AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene032091

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene032091.t1 MTR_2g081600 95.575 113 5 0 25 137 1 113 3.50e-78 227
MS.gene032091.t1 MTR_2g081630 95.614 114 4 1 25 137 1 114 1.15e-76 223
MS.gene032091.t1 MTR_1g082660 63.855 83 29 1 45 127 100 181 7.55e-32 114
MS.gene032091.t1 MTR_3g099180 63.855 83 29 1 45 127 54 135 1.26e-31 112
MS.gene032091.t1 MTR_3g099180 63.855 83 29 1 45 127 54 135 1.29e-31 112
MS.gene032091.t1 MTR_7g113680 61.446 83 31 1 45 127 151 232 3.74e-30 110
MS.gene032091.t1 MTR_2g023340 57.317 82 34 1 47 128 86 166 5.66e-25 95.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene032091.t1 AT3G48590 59.341 91 36 1 45 135 64 153 2.34e-32 114
MS.gene032091.t1 AT1G54830 63.855 83 29 1 45 127 69 150 2.20e-31 111
MS.gene032091.t1 AT1G54830 63.855 83 29 1 45 127 69 150 2.20e-31 111
MS.gene032091.t1 AT1G54830 63.855 83 29 1 45 127 69 150 2.20e-31 111
MS.gene032091.t1 AT1G08970 63.855 83 29 1 45 127 79 160 5.04e-31 111
MS.gene032091.t1 AT1G08970 63.855 83 29 1 45 127 79 160 5.04e-31 111
MS.gene032091.t1 AT1G08970 63.855 83 29 1 45 127 79 160 5.04e-31 111
MS.gene032091.t1 AT1G08970 63.855 83 29 1 45 127 79 160 5.04e-31 111
MS.gene032091.t1 AT5G63470 63.855 83 29 1 45 127 77 158 5.19e-31 111
MS.gene032091.t1 AT5G63470 63.855 83 29 1 45 127 77 158 5.19e-31 111
MS.gene032091.t1 AT1G56170 57.831 83 34 1 45 127 75 156 3.39e-30 108
MS.gene032091.t1 AT1G56170 57.831 83 34 1 45 127 75 156 3.39e-30 108
MS.gene032091.t1 AT5G50480 50.538 93 43 2 47 137 55 146 6.84e-25 94.7
MS.gene032091.t1 AT5G27910 57.895 76 31 1 45 120 35 109 3.31e-22 87.4
MS.gene032091.t1 AT5G50490 39.806 103 60 2 17 119 8 108 3.09e-18 77.0
MS.gene032091.t1 AT5G50470 39.796 98 50 3 45 134 62 158 8.91e-17 73.6
MS.gene032091.t1 AT5G38140 39.806 103 50 3 23 124 53 144 2.88e-15 69.3

Find 16 sgRNAs with CRISPR-Local

Find 18 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACAAGAAGGTCTTGGATTA+TGG 0.238491 2.3:+16566031 MS.gene032091:CDS
GCATATTCAGGTATAGTAAA+TGG 0.350320 2.3:+16565864 MS.gene032091:CDS
AGACAAGCAGGTGCATATTC+AGG 0.363661 2.3:+16565852 MS.gene032091:CDS
CATGATAGTGGCATCATTAG+TGG 0.365943 2.3:-16566159 None:intergenic
GAAGACGTGAAAATGATATC+AGG 0.404379 2.3:+16565957 MS.gene032091:CDS
AGTTTACATTTGCATGATAG+TGG 0.407452 2.3:-16566171 None:intergenic
TCTTGGATTATGGCTATTGA+TGG 0.412219 2.3:+16566041 MS.gene032091:CDS
AAGAACTTACAAGAAGGTCT+TGG 0.420089 2.3:+16566024 MS.gene032091:CDS
TATCTTCTTTATTCTTGCTA+AGG 0.439544 2.3:-16565919 None:intergenic
ATCTTCTTTATTCTTGCTAA+GGG 0.456949 2.3:-16565918 None:intergenic
AATGGTGGCATAGGAAGAAC+AGG 0.475968 2.3:+16565882 MS.gene032091:CDS
GGTATAGTAAATGGTGGCAT+AGG 0.554867 2.3:+16565873 MS.gene032091:CDS
AGGAACAATATGAGACAAGC+AGG 0.582630 2.3:+16565840 MS.gene032091:CDS
CTTGCTAAGGGTAATGAATG+TGG 0.583369 2.3:-16565906 None:intergenic
TCATTGAAGAACTTACAAGA+AGG 0.590491 2.3:+16566018 MS.gene032091:CDS
TATTCAGGTATAGTAAATGG+TGG 0.667600 2.3:+16565867 MS.gene032091:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGATTTTTTGATCACTT+TGG + chr2.3:16566121-16566140 MS.gene032091:CDS 20.0%
! ATCTTCTTTATTCTTGCTAA+GGG - chr2.3:16565921-16565940 None:intergenic 25.0%
! TATCTTCTTTATTCTTGCTA+AGG - chr2.3:16565922-16565941 None:intergenic 25.0%
GCATATTCAGGTATAGTAAA+TGG + chr2.3:16565864-16565883 MS.gene032091:CDS 30.0%
TATTCAGGTATAGTAAATGG+TGG + chr2.3:16565867-16565886 MS.gene032091:CDS 30.0%
TCATTGAAGAACTTACAAGA+AGG + chr2.3:16566018-16566037 MS.gene032091:CDS 30.0%
!! CAAGCTTTTGAGAAAACAAT+TGG - chr2.3:16565990-16566009 None:intergenic 30.0%
AAGAACTTACAAGAAGGTCT+TGG + chr2.3:16566024-16566043 MS.gene032091:CDS 35.0%
AGAGAAACAGAGAAAAACAG+AGG + chr2.3:16565820-16565839 MS.gene032091:CDS 35.0%
GAAGACGTGAAAATGATATC+AGG + chr2.3:16565957-16565976 MS.gene032091:CDS 35.0%
TACAAGAAGGTCTTGGATTA+TGG + chr2.3:16566031-16566050 MS.gene032091:CDS 35.0%
TCTTGGATTATGGCTATTGA+TGG + chr2.3:16566041-16566060 MS.gene032091:CDS 35.0%
AGGAACAATATGAGACAAGC+AGG + chr2.3:16565840-16565859 MS.gene032091:CDS 40.0%
CTTGCTAAGGGTAATGAATG+TGG - chr2.3:16565909-16565928 None:intergenic 40.0%
GGTATAGTAAATGGTGGCAT+AGG + chr2.3:16565873-16565892 MS.gene032091:CDS 40.0%
!! CATGATAGTGGCATCATTAG+TGG - chr2.3:16566162-16566181 None:intergenic 40.0%
AATGGTGGCATAGGAAGAAC+AGG + chr2.3:16565882-16565901 MS.gene032091:CDS 45.0%
AGACAAGCAGGTGCATATTC+AGG + chr2.3:16565852-16565871 MS.gene032091:CDS 45.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 16565777 16566190 16565777 ID=MS.gene032091
chr2.3 mRNA 16565777 16566190 16565777 ID=MS.gene032091.t1;Parent=MS.gene032091
chr2.3 exon 16565777 16566190 16565777 ID=MS.gene032091.t1.exon1;Parent=MS.gene032091.t1
chr2.3 CDS 16565777 16566190 16565777 ID=cds.MS.gene032091.t1;Parent=MS.gene032091.t1
Gene Sequence

>MS.gene032091

ACAAACAACTCTATAACACAGTTAAAGTTAAACTCAAAAACAGAGAGAAACAGAGAAAAACAGAGGAACAATATGAGACAAGCAGGTGCATATTCAGGTATAGTAAATGGTGGCATAGGAAGAACAGGTCCACATTCATTACCCTTAGCAAGAATAAAGAAGATAATGAAGAATTCTAGTGAAGACGTGAAAATGATATCAGGTGTTGCTCCAATTGTTTTCTCAAAAGCTTGTGAACTTTTCATTGAAGAACTTACAAGAAGGTCTTGGATTATGGCTATTGATGGTAAAAGAAGAACTTTGAATAAAGAAGATGTTGCTTCTGCTGTTATAGCTACTGATATTTTTGATTTTTTGATCACTTTGGTTTCTAATTCTGATTCCACTAATGATGCCACTATCATGCAAATGTAA
Protein sequence

>MS.gene032091.t1

TNNSITQLKLNSKTERNREKQRNNMRQAGAYSGIVNGGIGRTGPHSLPLARIKKIMKNSSEDVKMISGVAPIVFSKACELFIEELTRRSWIMAIDGKRRTLNKEDVASAVIATDIFDFLITLVSNSDSTNDATIMQM