AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1466190

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 115 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTGTAATTTGTGCATTAT+TGG 0.225543 tig0046177:-2002 Msa1466190:three_prime_UTR
TGCATTATTGGTTCCTTCAT+TGG 0.240192 tig0046177:-1990 Msa1466190:three_prime_UTR
TTTCAAATGTTTGTGCAATA+TGG 0.251188 tig0046177:-1865 Msa1466190:three_prime_UTR
ATAATTAAGATGAAACTAAT+TGG 0.284724 tig0046177:+1965 Msa1466190:intergenic
AAATGATGCCGCTGAGATTA+AGG 0.307981 tig0046177:-2785 Msa1466190:intron
GGTTGGACTGAGGCAGGTTT+CGG 0.378173 tig0046177:-2073 Msa1466190:three_prime_UTR
GTAGTCTTCTTTCAAATGTA+TGG 0.378293 tig0046177:+2370 Msa1466190:intergenic
TTTCGGCAAGATGGGTGTTT+CGG 0.388400 tig0046177:-2056 Msa1466190:three_prime_UTR
CGACTAATTAGAATCATTCA+AGG 0.432404 tig0046177:+2868 Msa1466190:intergenic
TACACTGGTTGGACTGAGGC+AGG 0.459434 tig0046177:-2079 Msa1466190:three_prime_UTR
AAACTAATTGGAACCAATGA+AGG 0.474797 tig0046177:+1977 Msa1466190:intergenic
CTTTGATAAATACTTTAGAA+AGG 0.476087 tig0046177:-1894 Msa1466190:three_prime_UTR
TGAGGCAGGTTTCGGCAAGA+TGG 0.486601 tig0046177:-2065 Msa1466190:three_prime_UTR
AGGCACGCAGTCTGTTACAC+TGG 0.491245 tig0046177:-2094 Msa1466190:three_prime_UTR
CAGACTGCGTGCCTCTTCAA+TGG 0.510928 tig0046177:+2103 Msa1466190:intergenic
ACAAGGACAGCATGTGCTGC+AGG 0.526864 tig0046177:-2173 Msa1466190:CDS
ACTACGTCTTGGTGGTCCAT+TGG 0.537769 tig0046177:-2352 Msa1466190:five_prime_UTR
GAGGCAGGTTTCGGCAAGAT+GGG 0.538244 tig0046177:-2064 Msa1466190:three_prime_UTR
TGCAGTCAATTCTCTGTACA+AGG 0.540808 tig0046177:-2190 Msa1466190:intron
GAAAGAAGACTACGTCTTGG+TGG 0.549879 tig0046177:-2360 Msa1466190:five_prime_UTR
AGTATTTATCAAAGCATCAA+AGG 0.582726 tig0046177:+1903 Msa1466190:intergenic
AGAAAGAGCAACCATTGAAG+AGG 0.585732 tig0046177:-2114 Msa1466190:three_prime_UTR
TTTGAAAGAAGACTACGTCT+TGG 0.593120 tig0046177:-2363 Msa1466190:five_prime_UTR
ACGCAGTCTGTTACACTGGT+TGG 0.593852 tig0046177:-2090 Msa1466190:three_prime_UTR
TCTTGGTGGTCCATTGGTGA+AGG 0.608383 tig0046177:-2346 Msa1466190:five_prime_UTR
GAAGGAAAACATCGCAACCA+TGG 0.618992 tig0046177:-2328 Msa1466190:exon
TCGCAACCATGGTTCTTGAG+AGG 0.620117 tig0046177:-2317 Msa1466190:intron
CTCTAACCTCTCAAGAACCA+TGG 0.655626 tig0046177:+2311 Msa1466190:intergenic
CAAGGACAGCATGTGCTGCA+GGG 0.666583 tig0046177:-2172 Msa1466190:CDS
CTGTTACACTGGTTGGACTG+AGG 0.672284 tig0046177:-2083 Msa1466190:three_prime_UTR
TCAGCTTACCTTAATCTCAG+CGG 0.688887 tig0046177:+2777 Msa1466190:intergenic
GGACAGCATGTGCTGCAGGG+TGG 0.776953 tig0046177:-2169 Msa1466190:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTTTTTATTCTAAATTTG+TGG + tig0046177:2179-2198 Msa1466190:intergenic 15.0%
!! TAAAACAAAATTAATCTTGT+AGG + tig0046177:2265-2284 Msa1466190:intergenic 15.0%
!! ATAATTAAGATGAAACTAAT+TGG + tig0046177:2770-2789 Msa1466190:intergenic 15.0%
!!! CTTTTTTTATTCTAAATTTG+TGG + tig0046177:2179-2198 Msa1466190:intergenic 15.0%
!! TAAAACAAAATTAATCTTGT+AGG + tig0046177:2265-2284 Msa1466190:intergenic 15.0%
!! ATAATTAAGATGAAACTAAT+TGG + tig0046177:2770-2789 Msa1466190:intergenic 15.0%
!!! ATGACCTTGTTTAAATAAAT+AGG + tig0046177:2488-2507 Msa1466190:intergenic 20.0%
!!! AATTGTAATTTGTGCATTAT+TGG - tig0046177:2730-2749 Msa1466190:intron 20.0%
!!! AATTATTATGTTGTTTTCCT+TGG - tig0046177:2784-2803 Msa1466190:intron 20.0%
!!! CTTTGATAAATACTTTAGAA+AGG - tig0046177:2838-2857 Msa1466190:five_prime_UTR 20.0%
!!! ATGACCTTGTTTAAATAAAT+AGG + tig0046177:2488-2507 Msa1466190:intergenic 20.0%
!!! AATTGTAATTTGTGCATTAT+TGG - tig0046177:2730-2749 Msa1466190:intron 20.0%
!!! AATTATTATGTTGTTTTCCT+TGG - tig0046177:2784-2803 Msa1466190:intron 20.0%
!!! CTTTGATAAATACTTTAGAA+AGG - tig0046177:2838-2857 Msa1466190:five_prime_UTR 20.0%
! ATCATAATTCAAAACCATGA+CGG + tig0046177:1996-2015 Msa1466190:intergenic 25.0%
! CATGCAAAGAATAAATCATA+TGG + tig0046177:2148-2167 Msa1466190:intergenic 25.0%
!! AAAAAAGTATGTTGAAAGCT+TGG - tig0046177:2192-2211 Msa1466190:intron 25.0%
!! CCTTGTTTAAATAAATAGGT+TGG + tig0046177:2484-2503 Msa1466190:intergenic 25.0%
! CCAACCTATTTATTTAAACA+AGG - tig0046177:2481-2500 Msa1466190:intron 25.0%
!! AGTATTTATCAAAGCATCAA+AGG + tig0046177:2832-2851 Msa1466190:intergenic 25.0%
! TTTCAAATGTTTGTGCAATA+TGG - tig0046177:2867-2886 Msa1466190:five_prime_UTR 25.0%
! ATCATAATTCAAAACCATGA+CGG + tig0046177:1996-2015 Msa1466190:intergenic 25.0%
! CATGCAAAGAATAAATCATA+TGG + tig0046177:2148-2167 Msa1466190:intergenic 25.0%
!! AAAAAAGTATGTTGAAAGCT+TGG - tig0046177:2192-2211 Msa1466190:intron 25.0%
!! CCTTGTTTAAATAAATAGGT+TGG + tig0046177:2484-2503 Msa1466190:intergenic 25.0%
! CCAACCTATTTATTTAAACA+AGG - tig0046177:2481-2500 Msa1466190:intron 25.0%
!! AGTATTTATCAAAGCATCAA+AGG + tig0046177:2832-2851 Msa1466190:intergenic 25.0%
GTTGCGAAAGAGTTAAATAA+TGG - tig0046177:2039-2058 Msa1466190:three_prime_UTR 30.0%
! TAAGCTTTGATTATGTCTCT+TGG - tig0046177:2283-2302 Msa1466190:intron 30.0%
!! GTATTTATTTTTCCTTGTGC+AGG - tig0046177:2330-2349 Msa1466190:exon 30.0%
GTAGTCTTCTTTCAAATGTA+TGG + tig0046177:2365-2384 Msa1466190:intergenic 30.0%
! GCAACGTGCTTTTATAATTT+TGG - tig0046177:2698-2717 Msa1466190:intron 30.0%
AAACTAATTGGAACCAATGA+AGG + tig0046177:2758-2777 Msa1466190:intergenic 30.0%
! ATATTTTGTTCATGAGACCA+AGG + tig0046177:2804-2823 Msa1466190:intergenic 30.0%
GTTGCGAAAGAGTTAAATAA+TGG - tig0046177:2039-2058 Msa1466190:three_prime_UTR 30.0%
! TAAGCTTTGATTATGTCTCT+TGG - tig0046177:2283-2302 Msa1466190:intron 30.0%
!! GTATTTATTTTTCCTTGTGC+AGG - tig0046177:2330-2349 Msa1466190:exon 30.0%
GTAGTCTTCTTTCAAATGTA+TGG + tig0046177:2365-2384 Msa1466190:intergenic 30.0%
! GCAACGTGCTTTTATAATTT+TGG - tig0046177:2698-2717 Msa1466190:intron 30.0%
AAACTAATTGGAACCAATGA+AGG + tig0046177:2758-2777 Msa1466190:intergenic 30.0%
! ATATTTTGTTCATGAGACCA+AGG + tig0046177:2804-2823 Msa1466190:intergenic 30.0%
AGGTAAGCTGAATCATGTTT+AGG - tig0046177:1967-1986 Msa1466190:three_prime_UTR 35.0%
GGTAAGCTGAATCATGTTTA+GGG - tig0046177:1968-1987 Msa1466190:three_prime_UTR 35.0%
TATTTAACTCTTTCGCAACG+TGG + tig0046177:2038-2057 Msa1466190:intergenic 35.0%
! TATTTTTCCTTGTGCAGGAA+CGG - tig0046177:2335-2354 Msa1466190:five_prime_UTR 35.0%
TTTGAAAGAAGACTACGTCT+TGG - tig0046177:2369-2388 Msa1466190:five_prime_UTR 35.0%
!! TGCATTATTGGTTCCTTCAT+TGG - tig0046177:2742-2761 Msa1466190:intron 35.0%
AGGTAAGCTGAATCATGTTT+AGG - tig0046177:1967-1986 Msa1466190:three_prime_UTR 35.0%
GGTAAGCTGAATCATGTTTA+GGG - tig0046177:1968-1987 Msa1466190:three_prime_UTR 35.0%
TATTTAACTCTTTCGCAACG+TGG + tig0046177:2038-2057 Msa1466190:intergenic 35.0%
! TATTTTTCCTTGTGCAGGAA+CGG - tig0046177:2335-2354 Msa1466190:five_prime_UTR 35.0%
TTTGAAAGAAGACTACGTCT+TGG - tig0046177:2369-2388 Msa1466190:five_prime_UTR 35.0%
!! TGCATTATTGGTTCCTTCAT+TGG - tig0046177:2742-2761 Msa1466190:intron 35.0%
AAATGATGCCGCTGAGATTA+AGG - tig0046177:1947-1966 Msa1466190:three_prime_UTR 40.0%
TCAGCTTACCTTAATCTCAG+CGG + tig0046177:1958-1977 Msa1466190:intergenic 40.0%
TGAATTATGATCACAGCCAC+AGG - tig0046177:2005-2024 Msa1466190:three_prime_UTR 40.0%
! ATTTTTCCTTGTGCAGGAAC+GGG - tig0046177:2336-2355 Msa1466190:five_prime_UTR 40.0%
TGCAGTCAATTCTCTGTACA+AGG - tig0046177:2542-2561 Msa1466190:intron 40.0%
AGAAAGAGCAACCATTGAAG+AGG - tig0046177:2618-2637 Msa1466190:intron 40.0%
AAATGATGCCGCTGAGATTA+AGG - tig0046177:1947-1966 Msa1466190:three_prime_UTR 40.0%
TCAGCTTACCTTAATCTCAG+CGG + tig0046177:1958-1977 Msa1466190:intergenic 40.0%
TGAATTATGATCACAGCCAC+AGG - tig0046177:2005-2024 Msa1466190:three_prime_UTR 40.0%
! ATTTTTCCTTGTGCAGGAAC+GGG - tig0046177:2336-2355 Msa1466190:five_prime_UTR 40.0%
TGCAGTCAATTCTCTGTACA+AGG - tig0046177:2542-2561 Msa1466190:intron 40.0%
AGAAAGAGCAACCATTGAAG+AGG - tig0046177:2618-2637 Msa1466190:intron 40.0%
TCATGTTTAGGGATCCGTCA+TGG - tig0046177:1979-1998 Msa1466190:three_prime_UTR 45.0%
! TTTTTCCTTGTGCAGGAACG+GGG - tig0046177:2337-2356 Msa1466190:five_prime_UTR 45.0%
GAAAGAAGACTACGTCTTGG+TGG - tig0046177:2372-2391 Msa1466190:five_prime_UTR 45.0%
! GCGATGTTTTCCTTCACCAA+TGG + tig0046177:2399-2418 Msa1466190:intergenic 45.0%
GAAGGAAAACATCGCAACCA+TGG - tig0046177:2404-2423 Msa1466190:intron 45.0%
CTCTAACCTCTCAAGAACCA+TGG + tig0046177:2424-2443 Msa1466190:intergenic 45.0%
TTTCGGCAAGATGGGTGTTT+CGG - tig0046177:2676-2695 Msa1466190:intron 45.0%
TCATGTTTAGGGATCCGTCA+TGG - tig0046177:1979-1998 Msa1466190:three_prime_UTR 45.0%
! TTTTTCCTTGTGCAGGAACG+GGG - tig0046177:2337-2356 Msa1466190:five_prime_UTR 45.0%
GAAAGAAGACTACGTCTTGG+TGG - tig0046177:2372-2391 Msa1466190:five_prime_UTR 45.0%
! GCGATGTTTTCCTTCACCAA+TGG + tig0046177:2399-2418 Msa1466190:intergenic 45.0%
GAAGGAAAACATCGCAACCA+TGG - tig0046177:2404-2423 Msa1466190:intron 45.0%
CTCTAACCTCTCAAGAACCA+TGG + tig0046177:2424-2443 Msa1466190:intergenic 45.0%
TTTCGGCAAGATGGGTGTTT+CGG - tig0046177:2676-2695 Msa1466190:intron 45.0%
! TTTTCCTTGTGCAGGAACGG+GGG - tig0046177:2338-2357 Msa1466190:five_prime_UTR 50.0%
! ACTACGTCTTGGTGGTCCAT+TGG - tig0046177:2380-2399 Msa1466190:five_prime_UTR 50.0%
! TCTTGGTGGTCCATTGGTGA+AGG - tig0046177:2386-2405 Msa1466190:intron 50.0%
TCGCAACCATGGTTCTTGAG+AGG - tig0046177:2415-2434 Msa1466190:intron 50.0%
ACGCAGTCTGTTACACTGGT+TGG - tig0046177:2642-2661 Msa1466190:intron 50.0%
! CTGTTACACTGGTTGGACTG+AGG - tig0046177:2649-2668 Msa1466190:intron 50.0%
! TTTTCCTTGTGCAGGAACGG+GGG - tig0046177:2338-2357 Msa1466190:five_prime_UTR 50.0%
! ACTACGTCTTGGTGGTCCAT+TGG - tig0046177:2380-2399 Msa1466190:five_prime_UTR 50.0%
! TCTTGGTGGTCCATTGGTGA+AGG - tig0046177:2386-2405 Msa1466190:intron 50.0%
TCGCAACCATGGTTCTTGAG+AGG - tig0046177:2415-2434 Msa1466190:intron 50.0%
ACGCAGTCTGTTACACTGGT+TGG - tig0046177:2642-2661 Msa1466190:intron 50.0%
! CTGTTACACTGGTTGGACTG+AGG - tig0046177:2649-2668 Msa1466190:intron 50.0%
ATGATCACAGCCACAGGTGC+TGG - tig0046177:2011-2030 Msa1466190:three_prime_UTR 55.0%
ACAAGGACAGCATGTGCTGC+AGG - tig0046177:2559-2578 Msa1466190:intron 55.0%
CAAGGACAGCATGTGCTGCA+GGG - tig0046177:2560-2579 Msa1466190:intron 55.0%
CAGACTGCGTGCCTCTTCAA+TGG + tig0046177:2632-2651 Msa1466190:intergenic 55.0%
AGGCACGCAGTCTGTTACAC+TGG - tig0046177:2638-2657 Msa1466190:intron 55.0%
! TACACTGGTTGGACTGAGGC+AGG - tig0046177:2653-2672 Msa1466190:intron 55.0%
GGTTGGACTGAGGCAGGTTT+CGG - tig0046177:2659-2678 Msa1466190:intron 55.0%
TGAGGCAGGTTTCGGCAAGA+TGG - tig0046177:2667-2686 Msa1466190:intron 55.0%
GAGGCAGGTTTCGGCAAGAT+GGG - tig0046177:2668-2687 Msa1466190:intron 55.0%
ATGATCACAGCCACAGGTGC+TGG - tig0046177:2011-2030 Msa1466190:three_prime_UTR 55.0%
ACAAGGACAGCATGTGCTGC+AGG - tig0046177:2559-2578 Msa1466190:intron 55.0%
CAAGGACAGCATGTGCTGCA+GGG - tig0046177:2560-2579 Msa1466190:intron 55.0%
CAGACTGCGTGCCTCTTCAA+TGG + tig0046177:2632-2651 Msa1466190:intergenic 55.0%
AGGCACGCAGTCTGTTACAC+TGG - tig0046177:2638-2657 Msa1466190:intron 55.0%
! TACACTGGTTGGACTGAGGC+AGG - tig0046177:2653-2672 Msa1466190:intron 55.0%
GGTTGGACTGAGGCAGGTTT+CGG - tig0046177:2659-2678 Msa1466190:intron 55.0%
TGAGGCAGGTTTCGGCAAGA+TGG - tig0046177:2667-2686 Msa1466190:intron 55.0%
GAGGCAGGTTTCGGCAAGAT+GGG - tig0046177:2668-2687 Msa1466190:intron 55.0%
GCAACGTGGACCAGCACCTG+TGG + tig0046177:2024-2043 Msa1466190:intergenic 65.0%
TGGTCCCCCGTTCCTGCACA+AGG + tig0046177:2345-2364 Msa1466190:intergenic 65.0%
GGACAGCATGTGCTGCAGGG+TGG - tig0046177:2563-2582 Msa1466190:intron 65.0%
GCAACGTGGACCAGCACCTG+TGG + tig0046177:2024-2043 Msa1466190:intergenic 65.0%
TGGTCCCCCGTTCCTGCACA+AGG + tig0046177:2345-2364 Msa1466190:intergenic 65.0%
GGACAGCATGTGCTGCAGGG+TGG - tig0046177:2563-2582 Msa1466190:intron 65.0%
Chromosome Type Strat End Strand Name
tig0046177 gene 1865 2889 1865 ID=Msa1466190;Name=Msa1466190
tig0046177 mRNA 1865 2889 1865 ID=Msa1466190-mRNA-1;Parent=Msa1466190;Name=Msa1466190-mRNA-1;_AED=0.24;_eAED=0.24;_QI=175|1|1|1|0.5|0.66|3|270|28
tig0046177 exon 1865 2207 1865 ID=Msa1466190-mRNA-1:exon:25014;Parent=Msa1466190-mRNA-1
tig0046177 exon 2318 2402 2318 ID=Msa1466190-mRNA-1:exon:25013;Parent=Msa1466190-mRNA-1
tig0046177 exon 2786 2889 2786 ID=Msa1466190-mRNA-1:exon:25012;Parent=Msa1466190-mRNA-1
tig0046177 five_prime_UTR 2786 2889 2786 ID=Msa1466190-mRNA-1:five_prime_utr;Parent=Msa1466190-mRNA-1
tig0046177 five_prime_UTR 2332 2402 2332 ID=Msa1466190-mRNA-1:five_prime_utr;Parent=Msa1466190-mRNA-1
tig0046177 CDS 2318 2331 2318 ID=Msa1466190-mRNA-1:cds;Parent=Msa1466190-mRNA-1
tig0046177 CDS 2135 2207 2135 ID=Msa1466190-mRNA-1:cds;Parent=Msa1466190-mRNA-1
tig0046177 three_prime_UTR 1865 2134 1865 ID=Msa1466190-mRNA-1:three_prime_utr;Parent=Msa1466190-mRNA-1
Gene Sequence

>Msa1466190

ATGGTTCTTGAGAGTCAATTCTCTGTACAAGGACAGCATGTGCTGCAGGGTGGTGCAAAACTTGTGTTAGTGACTTGCTTCTATTAG
Protein sequence

>Msa1466190

MVLESQFSVQGQHVLQGGAKLVLVTCFY*