AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0231100


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0231100 MtrunA17_Chr2g0277391 100.000 135 0 0 1 135 1 135 3.45e-95 270
Msa0231100 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
Msa0231100 AT4G15000.1 85.926 135 19 0 1 135 1 135 2.72e-83 240
Msa0231100 AT3G22230.1 85.926 135 19 0 1 135 1 135 3.91e-83 240
Msa0231100 AT2G32220.1 80.741 135 26 0 1 135 1 135 1.81e-78 228
Msa0231100 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_2:+3305380 None:intergenic
TACGGTCATTGCTTGGTTGC+AGG 0.251311 2_2:-3305606 Msa0231100:CDS
CACTCTGGATGTTGATTTGA+AGG 0.342388 2_2:-3305463 Msa0231100:CDS
TTCGAAGAAAGGTTCAAAAC+TGG 0.371776 2_2:-3305369 Msa0231100:CDS
AGGACGTTACGCTGGCAAAA+AGG 0.377725 2_2:-3305673 Msa0231100:CDS
AAGACGATCACCGCTTTGTT+TGG 0.378594 2_2:+3305699 None:intergenic
CACTGATGTTCTTCAGAGTA+AGG 0.400378 2_2:-3305430 Msa0231100:CDS
TCCTTCTTGATCACCTTAGC+TGG 0.435443 2_2:+3305570 None:intergenic
GGTTCAAAACTGGGAAGAAC+AGG 0.438118 2_2:-3305359 Msa0231100:CDS
TAAGAAGGTCACTGCTTTGA+AGG 0.444100 2_2:-3305406 Msa0231100:CDS
TGCAAAGAAATCGCGTGTTA+AGG 0.450525 2_2:-3305532 Msa0231100:CDS
ACGGTCATTGCTTGGTTGCA+GGG 0.480537 2_2:-3305605 Msa0231100:CDS
CCAAGAAGAGGTTCGAAGAA+AGG 0.486021 2_2:-3305380 Msa0231100:CDS
GGAACCCGTGAACGTGCTTA+CGG 0.489757 2_2:-3305624 Msa0231100:CDS
GGTGGTTCTTCACCAAGCTC+AGG 0.503030 2_2:-3305338 Msa0231100:CDS
AATGACCGTAAGCACGTTCA+CGG 0.519577 2_2:+3305619 None:intergenic
GCTAACTCAAAACCTGAGCT+TGG 0.550830 2_2:+3305326 None:intergenic
TCTTCAGAGTAAGGATAAGA+AGG 0.568239 2_2:-3305421 Msa0231100:CDS
GTCTTACAAGGACGTTACGC+TGG 0.570383 2_2:-3305681 Msa0231100:CDS
ACGTGCTTACGGTCATTGCT+TGG 0.573817 2_2:-3305613 Msa0231100:CDS
AAAGCGGTGATCGTCTTACA+AGG 0.580022 2_2:-3305693 Msa0231100:CDS
TATGCCAACACGTTACACTC+TGG 0.586595 2_2:-3305478 Msa0231100:CDS
ATCGTGAAGAACTTTGATGA+TGG 0.589985 2_2:-3305645 Msa0231100:CDS
TCGAAGAAAGGTTCAAAACT+GGG 0.592072 2_2:-3305368 Msa0231100:CDS
TCCAGCTAAGGTGATCAAGA+AGG 0.605612 2_2:-3305571 Msa0231100:CDS
ATGACCGTAAGCACGTTCAC+GGG 0.610478 2_2:+3305620 None:intergenic
GATCAAGAAGTATCCAGCTA+AGG 0.616060 2_2:-3305583 Msa0231100:CDS
CTTTGAAGGAGGCCAAGAAG+AGG 0.631043 2_2:-3305392 Msa0231100:CDS
ACATCCAGAGTGTAACGTGT+TGG 0.631735 2_2:+3305474 None:intergenic
GAAGGTCACTGCTTTGAAGG+AGG 0.643354 2_2:-3305403 Msa0231100:CDS
TCAAAACTGGGAAGAACAGG+TGG 0.653226 2_2:-3305356 Msa0231100:CDS
TCTGGATGTTGATTTGAAGG+AGG 0.686222 2_2:-3305460 Msa0231100:CDS
CTTACTCTGAAGAACATCAG+TGG 0.694910 2_2:+3305431 None:intergenic
ATTCTTGAAGCCAAACAAAG+CGG 0.699139 2_2:-3305709 Msa0231100:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATTCTTGAAGCCAAACAAAG+CGG - chr2_2:3305340-3305359 Msa0231100:CDS 35.0%
ATCGTGAAGAACTTTGATGA+TGG - chr2_2:3305404-3305423 Msa0231100:CDS 35.0%
! TGTTAAGGCTTTTGTGAAGT+TGG - chr2_2:3305532-3305551 Msa0231100:CDS 35.0%
TCTTCAGAGTAAGGATAAGA+AGG - chr2_2:3305628-3305647 Msa0231100:CDS 35.0%
TTCGAAGAAAGGTTCAAAAC+TGG - chr2_2:3305680-3305699 Msa0231100:CDS 35.0%
TCGAAGAAAGGTTCAAAACT+GGG - chr2_2:3305681-3305700 Msa0231100:CDS 35.0%
!! GATCAAGAAGTATCCAGCTA+AGG - chr2_2:3305466-3305485 Msa0231100:CDS 40.0%
TGCAAAGAAATCGCGTGTTA+AGG - chr2_2:3305517-3305536 Msa0231100:CDS 40.0%
!! CACTCTGGATGTTGATTTGA+AGG - chr2_2:3305586-3305605 Msa0231100:CDS 40.0%
!! TCTGGATGTTGATTTGAAGG+AGG - chr2_2:3305589-3305608 Msa0231100:CDS 40.0%
! CTTACTCTGAAGAACATCAG+TGG + chr2_2:3305621-3305640 None:intergenic 40.0%
CACTGATGTTCTTCAGAGTA+AGG - chr2_2:3305619-3305638 Msa0231100:CDS 40.0%
TAAGAAGGTCACTGCTTTGA+AGG - chr2_2:3305643-3305662 Msa0231100:CDS 40.0%
! AAGACGATCACCGCTTTGTT+TGG + chr2_2:3305353-3305372 None:intergenic 45.0%
AAAGCGGTGATCGTCTTACA+AGG - chr2_2:3305356-3305375 Msa0231100:CDS 45.0%
AATGACCGTAAGCACGTTCA+CGG + chr2_2:3305433-3305452 None:intergenic 45.0%
TCCAGCTAAGGTGATCAAGA+AGG - chr2_2:3305478-3305497 Msa0231100:CDS 45.0%
TCCTTCTTGATCACCTTAGC+TGG + chr2_2:3305482-3305501 None:intergenic 45.0%
TATGCCAACACGTTACACTC+TGG - chr2_2:3305571-3305590 Msa0231100:CDS 45.0%
ACATCCAGAGTGTAACGTGT+TGG + chr2_2:3305578-3305597 None:intergenic 45.0%
CCTTTCTTCGAACCTCTTCT+TGG + chr2_2:3305672-3305691 None:intergenic 45.0%
CCAAGAAGAGGTTCGAAGAA+AGG - chr2_2:3305669-3305688 Msa0231100:CDS 45.0%
GGTTCAAAACTGGGAAGAAC+AGG - chr2_2:3305690-3305709 Msa0231100:CDS 45.0%
TCAAAACTGGGAAGAACAGG+TGG - chr2_2:3305693-3305712 Msa0231100:CDS 45.0%
GTCTTACAAGGACGTTACGC+TGG - chr2_2:3305368-3305387 Msa0231100:CDS 50.0%
AGGACGTTACGCTGGCAAAA+AGG - chr2_2:3305376-3305395 Msa0231100:CDS 50.0%
ATGACCGTAAGCACGTTCAC+GGG + chr2_2:3305432-3305451 None:intergenic 50.0%
ACGTGCTTACGGTCATTGCT+TGG - chr2_2:3305436-3305455 Msa0231100:CDS 50.0%
TACGGTCATTGCTTGGTTGC+AGG - chr2_2:3305443-3305462 Msa0231100:CDS 50.0%
ACGGTCATTGCTTGGTTGCA+GGG - chr2_2:3305444-3305463 Msa0231100:CDS 50.0%
!! GAAGGTCACTGCTTTGAAGG+AGG - chr2_2:3305646-3305665 Msa0231100:CDS 50.0%
! CTTTGAAGGAGGCCAAGAAG+AGG - chr2_2:3305657-3305676 Msa0231100:CDS 50.0%
GGAACCCGTGAACGTGCTTA+CGG - chr2_2:3305425-3305444 Msa0231100:CDS 55.0%
GGTGGTTCTTCACCAAGCTC+AGG - chr2_2:3305711-3305730 Msa0231100:CDS 55.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 3305332 3305739 3305332 ID=Msa0231100;Name=Msa0231100
chr2_2 mRNA 3305332 3305739 3305332 ID=Msa0231100-mRNA-1;Parent=Msa0231100;Name=Msa0231100-mRNA-1;_AED=0.28;_eAED=0.29;_QI=0|-1|0|1|-1|1|1|0|135
chr2_2 exon 3305332 3305739 3305332 ID=Msa0231100-mRNA-1:exon:1313;Parent=Msa0231100-mRNA-1
chr2_2 CDS 3305332 3305739 3305332 ID=Msa0231100-mRNA-1:cds;Parent=Msa0231100-mRNA-1
Gene Sequence

>Msa0231100

ATGGTGAAATTCTTGAAGCCAAACAAAGCGGTGATCGTCTTACAAGGACGTTACGCTGGCAAAAAGGCTGTCATCGTGAAGAACTTTGATGATGGAACCCGTGAACGTGCTTACGGTCATTGCTTGGTTGCAGGGATCAAGAAGTATCCAGCTAAGGTGATCAAGAAGGATTCAGCTAAGAAAACTGCAAAGAAATCGCGTGTTAAGGCTTTTGTGAAGTTGGTTAACTATCAGCATCTTATGCCAACACGTTACACTCTGGATGTTGATTTGAAGGAGGTTGTTACCACTGATGTTCTTCAGAGTAAGGATAAGAAGGTCACTGCTTTGAAGGAGGCCAAGAAGAGGTTCGAAGAAAGGTTCAAAACTGGGAAGAACAGGTGGTTCTTCACCAAGCTCAGGTTTTGA

Protein sequence

>Msa0231100

MVKFLKPNKAVIVLQGRYAGKKAVIVKNFDDGTRERAYGHCLVAGIKKYPAKVIKKDSAKKTAKKSRVKAFVKLVNYQHLMPTRYTLDVDLKEVVTTDVLQSKDKKVTALKEAKKRFEERFKTGKNRWFFTKLRF*