AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1306850


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1306850 MtrunA17_Chr8g0377661 97.561 82 2 0 31 112 1 82 1.52e-52 159
Msa1306850 MtrunA17_Chr8g0377651 87.654 81 10 0 30 110 437 517 4.00e-42 144
Msa1306850 MtrunA17_Chr8g0377681 86.076 79 11 0 30 108 435 513 2.52e-41 142
Msa1306850 MtrunA17_Chr8g0377691 87.342 79 10 0 30 108 437 515 2.75e-41 142
Msa1306850 MtrunA17_Chr8g0377641 88.095 84 9 1 30 112 434 517 4.97e-41 141
Msa1306850 MtrunA17_Chr8g0377701 85.714 77 11 0 30 106 438 514 4.15e-37 130
Msa1306850 MtrunA17_Chr4g0037521 69.863 73 21 1 29 100 434 506 8.68e-26 100
Msa1306850 MtrunA17_Chr4g0037491 63.077 65 23 1 30 93 238 302 1.29e-20 84.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1306850 AT4G34880.1 69.444 72 21 1 30 100 390 461 3.47e-25 98.6
Msa1306850 AT4G34880.2 69.444 72 21 1 30 100 436 507 3.97e-25 98.6

Find 28 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTCTGACGGTGTGGATTCT+TGG 0.256519 8_4:+1794242 Msa1306850:CDS
TTTAGTAGCATACTTGCTAT+TGG 0.285041 8_4:+1794361 Msa1306850:CDS
CTTGCTATTGGAGGTTATCT+TGG 0.307365 8_4:+1794373 Msa1306850:CDS
TTGGTCTTGGAAGCTTAGTT+TGG 0.311340 8_4:+1794261 Msa1306850:CDS
ATGCTACTAAAGAATGAAAA+AGG 0.327148 8_4:-1794349 None:intergenic
CAGCCATTTGGAATTTGCTT+TGG 0.337732 8_4:+1794427 Msa1306850:CDS
CCATTTGGAATTTGCTTTGG+AGG 0.347630 8_4:+1794430 Msa1306850:CDS
ACGGTGTGGATTCTTGGTCT+TGG 0.417239 8_4:+1794248 Msa1306850:CDS
GTTCCAGCAGGATATGAAAA+AGG 0.427483 8_4:+1794403 Msa1306850:CDS
GTCTTGGAAGCTTAGTTTGG+AGG 0.439009 8_4:+1794264 Msa1306850:CDS
TTGTAACTTCCAACTTCCTA+AGG 0.444018 8_4:-1794531 None:intergenic
TAAGCAATCTCAATCAACTT+TGG 0.456653 8_4:-1794469 None:intergenic
AATCCACACCGTCAGACAAC+GGG 0.474967 8_4:-1794237 None:intergenic
GCCATCACCCCTTAGGAAGT+TGG 0.476560 8_4:+1794522 Msa1306850:CDS
ATTTGCTTTGGAGGTTTGAA+AGG 0.485064 8_4:+1794439 Msa1306850:CDS
AGTAGCATACTTGCTATTGG+AGG 0.497454 8_4:+1794364 Msa1306850:CDS
TCAGAAAGCCATCACCCCTT+AGG 0.498171 8_4:+1794515 Msa1306850:CDS
TCTTGGAAGCTTAGTTTGGA+GGG 0.501942 8_4:+1794265 Msa1306850:CDS
CTTGGAGTGATTGTTCCAGC+AGG 0.513725 8_4:+1794391 Msa1306850:CDS
TCCAACTTCCTAAGGGGTGA+TGG 0.529966 8_4:-1794523 None:intergenic
CCTCCAAAGCAAATTCCAAA+TGG 0.542753 8_4:-1794430 None:intergenic
GGCGAGTGCCCGTTGTCTGA+CGG 0.543749 8_4:+1794229 Msa1306850:CDS
TGTAACTTCCAACTTCCTAA+GGG 0.549765 8_4:-1794530 None:intergenic
TTTGCTTTGGAGGTTTGAAA+GGG 0.567329 8_4:+1794440 Msa1306850:CDS
AATAAATAAACTTGATGCTG+TGG 0.588874 8_4:+1794321 Msa1306850:CDS
GAATCCACACCGTCAGACAA+CGG 0.634170 8_4:-1794238 None:intergenic
GTGCCCGTTGTCTGACGGTG+TGG 0.634476 8_4:+1794234 Msa1306850:CDS
GTAACTTCCAACTTCCTAAG+GGG 0.639313 8_4:-1794529 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATAAATAAACTTGATGCTG+TGG + chr8_4:1794321-1794340 Msa1306850:CDS 25.0%
! ATGCTACTAAAGAATGAAAA+AGG - chr8_4:1794352-1794371 None:intergenic 25.0%
!! TTTAGTAGCATACTTGCTAT+TGG + chr8_4:1794361-1794380 Msa1306850:CDS 30.0%
TAAGCAATCTCAATCAACTT+TGG - chr8_4:1794472-1794491 None:intergenic 30.0%
TATGAAAAAGGTCAGCCATT+TGG + chr8_4:1794415-1794434 Msa1306850:CDS 35.0%
!! ATTTGCTTTGGAGGTTTGAA+AGG + chr8_4:1794439-1794458 Msa1306850:CDS 35.0%
!! TTTGCTTTGGAGGTTTGAAA+GGG + chr8_4:1794440-1794459 Msa1306850:CDS 35.0%
TGTAACTTCCAACTTCCTAA+GGG - chr8_4:1794533-1794552 None:intergenic 35.0%
TTGTAACTTCCAACTTCCTA+AGG - chr8_4:1794534-1794553 None:intergenic 35.0%
!! TTGGTCTTGGAAGCTTAGTT+TGG + chr8_4:1794261-1794280 Msa1306850:CDS 40.0%
! TCTTGGAAGCTTAGTTTGGA+GGG + chr8_4:1794265-1794284 Msa1306850:CDS 40.0%
!! AGTAGCATACTTGCTATTGG+AGG + chr8_4:1794364-1794383 Msa1306850:CDS 40.0%
!! CTTGCTATTGGAGGTTATCT+TGG + chr8_4:1794373-1794392 Msa1306850:CDS 40.0%
GTTCCAGCAGGATATGAAAA+AGG + chr8_4:1794403-1794422 Msa1306850:CDS 40.0%
!! TGACCTTTTTCATATCCTGC+TGG - chr8_4:1794409-1794428 None:intergenic 40.0%
! CAGCCATTTGGAATTTGCTT+TGG + chr8_4:1794427-1794446 Msa1306850:CDS 40.0%
CCTCCAAAGCAAATTCCAAA+TGG - chr8_4:1794433-1794452 None:intergenic 40.0%
! CCATTTGGAATTTGCTTTGG+AGG + chr8_4:1794430-1794449 Msa1306850:CDS 40.0%
GTAACTTCCAACTTCCTAAG+GGG - chr8_4:1794532-1794551 None:intergenic 40.0%
! GTCTTGGAAGCTTAGTTTGG+AGG + chr8_4:1794264-1794283 Msa1306850:CDS 45.0%
AATCCACACCGTCAGACAAC+GGG - chr8_4:1794240-1794259 None:intergenic 50.0%
GAATCCACACCGTCAGACAA+CGG - chr8_4:1794241-1794260 None:intergenic 50.0%
TGTCTGACGGTGTGGATTCT+TGG + chr8_4:1794242-1794261 Msa1306850:CDS 50.0%
ACGGTGTGGATTCTTGGTCT+TGG + chr8_4:1794248-1794267 Msa1306850:CDS 50.0%
CTTGGAGTGATTGTTCCAGC+AGG + chr8_4:1794391-1794410 Msa1306850:CDS 50.0%
TCAGAAAGCCATCACCCCTT+AGG + chr8_4:1794515-1794534 Msa1306850:CDS 50.0%
TCCAACTTCCTAAGGGGTGA+TGG - chr8_4:1794526-1794545 None:intergenic 50.0%
GCCATCACCCCTTAGGAAGT+TGG + chr8_4:1794522-1794541 Msa1306850:CDS 55.0%
GGCGAGTGCCCGTTGTCTGA+CGG + chr8_4:1794229-1794248 Msa1306850:CDS 65.0%
GTGCCCGTTGTCTGACGGTG+TGG + chr8_4:1794234-1794253 Msa1306850:CDS 65.0%
Chromosome Type Strat End Strand Name
chr8_4 gene 1794226 1794564 1794226 ID=Msa1306850;Name=Msa1306850
chr8_4 mRNA 1794226 1794564 1794226 ID=Msa1306850-mRNA-1;Parent=Msa1306850;Name=Msa1306850-mRNA-1;_AED=0.62;_eAED=0.62;_QI=0|-1|0|1|-1|1|1|0|112
chr8_4 exon 1794226 1794564 1794226 ID=Msa1306850-mRNA-1:exon:633;Parent=Msa1306850-mRNA-1
chr8_4 CDS 1794226 1794564 1794226 ID=Msa1306850-mRNA-1:cds;Parent=Msa1306850-mRNA-1
Gene Sequence

>Msa1306850

ATGGGCGAGTGCCCGTTGTCTGACGGTGTGGATTCTTGGTCTTGGAAGCTTAGTTTGGAGGGAGTGTACTCTGTTCGATCTGCATCTCTGATGAAAATAAATAAACTTGATGCTGTGGTAACACCTTTTTCATTCTTTAGTAGCATACTTGCTATTGGAGGTTATCTTGGAGTGATTGTTCCAGCAGGATATGAAAAAGGTCAGCCATTTGGAATTTGCTTTGGAGGTTTGAAAGGGTCAGAACCAAAGTTGATTGAGATTGCTTATTCATTTGAGCAAGCAACTTTGATCAGAAAGCCATCACCCCTTAGGAAGTTGGAAGTTACAAGTTTGAAGTAG

Protein sequence

>Msa1306850

MGECPLSDGVDSWSWKLSLEGVYSVRSASLMKINKLDAVVTPFSFFSSILAIGGYLGVIVPAGYEKGQPFGICFGGLKGSEPKLIEIAYSFEQATLIRKPSPLRKLEVTSLK*