AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1364410


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1364410 MtrunA17_Chr7g0249661 99.459 185 1 0 1 185 1 185 2.49e-136 378
Msa1364410 MtrunA17_Chr8g0378101 70.286 175 45 2 14 185 4 174 5.91e-75 223
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1364410 AT5G16250.1 67.914 187 54 3 1 185 1 183 2.01e-80 237
Msa1364410 AT3G02640.1 66.845 187 58 3 1 185 1 185 2.27e-77 229
Msa1364410 AT5G36800.2 61.582 177 55 4 18 185 44 216 4.24e-68 207
Msa1364410 AT5G36710.2 61.582 177 55 4 18 185 44 216 4.24e-68 207
Msa1364410 AT5G36800.1 61.582 177 55 4 18 185 9 181 6.43e-68 205
Msa1364410 AT5G36710.1 61.582 177 55 4 18 185 9 181 6.43e-68 205

Find 40 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCCATGTCTTCACCATTGC+TGG 0.213239 tig0018135:+2666 Msa1364410:CDS
ACCATTGCTGGAGCTGTTTC+AGG 0.221629 tig0018135:+2678 Msa1364410:CDS
TACTTGTAGGACTGTTGTTT+TGG 0.257403 tig0018135:+2968 Msa1364410:CDS
TTCTGCAACTATGTCCTCTT+AGG 0.263638 tig0018135:+2567 Msa1364410:CDS
GGATTGGCCATGGCCTTTCC+AGG 0.339796 tig0018135:+3025 Msa1364410:CDS
AAGTACTATGCTTGTGTTGA+AGG 0.382832 tig0018135:+2939 Msa1364410:CDS
AGAGGACATAGTTGCAGAAA+AGG 0.386856 tig0018135:-2563 None:intergenic
TGCAGAAAAGGAAGAGTTTG+TGG 0.401747 tig0018135:-2551 None:intergenic
CCGTTGGTATTCTGCTCATA+TGG 0.404355 tig0018135:+2722 Msa1364410:CDS
GTGAGTTGCAGTCTTATGTA+AGG 0.427295 tig0018135:+2820 Msa1364410:CDS
GTTTCAGGCTGTGCTGCTGT+TGG 0.438604 tig0018135:+2693 Msa1364410:CDS
TCAACAAGATGAAGATTTGA+AGG 0.442954 tig0018135:+3004 Msa1364410:CDS
TGAAGACATGGAGAAGGATA+AGG 0.461871 tig0018135:-2656 None:intergenic
AAGATGAAGATTTGAAGGAT+TGG 0.477591 tig0018135:+3009 Msa1364410:CDS
AGCTTGAAGCTGCACCTAAG+AGG 0.489271 tig0018135:-2581 None:intergenic
TGTCACCACTTCTTCAAACC+TGG 0.491339 tig0018135:-3043 None:intergenic
TGACGAGGTGTGATTGTAGC+TGG 0.504266 tig0018135:-2519 None:intergenic
AGGAAGAAGCCGCAGACGGA+AGG 0.533462 tig0018135:-2636 None:intergenic
TTGAAGGTGGGAATACTTGT+AGG 0.538479 tig0018135:+2955 Msa1364410:CDS
CTCCAGCAATGGTGAAGACA+TGG 0.539403 tig0018135:-2668 None:intergenic
CGCTTAGTCCCTTCCGTCTG+CGG 0.545876 tig0018135:+2627 Msa1364410:CDS
CTGCTGTTGGTGCTAACCGT+TGG 0.557004 tig0018135:+2706 Msa1364410:CDS
CCACTTCTTCAAACCTGGAA+AGG 0.564127 tig0018135:-3038 None:intergenic
TATGGTAGCTACTGTTCTAA+CGG 0.573662 tig0018135:+2740 Msa1364410:CDS
CTTCAAACCTGGAAAGGCCA+TGG 0.584648 tig0018135:-3032 None:intergenic
GGAAGAAGCCGCAGACGGAA+GGG 0.584820 tig0018135:-2635 None:intergenic
GCCTGAAACAGCTCCAGCAA+TGG 0.585887 tig0018135:-2679 None:intergenic
GAGTCAAAACAACCCACTCA+AGG 0.600902 tig0018135:-2902 None:intergenic
TACTATGCTTGTGTTGAAGG+TGG 0.611427 tig0018135:+2942 Msa1364410:CDS
AAGATTTGAAGGATTGGCCA+TGG 0.611621 tig0018135:+3015 Msa1364410:CDS
TGAGTTGCAGTCTTATGTAA+GGG 0.621403 tig0018135:+2821 Msa1364410:CDS
CAATGGTGAAGACATGGAGA+AGG 0.622789 tig0018135:-2662 None:intergenic
TCTTATGTAAGGGAAGAAGA+TGG 0.628672 tig0018135:+2831 Msa1364410:CDS
CTAAGCGGAGTGAAAGAGTG+AGG 0.630082 tig0018135:-2611 None:intergenic
TTGTGGATGTTGTAGTGACG+AGG 0.630615 tig0018135:-2534 None:intergenic
ACTATGCTTGTGTTGAAGGT+GGG 0.632872 tig0018135:+2943 Msa1364410:CDS
CGCAGACGGAAGGGACTAAG+CGG 0.641469 tig0018135:-2626 None:intergenic
GATAAGGAAGAAGCCGCAGA+CGG 0.647152 tig0018135:-2640 None:intergenic
CCATATGAGCAGAATACCAA+CGG 0.664716 tig0018135:-2722 None:intergenic
CGAGGTGTGATTGTAGCTGG+AGG 0.714233 tig0018135:-2516 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTCTAACGGCTATTTTTCAA+GGG + tig0018135:2754-2773 Msa1364410:CDS 30.0%
!!! TTTCTGTTCTTGTTTTTACG+AGG + tig0018135:2781-2800 Msa1364410:CDS 30.0%
TCAACAAGATGAAGATTTGA+AGG + tig0018135:3004-3023 Msa1364410:CDS 30.0%
AAGATGAAGATTTGAAGGAT+TGG + tig0018135:3009-3028 Msa1364410:CDS 30.0%
TATGGTAGCTACTGTTCTAA+CGG + tig0018135:2740-2759 Msa1364410:CDS 35.0%
!!! GTTCTAACGGCTATTTTTCA+AGG + tig0018135:2753-2772 Msa1364410:CDS 35.0%
! TGAGTTGCAGTCTTATGTAA+GGG + tig0018135:2821-2840 Msa1364410:CDS 35.0%
TCTTATGTAAGGGAAGAAGA+TGG + tig0018135:2831-2850 Msa1364410:CDS 35.0%
! TTTTGATCTTTTGCCTTGAG+TGG + tig0018135:2889-2908 Msa1364410:CDS 35.0%
! TTTGATCTTTTGCCTTGAGT+GGG + tig0018135:2890-2909 Msa1364410:CDS 35.0%
AAGTACTATGCTTGTGTTGA+AGG + tig0018135:2939-2958 Msa1364410:CDS 35.0%
!! TACTTGTAGGACTGTTGTTT+TGG + tig0018135:2968-2987 Msa1364410:CDS 35.0%
!!! ACTTGTAGGACTGTTGTTTT+GGG + tig0018135:2969-2988 Msa1364410:CDS 35.0%
TGCAGAAAAGGAAGAGTTTG+TGG - tig0018135:2554-2573 None:intergenic 40.0%
AGAGGACATAGTTGCAGAAA+AGG - tig0018135:2566-2585 None:intergenic 40.0%
TTCTGCAACTATGTCCTCTT+AGG + tig0018135:2567-2586 Msa1364410:CDS 40.0%
TGAAGACATGGAGAAGGATA+AGG - tig0018135:2659-2678 None:intergenic 40.0%
CCATATGAGCAGAATACCAA+CGG - tig0018135:2725-2744 None:intergenic 40.0%
!!! AACGGCTATTTTTCAAGGGT+CGG + tig0018135:2758-2777 Msa1364410:CDS 40.0%
! GTGAGTTGCAGTCTTATGTA+AGG + tig0018135:2820-2839 Msa1364410:CDS 40.0%
!!! TCAGTGATTTTGAAGCTGTC+TGG + tig0018135:2855-2874 Msa1364410:CDS 40.0%
TACTATGCTTGTGTTGAAGG+TGG + tig0018135:2942-2961 Msa1364410:CDS 40.0%
ACTATGCTTGTGTTGAAGGT+GGG + tig0018135:2943-2962 Msa1364410:CDS 40.0%
TTGAAGGTGGGAATACTTGT+AGG + tig0018135:2955-2974 Msa1364410:CDS 40.0%
!!! TGTTGTTTTGGGAAGTGCTA+AGG + tig0018135:2980-2999 Msa1364410:CDS 40.0%
!! AAGATTTGAAGGATTGGCCA+TGG + tig0018135:3015-3034 Msa1364410:CDS 40.0%
TTGTGGATGTTGTAGTGACG+AGG - tig0018135:2537-2556 None:intergenic 45.0%
CAATGGTGAAGACATGGAGA+AGG - tig0018135:2665-2684 None:intergenic 45.0%
CCGTTGGTATTCTGCTCATA+TGG + tig0018135:2722-2741 Msa1364410:CDS 45.0%
! ACGAGGACGAGTGATTTTCT+TGG + tig0018135:2798-2817 Msa1364410:CDS 45.0%
!!! GTGATTTTGAAGCTGTCTGG+TGG + tig0018135:2858-2877 Msa1364410:CDS 45.0%
GAGTCAAAACAACCCACTCA+AGG - tig0018135:2905-2924 None:intergenic 45.0%
!!! TGAGTGGGTTGTTTTGACTC+TGG + tig0018135:2905-2924 Msa1364410:CDS 45.0%
TGACGAGGTGTGATTGTAGC+TGG - tig0018135:2522-2541 None:intergenic 50.0%
AGCTTGAAGCTGCACCTAAG+AGG - tig0018135:2584-2603 None:intergenic 50.0%
CTAAGCGGAGTGAAAGAGTG+AGG - tig0018135:2614-2633 None:intergenic 50.0%
GATAAGGAAGAAGCCGCAGA+CGG - tig0018135:2643-2662 None:intergenic 50.0%
CTCCATGTCTTCACCATTGC+TGG + tig0018135:2666-2685 Msa1364410:CDS 50.0%
CTCCAGCAATGGTGAAGACA+TGG - tig0018135:2671-2690 None:intergenic 50.0%
! ACCATTGCTGGAGCTGTTTC+AGG + tig0018135:2678-2697 Msa1364410:CDS 50.0%
CGAGGTGTGATTGTAGCTGG+AGG - tig0018135:2519-2538 None:intergenic 55.0%
GCCTGAAACAGCTCCAGCAA+TGG - tig0018135:2682-2701 None:intergenic 55.0%
! GTTTCAGGCTGTGCTGCTGT+TGG + tig0018135:2693-2712 Msa1364410:CDS 55.0%
!! CTGCTGTTGGTGCTAACCGT+TGG + tig0018135:2706-2725 Msa1364410:CDS 55.0%
CGCAGACGGAAGGGACTAAG+CGG - tig0018135:2629-2648 None:intergenic 60.0%
CGCTTAGTCCCTTCCGTCTG+CGG + tig0018135:2627-2646 Msa1364410:CDS 60.0%
GGAAGAAGCCGCAGACGGAA+GGG - tig0018135:2638-2657 None:intergenic 60.0%
AGGAAGAAGCCGCAGACGGA+AGG - tig0018135:2639-2658 None:intergenic 60.0%
!! GGATTGGCCATGGCCTTTCC+AGG + tig0018135:3025-3044 Msa1364410:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0018135 gene 2495 3052 2495 ID=Msa1364410;Name=Msa1364410
tig0018135 mRNA 2495 3052 2495 ID=Msa1364410-mRNA-1;Parent=Msa1364410;Name=Msa1364410-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|185
tig0018135 exon 2495 3052 2495 ID=Msa1364410-mRNA-1:exon:13994;Parent=Msa1364410-mRNA-1
tig0018135 CDS 2495 3052 2495 ID=Msa1364410-mRNA-1:cds;Parent=Msa1364410-mRNA-1
Gene Sequence

>Msa1364410

ATGGGTCTCTCAATGAACAATCCTCCAGCTACAATCACACCTCGTCACTACAACATCCACAAACTCTTCCTTTTCTGCAACTATGTCCTCTTAGGTGCAGCTTCAAGCTGTATCTTCCTCACTCTTTCACTCCGCTTAGTCCCTTCCGTCTGCGGCTTCTTCCTTATCCTTCTCCATGTCTTCACCATTGCTGGAGCTGTTTCAGGCTGTGCTGCTGTTGGTGCTAACCGTTGGTATTCTGCTCATATGGTAGCTACTGTTCTAACGGCTATTTTTCAAGGGTCGGTTTCTGTTCTTGTTTTTACGAGGACGAGTGATTTTCTTGGTGAGTTGCAGTCTTATGTAAGGGAAGAAGATGGTTCAGTGATTTTGAAGCTGTCTGGTGGACTTGCTATTTTGATCTTTTGCCTTGAGTGGGTTGTTTTGACTCTGGCGTTTTTCTTGAAGTACTATGCTTGTGTTGAAGGTGGGAATACTTGTAGGACTGTTGTTTTGGGAAGTGCTAAGGTTCAACAAGATGAAGATTTGAAGGATTGGCCATGGCCTTTCCAGGTTTGA

Protein sequence

>Msa1364410

MGLSMNNPPATITPRHYNIHKLFLFCNYVLLGAASSCIFLTLSLRLVPSVCGFFLILLHVFTIAGAVSGCAAVGANRWYSAHMVATVLTAIFQGSVSVLVFTRTSDFLGELQSYVREEDGSVILKLSGGLAILIFCLEWVVLTLAFFLKYYACVEGGNTCRTVVLGSAKVQQDEDLKDWPWPFQV*