AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0173820


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0173820 MtrunA17_Chr1g0193951 99.301 143 1 0 1 143 1 143 2.12e-104 294
Msa0173820 MtrunA17_Chr6g0476661 40.260 77 46 0 42 118 3 79 1.89e-16 69.7
Msa0173820 MtrunA17_Chr1g0188281 32.500 80 54 0 39 118 34 113 6.85e-13 61.6
Msa0173820 MtrunA17_Chr6g0476721 32.258 93 63 0 45 137 36 128 1.74e-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
Msa0173820 AT2G32650.2 67.133 143 42 2 1 142 1 139 4.20e-65 195
Msa0173820 AT2G32650.1 67.133 143 42 2 1 142 1 139 4.20e-65 195
Msa0173820 AT2G32180.1 67.133 143 42 2 1 142 1 139 5.23e-65 194
Msa0173820 AT2G32180.2 67.133 143 42 2 1 142 1 139 5.23e-65 194
Msa0173820 AT4G10290.1 35.065 77 47 1 45 118 16 92 2.91e-11 57.4
Msa0173820 AT4G10300.1 29.703 101 69 1 18 118 17 115 4.06e-11 57.4

Find 39 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTTTCATGCAATTTGTTGC+CGG 0.346254 1_4:-59172779 Msa0173820:CDS
GAGGCTGATCTTTGGTTCAA+TGG 0.368609 1_4:-59172728 Msa0173820:CDS
ATGTTTCAAGATGGTCAGTA+TGG 0.381328 1_4:-59172898 Msa0173820:CDS
AGTGGTTTGAGGCTGATCTT+TGG 0.382114 1_4:-59172736 Msa0173820:CDS
CGTTATAGTTTCCGAGCATA+TGG 0.389309 1_4:-59172692 Msa0173820:CDS
ATGAAACGCTTGCTCCCTTC+AGG 0.397604 1_4:+59172794 None:intergenic
CTCCTTGAACCATTGTTGAT+AGG 0.416620 1_4:+59173052 None:intergenic
CTGCCAATCCCATGGCAACC+TGG 0.474702 1_4:+59172862 None:intergenic
ACCATTGTTGATAGGAGAAT+AGG 0.477458 1_4:+59173060 None:intergenic
TTGTTGCCGGAGATTTAATC+CGG 0.479684 1_4:-59172766 Msa0173820:CDS
CAATGTGAAGGTAGAAAGAA+AGG 0.481006 1_4:-59172948 Msa0173820:CDS
CCTCAAACCACTTCGGATAC+CGG 0.486692 1_4:+59172747 None:intergenic
AATCCAGGTTGCCATGGGAT+TGG 0.488234 1_4:-59172865 Msa0173820:CDS
CTCCTATCAACAATGGTTCA+AGG 0.489683 1_4:-59173054 Msa0173820:CDS
CGGATACCGGATTAAATCTC+CGG 0.495277 1_4:+59172760 None:intergenic
CAGGTTGCCATGGGATTGGC+AGG 0.499106 1_4:-59172861 Msa0173820:CDS
GGATTGGCAGGTAGACCAAC+TGG 0.504664 1_4:-59172849 Msa0173820:CDS
CCGGAAAATCCAGGTTGCCA+TGG 0.518583 1_4:-59172871 Msa0173820:CDS
CACATTGTATAATTCTTCCA+AGG 0.523416 1_4:+59172964 None:intergenic
AAACTATAACGTTCTTGATA+CGG 0.530071 1_4:+59172704 None:intergenic
CGGAAAATCCAGGTTGCCAT+GGG 0.538481 1_4:-59172870 Msa0173820:CDS
TATGGAAGACCGGAAAATCC+AGG 0.546447 1_4:-59172880 Msa0173820:CDS
AATGAAGATAGAGAAATCCT+TGG 0.554986 1_4:-59172981 Msa0173820:CDS
AGATGGTCAGTATGGAAGAC+CGG 0.563715 1_4:-59172890 Msa0173820:CDS
CTCAGCTTGATGTTTCAAGA+TGG 0.565626 1_4:-59172907 Msa0173820:CDS
CCGGTATCCGAAGTGGTTTG+AGG 0.566818 1_4:-59172747 Msa0173820:CDS
AATAATCATCACCATATGCT+CGG 0.568249 1_4:+59172681 None:intergenic
TCAAGTAACTCTTCTATGCG+AGG 0.580396 1_4:-59173019 Msa0173820:CDS
CAAGTAACTCTTCTATGCGA+GGG 0.589742 1_4:-59173018 Msa0173820:CDS
CTTCTTCTATGTACACCAGT+TGG 0.594279 1_4:+59172834 None:intergenic
ACCTATTCTCCTATCAACAA+TGG 0.597081 1_4:-59173061 Msa0173820:CDS
CAACTGGTGTACATAGAAGA+AGG 0.600561 1_4:-59172833 Msa0173820:CDS
AAGTGAGAGTTGTTCCTGAA+GGG 0.600643 1_4:-59172808 Msa0173820:CDS
GAAGTGAGAGTTGTTCCTGA+AGG 0.600726 1_4:-59172809 Msa0173820:CDS
TGGTCTACCTGCCAATCCCA+TGG 0.603266 1_4:+59172854 None:intergenic
GGAAGAATTATACAATGTGA+AGG 0.609686 1_4:-59172960 Msa0173820:CDS
ATTTAATCCGGTATCCGAAG+TGG 0.624736 1_4:-59172754 Msa0173820:CDS
AGATCAGCCTCAAACCACTT+CGG 0.631094 1_4:+59172740 None:intergenic
GTTGATAGGAGAATAGGTGA+AGG 0.653020 1_4:+59173066 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAACTATAACGTTCTTGATA+CGG + chr1_4:59173066-59173085 None:intergenic 25.0%
AATGAAGATAGAGAAATCCT+TGG - chr1_4:59172786-59172805 Msa0173820:CDS 30.0%
CACATTGTATAATTCTTCCA+AGG + chr1_4:59172806-59172825 None:intergenic 30.0%
GGAAGAATTATACAATGTGA+AGG - chr1_4:59172807-59172826 Msa0173820:CDS 30.0%
AATAATCATCACCATATGCT+CGG + chr1_4:59173089-59173108 None:intergenic 30.0%
ACCTATTCTCCTATCAACAA+TGG - chr1_4:59172706-59172725 Msa0173820:CDS 35.0%
! ACCATTGTTGATAGGAGAAT+AGG + chr1_4:59172710-59172729 None:intergenic 35.0%
CAATGTGAAGGTAGAAAGAA+AGG - chr1_4:59172819-59172838 Msa0173820:CDS 35.0%
ATGTTTCAAGATGGTCAGTA+TGG - chr1_4:59172869-59172888 Msa0173820:CDS 35.0%
! GTTGATAGGAGAATAGGTGA+AGG + chr1_4:59172704-59172723 None:intergenic 40.0%
CTCCTATCAACAATGGTTCA+AGG - chr1_4:59172713-59172732 Msa0173820:CDS 40.0%
CTCCTTGAACCATTGTTGAT+AGG + chr1_4:59172718-59172737 None:intergenic 40.0%
TCAAGTAACTCTTCTATGCG+AGG - chr1_4:59172748-59172767 Msa0173820:CDS 40.0%
CAAGTAACTCTTCTATGCGA+GGG - chr1_4:59172749-59172768 Msa0173820:CDS 40.0%
!!! TCAAGCTGAGCTAGTTTTTC+AGG + chr1_4:59172850-59172869 None:intergenic 40.0%
CTCAGCTTGATGTTTCAAGA+TGG - chr1_4:59172860-59172879 Msa0173820:CDS 40.0%
CTTCTTCTATGTACACCAGT+TGG + chr1_4:59172936-59172955 None:intergenic 40.0%
CAACTGGTGTACATAGAAGA+AGG - chr1_4:59172934-59172953 Msa0173820:CDS 40.0%
AAGTGAGAGTTGTTCCTGAA+GGG - chr1_4:59172959-59172978 Msa0173820:CDS 40.0%
!! CGTTTCATGCAATTTGTTGC+CGG - chr1_4:59172988-59173007 Msa0173820:CDS 40.0%
TTGTTGCCGGAGATTTAATC+CGG - chr1_4:59173001-59173020 Msa0173820:CDS 40.0%
ATTTAATCCGGTATCCGAAG+TGG - chr1_4:59173013-59173032 Msa0173820:CDS 40.0%
CGTTATAGTTTCCGAGCATA+TGG - chr1_4:59173075-59173094 Msa0173820:CDS 40.0%
AGATGGTCAGTATGGAAGAC+CGG - chr1_4:59172877-59172896 Msa0173820:CDS 45.0%
TATGGAAGACCGGAAAATCC+AGG - chr1_4:59172887-59172906 Msa0173820:CDS 45.0%
GAAGTGAGAGTTGTTCCTGA+AGG - chr1_4:59172958-59172977 Msa0173820:CDS 45.0%
CGGATACCGGATTAAATCTC+CGG + chr1_4:59173010-59173029 None:intergenic 45.0%
AGATCAGCCTCAAACCACTT+CGG + chr1_4:59173030-59173049 None:intergenic 45.0%
! AGTGGTTTGAGGCTGATCTT+TGG - chr1_4:59173031-59173050 Msa0173820:CDS 45.0%
! GAGGCTGATCTTTGGTTCAA+TGG - chr1_4:59173039-59173058 Msa0173820:CDS 45.0%
! CCATGGCAACCTGGATTTTC+CGG + chr1_4:59172899-59172918 None:intergenic 50.0%
CGGAAAATCCAGGTTGCCAT+GGG - chr1_4:59172897-59172916 Msa0173820:CDS 50.0%
AATCCAGGTTGCCATGGGAT+TGG - chr1_4:59172902-59172921 Msa0173820:CDS 50.0%
ATGAAACGCTTGCTCCCTTC+AGG + chr1_4:59172976-59172995 None:intergenic 50.0%
CCTCAAACCACTTCGGATAC+CGG + chr1_4:59173023-59173042 None:intergenic 50.0%
CCGGAAAATCCAGGTTGCCA+TGG - chr1_4:59172896-59172915 Msa0173820:CDS 55.0%
TGGTCTACCTGCCAATCCCA+TGG + chr1_4:59172916-59172935 None:intergenic 55.0%
! GGATTGGCAGGTAGACCAAC+TGG - chr1_4:59172918-59172937 Msa0173820:CDS 55.0%
CCGGTATCCGAAGTGGTTTG+AGG - chr1_4:59173020-59173039 Msa0173820:CDS 55.0%
CTGCCAATCCCATGGCAACC+TGG + chr1_4:59172908-59172927 None:intergenic 60.0%
! CAGGTTGCCATGGGATTGGC+AGG - chr1_4:59172906-59172925 Msa0173820:CDS 60.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 59172679 59173110 59172679 ID=Msa0173820;Name=Msa0173820
chr1_4 mRNA 59172679 59173110 59172679 ID=Msa0173820-mRNA-1;Parent=Msa0173820;Name=Msa0173820-mRNA-1;_AED=0.37;_eAED=0.38;_QI=0|-1|0|1|-1|1|1|0|143
chr1_4 exon 59172679 59173110 59172679 ID=Msa0173820-mRNA-1:exon:18538;Parent=Msa0173820-mRNA-1
chr1_4 CDS 59172679 59173110 59172679 ID=Msa0173820-mRNA-1:cds;Parent=Msa0173820-mRNA-1
Gene Sequence

>Msa0173820

ATGGCAAGCTTGTTGACATCAACCTTCACCTATTCTCCTATCAACAATGGTTCAAGGAGTTTGAGAAAATCAAGTAACTCTTCTATGCGAGGGTGTTGCGTAAAAGCAATGAAGATAGAGAAATCCTTGGAAGAATTATACAATGTGAAGGTAGAAAGAAAGGTGTCACCTGAAAAACTAGCTCAGCTTGATGTTTCAAGATGGTCAGTATGGAAGACCGGAAAATCCAGGTTGCCATGGGATTGGCAGGTAGACCAACTGGTGTACATAGAAGAAGGTGAAGTGAGAGTTGTTCCTGAAGGGAGCAAGCGTTTCATGCAATTTGTTGCCGGAGATTTAATCCGGTATCCGAAGTGGTTTGAGGCTGATCTTTGGTTCAATGGTCCGTATCAAGAACGTTATAGTTTCCGAGCATATGGTGATGATTATTGA

Protein sequence

>Msa0173820

MASLLTSTFTYSPINNGSRSLRKSSNSSMRGCCVKAMKIEKSLEELYNVKVERKVSPEKLAQLDVSRWSVWKTGKSRLPWDWQVDQLVYIEEGEVRVVPEGSKRFMQFVAGDLIRYPKWFEADLWFNGPYQERYSFRAYGDDY*