AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene03516

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03516.t1 MTR_1g101810 69.524 105 32 0 14 118 55 159 3.57e-47 154
MS.gene03516.t1 MTR_1g101810 69.524 105 32 0 14 118 85 189 1.19e-46 154
MS.gene03516.t1 MTR_8g033070 63.366 101 30 2 23 116 80 180 2.80e-37 129
MS.gene03516.t1 MTR_7g028160 56.383 94 41 0 19 112 46 139 2.12e-31 112
MS.gene03516.t1 MTR_1g038650 63.291 79 28 1 7 85 17 94 8.82e-29 104
MS.gene03516.t1 MTR_2g006150 56.842 95 41 0 16 110 123 217 4.70e-28 106
MS.gene03516.t1 MTR_2g006150 56.842 95 41 0 16 110 123 217 8.08e-28 105
MS.gene03516.t1 MTR_1g114380 59.494 79 30 1 7 85 19 95 2.19e-27 101
MS.gene03516.t1 MTR_5g039600 50.980 102 50 0 3 104 47 148 8.96e-27 102
MS.gene03516.t1 MTR_1g063870 69.841 63 19 0 23 85 49 111 2.02e-26 97.8
MS.gene03516.t1 MTR_4g108370 61.176 85 27 1 7 85 75 159 4.55e-26 100
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene03516.t1 AT2G45680 63.725 102 36 1 18 118 70 171 4.53e-38 131
MS.gene03516.t1 AT5G51910 67.778 90 28 1 12 100 45 134 7.71e-36 124
MS.gene03516.t1 AT5G51910 67.778 90 28 1 12 100 45 134 7.71e-36 124
MS.gene03516.t1 AT1G69690 74.603 63 16 0 23 85 52 114 5.84e-29 107
MS.gene03516.t1 AT1G35560 72.727 66 18 0 20 85 52 117 1.83e-28 106
MS.gene03516.t1 AT5G08330 66.667 69 23 0 17 85 25 93 7.98e-28 102
MS.gene03516.t1 AT3G27010 69.697 66 20 0 19 84 74 139 1.77e-27 103
MS.gene03516.t1 AT3G27010 69.697 66 20 0 19 84 74 139 1.77e-27 103
MS.gene03516.t1 AT5G23280 63.014 73 27 0 13 85 29 101 1.93e-27 101
MS.gene03516.t1 AT1G72010 72.464 69 19 0 17 85 57 125 3.37e-27 103
MS.gene03516.t1 AT1G58100 54.945 91 41 0 20 110 57 147 1.43e-25 99.4
MS.gene03516.t1 AT5G41030 62.319 69 26 0 20 88 65 133 2.66e-25 95.9
MS.gene03516.t1 AT3G47620 66.176 68 23 0 18 85 112 179 5.45e-25 98.2
MS.gene03516.t1 AT2G37000 71.186 59 17 0 23 81 43 101 1.87e-24 92.4
MS.gene03516.t1 AT3G45150 52.542 59 28 0 24 82 18 76 5.98e-18 75.1

Find 39 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCGGTGGCTTTGATGATTGC+AGG 0.311422 6.2:+38031203 None:intergenic
GGCTATGGCCGGAATTATTC+CGG 0.369975 6.2:+38031178 None:intergenic
TCGACCGACGCTGTCATTTG+TGG 0.382575 6.2:+38031383 None:intergenic
CAACTTTCCGCCCTCTGAAA+TGG 0.397867 6.2:+38031157 None:intergenic
CACCGGCACCGGAATAATTC+CGG 0.398178 6.2:-38031186 MS.gene03516:CDS
AAGTCTGATGGAGAAACAAT+AGG 0.400346 6.2:-38031248 MS.gene03516:CDS
GGTCTAGCTGCCGATGTTGT+TGG 0.412258 6.2:+38031128 None:intergenic
TTCCAGTTGACAAGAGATCT+TGG 0.413726 6.2:-38031275 MS.gene03516:CDS
GACCAAGATCTCTTGTCAAC+TGG 0.422669 6.2:+38031273 None:intergenic
TTCAGAGGGCGGAAAGTTGA+AGG 0.466569 6.2:-38031153 MS.gene03516:CDS
TTGCTGACAGTGTGACTCTT+CGG 0.478708 6.2:+38031315 None:intergenic
ATCCACAAATTAACCAATTG+AGG 0.488844 6.2:+38031067 None:intergenic
ATCATCAAAGCCACCGGCAC+CGG 0.497106 6.2:-38031197 MS.gene03516:CDS
GCTGTCATTTGTGGTCCAGC+GGG 0.499691 6.2:+38031392 None:intergenic
CCCTCTGAAATGGCTATGGC+CGG 0.502325 6.2:+38031167 None:intergenic
TGTCAGCAACATGTGCATCT+AGG 0.504146 6.2:-38031301 MS.gene03516:CDS
AAAAGCAAGAGAGCCTCAAT+TGG 0.505951 6.2:-38031080 MS.gene03516:CDS
GGCCGGAATTATTCCGGTGC+CGG 0.511782 6.2:+38031184 None:intergenic
AGTCTGATGGAGAAACAATA+GGG 0.517180 6.2:-38031247 MS.gene03516:CDS
TTTGTGTGACGGTCTTCTGA+TGG 0.527958 6.2:+38031353 None:intergenic
TCCGCCCTCTGAAATGGCTA+TGG 0.528278 6.2:+38031163 None:intergenic
CGGAATTATTCCGGTGCCGG+TGG 0.529649 6.2:+38031187 None:intergenic
CGCTGTCATTTGTGGTCCAG+CGG 0.534801 6.2:+38031391 None:intergenic
AAAACAGACGTTGAACCCGC+TGG 0.542316 6.2:-38031407 MS.gene03516:CDS
AGCTAGACCAGACTGCCAAA+AGG 0.550442 6.2:-38031114 MS.gene03516:CDS
GATCTTGGTCACAAGTCTGA+TGG 0.565835 6.2:-38031260 MS.gene03516:CDS
GTCCCTCCACCTTTGTGTGA+CGG 0.572278 6.2:+38031342 None:intergenic
AGACCGTCACACAAAGGTGG+AGG 0.580129 6.2:-38031345 MS.gene03516:CDS
CAGACTGCCAAAAGGCCCCA+AGG 0.604201 6.2:-38031106 MS.gene03516:CDS
GACCGTCACACAAAGGTGGA+GGG 0.618002 6.2:-38031344 MS.gene03516:CDS
TCCGGCCATAGCCATTTCAG+AGG 0.619818 6.2:-38031168 MS.gene03516:CDS
GCCATAGCCATTTCAGAGGG+CGG 0.621097 6.2:-38031164 MS.gene03516:CDS
CCTGCAATCATCAAAGCCAC+CGG 0.628378 6.2:-38031203 MS.gene03516:CDS
AGAAGACCGTCACACAAAGG+TGG 0.633680 6.2:-38031348 MS.gene03516:CDS
CCGGCCATAGCCATTTCAGA+GGG 0.636688 6.2:-38031167 MS.gene03516:CDS
GTTGAAGGTTCCAACAACAT+CGG 0.665250 6.2:-38031138 MS.gene03516:CDS
ATCAGAAGACCGTCACACAA+AGG 0.669750 6.2:-38031351 MS.gene03516:CDS
TGGACCACAAATGACAGCGT+CGG 0.681471 6.2:-38031387 MS.gene03516:CDS
CTGATGGAGAAACAATAGGG+TGG 0.705438 6.2:-38031244 MS.gene03516:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGTCTGATGGAGAAACAAT+AGG - chr6.2:38031244-38031263 MS.gene03516:CDS 35.0%
AGTCTGATGGAGAAACAATA+GGG - chr6.2:38031245-38031264 MS.gene03516:CDS 35.0%
AAAAGCAAGAGAGCCTCAAT+TGG - chr6.2:38031412-38031431 MS.gene03516:CDS 40.0%
GTTGAAGGTTCCAACAACAT+CGG - chr6.2:38031354-38031373 MS.gene03516:CDS 40.0%
TTCCAGTTGACAAGAGATCT+TGG - chr6.2:38031217-38031236 MS.gene03516:CDS 40.0%
!! CTCTCTTGCTTTTCTTCCTT+GGG + chr6.2:38031405-38031424 None:intergenic 40.0%
!! TCTCTTGCTTTTCTTCCTTG+GGG + chr6.2:38031404-38031423 None:intergenic 40.0%
ATCAGAAGACCGTCACACAA+AGG - chr6.2:38031141-38031160 MS.gene03516:CDS 45.0%
CTGATGGAGAAACAATAGGG+TGG - chr6.2:38031248-38031267 MS.gene03516:CDS 45.0%
GACCAAGATCTCTTGTCAAC+TGG + chr6.2:38031222-38031241 None:intergenic 45.0%
GATCTTGGTCACAAGTCTGA+TGG - chr6.2:38031232-38031251 MS.gene03516:CDS 45.0%
TGTCAGCAACATGTGCATCT+AGG - chr6.2:38031191-38031210 MS.gene03516:CDS 45.0%
TTGCTGACAGTGTGACTCTT+CGG + chr6.2:38031180-38031199 None:intergenic 45.0%
TTTGTGTGACGGTCTTCTGA+TGG + chr6.2:38031142-38031161 None:intergenic 45.0%
! TTTTCTTCCTTGGGGCCTTT+TGG + chr6.2:38031396-38031415 None:intergenic 45.0%
!! GCTCTCTTGCTTTTCTTCCT+TGG + chr6.2:38031406-38031425 None:intergenic 45.0%
AAAACAGACGTTGAACCCGC+TGG - chr6.2:38031085-38031104 MS.gene03516:CDS 50.0%
AGAAGACCGTCACACAAAGG+TGG - chr6.2:38031144-38031163 MS.gene03516:CDS 50.0%
AGCTAGACCAGACTGCCAAA+AGG - chr6.2:38031378-38031397 MS.gene03516:CDS 50.0%
CCTGCAATCATCAAAGCCAC+CGG - chr6.2:38031289-38031308 MS.gene03516:CDS 50.0%
GGCTATGGCCGGAATTATTC+CGG + chr6.2:38031317-38031336 None:intergenic 50.0%
TGGACCACAAATGACAGCGT+CGG - chr6.2:38031105-38031124 MS.gene03516:CDS 50.0%
TTCAGAGGGCGGAAAGTTGA+AGG - chr6.2:38031339-38031358 MS.gene03516:CDS 50.0%
! CAACTTTCCGCCCTCTGAAA+TGG + chr6.2:38031338-38031357 None:intergenic 50.0%
AGACCGTCACACAAAGGTGG+AGG - chr6.2:38031147-38031166 MS.gene03516:CDS 55.0%
ATCATCAAAGCCACCGGCAC+CGG - chr6.2:38031295-38031314 MS.gene03516:CDS 55.0%
CCGGCCATAGCCATTTCAGA+GGG - chr6.2:38031325-38031344 MS.gene03516:CDS 55.0%
GACCGTCACACAAAGGTGGA+GGG - chr6.2:38031148-38031167 MS.gene03516:CDS 55.0%
GCCATAGCCATTTCAGAGGG+CGG - chr6.2:38031328-38031347 MS.gene03516:CDS 55.0%
GGTCTAGCTGCCGATGTTGT+TGG + chr6.2:38031367-38031386 None:intergenic 55.0%
GTCCCTCCACCTTTGTGTGA+CGG + chr6.2:38031153-38031172 None:intergenic 55.0%
TCCGGCCATAGCCATTTCAG+AGG - chr6.2:38031324-38031343 MS.gene03516:CDS 55.0%
! CACCGGCACCGGAATAATTC+CGG - chr6.2:38031306-38031325 MS.gene03516:CDS 55.0%
! CGCTGTCATTTGTGGTCCAG+CGG + chr6.2:38031104-38031123 None:intergenic 55.0%
! GCTGTCATTTGTGGTCCAGC+GGG + chr6.2:38031103-38031122 None:intergenic 55.0%
! TCGACCGACGCTGTCATTTG+TGG + chr6.2:38031112-38031131 None:intergenic 55.0%
!! CCCTCTGAAATGGCTATGGC+CGG + chr6.2:38031328-38031347 None:intergenic 55.0%
!! CCGGTGGCTTTGATGATTGC+AGG + chr6.2:38031292-38031311 None:intergenic 55.0%
!! TCCGCCCTCTGAAATGGCTA+TGG + chr6.2:38031332-38031351 None:intergenic 55.0%
CAGACTGCCAAAAGGCCCCA+AGG - chr6.2:38031386-38031405 MS.gene03516:CDS 60.0%
GGCCGGAATTATTCCGGTGC+CGG + chr6.2:38031311-38031330 None:intergenic 60.0%
! CGGAATTATTCCGGTGCCGG+TGG + chr6.2:38031308-38031327 None:intergenic 60.0%
! CTTGGGGCCTTTTGGCAGTC+TGG + chr6.2:38031388-38031407 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 38031076 38031438 38031076 ID=MS.gene03516
chr6.2 mRNA 38031076 38031438 38031076 ID=MS.gene03516.t1;Parent=MS.gene03516
chr6.2 exon 38031076 38031438 38031076 ID=MS.gene03516.t1.exon1;Parent=MS.gene03516.t1
chr6.2 CDS 38031076 38031438 38031076 ID=cds.MS.gene03516.t1;Parent=MS.gene03516.t1
Gene Sequence

>MS.gene03516

ATGCATGGAAAAACAGACGTTGAACCCGCTGGACCACAAATGACAGCGTCGGTCGAAAAGAAACCATCAGAAGACCGTCACACAAAGGTGGAGGGACGTGTCCGAAGAGTCACACTGTCAGCAACATGTGCATCTAGGATCTTCCAGTTGACAAGAGATCTTGGTCACAAGTCTGATGGAGAAACAATAGGGTGGTTACTAGAACAAGCTGAACCTGCAATCATCAAAGCCACCGGCACCGGAATAATTCCGGCCATAGCCATTTCAGAGGGCGGAAAGTTGAAGGTTCCAACAACATCGGCAGCTAGACCAGACTGCCAAAAGGCCCCAAGGAAGAAAAGCAAGAGAGCCTCAATTGGTTAA
Protein sequence

>MS.gene03516.t1

MHGKTDVEPAGPQMTASVEKKPSEDRHTKVEGRVRRVTLSATCASRIFQLTRDLGHKSDGETIGWLLEQAEPAIIKATGTGIIPAIAISEGGKLKVPTTSAARPDCQKAPRKKSKRASIG