AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene003512

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003512.t1 MTR_4g073950 98.958 192 2 0 1 192 1 192 1.71e-143 397
MS.gene003512.t1 MTR_4g013350 56.579 152 65 1 41 192 47 197 5.65e-61 188
MS.gene003512.t1 MTR_4g013330 54.248 153 69 1 41 192 47 199 4.05e-59 184
MS.gene003512.t1 MTR_4g013320 53.947 152 69 1 41 192 49 199 2.31e-57 179
MS.gene003512.t1 MTR_4g013345 53.947 152 69 1 41 192 46 196 6.76e-57 178
MS.gene003512.t1 MTR_4g013325 52.055 146 69 1 47 192 55 199 4.25e-54 171
MS.gene003512.t1 MTR_7g093820 47.692 195 96 4 3 192 1 194 1.14e-51 164
MS.gene003512.t1 MTR_7g093830 52.288 153 71 2 41 192 42 193 2.02e-51 164
MS.gene003512.t1 MTR_4g013335 49.342 152 74 1 41 192 48 196 3.94e-51 163
MS.gene003512.t1 MTR_7g093850 50.980 153 73 2 41 192 43 194 1.59e-50 162
MS.gene003512.t1 MTR_1g054525 50.658 152 72 2 41 192 44 192 1.40e-49 159
MS.gene003512.t1 MTR_7g070390 47.647 170 82 2 23 192 30 192 2.06e-49 159
MS.gene003512.t1 MTR_4g013385 44.444 153 83 1 40 192 40 190 2.02e-45 149
MS.gene003512.t1 MTR_0433s0040 44.444 153 83 1 40 192 40 190 2.02e-45 149
MS.gene003512.t1 MTR_7g093790 47.059 153 79 2 41 192 40 191 2.40e-45 148
MS.gene003512.t1 MTR_4g074020 78.313 83 18 0 3 85 1 83 1.93e-44 143
MS.gene003512.t1 MTR_3g105640 46.053 152 81 1 42 192 37 188 2.04e-44 146
MS.gene003512.t1 MTR_4g013310 47.020 151 77 2 42 192 50 197 3.22e-44 145
MS.gene003512.t1 MTR_7g093870 41.818 165 92 2 32 192 29 193 9.19e-43 142
MS.gene003512.t1 MTR_4g013770 42.105 152 88 0 41 192 40 191 1.10e-42 142
MS.gene003512.t1 MTR_1g056370 42.208 154 86 2 39 191 34 185 1.27e-42 141
MS.gene003512.t1 MTR_5g096120 45.033 151 78 3 46 192 40 189 5.55e-40 134
MS.gene003512.t1 MTR_3g105630 38.542 192 110 4 4 192 3 189 3.40e-38 130
MS.gene003512.t1 MTR_4g078885 38.667 150 89 1 43 192 39 185 5.61e-35 122
MS.gene003512.t1 MTR_3g034030 37.333 150 91 1 43 192 39 185 2.40e-33 117
MS.gene003512.t1 MTR_4g013355 40.260 154 79 3 40 192 38 179 9.96e-33 115
MS.gene003512.t1 MTR_4g122110 39.216 153 92 1 40 192 29 180 5.26e-30 108
MS.gene003512.t1 MTR_4g122130 37.580 157 96 2 36 192 26 180 1.91e-28 105
MS.gene003512.t1 MTR_4g049550 32.432 148 99 1 42 189 29 175 1.80e-18 79.0
MS.gene003512.t1 MTR_8g099115 32.624 141 87 3 38 171 29 168 5.05e-18 78.2
MS.gene003512.t1 MTR_4g049570 31.944 144 97 1 46 189 33 175 8.29e-18 77.4
MS.gene003512.t1 MTR_8g099135 29.240 171 97 4 8 171 11 164 3.08e-15 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003512.t1 AT2G21100 57.895 190 76 3 3 191 1 187 2.08e-79 235
MS.gene003512.t1 AT2G21100 57.895 190 76 3 3 191 1 187 2.08e-79 235
MS.gene003512.t1 AT1G58170 47.853 163 80 2 34 192 24 185 2.75e-50 161
MS.gene003512.t1 AT5G42510 52.258 155 71 2 37 191 31 182 1.06e-49 159
MS.gene003512.t1 AT5G49040 42.857 189 101 3 10 192 4 191 4.65e-48 155
MS.gene003512.t1 AT5G42500 50.649 154 73 2 38 191 35 185 2.61e-47 153
MS.gene003512.t1 AT1G55210 46.053 152 78 1 41 192 40 187 6.32e-47 152
MS.gene003512.t1 AT1G55210 46.053 152 78 1 41 192 40 187 6.32e-47 152
MS.gene003512.t1 AT3G13650 39.683 189 100 3 8 192 8 186 1.92e-46 151
MS.gene003512.t1 AT1G65870 46.452 155 82 1 37 191 36 189 2.22e-44 146
MS.gene003512.t1 AT1G22900 46.452 155 80 2 37 191 42 193 2.55e-43 143
MS.gene003512.t1 AT2G21110 46.452 155 80 1 41 192 32 186 1.76e-42 141
MS.gene003512.t1 AT3G13662 44.604 139 73 1 41 179 38 172 7.11e-40 134
MS.gene003512.t1 AT3G13660 49.565 115 58 0 78 192 11 125 1.69e-38 129
MS.gene003512.t1 AT5G49030 47.826 138 71 1 41 178 41 177 3.20e-37 137
MS.gene003512.t1 AT4G38700 39.744 156 89 3 42 192 35 190 7.57e-37 127
MS.gene003512.t1 AT3G58090 49.541 109 55 0 83 191 163 271 1.28e-30 113
MS.gene003512.t1 AT4G11210 36.458 96 60 1 80 175 72 166 1.11e-13 66.6
MS.gene003512.t1 AT4G11190 30.709 127 86 2 50 175 41 166 4.91e-11 59.3

Find 50 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGGCCCACGAGCTTGGATTT+TGG 0.153982 4.3:-33022542 None:intergenic
GGATCAGATGTTTCAGTTAA+AGG 0.192736 4.3:-33022521 None:intergenic
TGAATTTAAAAGCAGGGAAT+TGG 0.267666 4.3:+33022333 MS.gene003512:CDS
TTTAAATTCAAGCTTTGAAT+TGG 0.322119 4.3:-33022320 None:intergenic
GGTAGCACATTTGCTCTTGT+TGG 0.341517 4.3:+33022653 MS.gene003512:CDS
GAACTGTGTAAGGTATGTTT+TGG 0.344125 4.3:-33022474 None:intergenic
ATGCCTGTTGTTGGAGGTAC+TGG 0.347518 4.3:+33022707 MS.gene003512:CDS
GAATTTAAAAGCAGGGAATT+GGG 0.356220 4.3:+33022334 MS.gene003512:CDS
ATGCCATTGCTAAGACTCAT+TGG 0.400986 4.3:+33022753 MS.gene003512:CDS
TTTGTGGATGGGCCGTATAA+TGG 0.409954 4.3:+33022632 MS.gene003512:CDS
GCAAATGTGCTACCATTATA+CGG 0.416384 4.3:-33022644 None:intergenic
TTGAGCTACTCCTTTGTGGA+TGG 0.418314 4.3:+33022620 MS.gene003512:CDS
TCATCGTGTCAGCAGGAGAT+TGG 0.421466 4.3:+33022584 MS.gene003512:CDS
GTCGTTGAGCTACTCCTTTG+TGG 0.422168 4.3:+33022616 MS.gene003512:CDS
TCAGCCACCTTGATCGCACT+TGG 0.429128 4.3:-33022437 None:intergenic
ACAACAGGCATCTCACGAAC+CGG 0.432988 4.3:-33022695 None:intergenic
AAATTCAAGCTTTGAATTGG+TGG 0.434298 4.3:-33022317 None:intergenic
TTGTGCTCGGCCCACGAGCT+TGG 0.436650 4.3:-33022549 None:intergenic
CATCGTGTCAGCAGGAGATT+GGG 0.452951 4.3:+33022585 MS.gene003512:CDS
GTTCGTGAGATGCCTGTTGT+TGG 0.459287 4.3:+33022698 MS.gene003512:CDS
CATTGGATTGATATTACTAC+TGG 0.460050 4.3:+33022770 MS.gene003512:CDS
TAATGTTTCCGAACTGTGTA+AGG 0.464436 4.3:-33022484 None:intergenic
ACTACTGGTGATGCTATTGT+TGG 0.469577 4.3:+33022785 MS.gene003512:CDS
TCACGAACCGGGTTCATAGC+AGG 0.470658 4.3:-33022683 None:intergenic
CAAAGCTTGAATTTAAAAGC+AGG 0.474536 4.3:+33022326 MS.gene003512:CDS
AAAACATACCTTACACAGTT+CGG 0.481108 4.3:+33022476 MS.gene003512:CDS
TGTCGTGGAAATAGAATTGA+AGG 0.486021 4.3:-33022397 None:intergenic
TGAGCTACTCCTTTGTGGAT+GGG 0.497718 4.3:+33022621 MS.gene003512:CDS
AGTCCAGTACCTCCAACAAC+AGG 0.500575 4.3:-33022710 None:intergenic
TTCAAGCTTTGAATTGGTGG+TGG 0.503760 4.3:-33022314 None:intergenic
TTACGCGTCATCGTGTCAGC+AGG 0.513526 4.3:+33022577 MS.gene003512:CDS
AAAGCTTGAATTTAAAAGCA+GGG 0.524166 4.3:+33022327 MS.gene003512:CDS
CGTGAGATGCCTGTTGTTGG+AGG 0.525744 4.3:+33022701 MS.gene003512:CDS
TGGCATAACCCCTTGCCATA+CGG 0.526929 4.3:-33022736 None:intergenic
TATTTCCACGACACACTAAG+TGG 0.531204 4.3:+33022407 MS.gene003512:CDS
CAGCCACCTTGATCGCACTT+GGG 0.549806 4.3:-33022436 None:intergenic
AAGCTCGTGGGCCGAGCACA+AGG 0.551866 4.3:+33022551 MS.gene003512:CDS
ACAGTTCGGAAACATTATGA+TGG 0.564400 4.3:+33022490 MS.gene003512:CDS
AATTTAAAAGCAGGGAATTG+GGG 0.569985 4.3:+33022335 MS.gene003512:CDS
CACGAACCGGGTTCATAGCA+GGG 0.575135 4.3:-33022682 None:intergenic
TGATCCAAAATCCAAGCTCG+TGG 0.590503 4.3:+33022538 MS.gene003512:CDS
CAACAGGCATCTCACGAACC+GGG 0.593590 4.3:-33022694 None:intergenic
ACGCGTAAATACCTTGTGCT+CGG 0.608058 4.3:-33022562 None:intergenic
AAAGAACCCTGCTATGAACC+CGG 0.622651 4.3:+33022676 MS.gene003512:CDS
GATCCAAAATCCAAGCTCGT+GGG 0.650480 4.3:+33022539 MS.gene003512:CDS
AATCCAATGAGTCTTAGCAA+TGG 0.659713 4.3:-33022756 None:intergenic
ATGCTATTAATAATGAACGA+GGG 0.668500 4.3:-33022819 None:intergenic
ATTATACGGCCCATCCACAA+AGG 0.683112 4.3:-33022630 None:intergenic
AAACCCAAGTGCGATCAAGG+TGG 0.716624 4.3:+33022433 MS.gene003512:CDS
AATGCTATTAATAATGAACG+AGG 0.719484 4.3:-33022820 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAATTCAAGCTTTGAAT+TGG - chr4.3:33022323-33022342 None:intergenic 20.0%
! AAAGCTTGAATTTAAAAGCA+GGG + chr4.3:33022327-33022346 MS.gene003512:CDS 25.0%
AAAACATACCTTACACAGTT+CGG + chr4.3:33022476-33022495 MS.gene003512:CDS 30.0%
AATTTAAAAGCAGGGAATTG+GGG + chr4.3:33022335-33022354 MS.gene003512:CDS 30.0%
CAAAGCTTGAATTTAAAAGC+AGG + chr4.3:33022326-33022345 MS.gene003512:CDS 30.0%
CATTGGATTGATATTACTAC+TGG + chr4.3:33022770-33022789 MS.gene003512:CDS 30.0%
GAATTTAAAAGCAGGGAATT+GGG + chr4.3:33022334-33022353 MS.gene003512:CDS 30.0%
TGAATTTAAAAGCAGGGAAT+TGG + chr4.3:33022333-33022352 MS.gene003512:CDS 30.0%
!! AAATTCAAGCTTTGAATTGG+TGG - chr4.3:33022320-33022339 None:intergenic 30.0%
AATCCAATGAGTCTTAGCAA+TGG - chr4.3:33022759-33022778 None:intergenic 35.0%
ACAGTTCGGAAACATTATGA+TGG + chr4.3:33022490-33022509 MS.gene003512:CDS 35.0%
GCAAATGTGCTACCATTATA+CGG - chr4.3:33022647-33022666 None:intergenic 35.0%
GGATCAGATGTTTCAGTTAA+AGG - chr4.3:33022524-33022543 None:intergenic 35.0%
TAATGTTTCCGAACTGTGTA+AGG - chr4.3:33022487-33022506 None:intergenic 35.0%
TGTCGTGGAAATAGAATTGA+AGG - chr4.3:33022400-33022419 None:intergenic 35.0%
! GAACTGTGTAAGGTATGTTT+TGG - chr4.3:33022477-33022496 None:intergenic 35.0%
!!! TATGTTTTGGTCTTGTCTAC+AGG - chr4.3:33022464-33022483 None:intergenic 35.0%
AAAAAACCCAAGTGCGATCA+AGG + chr4.3:33022430-33022449 MS.gene003512:CDS 40.0%
ATGCCATTGCTAAGACTCAT+TGG + chr4.3:33022753-33022772 MS.gene003512:CDS 40.0%
TATTTCCACGACACACTAAG+TGG + chr4.3:33022407-33022426 MS.gene003512:CDS 40.0%
! ACTACTGGTGATGCTATTGT+TGG + chr4.3:33022785-33022804 MS.gene003512:CDS 40.0%
! TTTTTCCACTTAGTGTGTCG+TGG - chr4.3:33022415-33022434 None:intergenic 40.0%
!! TTCAAGCTTTGAATTGGTGG+TGG - chr4.3:33022317-33022336 None:intergenic 40.0%
AAAGAACCCTGCTATGAACC+CGG + chr4.3:33022676-33022695 MS.gene003512:CDS 45.0%
ACGCGTAAATACCTTGTGCT+CGG - chr4.3:33022565-33022584 None:intergenic 45.0%
ATTATACGGCCCATCCACAA+AGG - chr4.3:33022633-33022652 None:intergenic 45.0%
GATCCAAAATCCAAGCTCGT+GGG + chr4.3:33022539-33022558 MS.gene003512:CDS 45.0%
GGTAGCACATTTGCTCTTGT+TGG + chr4.3:33022653-33022672 MS.gene003512:CDS 45.0%
TGAGCTACTCCTTTGTGGAT+GGG + chr4.3:33022621-33022640 MS.gene003512:CDS 45.0%
TGATCCAAAATCCAAGCTCG+TGG + chr4.3:33022538-33022557 MS.gene003512:CDS 45.0%
TTGAGCTACTCCTTTGTGGA+TGG + chr4.3:33022620-33022639 MS.gene003512:CDS 45.0%
TTTGTGGATGGGCCGTATAA+TGG + chr4.3:33022632-33022651 MS.gene003512:CDS 45.0%
! TGGACTTTTCCGTATGGCAA+GGG + chr4.3:33022727-33022746 MS.gene003512:CDS 45.0%
!!! AGGTACTGGACTTTTCCGTA+TGG + chr4.3:33022721-33022740 MS.gene003512:CDS 45.0%
AAACCCAAGTGCGATCAAGG+TGG + chr4.3:33022433-33022452 MS.gene003512:CDS 50.0%
ACAACAGGCATCTCACGAAC+CGG - chr4.3:33022698-33022717 None:intergenic 50.0%
AGTCCAGTACCTCCAACAAC+AGG - chr4.3:33022713-33022732 None:intergenic 50.0%
CATCGTGTCAGCAGGAGATT+GGG + chr4.3:33022585-33022604 MS.gene003512:CDS 50.0%
GTCGTTGAGCTACTCCTTTG+TGG + chr4.3:33022616-33022635 MS.gene003512:CDS 50.0%
GTTCGTGAGATGCCTGTTGT+TGG + chr4.3:33022698-33022717 MS.gene003512:CDS 50.0%
TCATCGTGTCAGCAGGAGAT+TGG + chr4.3:33022584-33022603 MS.gene003512:CDS 50.0%
TGGCATAACCCCTTGCCATA+CGG - chr4.3:33022739-33022758 None:intergenic 50.0%
! ATGCCTGTTGTTGGAGGTAC+TGG + chr4.3:33022707-33022726 MS.gene003512:CDS 50.0%
! CTGGACTTTTCCGTATGGCA+AGG + chr4.3:33022726-33022745 MS.gene003512:CDS 50.0%
! GGACTTTTCCGTATGGCAAG+GGG + chr4.3:33022728-33022747 MS.gene003512:CDS 50.0%
CAACAGGCATCTCACGAACC+GGG - chr4.3:33022697-33022716 None:intergenic 55.0%
CACGAACCGGGTTCATAGCA+GGG - chr4.3:33022685-33022704 None:intergenic 55.0%
CAGCCACCTTGATCGCACTT+GGG - chr4.3:33022439-33022458 None:intergenic 55.0%
CGTGAGATGCCTGTTGTTGG+AGG + chr4.3:33022701-33022720 MS.gene003512:CDS 55.0%
TCACGAACCGGGTTCATAGC+AGG - chr4.3:33022686-33022705 None:intergenic 55.0%
TCAGCCACCTTGATCGCACT+TGG - chr4.3:33022440-33022459 None:intergenic 55.0%
TTACGCGTCATCGTGTCAGC+AGG + chr4.3:33022577-33022596 MS.gene003512:CDS 55.0%
! CGGCCCACGAGCTTGGATTT+TGG - chr4.3:33022545-33022564 None:intergenic 60.0%
AAGCTCGTGGGCCGAGCACA+AGG + chr4.3:33022551-33022570 MS.gene003512:CDS 65.0%
TTGTGCTCGGCCCACGAGCT+TGG - chr4.3:33022552-33022571 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 33022257 33022835 33022257 ID=MS.gene003512
chr4.3 mRNA 33022257 33022835 33022257 ID=MS.gene003512.t1;Parent=MS.gene003512
chr4.3 exon 33022257 33022835 33022257 ID=MS.gene003512.t1.exon1;Parent=MS.gene003512.t1
chr4.3 CDS 33022257 33022835 33022257 ID=cds.MS.gene003512.t1;Parent=MS.gene003512.t1
Gene Sequence

>MS.gene003512

ATGAAAATGTCTAAGCAAAATGTGCTTGTGATGATACTTCTAATAAGTGCTATACTTCCACCACCAATTCAAAGCTTGAATTTAAAAGCAGGGAATTGGGGTGAAACTTTTCAAAACAAGAAACAAGAAACAGAAACAAACCTTCAATTCTATTTCCACGACACACTAAGTGGAAAAAACCCAAGTGCGATCAAGGTGGCTGAACCTGTAGACAAGACCAAAACATACCTTACACAGTTCGGAAACATTATGATGGCAGATGATCCTTTAACTGAAACATCTGATCCAAAATCCAAGCTCGTGGGCCGAGCACAAGGTATTTACGCGTCATCGTGTCAGCAGGAGATTGGGCTTCTTATGTCGTTGAGCTACTCCTTTGTGGATGGGCCGTATAATGGTAGCACATTTGCTCTTGTTGGAAAGAACCCTGCTATGAACCCGGTTCGTGAGATGCCTGTTGTTGGAGGTACTGGACTTTTCCGTATGGCAAGGGGTTATGCCATTGCTAAGACTCATTGGATTGATATTACTACTGGTGATGCTATTGTTGGCTACAATGTCACCCTCGTTCATTATTAA
Protein sequence

>MS.gene003512.t1

MKMSKQNVLVMILLISAILPPPIQSLNLKAGNWGETFQNKKQETETNLQFYFHDTLSGKNPSAIKVAEPVDKTKTYLTQFGNIMMADDPLTETSDPKSKLVGRAQGIYASSCQQEIGLLMSLSYSFVDGPYNGSTFALVGKNPAMNPVREMPVVGGTGLFRMARGYAIAKTHWIDITTGDAIVGYNVTLVHY