AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene003946

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003946.t1 MTR_2g098160 74.332 187 33 2 1 187 1 172 3.62e-97 279
MS.gene003946.t1 MTR_4g065570 84.713 157 4 1 31 187 1 137 5.94e-92 265
MS.gene003946.t1 MTR_7g092400 58.378 185 61 4 3 187 92 260 4.44e-70 213
MS.gene003946.t1 MTR_0249s0070 55.676 185 63 3 3 187 4 169 5.19e-68 205
MS.gene003946.t1 MTR_0249s0070 55.676 185 63 3 3 187 12 177 6.04e-68 205
MS.gene003946.t1 MTR_7g104320 40.217 184 92 5 4 187 3 168 1.01e-39 133
MS.gene003946.t1 MTR_4g053440 39.674 184 95 4 4 187 3 170 1.16e-39 133
MS.gene003946.t1 MTR_2g086190 40.462 173 71 4 15 187 10 150 2.30e-38 129
MS.gene003946.t1 MTR_1g060380 43.243 185 73 6 4 187 3 156 3.56e-35 121
MS.gene003946.t1 MTR_8g036980 65.574 61 21 0 127 187 91 151 1.58e-26 99.0
MS.gene003946.t1 MTR_3g028010 59.016 61 25 0 127 187 103 163 1.61e-23 91.7
MS.gene003946.t1 MTR_1g100773 30.814 172 82 5 15 185 3 138 1.05e-22 89.0
MS.gene003946.t1 MTR_7g114920 30.000 170 77 4 15 184 3 130 4.48e-22 87.0
MS.gene003946.t1 MTR_3g025570 72.727 44 12 0 122 165 4 47 2.74e-19 79.3
MS.gene003946.t1 MTR_2g054650 30.409 171 70 4 15 185 4 125 2.54e-17 74.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003946.t1 AT1G51200 59.358 187 62 4 1 187 1 173 9.22e-64 194
MS.gene003946.t1 AT1G51200 59.358 187 62 4 1 187 1 173 9.22e-64 194
MS.gene003946.t1 AT1G51200 59.358 187 62 4 1 187 1 173 9.22e-64 194
MS.gene003946.t1 AT1G51200 59.358 187 62 4 1 187 1 173 9.22e-64 194
MS.gene003946.t1 AT2G36320 41.573 178 76 3 12 187 10 161 1.50e-42 140
MS.gene003946.t1 AT2G27580 39.306 173 86 3 15 187 10 163 2.33e-39 132
MS.gene003946.t1 AT2G27580 39.306 173 86 3 15 187 10 163 2.33e-39 132
MS.gene003946.t1 AT4G12040 36.313 179 97 3 11 187 12 175 1.19e-38 130
MS.gene003946.t1 AT4G12040 36.313 179 97 3 11 187 12 175 1.19e-38 130
MS.gene003946.t1 AT1G12440 38.636 176 88 1 12 187 13 168 3.00e-38 129
MS.gene003946.t1 AT1G12440 38.636 176 88 1 12 187 13 168 3.00e-38 129
MS.gene003946.t1 AT1G12440 38.636 176 88 1 12 187 13 168 3.00e-38 129
MS.gene003946.t1 AT4G22820 36.994 173 94 2 15 187 19 176 3.84e-37 127
MS.gene003946.t1 AT4G22820 36.994 173 94 2 15 187 19 176 3.84e-37 127
MS.gene003946.t1 AT3G52800 41.489 188 86 5 4 187 3 170 9.51e-36 123
MS.gene003946.t1 AT3G52800 41.489 188 86 5 4 187 3 170 9.51e-36 123
MS.gene003946.t1 AT3G12630 37.349 166 67 5 23 187 31 160 3.53e-28 103
MS.gene003946.t1 AT4G14225 32.948 173 64 2 15 187 5 125 8.66e-26 96.3
MS.gene003946.t1 AT4G25380 28.409 176 65 4 18 187 10 130 3.06e-22 87.4

Find 49 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGGCTTAGAGATAGTTTC+AGG 0.302295 4.1:+35413027 None:intergenic
TTCGGACCATCCTTCGGCTT+TGG 0.323240 4.1:+35412970 None:intergenic
ATGCACAATATAGGACCTTC+AGG 0.357857 4.1:+35413291 None:intergenic
GTTTCAGCATCATGTCTTTG+TGG 0.367335 4.1:+35413214 None:intergenic
AGCTTCTCAGCCTTGACAAC+CGG 0.380344 4.1:+35412796 None:intergenic
CTTGACAACCGGATTTGCTT+TGG 0.394350 4.1:+35412807 None:intergenic
TTGCAGTTGCTGCAACGTTT+CGG 0.398329 4.1:+35412952 None:intergenic
TCCCTTGGAAATATTATGAA+TGG 0.415286 4.1:-35413165 MS.gene003946:CDS
AGTTTCAGGTTCCACAGAAA+TGG 0.422622 4.1:+35413041 None:intergenic
CAAAGACATGATGCTGAAAC+AGG 0.424095 4.1:-35413211 MS.gene003946:CDS
AATAAGCGAGTTGGTTTGAC+AGG 0.426782 4.1:-35412931 MS.gene003946:CDS
CAACGTTTCGGACCATCCTT+CGG 0.445047 4.1:+35412964 None:intergenic
TGCCATAGCCAAAGCAAATC+CGG 0.453351 4.1:-35412815 MS.gene003946:CDS
CAGTTGTTGATGCACAATAT+AGG 0.453708 4.1:+35413282 None:intergenic
AACCGGATTTGCTTTGGCTA+TGG 0.464324 4.1:+35412813 None:intergenic
TTAGGTTCCACGGAAATGGC+TGG 0.467021 4.1:+35413087 None:intergenic
TCAGGTTCCACAGAAATGGC+TGG 0.480113 4.1:+35413045 None:intergenic
GCACTTAGAGCACATGTTCA+TGG 0.487125 4.1:+35413236 None:intergenic
CCCTTGGAAATATTATGAAT+GGG 0.495769 4.1:-35413164 MS.gene003946:CDS
CAGAAGTGCGGTAATCGAAC+GGG 0.502252 4.1:+35412845 None:intergenic
AAGGGATGATGCTGCAAGAT+GGG 0.510002 4.1:+35413182 None:intergenic
ACGCTGGCAGCAGTAACAAC+AGG 0.516439 4.1:+35413117 None:intergenic
CCCATTCATAATATTTCCAA+GGG 0.520390 4.1:+35413164 None:intergenic
ACCCATTCATAATATTTCCA+AGG 0.526039 4.1:+35413163 None:intergenic
CAAGGGATGATGCTGCAAGA+TGG 0.532070 4.1:+35413181 None:intergenic
AGCAACTGCAATAAGCGAGT+TGG 0.543723 4.1:-35412940 MS.gene003946:CDS
AGCGATGTACAGCACAGAAA+AGG 0.543830 4.1:+35412887 None:intergenic
CAGGTTCCACAGAAATGGCT+GGG 0.544362 4.1:+35413046 None:intergenic
CATCTTGCAGCATCATCCCT+TGG 0.544464 4.1:-35413180 MS.gene003946:CDS
TTTATTTGGCTCAGGTTCAG+AGG 0.556901 4.1:-35413004 MS.gene003946:CDS
GCAGAAGTGCGGTAATCGAA+CGG 0.558885 4.1:+35412844 None:intergenic
TAGGTTCCACGGAAATGGCT+GGG 0.559679 4.1:+35413088 None:intergenic
TGCACAATATAGGACCTTCA+GGG 0.559940 4.1:+35413292 None:intergenic
CAAAGCAAATCCGGTTGTCA+AGG 0.564430 4.1:-35412806 MS.gene003946:CDS
AATGGCTGGGATATCGACAC+TGG 0.589398 4.1:+35413059 None:intergenic
CATGATGCTGAAACAGGAGC+AGG 0.593551 4.1:-35413205 MS.gene003946:CDS
ACAGGGTTTAATTGTCGATG+TGG 0.597602 4.1:-35412913 MS.gene003946:CDS
GGTGATCCAAAGCCGAAGGA+TGG 0.601061 4.1:-35412976 MS.gene003946:CDS
CGATATCCCAGCCATTTCTG+TGG 0.616564 4.1:-35413052 MS.gene003946:CDS
TGGCATCTCGTGCAGAAGTG+CGG 0.628982 4.1:+35412833 None:intergenic
GAGTGGTGATCCAAAGCCGA+AGG 0.630939 4.1:-35412980 MS.gene003946:CDS
GGATATCCCAGCCATTTCCG+TGG 0.638474 4.1:-35413094 MS.gene003946:CDS
GCACAATATAGGACCTTCAG+GGG 0.644318 4.1:+35413293 None:intergenic
ATAAGCGAGTTGGTTTGACA+GGG 0.651214 4.1:-35412930 MS.gene003946:CDS
AATGGCTGGGATATCCACGC+TGG 0.652769 4.1:+35413101 None:intergenic
GGCTCAGGTTCAGAGGAGAG+TGG 0.659270 4.1:-35412997 MS.gene003946:CDS
TGTTGTTACTGCTGCCAGCG+TGG 0.668169 4.1:-35413115 MS.gene003946:CDS
ATATTGTGCATCAACAACTG+TGG 0.675543 4.1:-35413279 MS.gene003946:CDS
CACAATATAGGACCTTCAGG+GGG 0.733275 4.1:+35413294 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATCTCTAAGCCTTTTTTATT+TGG - chr4.1:35413089-35413108 MS.gene003946:CDS 25.0%
ACCCATTCATAATATTTCCA+AGG + chr4.1:35412947-35412966 None:intergenic 30.0%
CCCATTCATAATATTTCCAA+GGG + chr4.1:35412946-35412965 None:intergenic 30.0%
CCCTTGGAAATATTATGAAT+GGG - chr4.1:35412943-35412962 MS.gene003946:CDS 30.0%
TCCCTTGGAAATATTATGAA+TGG - chr4.1:35412942-35412961 MS.gene003946:CDS 30.0%
! ATCAACAACTGTGGATTTTT+CGG - chr4.1:35412837-35412856 MS.gene003946:CDS 30.0%
AAAGGCTTAGAGATAGTTTC+AGG + chr4.1:35413083-35413102 None:intergenic 35.0%
ATATTGTGCATCAACAACTG+TGG - chr4.1:35412828-35412847 MS.gene003946:CDS 35.0%
CAGTTGTTGATGCACAATAT+AGG + chr4.1:35412828-35412847 None:intergenic 35.0%
GAACCTGAGCCAAATAAAAA+AGG + chr4.1:35413101-35413120 None:intergenic 35.0%
! ATATCGACACTGGAAGTTTT+AGG + chr4.1:35413041-35413060 None:intergenic 35.0%
!!! AAGCCTTTTTTATTTGGCTC+AGG - chr4.1:35413095-35413114 MS.gene003946:CDS 35.0%
ACAGGGTTTAATTGTCGATG+TGG - chr4.1:35413194-35413213 MS.gene003946:CDS 40.0%
ATGCACAATATAGGACCTTC+AGG + chr4.1:35412819-35412838 None:intergenic 40.0%
CAAAGACATGATGCTGAAAC+AGG - chr4.1:35412896-35412915 MS.gene003946:CDS 40.0%
GTTTCAGCATCATGTCTTTG+TGG + chr4.1:35412896-35412915 None:intergenic 40.0%
TGCACAATATAGGACCTTCA+GGG + chr4.1:35412818-35412837 None:intergenic 40.0%
! TTTATTTGGCTCAGGTTCAG+AGG - chr4.1:35413103-35413122 MS.gene003946:CDS 40.0%
!! AATAAGCGAGTTGGTTTGAC+AGG - chr4.1:35413176-35413195 MS.gene003946:CDS 40.0%
!! AGTTTCAGGTTCCACAGAAA+TGG + chr4.1:35413069-35413088 None:intergenic 40.0%
!! ATAAGCGAGTTGGTTTGACA+GGG - chr4.1:35413177-35413196 MS.gene003946:CDS 40.0%
!!! ACTGGAAGTTTTAGGTTCCA+CGG + chr4.1:35413033-35413052 None:intergenic 40.0%
!!! AGTTTTAGGTTCCACGGAAA+TGG + chr4.1:35413027-35413046 None:intergenic 40.0%
AAGGGATGATGCTGCAAGAT+GGG + chr4.1:35412928-35412947 None:intergenic 45.0%
AGCAACTGCAATAAGCGAGT+TGG - chr4.1:35413167-35413186 MS.gene003946:CDS 45.0%
AGCGATGTACAGCACAGAAA+AGG + chr4.1:35413223-35413242 None:intergenic 45.0%
CAAAGCAAATCCGGTTGTCA+AGG - chr4.1:35413301-35413320 MS.gene003946:CDS 45.0%
CACAATATAGGACCTTCAGG+GGG + chr4.1:35412816-35412835 None:intergenic 45.0%
GCACAATATAGGACCTTCAG+GGG + chr4.1:35412817-35412836 None:intergenic 45.0%
GCACTTAGAGCACATGTTCA+TGG + chr4.1:35412874-35412893 None:intergenic 45.0%
TGCCATAGCCAAAGCAAATC+CGG - chr4.1:35413292-35413311 MS.gene003946:CDS 45.0%
TTGCAGTTGCTGCAACGTTT+CGG + chr4.1:35413158-35413177 None:intergenic 45.0%
! AACCGGATTTGCTTTGGCTA+TGG + chr4.1:35413297-35413316 None:intergenic 45.0%
! CTTGACAACCGGATTTGCTT+TGG + chr4.1:35413303-35413322 None:intergenic 45.0%
AATGGCTGGGATATCGACAC+TGG + chr4.1:35413051-35413070 None:intergenic 50.0%
AGCTTCTCAGCCTTGACAAC+CGG + chr4.1:35413314-35413333 None:intergenic 50.0%
CAACGTTTCGGACCATCCTT+CGG + chr4.1:35413146-35413165 None:intergenic 50.0%
CAAGGGATGATGCTGCAAGA+TGG + chr4.1:35412929-35412948 None:intergenic 50.0%
CAGGTTCCACAGAAATGGCT+GGG + chr4.1:35413064-35413083 None:intergenic 50.0%
CATCTTGCAGCATCATCCCT+TGG - chr4.1:35412927-35412946 MS.gene003946:CDS 50.0%
CATGATGCTGAAACAGGAGC+AGG - chr4.1:35412902-35412921 MS.gene003946:CDS 50.0%
CGATATCCCAGCCATTTCTG+TGG - chr4.1:35413055-35413074 MS.gene003946:CDS 50.0%
TAGGTTCCACGGAAATGGCT+GGG + chr4.1:35413022-35413041 None:intergenic 50.0%
TCAGGTTCCACAGAAATGGC+TGG + chr4.1:35413065-35413084 None:intergenic 50.0%
TTAGGTTCCACGGAAATGGC+TGG + chr4.1:35413023-35413042 None:intergenic 50.0%
! CAGAAGTGCGGTAATCGAAC+GGG + chr4.1:35413265-35413284 None:intergenic 50.0%
! GCAGAAGTGCGGTAATCGAA+CGG + chr4.1:35413266-35413285 None:intergenic 50.0%
AATGGCTGGGATATCCACGC+TGG + chr4.1:35413009-35413028 None:intergenic 55.0%
ACGCTGGCAGCAGTAACAAC+AGG + chr4.1:35412993-35413012 None:intergenic 55.0%
GAATGTCAAGCTCCCCCTGA+AGG - chr4.1:35412801-35412820 MS.gene003946:CDS 55.0%
GAGTGGTGATCCAAAGCCGA+AGG - chr4.1:35413127-35413146 MS.gene003946:CDS 55.0%
GGATATCCCAGCCATTTCCG+TGG - chr4.1:35413013-35413032 MS.gene003946:CDS 55.0%
GGTGATCCAAAGCCGAAGGA+TGG - chr4.1:35413131-35413150 MS.gene003946:CDS 55.0%
TGGCATCTCGTGCAGAAGTG+CGG + chr4.1:35413277-35413296 None:intergenic 55.0%
TGTTGTTACTGCTGCCAGCG+TGG - chr4.1:35412992-35413011 MS.gene003946:CDS 55.0%
TTCGGACCATCCTTCGGCTT+TGG + chr4.1:35413140-35413159 None:intergenic 55.0%
GGCTCAGGTTCAGAGGAGAG+TGG - chr4.1:35413110-35413129 MS.gene003946:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 35412783 35413346 35412783 ID=MS.gene003946
chr4.1 mRNA 35412783 35413346 35412783 ID=MS.gene003946.t1;Parent=MS.gene003946
chr4.1 exon 35412783 35413346 35412783 ID=MS.gene003946.t1.exon1;Parent=MS.gene003946.t1
chr4.1 CDS 35412783 35413346 35412783 ID=cds.MS.gene003946.t1;Parent=MS.gene003946.t1
Gene Sequence

>MS.gene003946

ATGGAACATGAAAAGACTGAATGTCAAGCTCCCCCTGAAGGTCCTATATTGTGCATCAACAACTGTGGATTTTTCGGAAGTGCAGCTACCATGAACATGTGCTCTAAGTGCCACAAAGACATGATGCTGAAACAGGAGCAGGCCCATCTTGCAGCATCATCCCTTGGAAATATTATGAATGGGTCTACAAGCAACACTGAAAAAGAACCTGTTGTTACTGCTGCCAGCGTGGATATCCCAGCCATTTCCGTGGAACCTAAAACTTCCAGTGTCGATATCCCAGCCATTTCTGTGGAACCTGAAACTATCTCTAAGCCTTTTTTATTTGGCTCAGGTTCAGAGGAGAGTGGTGATCCAAAGCCGAAGGATGGTCCGAAACGTTGCAGCAACTGCAATAAGCGAGTTGGTTTGACAGGGTTTAATTGTCGATGTGGCAACCTTTTCTGTGCTGTACATCGCTACTCAGACAAGCATGATTGCCCGTTCGATTACCGCACTTCTGCACGAGATGCCATAGCCAAAGCAAATCCGGTTGTCAAGGCTGAGAAGCTTGATAAGATCTGA
Protein sequence

>MS.gene003946.t1

MEHEKTECQAPPEGPILCINNCGFFGSAATMNMCSKCHKDMMLKQEQAHLAASSLGNIMNGSTSNTEKEPVVTAASVDIPAISVEPKTSSVDIPAISVEPETISKPFLFGSGSEESGDPKPKDGPKRCSNCNKRVGLTGFNCRCGNLFCAVHRYSDKHDCPFDYRTSARDAIAKANPVVKAEKLDKI