTGATCCGTACCTG+AGG + chr2.1:15787012-15787031 MS.gene35397:CDS 60.0%
GGTACGGATCACTAGGGCCA+GGG - chr2.1:15787010-15787029 None:intergenic 60.0%
TCACTAGGGCCAGGGACATC+TGG - chr2.1:15787002-15787021 None:intergenic 60.0%
CAATGACCTCGGGCCTCCTG+TGG + chr2.1:15788133-15788152 MS.gene35397:CDS 65.0%
CAGCAGCCACAGGAGGCCCG+AGG - chr2.1:15788142-15788161 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 15786635 15788205 15786635 ID=MS.gene35397
chr2.1 mRNA 15786635 15788205 15786635 ID=MS.gene35397.t1;Parent=MS.gene35397
chr2.1 exon 15786635 15786832 15786635 ID=MS.gene35397.t1.exon1;Parent=MS.gene35397.t1
chr2.1 CDS 15786635 15786832 15786635 ID=cds.MS.gene35397.t1;Parent=MS.gene35397.t1
chr2.1 exon 15786987 15787048 15786987 ID=MS.gene35397.t1.exon2;Parent=MS.gene35397.t1
chr2.1 CDS 15786987 15787048 15786987 ID=cds.MS.gene35397.t1;Parent=MS.gene35397.t1
chr2.1 exon 15787836 15787876 15787836 ID=MS.gene35397.t1.exon3;Parent=MS.gene35397.t1
chr2.1 CDS 15787836 15787876 15787836 ID=cds.MS.gene35397.t1;Parent=MS.gene35397.t1
chr2.1 exon 15787985 15788205 15787985 ID=MS.gene35397.t1.exon4;Parent=MS.gene35397.t1
chr2.1 CDS 15787985 15788205 15787985 ID=cds.MS.gene35397.t1;Parent=MS.gene35397.t1
Gene Sequence

>MS.gene35397

ATGAGTATTGCAACAGATCCTCTTGCTATTGGGAGAGTGATTGGAGATGTAGTTGATTATTTCACTTCAACTATGAAAATGTCTGTCACTTACAACACTAAGCAAGTTTACAATGGTCATGAGTTTTTTCCTTCCTCAGTTACCACTAAACCTAAAGTTCAGATTCATGGTGGTGATATGAGATCTTTCTTCACTTTGGTACAAATCTCTCACCAAATCATTACTTCTTTATTTCTTCTTTTTTTTCATCTTACTGTTTTCATATGTATGCATGACACACCTTGTCCTTGAGTTCCTTACTTCAATATATTCTATTTTTTCTGTAATTATTTTTTCTTGAATTTTCTTTCAGGTCATGACAGATCCAGATGTCCCTGGCCCTAGTGATCCGTACCTGAGGGAACACTTGCACTGGTATGCAATACATACTACTTGAACAAAATGTTAATATAAAATTTACTTGAACTGAATTATTAAATCAAATCTGTGTGTTTTGAGTGGTAAGAAGCTTTATAAAATTTCATTAATATTTTAAGAGTTGATTAATCTAAAACATTTGAAGAAATTAGTCTCCTCTGATGCATGCAAAGTATATCCTATAATAAGCATTTGTTATTAAATATAAGGATAATTATGTATAATTTAAGTAATATAGATAGGAGTATATAGCATGCATGAATAAAGAACCAAAGGAAAGAAAATTAGAATTTCATGCATAAATAATTAGAAAAGAATTAAAGGCATCATGCATATAATACTAACTCCACTCCAGTCTCAAATATAAACAATGAACAAACTTTTTTGGTGATCTAAAATATGGATTTGTCTAATATGGACATCCCAAAAAGAGTCTACCATTTTTTAATAAAAAGTTGAATTTTATAAAAACAAAACAAATATGAAAGAAATTTAATATTTTATTCAAATTTACTAAAAATAAGGGTTAACCTTTTTTATCATGTTCAATGCTAAATTATTCTTCATTTTTATCAAAAAAAAATTACTCTTCAATTAATTTAGTTTTTTTTTTCAATAACTCATATTTTCAAGGAACAAATTTCTATGATAGACAATTTAAAAATACAAATTCCTTTTTGAAATTCTTTTTTGATTACTTTAAATGGTGTGAAAGTAGTATTTTTTATTTATATTAAGCTGGTCATAAACAAAGTTTCTAACCTATTTTAATTGTGCATCACAGGATAGTCACAGATATACCAGGCACAACTGATGCTACATTTGGTAATCAAAGTCCTCTAATATGGTCACATCAATTATATATATTAAAGAGTTTCTTTTCACTTTAATTATGATATTATATATATGCTTTAATTAATTGAAAATGAACAGGGAAAGAAGTGATGAAATATGAAATGCCACGTCCAAACATAGGAATCCATAGGTTTGTGTTCCTTCTTTACAAGCAGAAGCGCAGACAAACAGTGATGAAAATACCAACATCAAGGGATCTCTTTAACACAAAGAAATTTGCACAAGACAATGACCTCGGGCCTCCTGTGGCTGCTGTTTTTTTCAATGCACAGAGAGAAACAGCTGCCAGAAGACGTTGA
Protein sequence

>MS.gene35397.t1

MSIATDPLAIGRVIGDVVDYFTSTMKMSVTYNTKQVYNGHEFFPSSVTTKPKVQIHGGDMRSFFTLVMTDPDVPGPSDPYLREHLHWIVTDIPGTTDATFGKEVMKYEMPRPNIGIHRFVFLLYKQKRRQTVMKIPTSRDLFNTKKFAQDNDLGPPVAAVFFNAQRETAARRR