AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1450970


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1450970 MtrunA17_Chr4g0073821 100.000 77 0 0 1 77 1 77 7.81e-51 153
Msa1450970 MtrunA17_Chr4g0073811 81.333 75 14 0 1 75 1 75 1.22e-40 127
Msa1450970 MtrunA17_Chr7g0271271 70.833 48 13 1 8 55 6 52 2.43e-16 65.9
Msa1450970 MtrunA17_Chr7g0271281 62.500 48 17 1 8 55 6 52 2.29e-14 60.8
Msa1450970 MtrunA17_Chr6g0462381 55.769 52 22 1 5 56 3 53 1.91e-13 58.5
Msa1450970 MtrunA17_Chr7g0271261 61.702 47 17 1 9 55 7 52 1.58e-12 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1450970 AT4G28088.1 80.263 76 14 1 1 75 1 76 8.21e-41 128
Msa1450970 AT2G24040.1 79.167 72 15 0 1 72 1 72 6.85e-38 121
Msa1450970 AT4G30660.1 75.342 73 18 0 1 73 1 73 4.70e-37 119
Msa1450970 AT4G30660.2 75.342 73 18 0 1 73 1 73 4.70e-37 119
Msa1450970 AT4G30650.1 63.514 74 26 1 1 74 1 73 2.63e-27 94.4
Msa1450970 AT2G38905.1 66.667 51 16 1 6 56 4 53 1.36e-15 64.3
Msa1450970 AT3G05880.1 69.565 46 13 1 10 55 8 52 1.71e-14 61.6
Msa1450970 AT3G05890.1 67.391 46 14 1 10 55 8 52 2.92e-14 60.8
Msa1450970 AT2G24040.2 75.000 32 8 0 1 32 1 32 4.71e-13 57.8

Find 30 sgRNAs with CRISPR-Local

Find 89 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGCTGTGTTGCTCCCTCCTT+TGG 0.237778 tig0033155:+2254 Msa1450970:CDS
AGATTTGAGTTAGGTCAATT+TGG 0.259030 tig0033155:+2744 Msa1450970:three_prime_UTR
GATCATCACTTGTTCTTGTT+TGG 0.268370 tig0033155:+2157 Msa1450970:five_prime_UTR
AATTCATGTAGAAAATTATA+TGG 0.289444 tig0033155:+2838 Msa1450970:three_prime_UTR
TGATGTGATTGTTGATTGTT+TGG 0.361552 tig0033155:+2861 Msa1450970:three_prime_UTR
ATTGTGGTTTACTCGAAAAC+TGG 0.367118 tig0033155:+2790 Msa1450970:three_prime_UTR
ATCACGATCAATAAAGATAA+TGG 0.374759 tig0033155:-2599 Msa1450970:intergenic
GTGATGATCATCTAAAGTTT+AGG 0.388258 tig0033155:-2143 Msa1450970:intergenic
TGCTTGCTCCTTACAATACT+AGG 0.414159 tig0033155:+2544 Msa1450970:CDS
CTTGTTCTTGTTTGGATCGC+GGG 0.438467 tig0033155:+2165 Msa1450970:five_prime_UTR
TTCTCTTTGAGATTTGAGTT+AGG 0.454642 tig0033155:+2735 Msa1450970:three_prime_UTR
TAAAGTGGTTAGTTATATTG+TGG 0.465212 tig0033155:+2926 Msa1450970:three_prime_UTR
ACAATACTAGGATATCTTCC+TGG 0.469622 tig0033155:+2556 Msa1450970:CDS
GCTGTGTTGCTCCCTCCTTT+GGG 0.470326 tig0033155:+2255 Msa1450970:CDS
TTGAGTTAGGTCAATTTGGA+TGG 0.478573 tig0033155:+2748 Msa1450970:three_prime_UTR
ATCAGTACTTTGATGAATAT+AGG 0.494017 tig0033155:+2620 Msa1450970:CDS
ATCAAATTATGAAAATAAAG+TGG 0.499775 tig0033155:+2911 Msa1450970:three_prime_UTR
GAAGATATCCTAGTATTGTA+AGG 0.501846 tig0033155:-2552 Msa1450970:intergenic
TTGCATTATTCGTTTCATTG+TGG 0.556335 tig0033155:+2774 Msa1450970:three_prime_UTR
TTGGGTGTTTGTCTCCGCCA+TGG 0.565764 tig0033155:+2273 Msa1450970:CDS
ACTTGTTCTTGTTTGGATCG+CGG 0.583202 tig0033155:+2164 Msa1450970:five_prime_UTR
CAAGAATAATAAAATTCAAG+TGG 0.594545 tig0033155:-2702 Msa1450960:intergenic
GGAGACAAACACCCAAAGGA+GGG 0.610468 tig0033155:-2266 Msa1450960:intergenic
CGGAGACAAACACCCAAAGG+AGG 0.614116 tig0033155:-2267 Msa1450960:intergenic
TGGCGGAGACAAACACCCAA+AGG 0.638625 tig0033155:-2270 Msa1450960:intergenic
TAGAGAGCATAAATTATACC+AGG 0.643088 tig0033155:-2574 Msa1450960:intergenic
TATTGTGATTGTGCATACAA+AGG 0.645143 tig0033155:-2646 Msa1450960:intergenic
GACATACAGTGCAGCAACCA+TGG 0.648406 tig0033155:-2290 Msa1450960:intergenic
CAGCAAATTTCACAACGTGA+AGG 0.664232 tig0033155:-2219 Msa1450960:intergenic
ATACAGTGCAGCAACCATGG+CGG 0.788306 tig0033155:-2287 Msa1450960:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAATTTCATTAAAATCA+TGG - tig0033155:2497-2516 Msa1450970:intergenic 10.0%
!! AAATAATTTCATTAAAATCA+TGG - tig0033155:2497-2516 Msa1450970:intergenic 10.0%
!! ACTAAAAAATCATGAAAAAT+TGG - tig0033155:2390-2409 Msa1450970:intergenic 15.0%
!! AATTCATGTAGAAAATTATA+TGG + tig0033155:2838-2857 Msa1450970:three_prime_UTR 15.0%
!! ATCAAATTATGAAAATAAAG+TGG + tig0033155:2911-2930 Msa1450970:three_prime_UTR 15.0%
!! ACTAAAAAATCATGAAAAAT+TGG - tig0033155:2390-2409 Msa1450970:intergenic 15.0%
!! AATTCATGTAGAAAATTATA+TGG + tig0033155:2838-2857 Msa1450970:three_prime_UTR 15.0%
!! ATCAAATTATGAAAATAAAG+TGG + tig0033155:2911-2930 Msa1450970:three_prime_UTR 15.0%
!! AAAGGAAAAAAGAAGTAAAA+GGG - tig0033155:2353-2372 Msa1450970:intergenic 20.0%
!! AAAAGGAAAAAAGAAGTAAA+AGG - tig0033155:2354-2373 Msa1450970:intergenic 20.0%
!!! AATCATGAAAAATTGGATTT+TGG - tig0033155:2383-2402 Msa1450970:intergenic 20.0%
!!! GAAATTATTTTAATTTGTGC+AGG + tig0033155:2507-2526 Msa1450970:intron 20.0%
!! CAAGAATAATAAAATTCAAG+TGG - tig0033155:2705-2724 Msa1450970:intergenic 20.0%
!! AAAGGAAAAAAGAAGTAAAA+GGG - tig0033155:2353-2372 Msa1450970:intergenic 20.0%
!! AAAAGGAAAAAAGAAGTAAA+AGG - tig0033155:2354-2373 Msa1450970:intergenic 20.0%
!!! AATCATGAAAAATTGGATTT+TGG - tig0033155:2383-2402 Msa1450970:intergenic 20.0%
!!! GAAATTATTTTAATTTGTGC+AGG + tig0033155:2507-2526 Msa1450970:intron 20.0%
!! CAAGAATAATAAAATTCAAG+TGG - tig0033155:2705-2724 Msa1450970:intergenic 20.0%
! ATCACGATCAATAAAGATAA+TGG - tig0033155:2602-2621 Msa1450970:intergenic 25.0%
! ATCAGTACTTTGATGAATAT+AGG + tig0033155:2620-2639 Msa1450970:CDS 25.0%
!! TAAAGTGGTTAGTTATATTG+TGG + tig0033155:2926-2945 Msa1450970:three_prime_UTR 25.0%
! ATCACGATCAATAAAGATAA+TGG - tig0033155:2602-2621 Msa1450970:intergenic 25.0%
! ATCAGTACTTTGATGAATAT+AGG + tig0033155:2620-2639 Msa1450970:CDS 25.0%
! GTGATGATCATCTAAAGTTT+AGG - tig0033155:2146-2165 Msa0051080:intergenic 30.0%
! TTGGATTTTGGATGTGAAAA+AGG - tig0033155:2371-2390 Msa1450970:intergenic 30.0%
GAAGATATCCTAGTATTGTA+AGG - tig0033155:2555-2574 Msa1450970:intergenic 30.0%
! TAGAGAGCATAAATTATACC+AGG - tig0033155:2577-2596 Msa1450970:intergenic 30.0%
TATTGTGATTGTGCATACAA+AGG - tig0033155:2649-2668 Msa1450970:intergenic 30.0%
!! TTCTCTTTGAGATTTGAGTT+AGG + tig0033155:2735-2754 Msa1450970:three_prime_UTR 30.0%
! AGATTTGAGTTAGGTCAATT+TGG + tig0033155:2744-2763 Msa1450970:three_prime_UTR 30.0%
TTGCATTATTCGTTTCATTG+TGG + tig0033155:2774-2793 Msa1450970:three_prime_UTR 30.0%
! TGATGTGATTGTTGATTGTT+TGG + tig0033155:2861-2880 Msa1450970:three_prime_UTR 30.0%
! GTGATGATCATCTAAAGTTT+AGG - tig0033155:2146-2165 Msa1450970:intergenic 30.0%
! TTGGATTTTGGATGTGAAAA+AGG - tig0033155:2371-2390 Msa1450970:intergenic 30.0%
GAAGATATCCTAGTATTGTA+AGG - tig0033155:2555-2574 Msa1450970:intergenic 30.0%
! TAGAGAGCATAAATTATACC+AGG - tig0033155:2577-2596 Msa1450970:intergenic 30.0%
TATTGTGATTGTGCATACAA+AGG - tig0033155:2649-2668 Msa1450970:intergenic 30.0%
!! TTCTCTTTGAGATTTGAGTT+AGG + tig0033155:2735-2754 Msa1450970:three_prime_UTR 30.0%
! AGATTTGAGTTAGGTCAATT+TGG + tig0033155:2744-2763 Msa1450970:three_prime_UTR 30.0%
TTGCATTATTCGTTTCATTG+TGG + tig0033155:2774-2793 Msa1450970:three_prime_UTR 30.0%
! TGATGTGATTGTTGATTGTT+TGG + tig0033155:2861-2880 Msa1450970:three_prime_UTR 30.0%
GATCATCACTTGTTCTTGTT+TGG + tig0033155:2157-2176 Msa1450970:five_prime_UTR 35.0%
!!! CATTTTTTCTGGCTTCTTGT+TGG - tig0033155:2199-2218 Msa1450970:intergenic 35.0%
TTACAATCATTGTGAGTGAC+AGG + tig0033155:2465-2484 Msa1450970:intron 35.0%
ACAATACTAGGATATCTTCC+TGG + tig0033155:2556-2575 Msa1450970:CDS 35.0%
TTGAGTTAGGTCAATTTGGA+TGG + tig0033155:2748-2767 Msa1450970:three_prime_UTR 35.0%
ATTGTGGTTTACTCGAAAAC+TGG + tig0033155:2790-2809 Msa1450970:three_prime_UTR 35.0%
GATCATCACTTGTTCTTGTT+TGG + tig0033155:2157-2176 Msa1450970:five_prime_UTR 35.0%
!!! CATTTTTTCTGGCTTCTTGT+TGG - tig0033155:2199-2218 Msa1450970:intergenic 35.0%
TTACAATCATTGTGAGTGAC+AGG + tig0033155:2465-2484 Msa1450970:intron 35.0%
ACAATACTAGGATATCTTCC+TGG + tig0033155:2556-2575 Msa1450970:CDS 35.0%
TTGAGTTAGGTCAATTTGGA+TGG + tig0033155:2748-2767 Msa1450970:three_prime_UTR 35.0%
ATTGTGGTTTACTCGAAAAC+TGG + tig0033155:2790-2809 Msa1450970:three_prime_UTR 35.0%
! ACTTGTTCTTGTTTGGATCG+CGG + tig0033155:2164-2183 Msa1450970:five_prime_UTR 40.0%
!!! CAACGTGAAGGCATTTTTTC+TGG - tig0033155:2210-2229 Msa1450970:intergenic 40.0%
CAGCAAATTTCACAACGTGA+AGG - tig0033155:2222-2241 Msa1450970:intergenic 40.0%
TGCTTGCTCCTTACAATACT+AGG + tig0033155:2544-2563 Msa1450970:CDS 40.0%
! ACTTGTTCTTGTTTGGATCG+CGG + tig0033155:2164-2183 Msa1450970:five_prime_UTR 40.0%
!!! CAACGTGAAGGCATTTTTTC+TGG - tig0033155:2210-2229 Msa1450970:intergenic 40.0%
CAGCAAATTTCACAACGTGA+AGG - tig0033155:2222-2241 Msa1450970:intergenic 40.0%
TGCTTGCTCCTTACAATACT+AGG + tig0033155:2544-2563 Msa1450970:CDS 40.0%
! CTTGTTCTTGTTTGGATCGC+GGG + tig0033155:2165-2184 Msa1450970:five_prime_UTR 45.0%
TCTCTCTCCATCACTTCCAT+GGG + tig0033155:2321-2340 Msa1450970:intron 45.0%
AGTAAAAGGGTAGATCCCCA+TGG - tig0033155:2340-2359 Msa1450970:intergenic 45.0%
! CTTGTTCTTGTTTGGATCGC+GGG + tig0033155:2165-2184 Msa1450970:five_prime_UTR 45.0%
TCTCTCTCCATCACTTCCAT+GGG + tig0033155:2321-2340 Msa1450970:intron 45.0%
AGTAAAAGGGTAGATCCCCA+TGG - tig0033155:2340-2359 Msa1450970:intergenic 45.0%
GGAGACAAACACCCAAAGGA+GGG - tig0033155:2269-2288 Msa1450970:intergenic 50.0%
ATACAGTGCAGCAACCATGG+CGG - tig0033155:2290-2309 Msa1450970:intergenic 50.0%
GACATACAGTGCAGCAACCA+TGG - tig0033155:2293-2312 Msa1450970:intergenic 50.0%
CTCTCTCTCCATCACTTCCA+TGG + tig0033155:2320-2339 Msa1450970:intron 50.0%
CTCTCTCCATCACTTCCATG+GGG + tig0033155:2322-2341 Msa1450970:intron 50.0%
GTAGATCCCCATGGAAGTGA+TGG - tig0033155:2331-2350 Msa1450970:intergenic 50.0%
GGAGACAAACACCCAAAGGA+GGG - tig0033155:2269-2288 Msa1450970:intergenic 50.0%
ATACAGTGCAGCAACCATGG+CGG - tig0033155:2290-2309 Msa1450970:intergenic 50.0%
GACATACAGTGCAGCAACCA+TGG - tig0033155:2293-2312 Msa1450970:intergenic 50.0%
CTCTCTCTCCATCACTTCCA+TGG + tig0033155:2320-2339 Msa1450970:intron 50.0%
CTCTCTCCATCACTTCCATG+GGG + tig0033155:2322-2341 Msa1450970:intron 50.0%
GTAGATCCCCATGGAAGTGA+TGG - tig0033155:2331-2350 Msa1450970:intergenic 50.0%
! GCTGTGTTGCTCCCTCCTTT+GGG + tig0033155:2255-2274 Msa1450970:CDS 55.0%
CGGAGACAAACACCCAAAGG+AGG - tig0033155:2270-2289 Msa1450970:intergenic 55.0%
TGGCGGAGACAAACACCCAA+AGG - tig0033155:2273-2292 Msa1450970:intergenic 55.0%
TTGGGTGTTTGTCTCCGCCA+TGG + tig0033155:2273-2292 Msa1450970:CDS 55.0%
! GCTGTGTTGCTCCCTCCTTT+GGG + tig0033155:2255-2274 Msa1450970:CDS 55.0%
CGGAGACAAACACCCAAAGG+AGG - tig0033155:2270-2289 Msa1450970:intergenic 55.0%
TGGCGGAGACAAACACCCAA+AGG - tig0033155:2273-2292 Msa1450970:intergenic 55.0%
TTGGGTGTTTGTCTCCGCCA+TGG + tig0033155:2273-2292 Msa1450970:CDS 55.0%
! CGCTGTGTTGCTCCCTCCTT+TGG + tig0033155:2254-2273 Msa1450970:CDS 60.0%
! CGCTGTGTTGCTCCCTCCTT+TGG + tig0033155:2254-2273 Msa1450970:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0033155 gene 2111 2948 2111 ID=Msa1450970;Name=Msa1450970
tig0033155 mRNA 2111 2948 2111 ID=Msa1450970-mRNA-1;Parent=Msa1450970;Name=Msa1450970-mRNA-1;_AED=0.30;_eAED=0.30;_QI=105|1|1|1|1|1|2|276|77
tig0033155 exon 2111 2305 2111 ID=Msa1450970-mRNA-1:exon:17764;Parent=Msa1450970-mRNA-1
tig0033155 exon 2529 2948 2529 ID=Msa1450970-mRNA-1:exon:17765;Parent=Msa1450970-mRNA-1
tig0033155 five_prime_UTR 2111 2215 2111 ID=Msa1450970-mRNA-1:five_prime_utr;Parent=Msa1450970-mRNA-1
tig0033155 CDS 2216 2305 2216 ID=Msa1450970-mRNA-1:cds;Parent=Msa1450970-mRNA-1
tig0033155 CDS 2529 2672 2529 ID=Msa1450970-mRNA-1:cds;Parent=Msa1450970-mRNA-1
tig0033155 three_prime_UTR 2673 2948 2673 ID=Msa1450970-mRNA-1:three_prime_utr;Parent=Msa1450970-mRNA-1
Gene Sequence

>Msa1450970

ATGCCTTCACGTTGTGAAATTTGCTGTGAGATTATGATCGCTGTGTTGCTCCCTCCTTTGGGTGTTTGTCTCCGCCATGGTTGCTGCACTGTTGAATTCATTATTTGCTTGCTCCTTACAATACTAGGATATCTTCCTGGTATAATTTATGCTCTCTATGCCATTATCTTTATTGATCGTGATCAGTACTTTGATGAATATAGGCGTCCTTTGTATGCACAATCACAATACTAG

Protein sequence

>Msa1450970

MPSRCEICCEIMIAVLLPPLGVCLRHGCCTVEFIICLLLTILGYLPGIIYALYAIIFIDRDQYFDEYRRPLYAQSQY*