AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0531050


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0531050 MtrunA17_Chr4g0004071 86.290 124 13 1 1 120 1 124 6.46e-72 217
Msa0531050 MtrunA17_Chr4g0004061 79.032 124 22 1 1 120 1 124 3.22e-66 202
Msa0531050 MtrunA17_Chr7g0256741 36.800 125 74 2 1 120 1 125 7.65e-22 87.8
Msa0531050 MtrunA17_Chr3g0138351 37.008 127 71 4 1 120 1 125 6.16e-20 82.8
Msa0531050 MtrunA17_Chr1g0148781 31.538 130 78 4 1 120 1 129 1.26e-16 73.9
Msa0531050 MtrunA17_Chr4g0009541 32.000 125 78 3 1 120 1 123 5.52e-13 63.5
Msa0531050 MtrunA17_Chr4g0009561 31.405 121 75 4 8 120 6 126 6.49e-13 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0531050 AT1G52820.2 56.693 127 48 2 1 120 1 127 8.50e-46 149
Msa0531050 AT1G52820.1 56.693 127 48 2 1 120 1 127 3.62e-45 149
Msa0531050 AT1G52810.1 50.000 118 55 1 7 120 10 127 6.29e-35 122
Msa0531050 AT1G28030.1 51.261 119 53 2 3 117 7 124 2.60e-31 113
Msa0531050 AT4G03070.1 47.863 117 52 3 7 118 12 124 1.07e-29 108
Msa0531050 AT1G52790.1 43.220 118 62 2 8 120 4 121 5.26e-28 104
Msa0531050 AT1G52800.1 41.525 118 64 2 8 120 9 126 8.36e-26 98.6
Msa0531050 AT4G03050.2 43.478 115 58 2 8 118 7 118 1.10e-23 94.4
Msa0531050 AT4G03050.1 43.478 115 58 2 8 118 7 118 1.10e-23 94.4
Msa0531050 AT1G15540.1 29.839 124 74 3 1 115 1 120 7.64e-15 69.3
Msa0531050 AT1G15540.4 29.839 124 74 3 1 115 1 120 7.64e-15 69.3
Msa0531050 AT1G15540.3 29.839 124 74 3 1 115 8 127 8.35e-15 69.3
Msa0531050 AT1G15540.2 29.839 124 74 3 1 115 4 123 8.42e-15 68.9

Find 31 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCATCCGGCCACAAGATAT+TGG 0.302776 4_1:-5171429 None:intergenic
TAACTCCCAATTGGGACTTT+TGG 0.307103 4_1:-5171153 None:intergenic
CTCTTCTAGTGAAGTAAATA+TGG 0.310135 4_1:-5171261 None:intergenic
AGGTTATTGAAGTCAATTAT+TGG 0.351381 4_1:-5171119 None:intergenic
AGTGAAGTCCCAAGTCTATA+AGG 0.368829 4_1:+5171175 Msa0531050:CDS
AAGCCTTATGATGGCTATCT+TGG 0.371205 4_1:+5171329 Msa0531050:intron
GGACTTCACTAACTCCCAAT+TGG 0.386844 4_1:-5171162 None:intergenic
TATAAGGCATTAGCAGAGTA+TGG 0.406334 4_1:+5171191 Msa0531050:CDS
TGGAAGCCAAAAGTCCCAAT+TGG 0.421664 4_1:+5171147 Msa0531050:CDS
CTGCTAATGCCTTATAGACT+TGG 0.437929 4_1:-5171184 None:intergenic
TTGAGTAGCTTAGTCTCTAA+AGG 0.454248 4_1:-5171296 None:intergenic
CTCTCATAAAGTGGAACTAC+AGG 0.468829 4_1:-5171359 None:intergenic
GACTTCACTAACTCCCAATT+GGG 0.486736 4_1:-5171161 None:intergenic
TGAGTAGCTTAGTCTCTAAA+GGG 0.493999 4_1:-5171295 None:intergenic
TGACCAAGATAGCCATCATA+AGG 0.499656 4_1:-5171332 None:intergenic
ATGGCTTTGCGAAGGTGTAA+AGG 0.500853 4_1:-5171242 None:intergenic
ACCAATATCTTGTGGCCGGA+TGG 0.502522 4_1:+5171428 Msa0531050:CDS
AATTATTGGAAGCTTTAGAA+TGG 0.504433 4_1:-5171105 None:intergenic
GTGTCTAATAAGCCTTATGA+TGG 0.509211 4_1:+5171320 Msa0531050:intron
GGAAGCCAAAAGTCCCAATT+GGG 0.510341 4_1:+5171148 Msa0531050:CDS
TGACTTCAATAACCTCAACT+TGG 0.518399 4_1:+5171127 Msa0531050:CDS
ATGGCCATCCTCTCATAAAG+TGG 0.539466 4_1:-5171368 None:intergenic
CACGACCAATATCTTGTGGC+CGG 0.542340 4_1:+5171424 Msa0531050:CDS
TGCTAATGCCTTATAGACTT+GGG 0.570558 4_1:-5171183 None:intergenic
CTGTAGTTCCACTTTATGAG+AGG 0.580451 4_1:+5171360 Msa0531050:CDS
AGTTCCACTTTATGAGAGGA+TGG 0.582196 4_1:+5171364 Msa0531050:CDS
TAAGATATTTGCATCCTCGA+TGG 0.613439 4_1:-5171387 None:intergenic
AAAGCACGACCAATATCTTG+TGG 0.639997 4_1:+5171420 Msa0531050:CDS
AAGTAAATATGGCTTTGCGA+AGG 0.659208 4_1:-5171250 None:intergenic
GTAGCTTAGTCTCTAAAGGG+AGG 0.695642 4_1:-5171292 None:intergenic
TTATGAGAGGATGGCCATCG+AGG 0.726896 4_1:+5171373 Msa0531050:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTATTGGAAGCTTTAGAA+TGG - chr4_1:5171108-5171127 None:intergenic 25.0%
! AGGTTATTGAAGTCAATTAT+TGG - chr4_1:5171122-5171141 None:intergenic 25.0%
CTCTTCTAGTGAAGTAAATA+TGG - chr4_1:5171264-5171283 None:intergenic 30.0%
TGACTTCAATAACCTCAACT+TGG + chr4_1:5171127-5171146 Msa0531050:CDS 35.0%
TGCTAATGCCTTATAGACTT+GGG - chr4_1:5171186-5171205 None:intergenic 35.0%
! TATAAGGCATTAGCAGAGTA+TGG + chr4_1:5171191-5171210 Msa0531050:CDS 35.0%
! AAGTAAATATGGCTTTGCGA+AGG - chr4_1:5171253-5171272 None:intergenic 35.0%
TGAGTAGCTTAGTCTCTAAA+GGG - chr4_1:5171298-5171317 None:intergenic 35.0%
TTGAGTAGCTTAGTCTCTAA+AGG - chr4_1:5171299-5171318 None:intergenic 35.0%
! GTGTCTAATAAGCCTTATGA+TGG + chr4_1:5171320-5171339 Msa0531050:intron 35.0%
TAAGATATTTGCATCCTCGA+TGG - chr4_1:5171390-5171409 None:intergenic 35.0%
! TAACTCCCAATTGGGACTTT+TGG - chr4_1:5171156-5171175 None:intergenic 40.0%
GACTTCACTAACTCCCAATT+GGG - chr4_1:5171164-5171183 None:intergenic 40.0%
AGTGAAGTCCCAAGTCTATA+AGG + chr4_1:5171175-5171194 Msa0531050:CDS 40.0%
CTGCTAATGCCTTATAGACT+TGG - chr4_1:5171187-5171206 None:intergenic 40.0%
! AAGCCTTATGATGGCTATCT+TGG + chr4_1:5171329-5171348 Msa0531050:intron 40.0%
TGACCAAGATAGCCATCATA+AGG - chr4_1:5171335-5171354 None:intergenic 40.0%
CTCTCATAAAGTGGAACTAC+AGG - chr4_1:5171362-5171381 None:intergenic 40.0%
CTGTAGTTCCACTTTATGAG+AGG + chr4_1:5171360-5171379 Msa0531050:CDS 40.0%
AGTTCCACTTTATGAGAGGA+TGG + chr4_1:5171364-5171383 Msa0531050:CDS 40.0%
AAAGCACGACCAATATCTTG+TGG + chr4_1:5171420-5171439 Msa0531050:CDS 40.0%
!!! GACTTTTGGCTTCCAAGTTG+AGG - chr4_1:5171142-5171161 None:intergenic 45.0%
TGGAAGCCAAAAGTCCCAAT+TGG + chr4_1:5171147-5171166 Msa0531050:CDS 45.0%
GGAAGCCAAAAGTCCCAATT+GGG + chr4_1:5171148-5171167 Msa0531050:CDS 45.0%
GGACTTCACTAACTCCCAAT+TGG - chr4_1:5171165-5171184 None:intergenic 45.0%
! ATGGCTTTGCGAAGGTGTAA+AGG - chr4_1:5171245-5171264 None:intergenic 45.0%
! GTAGCTTAGTCTCTAAAGGG+AGG - chr4_1:5171295-5171314 None:intergenic 45.0%
ATGGCCATCCTCTCATAAAG+TGG - chr4_1:5171371-5171390 None:intergenic 45.0%
TTATGAGAGGATGGCCATCG+AGG + chr4_1:5171373-5171392 Msa0531050:CDS 50.0%
CACGACCAATATCTTGTGGC+CGG + chr4_1:5171424-5171443 Msa0531050:CDS 50.0%
ACCAATATCTTGTGGCCGGA+TGG + chr4_1:5171428-5171447 Msa0531050:CDS 50.0%
TCCATCCGGCCACAAGATAT+TGG - chr4_1:5171432-5171451 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 5171092 5171463 5171092 ID=Msa0531050;Name=Msa0531050
chr4_1 mRNA 5171092 5171463 5171092 ID=Msa0531050-mRNA-1;Parent=Msa0531050;Name=Msa0531050-mRNA-1;_AED=0.41;_eAED=0.41;_QI=0|0|0|1|0|0|2|0|120
chr4_1 exon 5171092 5171319 5171092 ID=Msa0531050-mRNA-1:exon:1615;Parent=Msa0531050-mRNA-1
chr4_1 exon 5171332 5171463 5171332 ID=Msa0531050-mRNA-1:exon:1616;Parent=Msa0531050-mRNA-1
chr4_1 CDS 5171092 5171319 5171092 ID=Msa0531050-mRNA-1:cds;Parent=Msa0531050-mRNA-1
chr4_1 CDS 5171332 5171463 5171332 ID=Msa0531050-mRNA-1:cds;Parent=Msa0531050-mRNA-1
Gene Sequence

>Msa0531050

ATGGGCTCAGAAACCATTCTAAAGCTTCCAATAATTGACTTCAATAACCTCAACTTGGAAGCCAAAAGTCCCAATTGGGAGTTAGTGAAGTCCCAAGTCTATAAGGCATTAGCAGAGTATGGTTGCTTCGAAGCAATTTTTGATAAAGTTCCTTTACACCTTCGCAAAGCCATATTTACTTCACTAGAAGAGCTCTTTGACCTCCCTTTAGAGACTAAGCTACTCAATCCTTATGATGGCTATCTTGGTCAATATCCTGTAGTTCCACTTTATGAGAGGATGGCCATCGAGGATGCAAATATCTTAGAGAAAGTAAAAAGCACGACCAATATCTTGTGGCCGGATGGAAACAAAATTTTT

Protein sequence

>Msa0531050

MGSETILKLPIIDFNNLNLEAKSPNWELVKSQVYKALAEYGCFEAIFDKVPLHLRKAIFTSLEELFDLPLETKLLNPYDGYLGQYPVVPLYERMAIEDANILEKVKSTTNILWPDGNKIF