AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene009644

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene009644.t1 MTR_5g075790 86.758 219 18 6 1 211 9 224 5.20e-129 362
MS.gene009644.t1 MTR_5g075760 83.945 218 26 5 1 211 1 216 3.01e-124 350
MS.gene009644.t1 MTR_1g083180 50.000 142 53 2 62 201 19 144 4.09e-37 128
MS.gene009644.t1 MTR_1g111830 38.624 189 101 6 12 188 23 208 5.88e-32 116
MS.gene009644.t1 MTR_8g063600 39.227 181 98 7 8 178 5 183 1.26e-29 111
MS.gene009644.t1 MTR_8g063870 39.205 176 95 7 7 178 2 169 3.47e-28 107
MS.gene009644.t1 MTR_7g067080 33.981 206 113 10 2 188 24 225 1.06e-21 90.9
MS.gene009644.t1 MTR_3g462790 36.747 166 85 7 4 152 34 196 1.64e-21 90.5
MS.gene009644.t1 MTR_4g111975 30.493 223 105 11 13 187 8 228 4.72e-20 86.3
MS.gene009644.t1 MTR_5g069710 32.275 189 102 8 2 171 18 199 1.01e-19 85.5
MS.gene009644.t1 MTR_5g081860 30.808 198 119 7 12 199 26 215 1.12e-17 79.3
MS.gene009644.t1 MTR_5g027570 48.837 86 41 2 105 187 93 178 4.04e-16 74.3
MS.gene009644.t1 MTR_5g088010 41.346 104 54 4 89 187 47 148 1.47e-15 73.2
MS.gene009644.t1 MTR_5g088060 45.455 88 43 3 105 187 273 360 5.72e-14 70.1
MS.gene009644.t1 MTR_5g488160 45.455 88 43 3 105 187 273 360 5.72e-14 70.1
MS.gene009644.t1 MTR_2g090305 42.683 82 43 3 106 185 30 109 3.60e-13 65.9
MS.gene009644.t1 MTR_4g107230 43.421 76 39 2 78 149 55 130 9.18e-13 65.9
MS.gene009644.t1 MTR_5g027550 42.169 83 44 3 70 151 46 125 9.19e-13 65.5
MS.gene009644.t1 MTR_4g100630 37.000 100 59 3 73 170 64 161 1.17e-12 65.9
MS.gene009644.t1 MTR_2g100930 42.466 73 39 2 95 166 100 170 3.46e-12 64.7
MS.gene009644.t1 MTR_5g037080 43.421 76 31 2 76 150 85 149 8.03e-12 63.5
MS.gene009644.t1 MTR_8g101650 45.205 73 37 2 106 177 107 177 9.35e-12 63.2
MS.gene009644.t1 MTR_3g104370 57.692 52 21 1 106 156 93 144 1.04e-11 62.4
MS.gene009644.t1 MTR_1g048660 51.852 54 25 1 103 155 11 64 1.16e-11 59.3
MS.gene009644.t1 MTR_6g092540 51.613 62 27 2 106 166 99 158 2.26e-11 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene009644.t1 AT5G04760 36.757 185 87 5 10 178 3 173 3.59e-26 100
MS.gene009644.t1 AT5G08520 35.754 179 90 7 13 171 12 185 3.04e-24 97.4
MS.gene009644.t1 AT3G10580 37.333 150 87 3 13 160 8 152 8.13e-23 92.8
MS.gene009644.t1 AT3G10580 38.732 142 80 3 13 152 8 144 1.30e-22 93.2
MS.gene009644.t1 AT5G23650 36.158 177 92 6 1 158 1 175 6.78e-21 89.4
MS.gene009644.t1 AT2G38090 31.132 212 107 10 2 189 18 214 3.89e-20 86.7
MS.gene009644.t1 AT4G09450 37.415 147 82 4 12 156 6 144 1.49e-19 83.2
MS.gene009644.t1 AT5G58900 32.240 183 102 6 8 171 29 208 3.36e-19 84.0
MS.gene009644.t1 AT5G01200 31.980 197 105 7 2 171 19 213 5.50e-19 82.8
MS.gene009644.t1 AT1G49010 30.457 197 96 8 13 171 8 201 3.30e-18 81.6
MS.gene009644.t1 AT5G05790 31.902 163 93 3 9 157 27 185 9.11e-18 79.7
MS.gene009644.t1 AT5G05790 31.902 163 93 3 9 157 27 185 9.11e-18 79.7
MS.gene009644.t1 AT3G11280 33.333 150 94 4 13 157 33 181 7.55e-17 77.0
MS.gene009644.t1 AT3G11280 33.333 150 94 4 13 157 33 181 7.55e-17 77.0
MS.gene009644.t1 AT5G47390 37.288 118 52 5 76 186 79 181 3.49e-15 73.6
MS.gene009644.t1 AT3G10590 29.050 179 105 6 8 169 2 175 5.06e-13 65.9
MS.gene009644.t1 AT1G70000 44.304 79 39 2 73 150 71 145 1.07e-12 65.5
MS.gene009644.t1 AT1G70000 44.304 79 39 2 73 150 71 145 1.07e-12 65.5
MS.gene009644.t1 AT5G61620 43.529 85 45 2 100 183 104 186 9.38e-11 60.5

Find 43 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGCATTTCCTTCACCAAAA+TGG 0.297505 5.3:+60702173 MS.gene009644:CDS
TTGAATTTCAACATTTAATT+CGG 0.308654 5.3:-60702362 None:intergenic
TTCTTAGTCTTATTCTTAGT+TGG 0.323967 5.3:-60701585 None:intergenic
AGATTCATAAGAAGGGAAAT+TGG 0.369394 5.3:+60702090 MS.gene009644:CDS
GTCCTTACTGAGAAGAGGTT+TGG 0.374736 5.3:-60702261 None:intergenic
TTAGTCTTATTCTTAGTTGG+AGG 0.415408 5.3:-60701582 None:intergenic
GAAAATCTTGCTCTTGTTTG+CGG 0.422028 5.3:+60701417 MS.gene009644:CDS
ATAAAATCATCTGAGTTTGT+TGG 0.441615 5.3:-60701522 None:intergenic
CTTCAACATTACCTCATTGA+AGG 0.462445 5.3:+60702229 MS.gene009644:CDS
GGGAATCGAGATTCATAAGA+AGG 0.470381 5.3:+60702082 MS.gene009644:CDS
ATGAACTACACAAATAATGA+TGG 0.488615 5.3:+60701306 MS.gene009644:CDS
TCCCATGAGGTAGGAGGAGA+TGG 0.491481 5.3:-60702290 None:intergenic
CTCAAGATATTCAAAGAGAA+TGG 0.491655 5.3:-60701373 None:intergenic
GCATGGCTAGCACATTGACT+TGG 0.494579 5.3:-60702146 None:intergenic
TTCAACATTTAATTCGGATG+AGG 0.495392 5.3:-60702356 None:intergenic
CTAAGAAAGTGGTGAAACAT+TGG 0.507701 5.3:+60701601 MS.gene009644:CDS
TTCCATCTCCTCCTACCTCA+TGG 0.508016 5.3:+60702288 MS.gene009644:CDS
GGATGAGGATAAAGAAGAGC+TGG 0.516096 5.3:-60702341 None:intergenic
TTCCAAACCTCTTCTCAGTA+AGG 0.524962 5.3:+60702259 MS.gene009644:CDS
TAAGAATAAGACTAAGAAAG+TGG 0.531612 5.3:+60701590 MS.gene009644:CDS
TTCAACATTACCTCATTGAA+GGG 0.537386 5.3:+60702230 MS.gene009644:CDS
GAGCTGGAACATAGAGAAGA+GGG 0.552512 5.3:-60702325 None:intergenic
TCCATCTCCTCCTACCTCAT+GGG 0.558700 5.3:+60702289 MS.gene009644:CDS
AGGAAGTACAAGAAGGTCGA+TGG 0.560186 5.3:+60701394 MS.gene009644:CDS
ATGTTGTCCTTACTGAGAAG+AGG 0.560674 5.3:-60702266 None:intergenic
CATTCTCTTTGAATATCTTG+AGG 0.571841 5.3:+60701374 MS.gene009644:CDS
GAAAATCAAAGGAGTGGACA+TGG 0.573641 5.3:+60701328 MS.gene009644:CDS
GGAATCGAGATTCATAAGAA+GGG 0.583688 5.3:+60702083 MS.gene009644:CDS
AAATAATGATGGAAAATCAA+AGG 0.595595 5.3:+60701317 MS.gene009644:CDS
TCTCCTCCTACCTCATGGGA+TGG 0.596171 5.3:+60702293 MS.gene009644:CDS
AGAGCTGGAACATAGAGAAG+AGG 0.602888 5.3:-60702326 None:intergenic
GCATGACTTAGCACTCATTG+AGG 0.603466 5.3:+60701482 MS.gene009644:CDS
GACTTAGCACTCATTGAGGA+AGG 0.612605 5.3:+60701486 MS.gene009644:CDS
ATGATGGAAAATCAAAGGAG+TGG 0.613850 5.3:+60701322 MS.gene009644:CDS
TTTCCATCCCATGAGGTAGG+AGG 0.614524 5.3:-60702296 None:intergenic
TATCTTGAGGAAGTACAAGA+AGG 0.618040 5.3:+60701387 MS.gene009644:CDS
GGAATGATCTCCCTTCAATG+AGG 0.623973 5.3:-60702240 None:intergenic
AAATTTCCATCCCATGAGGT+AGG 0.632795 5.3:-60702299 None:intergenic
CTGGAACATAGAGAAGAGGG+TGG 0.633901 5.3:-60702322 None:intergenic
GGAAGTACAAGAAGGTCGAT+GGG 0.635752 5.3:+60701395 MS.gene009644:CDS
AAAATCAAAGGAGTGGACAT+GGG 0.673138 5.3:+60701329 MS.gene009644:CDS
ATTGGAGTGAAGAAGAACAC+AGG 0.701675 5.3:+60701619 MS.gene009644:CDS
GTGGAAATTTCCATCCCATG+AGG 0.722495 5.3:-60702303 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATCAACAAATAAAAAAA+GGG + chr5.3:60701841-60701860 MS.gene009644:intron 10.0%
!!! TTTTATCAACAAATAAAAAA+AGG + chr5.3:60701840-60701859 MS.gene009644:intron 10.0%
!!! TTTTTTTATTTGTTGATAAA+AGG - chr5.3:60701841-60701860 None:intergenic 10.0%
!!! AGTCAATTTAATTTATATCA+TGG - chr5.3:60702027-60702046 None:intergenic 15.0%
!!! TTTACTAATTTCTCTTTTTA+CGG - chr5.3:60701743-60701762 None:intergenic 15.0%
!! TTAAATTGGATTCAAAAGAA+AGG + chr5.3:60701911-60701930 MS.gene009644:intron 20.0%
!!! AAATAATGATGGAAAATCAA+AGG + chr5.3:60701317-60701336 MS.gene009644:CDS 20.0%
!!! TTTCTTTTGAATCCAATTTA+AGG - chr5.3:60701912-60701931 None:intergenic 20.0%
!!! TTTTATAGGTTATTTGTAGA+GGG + chr5.3:60702062-60702081 MS.gene009644:intron 20.0%
!!! TTTTTATAGGTTATTTGTAG+AGG + chr5.3:60702061-60702080 MS.gene009644:intron 20.0%
! ATAAAATCATCTGAGTTTGT+TGG - chr5.3:60701525-60701544 None:intergenic 25.0%
! ATGAACTACACAAATAATGA+TGG + chr5.3:60701306-60701325 MS.gene009644:CDS 25.0%
! CCTATAAAAAAAATGATGAG+AGG - chr5.3:60702051-60702070 None:intergenic 25.0%
! TAAGAATAAGACTAAGAAAG+TGG + chr5.3:60701590-60701609 MS.gene009644:CDS 25.0%
! TACTACCTTATTCCTTAAAT+TGG + chr5.3:60701897-60701916 MS.gene009644:intron 25.0%
! TGAATCCAATTTAAGGAATA+AGG - chr5.3:60701905-60701924 None:intergenic 25.0%
! TTGACACTAACATATGTATT+GGG + chr5.3:60701980-60701999 MS.gene009644:intron 25.0%
!! TTATTTTCTTCTTCTTCATG+TGG + chr5.3:60701691-60701710 MS.gene009644:intron 25.0%
!!! CCTCTCATCATTTTTTTTAT+AGG + chr5.3:60702048-60702067 MS.gene009644:intron 25.0%
!!! TCAGATGATTTTATTTCGAA+AGG + chr5.3:60701531-60701550 MS.gene009644:CDS 25.0%
!!! TCTTTTTTGATGTACCATTT+TGG - chr5.3:60702190-60702209 None:intergenic 25.0%
!!! TTCTTAGTCTTATTCTTAGT+TGG - chr5.3:60701588-60701607 None:intergenic 25.0%
AGATTCATAAGAAGGGAAAT+TGG + chr5.3:60702090-60702109 MS.gene009644:CDS 30.0%
CATTCTCTTTGAATATCTTG+AGG + chr5.3:60701374-60701393 MS.gene009644:CDS 30.0%
CTCAAGATATTCAAAGAGAA+TGG - chr5.3:60701376-60701395 None:intergenic 30.0%
CTTGACACTAACATATGTAT+TGG + chr5.3:60701979-60701998 MS.gene009644:intron 30.0%
TTCAACATTACCTCATTGAA+GGG + chr5.3:60702230-60702249 MS.gene009644:CDS 30.0%
!! TTAGTCTTATTCTTAGTTGG+AGG - chr5.3:60701585-60701604 None:intergenic 30.0%
AAAATCAAAGGAGTGGACAT+GGG + chr5.3:60701329-60701348 MS.gene009644:CDS 35.0%
AAGCATTTCCTTCACCAAAA+TGG + chr5.3:60702173-60702192 MS.gene009644:CDS 35.0%
CTAAGAAAGTGGTGAAACAT+TGG + chr5.3:60701601-60701620 MS.gene009644:CDS 35.0%
CTTCAACATTACCTCATTGA+AGG + chr5.3:60702229-60702248 MS.gene009644:CDS 35.0%
GGAATCGAGATTCATAAGAA+GGG + chr5.3:60702083-60702102 MS.gene009644:CDS 35.0%
! ATGATGGAAAATCAAAGGAG+TGG + chr5.3:60701322-60701341 MS.gene009644:CDS 35.0%
! CTTTTATTCGAAGAACACCT+TGG + chr5.3:60701764-60701783 MS.gene009644:intron 35.0%
! GAAAATCTTGCTCTTGTTTG+CGG + chr5.3:60701417-60701436 MS.gene009644:CDS 35.0%
! TATCTTGAGGAAGTACAAGA+AGG + chr5.3:60701387-60701406 MS.gene009644:CDS 35.0%
!! ACACCTTGGTTTTTCTGAAA+AGG + chr5.3:60701778-60701797 MS.gene009644:intron 35.0%
!! CACCTTGGTTTTTCTGAAAA+GGG + chr5.3:60701779-60701798 MS.gene009644:intron 35.0%
!! TTGATGTACCATTTTGGTGA+AGG - chr5.3:60702184-60702203 None:intergenic 35.0%
AAATTTCCATCCCATGAGGT+AGG - chr5.3:60702302-60702321 None:intergenic 40.0%
ATGTTGTCCTTACTGAGAAG+AGG - chr5.3:60702269-60702288 None:intergenic 40.0%
ATTGGAGTGAAGAAGAACAC+AGG + chr5.3:60701619-60701638 MS.gene009644:CDS 40.0%
GAAAATCAAAGGAGTGGACA+TGG + chr5.3:60701328-60701347 MS.gene009644:CDS 40.0%
GGGAATCGAGATTCATAAGA+AGG + chr5.3:60702082-60702101 MS.gene009644:CDS 40.0%
TTCCAAACCTCTTCTCAGTA+AGG + chr5.3:60702259-60702278 MS.gene009644:CDS 40.0%
! GAAGGAAATGCTTTTGAGCA+TGG - chr5.3:60702166-60702185 None:intergenic 40.0%
! GTCCCTTTTCAGAAAAACCA+AGG - chr5.3:60701784-60701803 None:intergenic 40.0%
AGAGCTGGAACATAGAGAAG+AGG - chr5.3:60702329-60702348 None:intergenic 45.0%
CGGAATTCACACCATGCATA+AGG - chr5.3:60701723-60701742 None:intergenic 45.0%
GACTTAGCACTCATTGAGGA+AGG + chr5.3:60701486-60701505 MS.gene009644:CDS 45.0%
GAGCTGGAACATAGAGAAGA+GGG - chr5.3:60702328-60702347 None:intergenic 45.0%
GCATGACTTAGCACTCATTG+AGG + chr5.3:60701482-60701501 MS.gene009644:CDS 45.0%
GGAATGATCTCCCTTCAATG+AGG - chr5.3:60702243-60702262 None:intergenic 45.0%
GGATGAGGATAAAGAAGAGC+TGG - chr5.3:60702344-60702363 None:intergenic 45.0%
GTCCTTACTGAGAAGAGGTT+TGG - chr5.3:60702264-60702283 None:intergenic 45.0%
GTGGAAATTTCCATCCCATG+AGG - chr5.3:60702306-60702325 None:intergenic 45.0%
! AGGAAGTACAAGAAGGTCGA+TGG + chr5.3:60701394-60701413 MS.gene009644:CDS 45.0%
! GGAAGTACAAGAAGGTCGAT+GGG + chr5.3:60701395-60701414 MS.gene009644:CDS 45.0%
CTGGAACATAGAGAAGAGGG+TGG - chr5.3:60702325-60702344 None:intergenic 50.0%
TCCATCTCCTCCTACCTCAT+GGG + chr5.3:60702289-60702308 MS.gene009644:CDS 50.0%
TGTGGACGAGTCCTTATGCA+TGG + chr5.3:60701709-60701728 MS.gene009644:intron 50.0%
TTCCATCTCCTCCTACCTCA+TGG + chr5.3:60702288-60702307 MS.gene009644:CDS 50.0%
TTTCCATCCCATGAGGTAGG+AGG - chr5.3:60702299-60702318 None:intergenic 50.0%
! GCATGGCTAGCACATTGACT+TGG - chr5.3:60702149-60702168 None:intergenic 50.0%
TCCCATGAGGTAGGAGGAGA+TGG - chr5.3:60702293-60702312 None:intergenic 55.0%
TCTCCTCCTACCTCATGGGA+TGG + chr5.3:60702293-60702312 MS.gene009644:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 60701306 60702370 60701306 ID=MS.gene009644
chr5.3 mRNA 60701306 60702370 60701306 ID=MS.gene009644.t1;Parent=MS.gene009644
chr5.3 exon 60701306 60701640 60701306 ID=MS.gene009644.t1.exon1;Parent=MS.gene009644.t1
chr5.3 CDS 60701306 60701640 60701306 ID=cds.MS.gene009644.t1;Parent=MS.gene009644.t1
chr5.3 exon 60702070 60702370 60702070 ID=MS.gene009644.t1.exon2;Parent=MS.gene009644.t1
chr5.3 CDS 60702070 60702370 60702070 ID=cds.MS.gene009644.t1;Parent=MS.gene009644.t1
Gene Sequence

>MS.gene009644

ATGAACTACACAAATAATGATGGAAAATCAAAGGAGTGGACATGGGATGAAAATAAAATCTTTGAGACCATTCTCTTTGAATATCTTGAGGAAGTACAAGAAGGTCGATGGGAAAATCTTGCTCTTGTTTGCGGTCGATCATCAACTGAAGTAAAAGAACACTATGAGACATTGTTGCATGACTTAGCACTCATTGAGGAAGGTCTTGTCGATTTTCCAACAAACTCAGATGATTTTATTTCGAAAGGCAATGCTTCAATCGATGAGAAGAAAGCTCCTCCAACTAAGAATAAGACTAAGAAAGTGGTGAAACATTGGAGTGAAGAAGAACACAGGTATATATATACTTATTTAGAAAAAACTAACTTACACTTTATTTTTAATTTTATTTTCTTCTTCTTCATGTGGACGAGTCCTTATGCATGGTGTGAATTCCGTAAAAAGAGAAATTAGTAAATCTTTTATTCGAAGAACACCTTGGTTTTTCTGAAAAGGGACATTATTTTTATTGTGTTAAATTTAAAAGTTTATTCCTTTTATCAACAAATAAAAAAAGGGATGAATAAATATTTTAGTTGATAATTTTTGTGTTACTACCTTATTCCTTAAATTGGATTCAAAAGAAAGGTATAACAAACTTGAAGAAATAAAAAAAAAAAAATTGTTAATGTATCTTGACACTAACATATGTATTGGGTTTTCTATGTTTTTCTTTTCACCATGATATAAATTAAATTGACTACCTCTCATCATTTTTTTTATAGGTTATTTGTAGAGGGAATCGAGATTCATAAGAAGGGAAATTGGAAAATGATTTCACAACATGTTCGTACAAGAACTCCAAGTCAATGTGCTAGCCATGCTCAAAAGCATTTCCTTCACCAAAATGGTACATCAAAAAAGATTTATAAAAAAAGAAGCAACTTCAACATTACCTCATTGAAGGGAGATCATTCCAAACCTCTTCTCAGTAAGGACAACATTCCATCTCCTCCTACCTCATGGGATGGAAATTTCCACCCTCTTCTCTATGTTCCAGCTCTTCTTTATCCTCATCCGAATTAA
Protein sequence

>MS.gene009644.t1

MNYTNNDGKSKEWTWDENKIFETILFEYLEEVQEGRWENLALVCGRSSTEVKEHYETLLHDLALIEEGLVDFPTNSDDFISKGNASIDEKKAPPTKNKTKKVVKHWSEEEHRLFVEGIEIHKKGNWKMISQHVRTRTPSQCASHAQKHFLHQNGTSKKIYKKRSNFNITSLKGDHSKPLLSKDNIPSPPTSWDGNFHPLLYVPALLYPHPN