AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24498

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24498.t1 MTR_1g017570 97.241 145 4 0 1 145 1 145 1.28e-101 287
MS.gene24498.t1 MTR_3g103360 58.333 144 56 2 1 144 1 140 7.77e-50 156
MS.gene24498.t1 MTR_4g097440 47.154 123 47 3 22 128 23 143 8.44e-20 80.9
MS.gene24498.t1 MTR_5g015090 45.082 122 51 3 31 139 22 140 5.91e-18 75.9
MS.gene24498.t1 MTR_8g086020 41.584 101 53 2 45 143 18 114 1.11e-14 67.4
MS.gene24498.t1 MTR_1g087040 37.273 110 62 2 34 143 4 106 1.64e-13 63.9
MS.gene24498.t1 MTR_1g022495 41.111 90 51 1 35 124 7 94 2.37e-12 61.2
MS.gene24498.t1 MTR_3g117120 43.902 82 44 1 43 124 15 94 2.61e-12 60.8
MS.gene24498.t1 MTR_4g070860 43.750 80 43 1 45 124 17 94 3.11e-12 60.8
MS.gene24498.t1 MTR_7g029400 44.156 77 43 0 59 135 83 159 1.52e-11 59.7
MS.gene24498.t1 MTR_8g015250 42.857 77 44 0 59 135 73 149 2.26e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24498.t1 AT3G49760 38.849 139 77 2 9 139 13 151 1.26e-20 82.8
MS.gene24498.t1 AT2G22850 45.783 83 45 0 57 139 126 208 2.25e-15 70.5
MS.gene24498.t1 AT2G22850 45.783 83 45 0 57 139 126 208 2.25e-15 70.5
MS.gene24498.t1 AT2G18160 43.750 80 45 0 45 124 16 95 5.69e-14 65.9
MS.gene24498.t1 AT1G75390 41.667 84 49 0 45 128 26 109 3.21e-13 63.9
MS.gene24498.t1 AT4G37730 51.471 68 33 0 57 124 194 261 3.83e-13 65.5
MS.gene24498.t1 AT1G75390 41.463 82 48 0 43 124 24 105 9.87e-13 61.2
MS.gene24498.t1 AT1G59530 39.344 122 68 2 18 139 14 129 9.91e-12 59.3
MS.gene24498.t1 AT5G15830 38.835 103 59 2 26 128 44 142 9.92e-12 60.1

Find 46 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCCCTCATGGCAACACTTT+TGG 0.232653 1.1:+4948121 MS.gene24498:CDS
CGATTTGAACCGGTTGAGAA+TGG 0.382249 1.1:+4948007 MS.gene24498:CDS
TTGTGAACCGGACCCTGGAC+TGG 0.414459 1.1:-4947865 None:intergenic
ACCGGTTGAGAATGGAAAAC+CGG 0.420192 1.1:+4948015 MS.gene24498:CDS
GGTCCGGCTCACGTGTGTTC+CGG 0.430584 1.1:+4947770 MS.gene24498:CDS
TAAGGAGAATGCAATCAAAC+CGG 0.448119 1.1:+4947928 MS.gene24498:CDS
ACCTCACGAACGATTTGAAC+CGG 0.459693 1.1:+4947997 MS.gene24498:CDS
ACGACTGGATCCTTGTGAAC+CGG 0.467778 1.1:-4947877 None:intergenic
GATCCTTGTGAACCGGACCC+TGG 0.468796 1.1:-4947870 None:intergenic
ATTGCATGGTTAACCCTAGC+TGG 0.474346 1.1:-4948049 None:intergenic
GGACCGGATACTCCTCTTCA+TGG 0.477097 1.1:-4947752 None:intergenic
GTGAACATGGTTTCATGAAC+CGG 0.479700 1.1:-4947789 None:intergenic
CCTGGACTGGATGGATCAAC+CGG 0.484260 1.1:-4947852 None:intergenic
CCGGTTGATCCATCCAGTCC+AGG 0.489171 1.1:+4947852 MS.gene24498:CDS
GATCAACCGGTTGGTTAATG+AGG 0.507162 1.1:-4947839 None:intergenic
GAACCGGAACACACGTGAGC+CGG 0.519769 1.1:-4947773 None:intergenic
GGTCGAGTAAACCGCACGAC+TGG 0.523402 1.1:-4947892 None:intergenic
GATCCATCCAGTCCAGGGTC+CGG 0.524687 1.1:+4947858 MS.gene24498:CDS
CTTCCATGAAGAGGAGTATC+CGG 0.526400 1.1:+4947749 MS.gene24498:CDS
GGAACACACGTGAGCCGGAC+CGG 0.528631 1.1:-4947768 None:intergenic
GTTCACACAAGGCGAAATAG+AGG 0.540753 1.1:+4947806 MS.gene24498:CDS
ATCCAAAAGTGTTGCCATGA+GGG 0.543780 1.1:-4948123 None:intergenic
TATTTCGCCTTGTGTGAACA+TGG 0.548387 1.1:-4947802 None:intergenic
CCGGTTGAGAATGGAAAACC+GGG 0.557045 1.1:+4948016 MS.gene24498:CDS
AATCAAACCGGGAGTCGGCT+AGG 0.560261 1.1:+4947940 MS.gene24498:CDS
ATCAGAATCAATGTCCCTCA+TGG 0.566320 1.1:+4948109 MS.gene24498:CDS
GAACCGGACCCTGGACTGGA+TGG 0.582397 1.1:-4947861 None:intergenic
ATGAAGAGGAGTATCCGGTC+CGG 0.588642 1.1:+4947754 MS.gene24498:CDS
AGCAATGTCCTTCCATGAAG+AGG 0.590028 1.1:+4947740 None:intergenic
AGTCCAGGGTCCGGTTCACA+AGG 0.591544 1.1:+4947867 MS.gene24498:CDS
ACCGGTTCAAATCGTTCGTG+AGG 0.594738 1.1:-4947998 None:intergenic
CGGATACTCCTCTTCATGGA+AGG 0.596073 1.1:-4947748 None:intergenic
CGGTTGATCCATCCAGTCCA+GGG 0.598027 1.1:+4947853 MS.gene24498:CDS
GACTGGATGGATCAACCGGT+TGG 0.601414 1.1:-4947848 None:intergenic
GTGACCGCCTAGCCGACTCC+CGG 0.602249 1.1:-4947947 None:intergenic
TAATATGAGATTGTATTGCA+TGG 0.609971 1.1:-4948063 None:intergenic
ATCAACCGGTTGGTTAATGA+GGG 0.611428 1.1:-4947838 None:intergenic
AATGCAATCAAACCGGGAGT+CGG 0.621410 1.1:+4947935 MS.gene24498:CDS
ATACAATCTCATATTATCAA+CGG 0.623568 1.1:+4948070 MS.gene24498:CDS
AAGGAGAATGCAATCAAACC+GGG 0.631263 1.1:+4947929 MS.gene24498:CDS
CATGAAACCATGTTCACACA+AGG 0.636957 1.1:+4947795 MS.gene24498:CDS
TTCACAAGGATCCAGTCGTG+CGG 0.658093 1.1:+4947881 MS.gene24498:CDS
GATCCAAAAGTGTTGCCATG+AGG 0.664933 1.1:-4948124 None:intergenic
AGTCGGCTAGGCGGTCACGT+TGG 0.676204 1.1:+4947952 MS.gene24498:CDS
GGTCACGTTGGAGAAAGAAG+CGG 0.707696 1.1:+4947964 MS.gene24498:CDS
CAAACCGGGAGTCGGCTAGG+CGG 0.728540 1.1:+4947943 MS.gene24498:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATACAATCTCATATTATCAA+CGG + chr1.1:4948070-4948089 MS.gene24498:CDS 20.0%
! TAATATGAGATTGTATTGCA+TGG - chr1.1:4948066-4948085 None:intergenic 25.0%
! CAACACTTTTGGATCTATAT+CGG + chr1.1:4948132-4948151 MS.gene24498:CDS 30.0%
!!! TTCTCCTTATTTTTCTCTCA+CGG - chr1.1:4947917-4947936 None:intergenic 30.0%
TAAGGAGAATGCAATCAAAC+CGG + chr1.1:4947928-4947947 MS.gene24498:CDS 35.0%
! ATTTTCCCTCATTAACCAAC+CGG + chr1.1:4947833-4947852 MS.gene24498:CDS 35.0%
!!! TCTCCTTATTTTTCTCTCAC+GGG - chr1.1:4947916-4947935 None:intergenic 35.0%
AAGGAGAATGCAATCAAACC+GGG + chr1.1:4947929-4947948 MS.gene24498:CDS 40.0%
ATCAGAATCAATGTCCCTCA+TGG + chr1.1:4948109-4948128 MS.gene24498:CDS 40.0%
CATGAAACCATGTTCACACA+AGG + chr1.1:4947795-4947814 MS.gene24498:CDS 40.0%
GGGAACTAAAAAACCAGCTA+GGG + chr1.1:4948036-4948055 MS.gene24498:CDS 40.0%
GTGAACATGGTTTCATGAAC+CGG - chr1.1:4947792-4947811 None:intergenic 40.0%
TATTTCGCCTTGTGTGAACA+TGG - chr1.1:4947805-4947824 None:intergenic 40.0%
! ATCAACCGGTTGGTTAATGA+GGG - chr1.1:4947841-4947860 None:intergenic 40.0%
!! ATCCAAAAGTGTTGCCATGA+GGG - chr1.1:4948126-4948145 None:intergenic 40.0%
!!! CTAGCTGGTTTTTTAGTTCC+CGG - chr1.1:4948037-4948056 None:intergenic 40.0%
AATGCAATCAAACCGGGAGT+CGG + chr1.1:4947935-4947954 MS.gene24498:CDS 45.0%
ACCGGTTGAGAATGGAAAAC+CGG + chr1.1:4948015-4948034 MS.gene24498:CDS 45.0%
ACCTCACGAACGATTTGAAC+CGG + chr1.1:4947997-4948016 MS.gene24498:CDS 45.0%
ATTGCATGGTTAACCCTAGC+TGG - chr1.1:4948052-4948071 None:intergenic 45.0%
CGACCCGTGAGAGAAAAATA+AGG + chr1.1:4947910-4947929 MS.gene24498:CDS 45.0%
CGATTTGAACCGGTTGAGAA+TGG + chr1.1:4948007-4948026 MS.gene24498:CDS 45.0%
CGGGAACTAAAAAACCAGCT+AGG + chr1.1:4948035-4948054 MS.gene24498:CDS 45.0%
GTTCACACAAGGCGAAATAG+AGG + chr1.1:4947806-4947825 MS.gene24498:CDS 45.0%
! GATCAACCGGTTGGTTAATG+AGG - chr1.1:4947842-4947861 None:intergenic 45.0%
!! CTTCCATGAAGAGGAGTATC+CGG + chr1.1:4947749-4947768 MS.gene24498:CDS 45.0%
!! GATCCAAAAGTGTTGCCATG+AGG - chr1.1:4948127-4948146 None:intergenic 45.0%
ACGACTGGATCCTTGTGAAC+CGG - chr1.1:4947880-4947899 None:intergenic 50.0%
CCGGTTGAGAATGGAAAACC+GGG + chr1.1:4948016-4948035 MS.gene24498:CDS 50.0%
CGGATACTCCTCTTCATGGA+AGG - chr1.1:4947751-4947770 None:intergenic 50.0%
GGTCACGTTGGAGAAAGAAG+CGG + chr1.1:4947964-4947983 MS.gene24498:CDS 50.0%
TTCACAAGGATCCAGTCGTG+CGG + chr1.1:4947881-4947900 MS.gene24498:CDS 50.0%
! ACCGGTTCAAATCGTTCGTG+AGG - chr1.1:4948001-4948020 None:intergenic 50.0%
! CCCGGTTTTCCATTCTCAAC+CGG - chr1.1:4948019-4948038 None:intergenic 50.0%
! GTCCCTCATGGCAACACTTT+TGG + chr1.1:4948121-4948140 MS.gene24498:CDS 50.0%
!! ATGAAGAGGAGTATCCGGTC+CGG + chr1.1:4947754-4947773 MS.gene24498:CDS 50.0%
AATCAAACCGGGAGTCGGCT+AGG + chr1.1:4947940-4947959 MS.gene24498:CDS 55.0%
CGGTTGATCCATCCAGTCCA+GGG + chr1.1:4947853-4947872 MS.gene24498:CDS 55.0%
GACTGGATGGATCAACCGGT+TGG - chr1.1:4947851-4947870 None:intergenic 55.0%
GGACCGGATACTCCTCTTCA+TGG - chr1.1:4947755-4947774 None:intergenic 55.0%
! CCTGGACTGGATGGATCAAC+CGG - chr1.1:4947855-4947874 None:intergenic 55.0%
AGTCCAGGGTCCGGTTCACA+AGG + chr1.1:4947867-4947886 MS.gene24498:CDS 60.0%
CCGGTTGATCCATCCAGTCC+AGG + chr1.1:4947852-4947871 MS.gene24498:CDS 60.0%
GAACCGGAACACACGTGAGC+CGG - chr1.1:4947776-4947795 None:intergenic 60.0%
GATCCATCCAGTCCAGGGTC+CGG + chr1.1:4947858-4947877 MS.gene24498:CDS 60.0%
GATCCTTGTGAACCGGACCC+TGG - chr1.1:4947873-4947892 None:intergenic 60.0%
GGTCGAGTAAACCGCACGAC+TGG - chr1.1:4947895-4947914 None:intergenic 60.0%
TTGTGAACCGGACCCTGGAC+TGG - chr1.1:4947868-4947887 None:intergenic 60.0%
AGTCGGCTAGGCGGTCACGT+TGG + chr1.1:4947952-4947971 MS.gene24498:CDS 65.0%
CAAACCGGGAGTCGGCTAGG+CGG + chr1.1:4947943-4947962 MS.gene24498:CDS 65.0%
GGAACACACGTGAGCCGGAC+CGG - chr1.1:4947771-4947790 None:intergenic 65.0%
GGTCCGGCTCACGTGTGTTC+CGG + chr1.1:4947770-4947789 MS.gene24498:CDS 65.0%
! GAACCGGACCCTGGACTGGA+TGG - chr1.1:4947864-4947883 None:intergenic 65.0%
! GTGACCGCCTAGCCGACTCC+CGG - chr1.1:4947950-4947969 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 4947744 4948181 4947744 ID=MS.gene24498
chr1.1 mRNA 4947744 4948181 4947744 ID=MS.gene24498.t1;Parent=MS.gene24498
chr1.1 exon 4947744 4948181 4947744 ID=MS.gene24498.t1.exon1;Parent=MS.gene24498.t1
chr1.1 CDS 4947744 4948181 4947744 ID=cds.MS.gene24498.t1;Parent=MS.gene24498.t1
Gene Sequence

>MS.gene24498

ATGTCCTTCCATGAAGAGGAGTATCCGGTCCGGCTCACGTGTGTTCCGGTTCATGAAACCATGTTCACACAAGGCGAAATAGAGGAGTTATTTTCCCTCATTAACCAACCGGTTGATCCATCCAGTCCAGGGTCCGGTTCACAAGGATCCAGTCGTGCGGTTTACTCGACCCGTGAGAGAAAAATAAGGAGAATGCAATCAAACCGGGAGTCGGCTAGGCGGTCACGTTGGAGAAAGAAGCGGCACGTAGAGAACCTCACGAACGATTTGAACCGGTTGAGAATGGAAAACCGGGAACTAAAAAACCAGCTAGGGTTAACCATGCAATACAATCTCATATTATCAACGGAGAATGAACGTCTAAGATCAGAATCAATGTCCCTCATGGCAACACTTTTGGATCTATATCGGACTTTAGAGACAATAATTTCGCAATAG
Protein sequence

>MS.gene24498.t1

MSFHEEEYPVRLTCVPVHETMFTQGEIEELFSLINQPVDPSSPGSGSQGSSRAVYSTRERKIRRMQSNRESARRSRWRKKRHVENLTNDLNRLRMENRELKNQLGLTMQYNLILSTENERLRSESMSLMATLLDLYRTLETIISQ