AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0188350


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0188350 MtrunA17_Chr2g0277391 100.000 135 0 0 1 135 1 135 3.45e-95 270
Msa0188350 MtrunA17_Chr2g0297101 99.259 135 1 0 1 135 1 135 1.53e-94 268
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0188350 AT4G15000.1 85.926 135 19 0 1 135 1 135 2.72e-83 240
Msa0188350 AT3G22230.1 85.926 135 19 0 1 135 1 135 3.91e-83 240
Msa0188350 AT2G32220.1 80.741 135 26 0 1 135 1 135 1.81e-78 228
Msa0188350 AT4G15000.2 84.553 123 19 0 1 123 1 123 1.46e-72 213

Find 34 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTTCTTCGAACCTCTTCT+TGG 0.194010 2_1:+3539759 None:intergenic
TACGGTCATTGCTTGGTTGC+AGG 0.251311 2_1:-3539985 Msa0188350:CDS
CACTCTGGATGTTGATTTGA+AGG 0.342388 2_1:-3539842 Msa0188350:CDS
TTCGAAGAAAGGTTCAAAAC+TGG 0.371776 2_1:-3539748 Msa0188350:CDS
AGGACGTTACGCTGGCAAAA+AGG 0.377725 2_1:-3540052 Msa0188350:CDS
AAGACGATCACCGCTTTGTT+TGG 0.378594 2_1:+3540078 None:intergenic
CACTGATGTTCTTCAGAGTA+AGG 0.400378 2_1:-3539809 Msa0188350:CDS
TCCTTCTTGATCACCTTAGC+TGG 0.435443 2_1:+3539949 None:intergenic
GGTTCAAAACTGGGAAGAAC+AGG 0.438118 2_1:-3539738 Msa0188350:CDS
TAAGAAGGTCACTGCTTTGA+AGG 0.444100 2_1:-3539785 Msa0188350:CDS
TGCAAAGAAATCGCGTGTTA+AGG 0.450525 2_1:-3539911 Msa0188350:CDS
ACGGTCATTGCTTGGTTGCA+GGG 0.480537 2_1:-3539984 Msa0188350:CDS
CCAAGAAGAGGTTCGAAGAA+AGG 0.486021 2_1:-3539759 Msa0188350:CDS
GGAACCCGTGAACGTGCTTA+CGG 0.489757 2_1:-3540003 Msa0188350:CDS
GGTGGTTCTTCACCAAGCTC+AGG 0.503030 2_1:-3539717 Msa0188350:CDS
AATGACCGTAAGCACGTTCA+CGG 0.519577 2_1:+3539998 None:intergenic
GCTAACTCAAAACCTGAGCT+TGG 0.550830 2_1:+3539705 None:intergenic
TCTTCAGAGTAAGGATAAGA+AGG 0.568239 2_1:-3539800 Msa0188350:CDS
GTCTTACAAGGACGTTACGC+TGG 0.570383 2_1:-3540060 Msa0188350:CDS
ACGTGCTTACGGTCATTGCT+TGG 0.573817 2_1:-3539992 Msa0188350:CDS
AAAGCGGTGATCGTCTTACA+AGG 0.580022 2_1:-3540072 Msa0188350:CDS
TATGCCAACACGTTACACTC+TGG 0.586595 2_1:-3539857 Msa0188350:CDS
ATCGTGAAGAACTTTGATGA+TGG 0.589985 2_1:-3540024 Msa0188350:CDS
TCGAAGAAAGGTTCAAAACT+GGG 0.592072 2_1:-3539747 Msa0188350:CDS
TCCAGCTAAGGTGATCAAGA+AGG 0.605612 2_1:-3539950 Msa0188350:CDS
ATGACCGTAAGCACGTTCAC+GGG 0.610478 2_1:+3539999 None:intergenic
GATCAAGAAGTATCCAGCTA+AGG 0.616060 2_1:-3539962 Msa0188350:CDS
CTTTGAAGGAGGCCAAGAAG+AGG 0.631043 2_1:-3539771 Msa0188350:CDS
ACATCCAGAGTGTAACGTGT+TGG 0.631735 2_1:+3539853 None:intergenic
GAAGGTCACTGCTTTGAAGG+AGG 0.643354 2_1:-3539782 Msa0188350:CDS
TCAAAACTGGGAAGAACAGG+TGG 0.653226 2_1:-3539735 Msa0188350:CDS
TCTGGATGTTGATTTGAAGG+AGG 0.686222 2_1:-3539839 Msa0188350:CDS
CTTACTCTGAAGAACATCAG+TGG 0.694910 2_1:+3539810 None:intergenic
ATTCTTGAAGCCAAACAAAG+CGG 0.699139 2_1:-3540088 Msa0188350:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATTCTTGAAGCCAAACAAAG+CGG - chr2_1:3539719-3539738 Msa0188350:CDS 35.0%
ATCGTGAAGAACTTTGATGA+TGG - chr2_1:3539783-3539802 Msa0188350:CDS 35.0%
! TGTTAAGGCTTTTGTGAAGT+TGG - chr2_1:3539911-3539930 Msa0188350:CDS 35.0%
TCTTCAGAGTAAGGATAAGA+AGG - chr2_1:3540007-3540026 Msa0188350:CDS 35.0%
TTCGAAGAAAGGTTCAAAAC+TGG - chr2_1:3540059-3540078 Msa0188350:CDS 35.0%
TCGAAGAAAGGTTCAAAACT+GGG - chr2_1:3540060-3540079 Msa0188350:CDS 35.0%
!! GATCAAGAAGTATCCAGCTA+AGG - chr2_1:3539845-3539864 Msa0188350:CDS 40.0%
TGCAAAGAAATCGCGTGTTA+AGG - chr2_1:3539896-3539915 Msa0188350:CDS 40.0%
!! CACTCTGGATGTTGATTTGA+AGG - chr2_1:3539965-3539984 Msa0188350:CDS 40.0%
!! TCTGGATGTTGATTTGAAGG+AGG - chr2_1:3539968-3539987 Msa0188350:CDS 40.0%
! CTTACTCTGAAGAACATCAG+TGG + chr2_1:3540000-3540019 None:intergenic 40.0%
CACTGATGTTCTTCAGAGTA+AGG - chr2_1:3539998-3540017 Msa0188350:CDS 40.0%
TAAGAAGGTCACTGCTTTGA+AGG - chr2_1:3540022-3540041 Msa0188350:CDS 40.0%
! AAGACGATCACCGCTTTGTT+TGG + chr2_1:3539732-3539751 None:intergenic 45.0%
AAAGCGGTGATCGTCTTACA+AGG - chr2_1:3539735-3539754 Msa0188350:CDS 45.0%
AATGACCGTAAGCACGTTCA+CGG + chr2_1:3539812-3539831 None:intergenic 45.0%
TCCAGCTAAGGTGATCAAGA+AGG - chr2_1:3539857-3539876 Msa0188350:CDS 45.0%
TCCTTCTTGATCACCTTAGC+TGG + chr2_1:3539861-3539880 None:intergenic 45.0%
TATGCCAACACGTTACACTC+TGG - chr2_1:3539950-3539969 Msa0188350:CDS 45.0%
ACATCCAGAGTGTAACGTGT+TGG + chr2_1:3539957-3539976 None:intergenic 45.0%
CCTTTCTTCGAACCTCTTCT+TGG + chr2_1:3540051-3540070 None:intergenic 45.0%
CCAAGAAGAGGTTCGAAGAA+AGG - chr2_1:3540048-3540067 Msa0188350:CDS 45.0%
GGTTCAAAACTGGGAAGAAC+AGG - chr2_1:3540069-3540088 Msa0188350:CDS 45.0%
TCAAAACTGGGAAGAACAGG+TGG - chr2_1:3540072-3540091 Msa0188350:CDS 45.0%
GTCTTACAAGGACGTTACGC+TGG - chr2_1:3539747-3539766 Msa0188350:CDS 50.0%
AGGACGTTACGCTGGCAAAA+AGG - chr2_1:3539755-3539774 Msa0188350:CDS 50.0%
ATGACCGTAAGCACGTTCAC+GGG + chr2_1:3539811-3539830 None:intergenic 50.0%
ACGTGCTTACGGTCATTGCT+TGG - chr2_1:3539815-3539834 Msa0188350:CDS 50.0%
TACGGTCATTGCTTGGTTGC+AGG - chr2_1:3539822-3539841 Msa0188350:CDS 50.0%
ACGGTCATTGCTTGGTTGCA+GGG - chr2_1:3539823-3539842 Msa0188350:CDS 50.0%
!! GAAGGTCACTGCTTTGAAGG+AGG - chr2_1:3540025-3540044 Msa0188350:CDS 50.0%
! CTTTGAAGGAGGCCAAGAAG+AGG - chr2_1:3540036-3540055 Msa0188350:CDS 50.0%
GGAACCCGTGAACGTGCTTA+CGG - chr2_1:3539804-3539823 Msa0188350:CDS 55.0%
GGTGGTTCTTCACCAAGCTC+AGG - chr2_1:3540090-3540109 Msa0188350:CDS 55.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 3539711 3540118 3539711 ID=Msa0188350;Name=Msa0188350
chr2_1 mRNA 3539711 3540118 3539711 ID=Msa0188350-mRNA-1;Parent=Msa0188350;Name=Msa0188350-mRNA-1;_AED=0.26;_eAED=0.27;_QI=0|-1|0|1|-1|1|1|0|135
chr2_1 exon 3539711 3540118 3539711 ID=Msa0188350-mRNA-1:exon:1509;Parent=Msa0188350-mRNA-1
chr2_1 CDS 3539711 3540118 3539711 ID=Msa0188350-mRNA-1:cds;Parent=Msa0188350-mRNA-1
Gene Sequence

>Msa0188350

ATGGTGAAATTCTTGAAGCCAAACAAAGCGGTGATCGTCTTACAAGGACGTTACGCTGGCAAAAAGGCTGTCATCGTGAAGAACTTTGATGATGGAACCCGTGAACGTGCTTACGGTCATTGCTTGGTTGCAGGGATCAAGAAGTATCCAGCTAAGGTGATCAAGAAGGATTCAGCTAAGAAAACTGCAAAGAAATCGCGTGTTAAGGCTTTTGTGAAGTTGGTTAACTATCAGCATCTTATGCCAACACGTTACACTCTGGATGTTGATTTGAAGGAGGTTGTTACCACTGATGTTCTTCAGAGTAAGGATAAGAAGGTCACTGCTTTGAAGGAGGCCAAGAAGAGGTTCGAAGAAAGGTTCAAAACTGGGAAGAACAGGTGGTTCTTCACCAAGCTCAGGTTTTGA

Protein sequence

>Msa0188350

MVKFLKPNKAVIVLQGRYAGKKAVIVKNFDDGTRERAYGHCLVAGIKKYPAKVIKKDSAKKTAKKSRVKAFVKLVNYQHLMPTRYTLDVDLKEVVTTDVLQSKDKKVTALKEAKKRFEERFKTGKNRWFFTKLRF*