AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1397000

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1397000 MtrunA17_Chr2g0309121 90.164 122 11 1 1 122 1 121 9.13e-76 220
Msa1397000 MtrunA17_Chr2g0281511 84.426 122 19 0 1 122 1 122 1.33e-72 212
Msa1397000 MtrunA17_Chr3g0081891 83.750 80 13 0 1 80 1 80 8.78e-44 137
Msa1397000 MtrunA17_Chr7g0276661 32.061 131 69 4 7 119 38 166 3.66e-16 70.5
Msa1397000 MtrunA17_Chr0c01g0489371 42.857 91 50 1 22 110 224 314 8.78e-16 71.6
Msa1397000 MtrunA17_Chr8g0356961 41.573 89 50 1 24 110 77 165 4.30e-15 67.8
Msa1397000 MtrunA17_Chr8g0372431 27.835 97 70 0 24 120 6 102 1.17e-13 62.0
Msa1397000 MtrunA17_Chr5g0434641 36.264 91 56 1 22 110 208 298 1.31e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGGTTATTGCTTCTATTT+TGG 0.132946 tig0022096:+13104 Msa1397000:CDS
GAAGTCAATGGTACTGAATT+AGG 0.159497 tig0022096:+13045 Msa1397000:CDS
TGTATGCTACCGTCGTTAAC+TGG 0.211996 tig0022096:+13464 Msa1397000:CDS
AAAATATCGATGTCCATTAT+TGG 0.234776 tig0022096:+13076 Msa1397000:CDS
TACCGGTTTCTTCATCAAAA+AGG 0.272684 tig0022096:-13297 Msa1397000:intergenic
TAACCTTATGCTTCCAATAA+TGG 0.277357 tig0022096:-13089 Msa1397000:intergenic
ATCAAAGTCATAAGATTTAC+CGG 0.326757 tig0022096:-13314 Msa1397000:intergenic
CCTCGATGTGTTGCGGAGAA+TGG 0.338723 tig0022096:+13247 Msa1397000:CDS
TTTGGATGGAAACAATGTTT+TGG 0.356448 tig0022096:+13122 Msa1397000:CDS
TAAGGAAACATGAATGAGAT+TGG 0.380138 tig0022096:+13018 None:intergenic
GTACAACTTTGTTCTTGAAA+AGG 0.417029 tig0022096:+13387 Msa1397000:CDS
AAGTCAATGGTACTGAATTA+GGG 0.437113 tig0022096:+13046 Msa1397000:CDS
TGTCCATTATTGGAAGCATA+AGG 0.460083 tig0022096:+13086 Msa1397000:CDS
CGGTCAATAATCCTCCTAAT+CGG 0.465785 tig0022096:+13440 Msa1397000:CDS
ACGGTAGCATACATCCGATT+AGG 0.477261 tig0022096:-13454 Msa1397000:intergenic
CTTGAAAAGGACCTAAAAGT+TGG 0.486000 tig0022096:+13400 Msa1397000:CDS
AGAAATACATAGGGAGAGAA+TGG 0.518052 tig0022096:+13365 Msa1397000:CDS
GTATGCTACCGTCGTTAACT+GGG 0.522932 tig0022096:+13465 Msa1397000:CDS
AACATGCATCAGAAATACAT+AGG 0.535430 tig0022096:+13355 Msa1397000:CDS
GAGATTGGAGTTGAAGTCAA+TGG 0.575541 tig0022096:+13033 Msa1397000:CDS
ACATGCATCAGAAATACATA+GGG 0.587826 tig0022096:+13356 Msa1397000:CDS
GTAGCATACATCCGATTAGG+AGG 0.600441 tig0022096:-13451 Msa1396990:intergenic
CCATTCTCCGCAACACATCG+AGG 0.699602 tig0022096:-13247 Msa1396990:intergenic
GAATCAGTCCCAGTTAACGA+CGG 0.733495 tig0022096:-13473 Msa1396990:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAATATCGATGTCCATTAT+TGG + tig0022096:13076-13095 Msa1397000:CDS 25.0%
!! TAAGGTTATTGCTTCTATTT+TGG + tig0022096:13104-13123 Msa1397000:CDS 25.0%
! ATCAAAGTCATAAGATTTAC+CGG - tig0022096:13317-13336 Msa1397000:intergenic 25.0%
! AAGTCAATGGTACTGAATTA+GGG + tig0022096:13046-13065 Msa1397000:CDS 30.0%
TAACCTTATGCTTCCAATAA+TGG - tig0022096:13092-13111 Msa1397000:intergenic 30.0%
!! GTTATTGCTTCTATTTTGGA+TGG + tig0022096:13108-13127 Msa1397000:CDS 30.0%
! TTTGGATGGAAACAATGTTT+TGG + tig0022096:13122-13141 Msa1397000:CDS 30.0%
AACATGCATCAGAAATACAT+AGG + tig0022096:13355-13374 Msa1397000:CDS 30.0%
ACATGCATCAGAAATACATA+GGG + tig0022096:13356-13375 Msa1397000:CDS 30.0%
GTACAACTTTGTTCTTGAAA+AGG + tig0022096:13387-13406 Msa1397000:CDS 30.0%
! AAATAACGTCACCAACTTTT+AGG - tig0022096:13414-13433 Msa1397000:intergenic 30.0%
! GAAGTCAATGGTACTGAATT+AGG + tig0022096:13045-13064 Msa1397000:CDS 35.0%
! TGTCCATTATTGGAAGCATA+AGG + tig0022096:13086-13105 Msa1397000:CDS 35.0%
!!! GGAAACAATGTTTTGGTTAG+TGG + tig0022096:13129-13148 Msa1397000:intron 35.0%
! CTCCTTTTTGATGAAGAAAC+CGG + tig0022096:13295-13314 Msa1397000:CDS 35.0%
!! TACCGGTTTCTTCATCAAAA+AGG - tig0022096:13300-13319 Msa1397000:intergenic 35.0%
AGAAATACATAGGGAGAGAA+TGG + tig0022096:13365-13384 Msa1397000:CDS 35.0%
CTTGAAAAGGACCTAAAAGT+TGG + tig0022096:13400-13419 Msa1397000:CDS 35.0%
!! TGGTGACGTTATTTTGTTCA+CGG + tig0022096:13420-13439 Msa1397000:CDS 35.0%
GAGATTGGAGTTGAAGTCAA+TGG + tig0022096:13033-13052 Msa1397000:CDS 40.0%
CGGTCAATAATCCTCCTAAT+CGG + tig0022096:13440-13459 Msa1397000:CDS 40.0%
! GCATTTTCCTCGATGTGTTG+CGG + tig0022096:13240-13259 Msa1397000:intron 45.0%
GTAGCATACATCCGATTAGG+AGG - tig0022096:13454-13473 Msa1397000:intergenic 45.0%
ACGGTAGCATACATCCGATT+AGG - tig0022096:13457-13476 Msa1397000:intergenic 45.0%
TGTATGCTACCGTCGTTAAC+TGG + tig0022096:13464-13483 Msa1397000:CDS 45.0%
GTATGCTACCGTCGTTAACT+GGG + tig0022096:13465-13484 Msa1397000:CDS 45.0%
CCATTCTCCGCAACACATCG+AGG - tig0022096:13250-13269 Msa1397000:intergenic 55.0%
CCTCGATGTGTTGCGGAGAA+TGG + tig0022096:13247-13266 Msa1397000:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0022096 gene 13027 13492 13027 ID=Msa1397000;Name=Msa1397000
tig0022096 mRNA 13027 13492 13027 ID=Msa1397000-mRNA-1;Parent=Msa1397000;Name=Msa1397000-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|122
tig0022096 exon 13027 13143 13027 ID=Msa1397000-mRNA-1:exon:15822;Parent=Msa1397000-mRNA-1
tig0022096 exon 13241 13492 13241 ID=Msa1397000-mRNA-1:exon:15823;Parent=Msa1397000-mRNA-1
tig0022096 CDS 13027 13143 13027 ID=Msa1397000-mRNA-1:cds;Parent=Msa1397000-mRNA-1
tig0022096 CDS 13241 13492 13241 ID=Msa1397000-mRNA-1:cds;Parent=Msa1397000-mRNA-1
Gene Sequence

>Msa1397000

ATGAATGAGATTGGAGTTGAAGTCAATGGTACTGAATTAGGGAATGTTCAAAATATCGATGTCCATTATTGGAAGCATAAGGTTATTGCTTCTATTTTGGATGGAAACAATGTTTTGCATTTTCCTCGATGTGTTGCGGAGAATGGTTTGTTTATCAATCAATCTAAAATTCTCCTTTTTGATGAAGAAACCGGTAAATCTTATGACTTTGATGTTCACACTACGTCAAAAAACATGCATCAGAAATACATAGGGAGAGAATGGTACAACTTTGTTCTTGAAAAGGACCTAAAAGTTGGTGACGTTATTTTGTTCACGGTCAATAATCCTCCTAATCGGATGTATGCTACCGTCGTTAACTGGGACTGA
Protein sequence

>Msa1397000

MNEIGVEVNGTELGNVQNIDVHYWKHKVIASILDGNNVLHFPRCVAENGLFINQSKILLFDEETGKSYDFDVHTTSKNMHQKYIGREWYNFVLEKDLKVGDVILFTVNNPPNRMYATVVNWD*