AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene004307

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004307.t1 MTR_2g017890 91.743 109 9 0 1 109 2 110 4.47e-70 214
MS.gene004307.t1 MTR_8g087540 60.331 121 46 1 1 121 1 119 4.80e-47 155
MS.gene004307.t1 MTR_6g043060 60.577 104 41 0 4 107 12 115 1.32e-43 145
MS.gene004307.t1 MTR_5g029680 62.626 99 37 0 9 107 27 125 2.20e-43 148
MS.gene004307.t1 MTR_4g077970 63.265 98 36 0 12 109 10 107 6.36e-43 147
MS.gene004307.t1 MTR_7g095680 63.441 93 34 0 13 105 48 140 3.19e-41 140
MS.gene004307.t1 MTR_2g100680 58.824 102 42 0 6 107 23 124 5.54e-41 141
MS.gene004307.t1 MTR_2g100670 56.637 113 43 1 1 107 14 126 7.26e-41 137
MS.gene004307.t1 MTR_8g083100 64.516 93 33 0 15 107 23 115 7.83e-41 141
MS.gene004307.t1 MTR_5g017470 60.638 94 37 0 14 107 9 102 1.03e-40 137
MS.gene004307.t1 MTR_2g100670 56.637 113 43 1 1 107 122 234 6.76e-40 137
MS.gene004307.t1 MTR_5g010680 58.095 105 43 1 2 105 11 115 6.79e-40 136
MS.gene004307.t1 MTR_1g061170 60.000 95 38 0 12 106 47 141 1.48e-39 137
MS.gene004307.t1 MTR_3g101870 61.000 100 38 1 8 106 17 116 3.53e-39 135
MS.gene004307.t1 MTR_8g105780 65.263 95 32 1 12 105 20 114 3.78e-39 134
MS.gene004307.t1 MTR_3g104550 58.947 95 39 0 13 107 45 139 4.84e-39 134
MS.gene004307.t1 MTR_1g102860 56.863 102 44 0 5 106 31 132 1.59e-38 132
MS.gene004307.t1 MTR_1g071360 56.436 101 44 0 5 105 23 123 5.07e-38 131
MS.gene004307.t1 MTR_1g071360 56.436 101 44 0 5 105 20 120 6.88e-38 131
MS.gene004307.t1 MTR_1g100777 54.717 106 47 1 3 107 6 111 9.02e-38 129
MS.gene004307.t1 MTR_6g086805 57.292 96 41 0 12 107 9 104 1.48e-37 130
MS.gene004307.t1 MTR_5g089170 57.000 100 42 1 8 106 18 117 2.29e-36 124
MS.gene004307.t1 MTR_0020s0020 55.319 94 42 0 14 107 33 126 2.57e-34 121
MS.gene004307.t1 MTR_7g091370 51.613 93 45 0 14 106 22 114 4.32e-34 118
MS.gene004307.t1 MTR_4g088900 43.519 108 57 1 14 117 33 140 3.60e-29 105
MS.gene004307.t1 MTR_4g045757 64.789 71 25 0 1 71 1 71 2.95e-28 99.0
MS.gene004307.t1 MTR_5g047190 50.000 92 39 2 22 106 1 92 7.05e-25 90.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene004307.t1 AT4G17750 68.421 95 30 0 13 107 51 145 1.31e-45 154
MS.gene004307.t1 AT4G13980 67.742 93 30 0 15 107 24 116 2.65e-42 145
MS.gene004307.t1 AT3G02990 63.830 94 34 0 12 105 21 114 3.48e-42 144
MS.gene004307.t1 AT5G03720 59.184 98 40 0 9 106 50 147 4.79e-42 143
MS.gene004307.t1 AT5G03720 59.184 98 40 0 9 106 50 147 4.79e-42 143
MS.gene004307.t1 AT1G32330 62.000 100 38 0 8 107 31 130 1.59e-41 143
MS.gene004307.t1 AT1G32330 62.000 100 38 0 8 107 31 130 1.76e-41 143
MS.gene004307.t1 AT2G26150 59.223 103 42 0 5 107 35 137 2.02e-41 140
MS.gene004307.t1 AT2G26150 59.223 103 42 0 5 107 35 137 2.02e-41 140
MS.gene004307.t1 AT1G46264 58.559 111 42 2 1 110 23 130 2.65e-40 137
MS.gene004307.t1 AT5G16820 60.417 96 38 0 10 105 23 118 3.38e-40 139
MS.gene004307.t1 AT5G16820 60.417 96 38 0 10 105 23 118 3.38e-40 139
MS.gene004307.t1 AT3G22830 58.824 102 42 0 5 106 52 153 4.14e-40 138
MS.gene004307.t1 AT4G18880 66.981 106 35 0 2 107 3 108 6.51e-40 137
MS.gene004307.t1 AT3G24520 61.702 94 36 0 12 105 15 108 2.21e-39 134
MS.gene004307.t1 AT5G62020 56.604 106 45 1 1 105 9 114 5.86e-39 132
MS.gene004307.t1 AT3G51910 56.000 100 44 0 5 104 20 119 1.54e-38 130
MS.gene004307.t1 AT5G43840 60.204 98 37 1 11 106 14 111 1.62e-38 131
MS.gene004307.t1 AT4G36990 60.606 99 38 1 12 109 11 109 4.47e-38 130
MS.gene004307.t1 AT5G45710 60.748 107 41 1 1 107 1 106 5.61e-37 128
MS.gene004307.t1 AT5G45710 60.748 107 41 1 1 107 1 106 5.61e-37 128
MS.gene004307.t1 AT2G41690 55.319 94 42 0 13 106 39 132 1.35e-36 125
MS.gene004307.t1 AT4G11660 58.696 92 38 0 14 105 59 150 2.37e-36 127
MS.gene004307.t1 AT5G54070 54.839 93 42 0 12 104 69 161 4.12e-36 126
MS.gene004307.t1 AT1G67970 58.763 97 39 1 12 107 17 113 2.54e-35 125
MS.gene004307.t1 AT3G63350 57.143 91 39 0 14 104 28 118 8.99e-35 121
MS.gene004307.t1 AT4G18870 48.864 88 45 0 14 101 146 233 8.43e-25 95.9
MS.gene004307.t1 AT4G18870 46.535 101 52 2 1 101 1 99 1.75e-23 92.4
MS.gene004307.t1 AT1G77570 36.667 90 54 2 15 101 27 116 4.80e-17 72.4
MS.gene004307.t1 AT4G19630 33.333 90 57 1 15 101 12 101 1.43e-13 63.2

Find 21 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACTGATGACATTGTTTCT+TGG 0.248061 2.3:+68816813 MS.gene004307:CDS
AACTGATGACATTGTTTCTT+GGG 0.286701 2.3:+68816814 MS.gene004307:CDS
TGAAACTTGAGAAGTTATTA+TGG 0.310950 2.3:-68816910 None:intergenic
TCTCACCAAGACTTATGATA+TGG 0.311693 2.3:+68816778 MS.gene004307:CDS
GGGAATGATGGAAGAAGCTC+AGG 0.447000 2.3:+68816727 None:intergenic
GAGAAAAGGAGGCACCTTAT+CGG 0.464277 2.3:-68816759 None:intergenic
TCATAAGTCTTGGTGAGAAA+AGG 0.480198 2.3:-68816773 None:intergenic
CTCAACCATATCATAAGTCT+TGG 0.489284 2.3:-68816783 None:intergenic
CATGAGCATTCTGCGAAGAA+TGG 0.490641 2.3:-68817662 None:intergenic
TCGCAGAATGCTCATGGCCA+AGG 0.501991 2.3:+68817669 MS.gene004307:CDS
TTATTATGGTTAAAGTATTG+AGG 0.507346 2.3:-68816896 None:intergenic
CGCAGAATGCTCATGGCCAA+GGG 0.508087 2.3:+68817670 MS.gene004307:CDS
GAAACAATGTCATCAGTTGA+AGG 0.519956 2.3:-68816809 None:intergenic
TCAGGGTAGTAGTTCCGATA+AGG 0.544906 2.3:+68816745 MS.gene004307:CDS
CATTCTTCGCAGAATGCTCA+TGG 0.549403 2.3:+68817663 MS.gene004307:CDS
CAAGACTTATGATATGGTTG+AGG 0.564774 2.3:+68816784 MS.gene004307:CDS
ACTGATGACATTGTTTCTTG+GGG 0.579964 2.3:+68816815 MS.gene004307:CDS
TAAGTCTTGGTGAGAAAAGG+AGG 0.608589 2.3:-68816770 None:intergenic
ATCTTATGAAGAATATCCAA+AGG 0.635890 2.3:+68817623 MS.gene004307:CDS
GCAGAATGCTCATGGCCAAG+GGG 0.714345 2.3:+68817671 MS.gene004307:CDS
GGAATGATGGAAGAAGCTCA+GGG 0.733848 2.3:+68816728 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAATAAATCAATCAAATC+AGG - chr2.3:68817169-68817188 None:intergenic 15.0%
!!! TATTGGTTTTTTTATTAAGT+TGG - chr2.3:68817371-68817390 None:intergenic 15.0%
!!! TTTTTGTTGTTAATTGTTAT+TGG - chr2.3:68817388-68817407 None:intergenic 15.0%
!! AAAAATTGATACACAACTAT+GGG + chr2.3:68817564-68817583 MS.gene004307:CDS 20.0%
!!! TTAAGCTTATGTATTTTCAT+AGG + chr2.3:68817185-68817204 MS.gene004307:intron 20.0%
!!! TTATTATGGTTAAAGTATTG+AGG - chr2.3:68816899-68816918 None:intergenic 20.0%
! AAGCAATAAAAAAACCTGAA+TGG - chr2.3:68817069-68817088 None:intergenic 25.0%
! AAGCAATCAATAAACCTTAA+TGG - chr2.3:68817506-68817525 None:intergenic 25.0%
! AGCAATCAATAAACCTTAAT+GGG - chr2.3:68817505-68817524 None:intergenic 25.0%
! ATAAAAGAACAAAGCTTGAT+TGG - chr2.3:68817326-68817345 None:intergenic 25.0%
! ATCTTATGAAGAATATCCAA+AGG + chr2.3:68817623-68817642 MS.gene004307:CDS 25.0%
! CTTTAATGTACTTCATTTCA+TGG + chr2.3:68816961-68816980 MS.gene004307:intron 25.0%
! GAAAAATTGATACACAACTA+TGG + chr2.3:68817563-68817582 MS.gene004307:CDS 25.0%
! TGAAACTTGAGAAGTTATTA+TGG - chr2.3:68816913-68816932 None:intergenic 25.0%
!! TTAGACTGTGTTATGTTTTT+CGG + chr2.3:68817087-68817106 MS.gene004307:intron 25.0%
!! TTTTTCTAATCATTCCATTC+AGG + chr2.3:68817052-68817071 MS.gene004307:intron 25.0%
!!! CTGATGAAAGTTTTATTGTT+TGG + chr2.3:68816843-68816862 MS.gene004307:CDS 25.0%
GTTAGAAAAATTGATCATCG+TGG + chr2.3:68817122-68817141 MS.gene004307:intron 30.0%
TGTGAGATAGCTTATGTTAT+AGG + chr2.3:68817280-68817299 MS.gene004307:intron 30.0%
! AACTGATGACATTGTTTCTT+GGG + chr2.3:68816814-68816833 MS.gene004307:CDS 30.0%
! CTTCTTTTTATCACCCATTA+AGG + chr2.3:68817489-68817508 MS.gene004307:intron 30.0%
! TTGAACTGTCTTATGGTTTT+TGG + chr2.3:68817524-68817543 MS.gene004307:intron 30.0%
!!! TATGGTTTTTGGTTTGATCA+GGG + chr2.3:68817535-68817554 MS.gene004307:intron 30.0%
!!! TTATGGTTTTTGGTTTGATC+AGG + chr2.3:68817534-68817553 MS.gene004307:intron 30.0%
CAAGACTTATGATATGGTTG+AGG + chr2.3:68816784-68816803 MS.gene004307:CDS 35.0%
CAGCTTAATACCTATGTAAG+CGG + chr2.3:68816938-68816957 MS.gene004307:intron 35.0%
CTCAACCATATCATAAGTCT+TGG - chr2.3:68816786-68816805 None:intergenic 35.0%
GAAACAATGTCATCAGTTGA+AGG - chr2.3:68816812-68816831 None:intergenic 35.0%
TACATTAAAGCCGCTTACAT+AGG - chr2.3:68816951-68816970 None:intergenic 35.0%
TCATAAGTCTTGGTGAGAAA+AGG - chr2.3:68816776-68816795 None:intergenic 35.0%
TCTCACCAAGACTTATGATA+TGG + chr2.3:68816778-68816797 MS.gene004307:CDS 35.0%
TGATTGCTTGAACTGTCTTA+TGG + chr2.3:68817517-68817536 MS.gene004307:intron 35.0%
! ACTGATGACATTGTTTCTTG+GGG + chr2.3:68816815-68816834 MS.gene004307:CDS 35.0%
! CAACTGATGACATTGTTTCT+TGG + chr2.3:68816813-68816832 MS.gene004307:CDS 35.0%
!! CAGAAGATCAAAGCATTGTT+TGG - chr2.3:68817455-68817474 None:intergenic 35.0%
TAAGTCTTGGTGAGAAAAGG+AGG - chr2.3:68816773-68816792 None:intergenic 40.0%
! CTAAAACTGTTTTGCGCCTT+TGG - chr2.3:68817642-68817661 None:intergenic 40.0%
CATGAGCATTCTGCGAAGAA+TGG - chr2.3:68817665-68817684 None:intergenic 45.0%
CATTCTTCGCAGAATGCTCA+TGG + chr2.3:68817663-68817682 MS.gene004307:CDS 45.0%
TCAGGGTAGTAGTTCCGATA+AGG + chr2.3:68816745-68816764 MS.gene004307:CDS 45.0%
!! GAGAAAAGGAGGCACCTTAT+CGG - chr2.3:68816762-68816781 None:intergenic 45.0%
CGCAGAATGCTCATGGCCAA+GGG + chr2.3:68817670-68817689 MS.gene004307:CDS 55.0%
GCAGAATGCTCATGGCCAAG+GGG + chr2.3:68817671-68817690 MS.gene004307:CDS 55.0%
TCGCAGAATGCTCATGGCCA+AGG + chr2.3:68817669-68817688 MS.gene004307:CDS 55.0%
TTAGTGGAGCAGCAACCCCT+TGG - chr2.3:68817689-68817708 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 68816734 68817708 68816734 ID=MS.gene004307
chr2.3 mRNA 68816734 68817708 68816734 ID=MS.gene004307.t1;Parent=MS.gene004307
chr2.3 exon 68816734 68816952 68816734 ID=MS.gene004307.t1.exon1;Parent=MS.gene004307.t1
chr2.3 CDS 68816734 68816952 68816734 ID=cds.MS.gene004307.t1;Parent=MS.gene004307.t1
chr2.3 exon 68817556 68817708 68817556 ID=MS.gene004307.t1.exon2;Parent=MS.gene004307.t1
chr2.3 CDS 68817556 68817708 68817556 ID=cds.MS.gene004307.t1;Parent=MS.gene004307.t1
Gene Sequence

>MS.gene004307

ATGGAAGAAGCTCAGGGTAGTAGTTCCGATAAGGTGCCTCCTTTTCTCACCAAGACTTATGATATGGTTGAGGATCCTTCAACTGATGACATTGTTTCTTGGGGTGCTACTGATGAAAGTTTTATTGTTTGGAATAAACTAGATTTTGAAAAAGATGTGTTGCCTCAATACTTTAACCATAATAACTTCTCAAGTTTCATCAGACAGCTTAATACCTATGTAAGCGGCTTTAATGTACTTCATTTCATGGATTTTTAAATTGTTTTGTTATTTCGTTAATGTATAATGTTTTGTTATTGTCTTAATGTTGTCTCTTTTTTTTTCTAATCATTCCATTCAGGTTTTTTTATTGCTTAGACTGTGTTATGTTTTTCGGTTTGATTATGTCGTTAGAAAAATTGATCATCGTGGATTTGTTAATTTTTTTATGAGCCTGATTTGATTGATTTATTTAAGCTTATGTATTTTCATAGGCACGCGTAAGACTAATTGAGATAGCTTATAGAAAAACAACTTCATAAGTTGTTCAGTTTATTTTATTTTCATTGTGAGATAGCTTATGTTATAGGCACTTTATTAAGTTGTTGATCCAATCAAGCTTTGTTCTTTTATTGTTACTGTATTTTCATCACTGCCAACTTAATAAAAAAACCAATAACAATTAACAACAAAAATCATATAAGTGTTTATGTTATAAACACTCAATTAACTTGCTCATCCAAACAATGCTTTGATCTTCTGTTTTTTTTCTCTCTCTTCTTTTTATCACCCATTAAGGTTTATTGATTGCTTGAACTGTCTTATGGTTTTTGGTTTGATCAGGGCTTTAGAAAAATTGATACACAACTATGGGAATACGCAAACGATGATTTCGTAAGAAATCAAAAACATCTTATGAAGAATATCCAAAGGCGCAAAACAGTTTTAGCCATTCTTCGCAGAATGCTCATGGCCAAGGGGTTGCTGCTCCACTAA
Protein sequence

>MS.gene004307.t1

MEEAQGSSSDKVPPFLTKTYDMVEDPSTDDIVSWGATDESFIVWNKLDFEKDVLPQYFNHNNFSSFIRQLNTYGFRKIDTQLWEYANDDFVRNQKHLMKNIQRRKTVLAILRRMLMAKGLLLH