AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene73041

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene73041.t1 MTR_3g034030 58.919 185 71 1 4 188 5 184 3.21e-78 231
MS.gene73041.t1 MTR_4g078885 59.116 181 69 1 8 188 9 184 4.00e-78 231
MS.gene73041.t1 MTR_1g056370 47.826 184 89 5 10 188 4 185 1.96e-53 169
MS.gene73041.t1 MTR_4g013350 50.331 151 73 1 40 188 46 196 5.58e-47 152
MS.gene73041.t1 MTR_4g013335 48.993 149 76 0 40 188 47 195 2.27e-45 148
MS.gene73041.t1 MTR_4g013345 48.344 151 76 1 40 188 45 195 8.09e-45 147
MS.gene73041.t1 MTR_1g054525 49.324 148 71 3 43 188 46 191 8.75e-45 147
MS.gene73041.t1 MTR_4g013330 46.405 153 78 1 40 188 46 198 1.18e-44 147
MS.gene73041.t1 MTR_4g013320 45.695 151 80 1 40 188 48 198 4.14e-42 140
MS.gene73041.t1 MTR_4g013325 47.222 144 74 1 47 188 55 198 4.12e-41 137
MS.gene73041.t1 MTR_7g093820 48.993 149 73 2 43 188 45 193 6.41e-41 137
MS.gene73041.t1 MTR_7g093790 48.000 150 73 4 43 188 42 190 1.07e-40 136
MS.gene73041.t1 MTR_4g073950 41.176 153 85 2 39 188 41 191 2.04e-40 135
MS.gene73041.t1 MTR_7g070390 42.473 186 101 3 7 188 8 191 3.82e-40 135
MS.gene73041.t1 MTR_7g093850 48.993 149 73 2 43 188 45 193 6.38e-40 134
MS.gene73041.t1 MTR_7g093830 46.309 149 77 2 43 188 44 192 2.80e-38 130
MS.gene73041.t1 MTR_4g013310 44.516 155 80 4 34 186 44 194 8.29e-37 127
MS.gene73041.t1 MTR_4g013385 38.776 147 89 1 43 188 43 189 5.08e-36 124
MS.gene73041.t1 MTR_0433s0040 38.776 147 89 1 43 188 43 189 5.08e-36 124
MS.gene73041.t1 MTR_4g013770 39.779 181 100 3 11 188 16 190 2.39e-34 120
MS.gene73041.t1 MTR_5g096120 38.220 191 99 5 7 188 8 188 6.34e-34 119
MS.gene73041.t1 MTR_7g093870 44.444 153 78 2 43 188 40 192 1.51e-32 116
MS.gene73041.t1 MTR_3g105630 40.397 151 85 2 43 188 38 188 2.92e-31 112
MS.gene73041.t1 MTR_3g105640 40.397 151 84 4 43 188 38 187 3.93e-30 109
MS.gene73041.t1 MTR_4g013355 35.484 155 88 2 36 188 34 178 7.87e-26 98.2
MS.gene73041.t1 MTR_4g049570 31.818 154 103 1 38 189 25 178 5.26e-21 85.5
MS.gene73041.t1 MTR_4g122110 34.483 145 93 1 46 188 35 179 5.27e-21 85.5
MS.gene73041.t1 MTR_4g049550 32.886 149 98 1 43 189 30 178 7.39e-21 85.1
MS.gene73041.t1 MTR_4g122130 31.548 168 97 2 3 168 8 159 2.94e-20 83.6
MS.gene73041.t1 MTR_1g046490 38.298 94 57 1 76 169 121 213 1.45e-12 64.3
MS.gene73041.t1 MTR_1g046800 39.362 94 56 1 76 169 135 227 2.42e-12 63.9
MS.gene73041.t1 MTR_1g046500 39.362 94 56 1 76 169 135 227 2.90e-12 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene73041.t1 AT1G65870 49.689 161 79 2 30 188 29 189 1.60e-48 156
MS.gene73041.t1 AT5G42500 44.785 163 86 2 28 188 25 185 1.56e-44 146
MS.gene73041.t1 AT2G21100 42.105 152 86 1 39 188 36 187 5.47e-43 142
MS.gene73041.t1 AT2G21100 42.105 152 86 1 39 188 36 187 5.47e-43 142
MS.gene73041.t1 AT1G22900 46.452 155 79 3 36 188 41 193 2.72e-42 140
MS.gene73041.t1 AT5G42510 44.516 155 82 2 36 188 30 182 1.44e-41 138
MS.gene73041.t1 AT3G13650 43.836 146 81 1 43 188 41 185 1.08e-40 136
MS.gene73041.t1 AT5G49040 44.966 149 78 3 43 188 43 190 9.30e-39 131
MS.gene73041.t1 AT1G58170 38.421 190 109 3 1 188 1 184 1.83e-38 130
MS.gene73041.t1 AT1G55210 44.295 149 82 1 40 188 39 186 2.11e-38 130
MS.gene73041.t1 AT1G55210 44.295 149 82 1 40 188 39 186 2.11e-38 130
MS.gene73041.t1 AT5G49030 48.438 128 64 1 43 168 43 170 1.36e-34 129
MS.gene73041.t1 AT3G13662 46.032 126 67 1 43 168 40 164 3.16e-33 117
MS.gene73041.t1 AT4G38700 42.208 154 81 3 43 188 36 189 3.27e-32 115
MS.gene73041.t1 AT3G58090 51.402 107 52 0 82 188 165 271 2.95e-31 114
MS.gene73041.t1 AT2G21110 36.667 150 89 1 45 188 36 185 2.56e-29 107
MS.gene73041.t1 AT3G13660 40.678 118 70 0 71 188 7 124 1.04e-26 99.0
MS.gene73041.t1 AT4G11210 28.495 186 126 4 1 186 1 179 1.32e-17 77.0
MS.gene73041.t1 AT4G23690 30.612 147 94 4 45 186 40 183 1.89e-12 63.2

Find 35 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGCTGTTGCTAAGAGTCTT+TGG 0.249586 3.2:+11662323 MS.gene73041:CDS
ACTAGTTCACCAAGTGGATT+TGG 0.311527 3.2:+11662046 MS.gene73041:CDS
TTCAAATGGCTACCTCTCTT+AGG 0.324065 3.2:+11661831 None:intergenic
TCGGCGGCACCGGCGTGTTT+AGG 0.331194 3.2:+11662287 MS.gene73041:CDS
TGCTGTTGCTAAGAGTCTTT+GGG 0.346946 3.2:+11662324 MS.gene73041:CDS
CTGCCTATTGTCGGCGGCAC+CGG 0.359439 3.2:+11662277 MS.gene73041:CDS
TCAGTGCTTTGTTGATTTGT+TGG 0.368171 3.2:-11661941 None:intergenic
GGTAGAGCTCAAGGGATGTT+TGG 0.378489 3.2:+11662130 MS.gene73041:CDS
AGCTCAAGGGATGTTTGGTT+TGG 0.396536 3.2:+11662135 MS.gene73041:CDS
ACGCCGGTGCCGCCGACAAT+AGG 0.397084 3.2:-11662280 None:intergenic
TCTCTAACCGTGTCTTGAAC+AGG 0.414606 3.2:-11662253 None:intergenic
CCACTTGGTGAACTAGTTGA+TGG 0.423861 3.2:-11662040 None:intergenic
GCTCTTGTTCTTCAGTTAAG+AGG 0.424118 3.2:-11662090 None:intergenic
ATCCCTTGAGCTCTACCAAC+AGG 0.451335 3.2:-11662124 None:intergenic
ATTTGTTGGTAACATGATGT+TGG 0.455637 3.2:-11661927 None:intergenic
TAACATGATGTTGGATTGTT+CGG 0.468734 3.2:-11661918 None:intergenic
GGTAGTACTCTTAGTATGCT+TGG 0.469670 3.2:+11662223 MS.gene73041:CDS
TCTATAATTTGTACAACCGT+TGG 0.476718 3.2:-11662016 None:intergenic
ATTTGGAACAACATTCATGA+TGG 0.515290 3.2:+11662063 MS.gene73041:CDS
AAACCTGTTGGTAGAGCTCA+AGG 0.516264 3.2:+11662121 MS.gene73041:CDS
CTTTACCTTCTAAGATGTCA+TGG 0.530269 3.2:-11661991 None:intergenic
GTTAGAGAACTGCCTATTGT+CGG 0.546616 3.2:+11662268 MS.gene73041:CDS
GAGCTAACCTCAAAACCTGT+TGG 0.575184 3.2:+11662109 MS.gene73041:CDS
TTGTTCGGAGAACAATCCAT+TGG 0.584508 3.2:-11661903 None:intergenic
TTGGCATCTTTGCATGATCG+TGG 0.594187 3.2:+11662154 MS.gene73041:CDS
ATCTTTGCATGATCGTGGAA+TGG 0.599273 3.2:+11662159 MS.gene73041:CDS
CTTAGAAGGTAAAGATCCAA+CGG 0.624749 3.2:+11662000 MS.gene73041:CDS
GAGAAAGAAGAACCTAAGAG+AGG 0.627560 3.2:-11661843 None:intergenic
GGCGTGTTTAGGTTTGCTAG+AGG 0.633858 3.2:+11662298 MS.gene73041:CDS
AAGAAATCCTGTTCAAGACA+CGG 0.645101 3.2:+11662246 MS.gene73041:CDS
CCATCAACTAGTTCACCAAG+TGG 0.652779 3.2:+11662040 MS.gene73041:CDS
AATGTTGTTCCAAATCCACT+TGG 0.683285 3.2:-11662055 None:intergenic
AGAGAACTGCCTATTGTCGG+CGG 0.685485 3.2:+11662271 MS.gene73041:CDS
AACCTGTTGGTAGAGCTCAA+GGG 0.691584 3.2:+11662122 MS.gene73041:CDS
TCTAGCAAACCTAAACACGC+CGG 0.712215 3.2:-11662296 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTAATCTTGCTTTTACTGA+AGG + chr3.2:11662190-11662209 MS.gene73041:CDS 25.0%
TAACATGATGTTGGATTGTT+CGG - chr3.2:11661921-11661940 None:intergenic 30.0%
! ATTTGGAACAACATTCATGA+TGG + chr3.2:11662063-11662082 MS.gene73041:CDS 30.0%
! TCTATAATTTGTACAACCGT+TGG - chr3.2:11662019-11662038 None:intergenic 30.0%
! TTTTACCATGACATCTTAGA+AGG + chr3.2:11661986-11662005 MS.gene73041:CDS 30.0%
!! ATTTGTTGGTAACATGATGT+TGG - chr3.2:11661930-11661949 None:intergenic 30.0%
AAGAAATCCTGTTCAAGACA+CGG + chr3.2:11662246-11662265 MS.gene73041:CDS 35.0%
AATGTTGTTCCAAATCCACT+TGG - chr3.2:11662058-11662077 None:intergenic 35.0%
CTTAGAAGGTAAAGATCCAA+CGG + chr3.2:11662000-11662019 MS.gene73041:CDS 35.0%
! GCTCAATTTTTCACTACCAA+TGG + chr3.2:11661887-11661906 MS.gene73041:CDS 35.0%
! TTTACTGAAGGTGATTTTGC+TGG + chr3.2:11662202-11662221 MS.gene73041:CDS 35.0%
!! CTTTACCTTCTAAGATGTCA+TGG - chr3.2:11661994-11662013 None:intergenic 35.0%
!! TCAGTGCTTTGTTGATTTGT+TGG - chr3.2:11661944-11661963 None:intergenic 35.0%
ATCTTTGCATGATCGTGGAA+TGG + chr3.2:11662159-11662178 MS.gene73041:CDS 40.0%
ATGCTGTTGCTAAGAGTCTT+TGG + chr3.2:11662323-11662342 MS.gene73041:CDS 40.0%
GAGAAAGAAGAACCTAAGAG+AGG - chr3.2:11661846-11661865 None:intergenic 40.0%
GCTCTTGTTCTTCAGTTAAG+AGG - chr3.2:11662093-11662112 None:intergenic 40.0%
GGTAGTACTCTTAGTATGCT+TGG + chr3.2:11662223-11662242 MS.gene73041:CDS 40.0%
GTTAGAGAACTGCCTATTGT+CGG + chr3.2:11662268-11662287 MS.gene73041:CDS 40.0%
TGCTGTTGCTAAGAGTCTTT+GGG + chr3.2:11662324-11662343 MS.gene73041:CDS 40.0%
TTGTTCGGAGAACAATCCAT+TGG - chr3.2:11661906-11661925 None:intergenic 40.0%
! ACTAGTTCACCAAGTGGATT+TGG + chr3.2:11662046-11662065 MS.gene73041:CDS 40.0%
AGCTCAAGGGATGTTTGGTT+TGG + chr3.2:11662135-11662154 MS.gene73041:CDS 45.0%
CCATCAACTAGTTCACCAAG+TGG + chr3.2:11662040-11662059 MS.gene73041:CDS 45.0%
GAGCTAACCTCAAAACCTGT+TGG + chr3.2:11662109-11662128 MS.gene73041:CDS 45.0%
TCTAGCAAACCTAAACACGC+CGG - chr3.2:11662299-11662318 None:intergenic 45.0%
TCTCTAACCGTGTCTTGAAC+AGG - chr3.2:11662256-11662275 None:intergenic 45.0%
TTGGCATCTTTGCATGATCG+TGG + chr3.2:11662154-11662173 MS.gene73041:CDS 45.0%
! AAACCTGTTGGTAGAGCTCA+AGG + chr3.2:11662121-11662140 MS.gene73041:CDS 45.0%
! AACCTGTTGGTAGAGCTCAA+GGG + chr3.2:11662122-11662141 MS.gene73041:CDS 45.0%
! AGCTCTACCAACAGGTTTTG+AGG - chr3.2:11662119-11662138 None:intergenic 45.0%
! CCACTTGGTGAACTAGTTGA+TGG - chr3.2:11662043-11662062 None:intergenic 45.0%
AGAGAACTGCCTATTGTCGG+CGG + chr3.2:11662271-11662290 MS.gene73041:CDS 50.0%
ATCCCTTGAGCTCTACCAAC+AGG - chr3.2:11662127-11662146 None:intergenic 50.0%
GGTAGAGCTCAAGGGATGTT+TGG + chr3.2:11662130-11662149 MS.gene73041:CDS 50.0%
!! GGCGTGTTTAGGTTTGCTAG+AGG + chr3.2:11662298-11662317 MS.gene73041:CDS 50.0%
CTGCCTATTGTCGGCGGCAC+CGG + chr3.2:11662277-11662296 MS.gene73041:CDS 65.0%
!! ACGCCGGTGCCGCCGACAAT+AGG - chr3.2:11662283-11662302 None:intergenic 70.0%
!! TCGGCGGCACCGGCGTGTTT+AGG + chr3.2:11662287-11662306 MS.gene73041:CDS 70.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 11661836 11662405 11661836 ID=MS.gene73041
chr3.2 mRNA 11661836 11662405 11661836 ID=MS.gene73041.t1;Parent=MS.gene73041
chr3.2 exon 11661836 11662405 11661836 ID=MS.gene73041.t1.exon1;Parent=MS.gene73041.t1
chr3.2 CDS 11661836 11662405 11661836 ID=cds.MS.gene73041.t1;Parent=MS.gene73041.t1
Gene Sequence

>MS.gene73041

ATGGCTACCTCTCTTAGGTTCTTCTTTCTCTTCACTCTCACTCTCATATTTGCTCAATTTTTCACTACCAATGGATTGTTCTCCGAACAATCCAACATCATGTTACCAACAAATCAACAAAGCACTGAAAAATTAACTCACTTGCACTTTTTTTACCATGACATCTTAGAAGGTAAAGATCCAACGGTTGTACAAATTATAGATCCATCAACTAGTTCACCAAGTGGATTTGGAACAACATTCATGATGGACAACCTCTTAACTGAAGAACAAGAGCTAACCTCAAAACCTGTTGGTAGAGCTCAAGGGATGTTTGGTTTGGCATCTTTGCATGATCGTGGAATGGTTATGTTAATTAATCTTGCTTTTACTGAAGGTGATTTTGCTGGTAGTACTCTTAGTATGCTTGGAAGAAATCCTGTTCAAGACACGGTTAGAGAACTGCCTATTGTCGGCGGCACCGGCGTGTTTAGGTTTGCTAGAGGTTATGCTGTTGCTAAGAGTCTTTGGGAGATTTCAACTTCTGAACATTTTGTTGTTGAGTATGATGTCACTGTTTCTCATCCATAG
Protein sequence

>MS.gene73041.t1

MATSLRFFFLFTLTLIFAQFFTTNGLFSEQSNIMLPTNQQSTEKLTHLHFFYHDILEGKDPTVVQIIDPSTSSPSGFGTTFMMDNLLTEEQELTSKPVGRAQGMFGLASLHDRGMVMLINLAFTEGDFAGSTLSMLGRNPVQDTVRELPIVGGTGVFRFARGYAVAKSLWEISTSEHFVVEYDVTVSHP