AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1172100

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1172100 MtrunA17_Chr4g0059251 95.395 152 4 1 1 152 1 149 6.87e-106 298
Msa1172100 MtrunA17_Chr3g0117901 50.407 123 32 5 22 135 20 122 3.59e-31 109
Msa1172100 MtrunA17_Chr6g0451141 42.857 126 57 6 17 137 25 140 6.72e-24 90.9
Msa1172100 MtrunA17_Chr2g0305131 46.835 79 35 4 58 134 57 130 3.28e-13 62.8
Msa1172100 MtrunA17_Chr4g0065221 28.889 135 88 4 1 133 9 137 3.84e-12 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1172100 AT5G62865.1 41.447 152 66 7 3 139 1 144 9.02e-19 78.6
Msa1172100 AT3G01430.1 34.194 155 59 6 14 137 21 163 1.08e-17 75.9
Msa1172100 AT3G48020.1 37.705 122 55 4 26 139 14 122 1.99e-16 71.6
Msa1172100 AT5G14895.1 35.252 139 60 7 17 137 24 150 3.40e-16 71.6

Find 56 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAGGCTCGGAGTTTCTTTA+AGG 0.198226 8_1:+1982163 None:intergenic
CCGGAACCGGAGGGTGAAAT+TGG 0.303837 8_1:-1981939 Msa1172100:CDS
CGAATGAAATTCTTCCATCT+TGG 0.312826 8_1:+1982122 None:intergenic
CCAATTTCACCCTCCGGTTC+CGG 0.326252 8_1:+1981939 None:intergenic
TGGTTGTGGTGGTGGTGGGA+TGG 0.347361 8_1:+1982219 None:intergenic
GGCGGTGGTTGTGGTGGTGG+TGG 0.369594 8_1:+1982214 None:intergenic
GGTTGTGGTGGTGGTGGGAT+GGG 0.371805 8_1:+1982220 None:intergenic
CCATCTATCGGCGGTGGTTG+TGG 0.375414 8_1:+1982205 None:intergenic
TAAGTCTGTTGCGCCGGAAC+CGG 0.391391 8_1:-1981952 Msa1172100:CDS
CACGCCGCCGTTCCGTTTGG+TGG 0.400297 8_1:-1982274 Msa1172100:CDS
CCACAACCACCGCCGATAGA+TGG 0.401522 8_1:-1982205 Msa1172100:CDS
GTCTGTTGCGCCGGAACCGG+AGG 0.417562 8_1:-1981949 Msa1172100:CDS
ATCGGCGGTGGTTGTGGTGG+TGG 0.420574 8_1:+1982211 None:intergenic
CCTCACGCCGCCGTTCCGTT+TGG 0.424502 8_1:-1982277 Msa1172100:CDS
GCCTGGTCGGAGATCGTCGC+TGG 0.451987 8_1:-1982146 Msa1172100:CDS
CGCAACAGACTTAATATTAA+CGG 0.461558 8_1:+1981962 None:intergenic
CCTTAAAGAAACTCCGAGCC+TGG 0.463778 8_1:-1982163 Msa1172100:CDS
TTGTCATACGCTTCGATCGA+TGG 0.470318 8_1:+1982087 None:intergenic
ACGGCGGCGTGAGGCGAAGC+AGG 0.472114 8_1:+1982286 None:intergenic
ATGAAGATAGCCACGACGAC+GGG 0.475007 8_1:-1982013 Msa1172100:CDS
CAAGATGGAAGAATTTCATT+CGG 0.477769 8_1:-1982121 Msa1172100:CDS
GCGGTGGTTGTGGTGGTGGT+GGG 0.485464 8_1:+1982215 None:intergenic
GAAGCAGGTGGGGAAACATA+AGG 0.500761 8_1:+1982301 None:intergenic
AACCCGCCAATTTCACCCTC+CGG 0.509850 8_1:+1981933 None:intergenic
GGTGGGATGGGATTGAGAAA+AGG 0.511993 8_1:+1982232 None:intergenic
AACCGGAGGGTGAAATTGGC+GGG 0.518811 8_1:-1981935 Msa1172100:CDS
GAACCGGAGGGTGAAATTGG+CGG 0.518878 8_1:-1981936 Msa1172100:CDS
GGCGTGAGGCGAAGCAGGTG+GGG 0.526513 8_1:+1982291 None:intergenic
GCGGCGTGAGGCGAAGCAGG+TGG 0.527709 8_1:+1982289 None:intergenic
CGACGATCTCCGACCAGGCT+CGG 0.535045 8_1:+1982150 None:intergenic
ACGCCGCCGTTCCGTTTGGT+GGG 0.538378 8_1:-1982273 Msa1172100:CDS
TAATATTAAGTCTGTTGCGC+CGG 0.541424 8_1:-1981958 Msa1172100:CDS
ACCAGCGACGATCTCCGACC+AGG 0.547492 8_1:+1982145 None:intergenic
GCGAACACGTTCCCACCAAA+CGG 0.551665 8_1:+1982262 None:intergenic
AGATCGTCGCTGGTCCAAGA+TGG 0.560579 8_1:-1982136 Msa1172100:CDS
GCCGCGAGACCACCATCTAT+CGG 0.563498 8_1:+1982193 None:intergenic
CACGTTCCCACCAAACGGAA+CGG 0.587139 8_1:+1982267 None:intergenic
AGACCACCATCTATCGGCGG+TGG 0.590655 8_1:+1982199 None:intergenic
CCAAACGGAACGGCGGCGTG+AGG 0.591562 8_1:+1982277 None:intergenic
TCTATCGGCGGTGGTTGTGG+TGG 0.591878 8_1:+1982208 None:intergenic
TATGCGTTAAACTTTGATGA+GGG 0.593416 8_1:-1982041 Msa1172100:CDS
GGGATGGGATTGAGAAAAGG+AGG 0.601763 8_1:+1982235 None:intergenic
TTATGCGTTAAACTTTGATG+AGG 0.610573 8_1:-1982042 Msa1172100:CDS
GCCGATAGATGGTGGTCTCG+CGG 0.626739 8_1:-1982194 Msa1172100:CDS
TCTGTTGCGCCGGAACCGGA+GGG 0.629319 8_1:-1981948 Msa1172100:CDS
AATGAAGATAGCCACGACGA+CGG 0.629695 8_1:-1982014 Msa1172100:CDS
AATTCCGAAACCCGTCGTCG+TGG 0.629946 8_1:+1982003 None:intergenic
ATGGGATTGAGAAAAGGAGG+CGG 0.635403 8_1:+1982238 None:intergenic
AAAGAAACTCCGAGCCTGGT+CGG 0.644913 8_1:-1982159 Msa1172100:CDS
TGATTCAAGCTCTAGCTCAA+CGG 0.647004 8_1:+1982358 None:intergenic
AAGTTTAACGCATAACTCAA+CGG 0.651799 8_1:+1982050 None:intergenic
GGAGTTTCTTTAAGGCGTTG+AGG 0.656051 8_1:+1982171 None:intergenic
CAACCACCGCCGATAGATGG+TGG 0.659317 8_1:-1982202 Msa1172100:CDS
GTTCCCACCAAACGGAACGG+CGG 0.663196 8_1:+1982270 None:intergenic
AACAGACTTAATATTAACGG+CGG 0.721385 8_1:+1981965 None:intergenic
GCGAGACCACCATCTATCGG+CGG 0.723063 8_1:+1982196 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
CAAGATGGAAGAATTTCATT+CGG - chr8_1:1982167-1982186 Msa1172100:CDS 30.0%
AAGTTTAACGCATAACTCAA+CGG + chr8_1:1982241-1982260 None:intergenic 30.0%
TTATGCGTTAAACTTTGATG+AGG - chr8_1:1982246-1982265 Msa1172100:CDS 30.0%
TATGCGTTAAACTTTGATGA+GGG - chr8_1:1982247-1982266 Msa1172100:CDS 30.0%
AACAGACTTAATATTAACGG+CGG + chr8_1:1982326-1982345 None:intergenic 30.0%
CGCAACAGACTTAATATTAA+CGG + chr8_1:1982329-1982348 None:intergenic 30.0%
CGAATGAAATTCTTCCATCT+TGG + chr8_1:1982169-1982188 None:intergenic 35.0%
TAATATTAAGTCTGTTGCGC+CGG - chr8_1:1982330-1982349 Msa1172100:CDS 35.0%
! TGATTCAAGCTCTAGCTCAA+CGG + chr8_1:1981933-1981952 None:intergenic 40.0%
! TCTCTTTTGTTGGAGATGAG+CGG + chr8_1:1981960-1981979 None:intergenic 40.0%
! TTTTGTTGGAGATGAGCGGT+TGG + chr8_1:1981956-1981975 None:intergenic 45.0%
! AGGCGCTTGATCTCTTTTGT+TGG + chr8_1:1981970-1981989 None:intergenic 45.0%
ATGGGATTGAGAAAAGGAGG+CGG + chr8_1:1982053-1982072 None:intergenic 45.0%
!! GGAGTTTCTTTAAGGCGTTG+AGG + chr8_1:1982120-1982139 None:intergenic 45.0%
TTGTCATACGCTTCGATCGA+TGG + chr8_1:1982204-1982223 None:intergenic 45.0%
AATGAAGATAGCCACGACGA+CGG - chr8_1:1982274-1982293 Msa1172100:CDS 45.0%
GAAGCAGGTGGGGAAACATA+AGG + chr8_1:1981990-1982009 None:intergenic 50.0%
GGGATGGGATTGAGAAAAGG+AGG + chr8_1:1982056-1982075 None:intergenic 50.0%
GGTGGGATGGGATTGAGAAA+AGG + chr8_1:1982059-1982078 None:intergenic 50.0%
CCAGGCTCGGAGTTTCTTTA+AGG + chr8_1:1982128-1982147 None:intergenic 50.0%
CCTTAAAGAAACTCCGAGCC+TGG - chr8_1:1982125-1982144 Msa1172100:CDS 50.0%
AAAGAAACTCCGAGCCTGGT+CGG - chr8_1:1982129-1982148 Msa1172100:CDS 50.0%
ATGAAGATAGCCACGACGAC+GGG - chr8_1:1982275-1982294 Msa1172100:CDS 50.0%
CACGTTCCCACCAAACGGAA+CGG + chr8_1:1982024-1982043 None:intergenic 55.0%
GCGAACACGTTCCCACCAAA+CGG + chr8_1:1982029-1982048 None:intergenic 55.0%
AGATCGTCGCTGGTCCAAGA+TGG - chr8_1:1982152-1982171 Msa1172100:CDS 55.0%
! ATAGCCACGACGACGGGTTT+CGG - chr8_1:1982281-1982300 Msa1172100:CDS 55.0%
AATTCCGAAACCCGTCGTCG+TGG + chr8_1:1982288-1982307 None:intergenic 55.0%
TAAGTCTGTTGCGCCGGAAC+CGG - chr8_1:1982336-1982355 Msa1172100:CDS 55.0%
CCAATTTCACCCTCCGGTTC+CGG + chr8_1:1982352-1982371 None:intergenic 55.0%
GAACCGGAGGGTGAAATTGG+CGG - chr8_1:1982352-1982371 Msa1172100:CDS 55.0%
AACCGGAGGGTGAAATTGGC+GGG - chr8_1:1982353-1982372 Msa1172100:CDS 55.0%
AACCCGCCAATTTCACCCTC+CGG + chr8_1:1982358-1982377 None:intergenic 55.0%
GTTCCCACCAAACGGAACGG+CGG + chr8_1:1982021-1982040 None:intergenic 60.0%
!! GGTTGTGGTGGTGGTGGGAT+GGG + chr8_1:1982071-1982090 None:intergenic 60.0%
!! TGGTTGTGGTGGTGGTGGGA+TGG + chr8_1:1982072-1982091 None:intergenic 60.0%
TCTATCGGCGGTGGTTGTGG+TGG + chr8_1:1982083-1982102 None:intergenic 60.0%
CCATCTATCGGCGGTGGTTG+TGG + chr8_1:1982086-1982105 None:intergenic 60.0%
CCACAACCACCGCCGATAGA+TGG - chr8_1:1982083-1982102 Msa1172100:CDS 60.0%
CAACCACCGCCGATAGATGG+TGG - chr8_1:1982086-1982105 Msa1172100:CDS 60.0%
AGACCACCATCTATCGGCGG+TGG + chr8_1:1982092-1982111 None:intergenic 60.0%
GCGAGACCACCATCTATCGG+CGG + chr8_1:1982095-1982114 None:intergenic 60.0%
! GCCGATAGATGGTGGTCTCG+CGG - chr8_1:1982094-1982113 Msa1172100:CDS 60.0%
GCCGCGAGACCACCATCTAT+CGG + chr8_1:1982098-1982117 None:intergenic 60.0%
CCGGAACCGGAGGGTGAAAT+TGG - chr8_1:1982349-1982368 Msa1172100:CDS 60.0%
ACGCCGCCGTTCCGTTTGGT+GGG - chr8_1:1982015-1982034 Msa1172100:CDS 65.0%
!! GCGGTGGTTGTGGTGGTGGT+GGG + chr8_1:1982076-1982095 None:intergenic 65.0%
ATCGGCGGTGGTTGTGGTGG+TGG + chr8_1:1982080-1982099 None:intergenic 65.0%
CGACGATCTCCGACCAGGCT+CGG + chr8_1:1982141-1982160 None:intergenic 65.0%
ACCAGCGACGATCTCCGACC+AGG + chr8_1:1982146-1982165 None:intergenic 65.0%
TCTGTTGCGCCGGAACCGGA+GGG - chr8_1:1982340-1982359 Msa1172100:CDS 65.0%
GGCGTGAGGCGAAGCAGGTG+GGG + chr8_1:1982000-1982019 None:intergenic 70.0%
CGGCGTGAGGCGAAGCAGGT+GGG + chr8_1:1982001-1982020 None:intergenic 70.0%
CCAAACGGAACGGCGGCGTG+AGG + chr8_1:1982014-1982033 None:intergenic 70.0%
CCTCACGCCGCCGTTCCGTT+TGG - chr8_1:1982011-1982030 Msa1172100:CDS 70.0%
CACGCCGCCGTTCCGTTTGG+TGG - chr8_1:1982014-1982033 Msa1172100:CDS 70.0%
!! GGCGGTGGTTGTGGTGGTGG+TGG + chr8_1:1982077-1982096 None:intergenic 70.0%
GCCTGGTCGGAGATCGTCGC+TGG - chr8_1:1982142-1982161 Msa1172100:CDS 70.0%
GTCTGTTGCGCCGGAACCGG+AGG - chr8_1:1982339-1982358 Msa1172100:CDS 70.0%
GCGGCGTGAGGCGAAGCAGG+TGG + chr8_1:1982002-1982021 None:intergenic 75.0%
ACGGCGGCGTGAGGCGAAGC+AGG + chr8_1:1982005-1982024 None:intergenic 75.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 1981926 1982384 1981926 ID=Msa1172100;Name=Msa1172100
chr8_1 mRNA 1981926 1982384 1981926 ID=Msa1172100-mRNA-1;Parent=Msa1172100;Name=Msa1172100-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|152
chr8_1 exon 1981926 1982384 1981926 ID=Msa1172100-mRNA-1:exon:732;Parent=Msa1172100-mRNA-1
chr8_1 CDS 1981926 1982384 1981926 ID=Msa1172100-mRNA-1:cds;Parent=Msa1172100-mRNA-1
Gene Sequence

>Msa1172100

ATGTCCGTTGAGCTAGAGCTTGAATCACCAACCGCTCATCTCCAACAAAAGAGATCAAGCGCCTTATGTTTCCCCACCTGCTTCGCCTCACGCCGCCGTTCCGTTTGGTGGGAACGTGTTCGCTCCGCCTCCTTTTCTCAATCCCATCCCACCACCACCACAACCACCGCCGATAGATGGTGGTCTCGCGGCCTCAACGCCTTAAAGAAACTCCGAGCCTGGTCGGAGATCGTCGCTGGTCCAAGATGGAAGAATTTCATTCGGAAATTCAACAACCATCGATCGAAGCGTATGACAAAGTGTCAATACGATCCGTTGAGTTATGCGTTAAACTTTGATGAGGGACAGAATGAAGATAGCCACGACGACGGGTTTCGGAATTTCTCTACGCGTTACGCCGCCGTTAATATTAAGTCTGTTGCGCCGGAACCGGAGGGTGAAATTGGCGGGTTAGTTTGA
Protein sequence

>Msa1172100

MSVELELESPTAHLQQKRSSALCFPTCFASRRRSVWWERVRSASFSQSHPTTTTTTADRWWSRGLNALKKLRAWSEIVAGPRWKNFIRKFNNHRSKRMTKCQYDPLSYALNFDEGQNEDSHDDGFRNFSTRYAAVNIKSVAPEPEGEIGGLV*