AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0732310


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0732310 MtrunA17_Chr4g0021021 66.092 174 41 2 28 190 46 212 2.20e-75 225
Msa0732310 MtrunA17_Chr3g0079081 59.195 174 50 3 28 190 74 237 8.07e-65 199
Msa0732310 MtrunA17_Chr7g0231961 55.435 92 37 1 29 120 11 98 3.25e-30 107
Msa0732310 MtrunA17_Chr7g0231951 62.264 53 19 1 130 181 11 63 2.75e-15 67.8
Msa0732310 MtrunA17_Chr5g0395991 29.221 154 81 6 30 180 7 135 1.85e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0732310 AT2G45010.2 52.597 154 61 3 29 181 32 174 1.96e-50 162
Msa0732310 AT2G45010.1 55.102 147 54 3 29 174 78 213 4.39e-50 162
Msa0732310 AT5G51400.1 49.673 153 65 3 30 181 79 220 7.15e-45 149

Find 42 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTGTCCTTGCGTACTATT+TGG 0.192370 5_1:-44521729 Msa0732310:CDS
TGTCGAAGGTTGCATTTCTT+TGG 0.228315 5_1:-44521640 Msa0732310:CDS
ACAAAAGAAATATCACTTAA+AGG 0.255348 5_1:-44521487 Msa0732310:CDS
GTGCATGTTGTGTGCATTGC+TGG 0.319796 5_1:-44521358 Msa0732310:CDS
GTCGAAGGTTGCATTTCTTT+GGG 0.327155 5_1:-44521639 Msa0732310:CDS
GCTGCAGCTGTCTTAATTCC+TGG 0.368615 5_1:-44521603 Msa0732310:CDS
GGAGATGAAGGGACGACTTT+CGG 0.392859 5_1:-44521303 Msa0732310:CDS
ACATGCTCATTGTTGTTAGT+AGG 0.397626 5_1:+44521224 None:intergenic
AGTAGGCTTCATCTCTTGAA+TGG 0.408840 5_1:+44521241 None:intergenic
CAACAATGAGCATGTTACTT+TGG 0.429504 5_1:-44521216 Msa0732310:CDS
GGGTTTATATTTCTCGTGGC+TGG 0.430171 5_1:-44521547 Msa0732310:CDS
GTGTGCATTGCTGGTTGCAC+TGG 0.444515 5_1:-44521349 Msa0732310:CDS
GGCATTAATCCATGGATGTC+AGG 0.444733 5_1:-44521582 Msa0732310:CDS
GTAGGCTTCATCTCTTGAAT+GGG 0.472668 5_1:+44521242 None:intergenic
TCAAGAGCACAGGGAGATGA+AGG 0.472835 5_1:-44521315 Msa0732310:CDS
GCAATTACACTGGTCAAGTT+CGG 0.476213 5_1:-44521518 Msa0732310:CDS
GCTTGAGGGAAGACACTCAT+TGG 0.480198 5_1:-44521692 Msa0732310:CDS
TTCATCTCTTGAATGGGAGG+AGG 0.490510 5_1:+44521248 None:intergenic
GCATGTTACTTTGGAGATGC+AGG 0.490868 5_1:-44521207 Msa0732310:CDS
TCATCTCTTGAATGGGAGGA+GGG 0.507184 5_1:+44521249 None:intergenic
CTCCCTGTGCTCTTGACACA+AGG 0.532100 5_1:+44521322 None:intergenic
TAATTCCTGGCATTAATCCA+TGG 0.537201 5_1:-44521590 Msa0732310:CDS
GTGCCTTGTGTCAAGAGCAC+AGG 0.538053 5_1:-44521325 Msa0732310:CDS
GACATCCATGGATTAATGCC+AGG 0.543556 5_1:+44521585 None:intergenic
ACGCAATGTACAAAGCTTGA+GGG 0.554563 5_1:-44521706 Msa0732310:CDS
GACGCAATGTACAAAGCTTG+AGG 0.564085 5_1:-44521707 Msa0732310:CDS
AAGGTACACAAGGCCACAGA+AGG 0.566842 5_1:-44521468 Msa0732310:CDS
GTGAGGGTTTATATTTCTCG+TGG 0.568607 5_1:-44521551 Msa0732310:CDS
ATGTCAGGTGTCATTTGTGA+GGG 0.571336 5_1:-44521567 Msa0732310:CDS
GATGTCAGGTGTCATTTGTG+AGG 0.575167 5_1:-44521568 Msa0732310:CDS
GGCTTCATCTCTTGAATGGG+AGG 0.588689 5_1:+44521245 None:intergenic
CAAATGACACCTGACATCCA+TGG 0.596465 5_1:+44521573 None:intergenic
TGCCTTGTGTCAAGAGCACA+GGG 0.601598 5_1:-44521324 Msa0732310:CDS
CAAATCAAGTACAATTTGAG+AGG 0.604742 5_1:+44521806 None:intergenic
GGGAAGACACTCATTGGACT+AGG 0.613183 5_1:-44521686 Msa0732310:CDS
TTGCGTCCAAATAGTACGCA+AGG 0.632285 5_1:+44521723 None:intergenic
AAAATGGCATGACAAATGCA+TGG 0.642333 5_1:+44521663 None:intergenic
GCACACAACATGCACAACAA+AGG 0.644804 5_1:+44521366 None:intergenic
CAAGAGCACAGGGAGATGAA+GGG 0.660978 5_1:-44521314 Msa0732310:CDS
ATATCACTTAAAGGTACACA+AGG 0.665076 5_1:-44521478 Msa0732310:CDS
CTGGTGTGTAGCAATTACAC+TGG 0.674179 5_1:-44521528 Msa0732310:CDS
AGGTACACAAGGCCACAGAA+GGG 0.689613 5_1:-44521467 Msa0732310:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAAAATGAAAGAATGTAAA+AGG + chr5_1:44521251-44521270 None:intergenic 20.0%
!!! TAAGTGATATTTCTTTTGTA+AGG + chr5_1:44521533-44521552 None:intergenic 20.0%
!! ACAAAAGAAATATCACTTAA+AGG - chr5_1:44521534-44521553 Msa0732310:CDS 20.0%
CAAATCAAGTACAATTTGAG+AGG + chr5_1:44521218-44521237 None:intergenic 30.0%
!! ATTCTTTCATTTTTCACTGC+AGG - chr5_1:44521256-44521275 Msa0732310:CDS 30.0%
! ATATCACTTAAAGGTACACA+AGG - chr5_1:44521543-44521562 Msa0732310:CDS 30.0%
!! ACATAATTTTAACCCTTCTG+TGG + chr5_1:44521569-44521588 None:intergenic 30.0%
TGTATAAATGTCGTTCTACA+TGG + chr5_1:44521592-44521611 None:intergenic 30.0%
AATTCTGCAATCATAAACAG+AGG + chr5_1:44521633-44521652 None:intergenic 30.0%
AAAATGGCATGACAAATGCA+TGG + chr5_1:44521361-44521380 None:intergenic 35.0%
AATGCAACCTTCGACAAAAA+TGG + chr5_1:44521377-44521396 None:intergenic 35.0%
TAATTCCTGGCATTAATCCA+TGG - chr5_1:44521431-44521450 Msa0732310:intron 35.0%
! ACATGCTCATTGTTGTTAGT+AGG + chr5_1:44521800-44521819 None:intergenic 35.0%
! CAACAATGAGCATGTTACTT+TGG - chr5_1:44521805-44521824 Msa0732310:CDS 35.0%
ACGCAATGTACAAAGCTTGA+GGG - chr5_1:44521315-44521334 Msa0732310:CDS 40.0%
!!! TGTCATGCCATTTTTGTCGA+AGG - chr5_1:44521367-44521386 Msa0732310:CDS 40.0%
TGTCGAAGGTTGCATTTCTT+TGG - chr5_1:44521381-44521400 Msa0732310:intron 40.0%
GTCGAAGGTTGCATTTCTTT+GGG - chr5_1:44521382-44521401 Msa0732310:intron 40.0%
!! ATGTCAGGTGTCATTTGTGA+GGG - chr5_1:44521454-44521473 Msa0732310:intron 40.0%
GTGAGGGTTTATATTTCTCG+TGG - chr5_1:44521470-44521489 Msa0732310:CDS 40.0%
GCAATTACACTGGTCAAGTT+CGG - chr5_1:44521503-44521522 Msa0732310:CDS 40.0%
GTAGGCTTCATCTCTTGAAT+GGG + chr5_1:44521782-44521801 None:intergenic 40.0%
AGTAGGCTTCATCTCTTGAA+TGG + chr5_1:44521783-44521802 None:intergenic 40.0%
! TTTTTCACTGCAGGCTTGAC+TGG - chr5_1:44521265-44521284 Msa0732310:CDS 45.0%
CTCTGTCCTTGCGTACTATT+TGG - chr5_1:44521292-44521311 Msa0732310:CDS 45.0%
TTGCGTCCAAATAGTACGCA+AGG + chr5_1:44521301-44521320 None:intergenic 45.0%
GACGCAATGTACAAAGCTTG+AGG - chr5_1:44521314-44521333 Msa0732310:CDS 45.0%
! GACATCCATGGATTAATGCC+AGG + chr5_1:44521439-44521458 None:intergenic 45.0%
GGCATTAATCCATGGATGTC+AGG - chr5_1:44521439-44521458 Msa0732310:intron 45.0%
CAAATGACACCTGACATCCA+TGG + chr5_1:44521451-44521470 None:intergenic 45.0%
!! GATGTCAGGTGTCATTTGTG+AGG - chr5_1:44521453-44521472 Msa0732310:intron 45.0%
GGGTTTATATTTCTCGTGGC+TGG - chr5_1:44521474-44521493 Msa0732310:CDS 45.0%
CTGGTGTGTAGCAATTACAC+TGG - chr5_1:44521493-44521512 Msa0732310:CDS 45.0%
GCACACAACATGCACAACAA+AGG + chr5_1:44521658-44521677 None:intergenic 45.0%
TCATCTCTTGAATGGGAGGA+GGG + chr5_1:44521775-44521794 None:intergenic 45.0%
TTCATCTCTTGAATGGGAGG+AGG + chr5_1:44521776-44521795 None:intergenic 45.0%
!! GCATGTTACTTTGGAGATGC+AGG - chr5_1:44521814-44521833 Msa0732310:CDS 45.0%
GCTTGAGGGAAGACACTCAT+TGG - chr5_1:44521329-44521348 Msa0732310:CDS 50.0%
GGGAAGACACTCATTGGACT+AGG - chr5_1:44521335-44521354 Msa0732310:CDS 50.0%
GCTGCAGCTGTCTTAATTCC+TGG - chr5_1:44521418-44521437 Msa0732310:intron 50.0%
AAGGTACACAAGGCCACAGA+AGG - chr5_1:44521553-44521572 Msa0732310:CDS 50.0%
AGGTACACAAGGCCACAGAA+GGG - chr5_1:44521554-44521573 Msa0732310:CDS 50.0%
GTGCATGTTGTGTGCATTGC+TGG - chr5_1:44521663-44521682 Msa0732310:CDS 50.0%
! TGCCTTGTGTCAAGAGCACA+GGG - chr5_1:44521697-44521716 Msa0732310:CDS 50.0%
! TCAAGAGCACAGGGAGATGA+AGG - chr5_1:44521706-44521725 Msa0732310:CDS 50.0%
! CAAGAGCACAGGGAGATGAA+GGG - chr5_1:44521707-44521726 Msa0732310:CDS 50.0%
GGAGATGAAGGGACGACTTT+CGG - chr5_1:44521718-44521737 Msa0732310:CDS 50.0%
GGCTTCATCTCTTGAATGGG+AGG + chr5_1:44521779-44521798 None:intergenic 50.0%
! GTGTGCATTGCTGGTTGCAC+TGG - chr5_1:44521672-44521691 Msa0732310:CDS 55.0%
! GTGCCTTGTGTCAAGAGCAC+AGG - chr5_1:44521696-44521715 Msa0732310:CDS 55.0%
CTCCCTGTGCTCTTGACACA+AGG + chr5_1:44521702-44521721 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 44521199 44521844 44521199 ID=Msa0732310;Name=Msa0732310
chr5_1 mRNA 44521199 44521844 44521199 ID=Msa0732310-mRNA-1;Parent=Msa0732310;Name=Msa0732310-mRNA-1;_AED=0.07;_eAED=0.07;_QI=0|0|0|1|0|0.5|2|0|190
chr5_1 exon 44521468 44521844 44521468 ID=Msa0732310-mRNA-1:exon:12651;Parent=Msa0732310-mRNA-1
chr5_1 exon 44521199 44521394 44521199 ID=Msa0732310-mRNA-1:exon:12650;Parent=Msa0732310-mRNA-1
chr5_1 CDS 44521468 44521844 44521468 ID=Msa0732310-mRNA-1:cds;Parent=Msa0732310-mRNA-1
chr5_1 CDS 44521199 44521394 44521199 ID=Msa0732310-mRNA-1:cds;Parent=Msa0732310-mRNA-1
Gene Sequence

>Msa0732310

TTGTATGTTAATAATACCTCTCAAATTGTACTTGATTTGCATATTGCATCCTTTTACATTCTTTCATTTTTCACTGCAGGCTTGACTGGACTGCTCTGTCCTTGCGTACTATTTGGACGCAATGTACAAAGCTTGAGGGAAGACACTCATTGGACTAGGCCATGCATTTGTCATGCCATTTTTGTCGAAGGTTGCATTTCTTTGGGTATAGCAAATGTAGCTGCAGCTGTCTTAATTCCTGGCATTAATCCATGGATGTCAGGTGTCATTTGTGAGGGTTTATATTTCTCGTGGCTGGTGTGTAGCAATTACACTGGTCAAGTTCGGCAATCCTTACAAAAGAAATATCACTTAAAGGTACACAAGGCCACAGAAGGAATTCACCTTTGTTGTGCATGTTGTGTGCATTGCTGGTTGCACTGGTGTGCCTTGTGTCAAGAGCACAGGGAGATGAAGGGACGACTTTCGGAAAATGTTTGTTCAAAAATGACAATTCTAAACCCTCCTCCCATTCAAGAGATGAAGCCTACTAACAACAATGAGCATGTTACTTTGGAGATGCAGGCTATGTAA

Protein sequence

>Msa0732310

LYVNNTSQIVLDLHIASFYILSFFTAGLTGLLCPCVLFGRNVQSLREDTHWTRPCICHAIFVEGCISLGIANVAAAVLIPGINPWMSGVICEGLYFSWLVCSNYTGQVRQSLQKKYHLKVHKATEGIHLCCACCVHCWLHWCALCQEHREMKGRLSENVCSKMTILNPPPIQEMKPTNNNEHVTLEMQAM*