AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1265770

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1265770 MtrunA17_Chr4g0071441 100.000 101 0 0 1 101 1 101 3.42e-70 204
Msa1265770 MtrunA17_Chr2g0299011 90.099 101 10 0 2 102 3 103 1.15e-62 185
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1265770 AT4G29850.1 82.178 101 18 0 2 102 3 103 3.37e-59 177
Msa1265770 AT2G19350.1 78.218 101 22 0 2 102 3 103 3.18e-56 169
Msa1265770 AT3G29170.1 40.659 91 54 0 10 100 29 119 1.09e-13 62.4
Msa1265770 AT3G29170.2 40.659 91 54 0 10 100 29 119 1.09e-13 62.4

Find 30 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGAACTCTCTCAGATTAT+AGG 0.162024 8_2:+70304628 None:intergenic
AGGTCTCTTCTTTGCAATAC+TGG 0.262488 8_2:-70304146 Msa1265770:CDS
GTATAGATGTTGATCTTCTA+TGG 0.296101 8_2:-70304000 Msa1265770:three_prime_UTR
AGCTGTAAATGTATTTGTTC+AGG 0.421470 8_2:+70303839 None:intergenic
GAATAACAAACCACCGATCA+AGG 0.440187 8_2:-70304538 Msa1265770:CDS
AAGATCAACATCTATACATA+AGG 0.483235 8_2:+70304006 None:intergenic
TCTATACATAAGGATGCTAC+TGG 0.485278 8_2:+70304016 None:intergenic
GGTCTCTTCTTTGCAATACT+GGG 0.489973 8_2:-70304145 Msa1265770:CDS
GATTGCATATTATGCTTACA+AGG 0.497760 8_2:-70304086 Msa1265770:CDS
TTCCGATGAAGACATGATGA+TGG 0.501107 8_2:-70304577 Msa1265770:CDS
GCTACTGGAGAAAACTATAC+AGG 0.517069 8_2:+70304031 None:intergenic
TTCCATCATCATGTCTTCAT+CGG 0.520845 8_2:+70304575 None:intergenic
TATCATCATCGGTTCTCTCA+TGG 0.531321 8_2:-70304472 Msa1265770:CDS
GGATCAATCTTGTTCATACC+AGG 0.533605 8_2:-70304124 Msa1265770:CDS
GAGAACCGATGATGATACCT+AGG 0.557809 8_2:+70304478 None:intergenic
TACCAGGTTTCTACTATACA+CGG 0.584090 8_2:-70304108 Msa1265770:CDS
TATGCTTACAAGGGATACAA+AGG 0.595286 8_2:-70304076 Msa1265770:CDS
TCCGAAAACGAGAAGAGCGA+CGG 0.605899 8_2:+70304503 None:intergenic
ATCCGTGTATAGTAGAAACC+TGG 0.613139 8_2:+70304106 None:intergenic
GCGAGAGCGATCTCCTTGAT+CGG 0.617044 8_2:+70304525 None:intergenic
GGAACCCTAGGTATCATCAT+CGG 0.618807 8_2:-70304483 Msa1265770:CDS
ATTGCATATTATGCTTACAA+GGG 0.625358 8_2:-70304085 Msa1265770:CDS
AGAGCGATCTCCTTGATCGG+TGG 0.654102 8_2:+70304528 None:intergenic
AGAACCGATGATGATACCTA+GGG 0.654644 8_2:+70304479 None:intergenic
TATACATTAGATGCAACGCA+AGG 0.662693 8_2:+70303954 None:intergenic
ATGGCTTACAATCACGTCGG+CGG 0.675872 8_2:-70304453 Msa1265770:CDS
GATGATGGAAACATCATACA+CGG 0.676748 8_2:-70304562 Msa1265770:CDS
GTCGGCGGTGACACTGCTCA+CGG 0.677770 8_2:-70304438 Msa1265770:intron
ACTGGAGAAAACTATACAGG+AGG 0.682610 8_2:+70304034 None:intergenic
CTCATGGCTTACAATCACGT+CGG 0.683421 8_2:-70304456 Msa1265770:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGACTAATATTAATTATTTT+AGG - chr8_2:70304299-70304318 Msa1265770:intron 10.0%
!!! AGACTAATATTAATTATTTT+AGG - chr8_2:70304299-70304318 Msa1265770:intron 10.0%
!!! TTTGTTATTGAATGATTTAT+AGG - chr8_2:70304346-70304365 Msa1265770:intron 15.0%
!!! TTTGTTATTGAATGATTTAT+AGG - chr8_2:70304346-70304365 Msa1265770:intron 15.0%
!!! AATTGATTCAGAAAATTTCT+TGG - chr8_2:70304177-70304196 Msa1265770:intron 20.0%
!!! AATTGATTCAGAAAATTTCT+TGG - chr8_2:70304177-70304196 Msa1265770:intron 20.0%
! AGAAACTTAATTCTGAATCA+AGG + chr8_2:70304140-70304159 None:intergenic 25.0%
! ATTGCATATTATGCTTACAA+GGG - chr8_2:70304427-70304446 Msa1265770:intron 25.0%
! AAGATCAACATCTATACATA+AGG + chr8_2:70304509-70304528 None:intergenic 25.0%
! AGGCAGAACAAATAAAAAAA+AGG + chr8_2:70304541-70304560 None:intergenic 25.0%
! AGAAACTTAATTCTGAATCA+AGG + chr8_2:70304140-70304159 None:intergenic 25.0%
! ATTGCATATTATGCTTACAA+GGG - chr8_2:70304427-70304446 Msa1265770:intron 25.0%
! AAGATCAACATCTATACATA+AGG + chr8_2:70304509-70304528 None:intergenic 25.0%
! AGGCAGAACAAATAAAAAAA+AGG + chr8_2:70304541-70304560 None:intergenic 25.0%
TTTGAACTCTCTCAGATTAT+AGG + chr8_2:70303887-70303906 None:intergenic 30.0%
GATTGCATATTATGCTTACA+AGG - chr8_2:70304426-70304445 Msa1265770:intron 30.0%
GTATAGATGTTGATCTTCTA+TGG - chr8_2:70304512-70304531 Msa1265770:CDS 30.0%
AGCTGTAAATGTATTTGTTC+AGG + chr8_2:70304676-70304695 None:intergenic 30.0%
TTTGAACTCTCTCAGATTAT+AGG + chr8_2:70303887-70303906 None:intergenic 30.0%
GATTGCATATTATGCTTACA+AGG - chr8_2:70304426-70304445 Msa1265770:intron 30.0%
GTATAGATGTTGATCTTCTA+TGG - chr8_2:70304512-70304531 Msa1265770:CDS 30.0%
AGCTGTAAATGTATTTGTTC+AGG + chr8_2:70304676-70304695 None:intergenic 30.0%
TTCCATCATCATGTCTTCAT+CGG + chr8_2:70303940-70303959 None:intergenic 35.0%
!! GATGATGGAAACATCATACA+CGG - chr8_2:70303950-70303969 Msa1265770:three_prime_UTR 35.0%
AGAACGATTGAAGGGAAAAA+GGG + chr8_2:70304115-70304134 None:intergenic 35.0%
AAGAACGATTGAAGGGAAAA+AGG + chr8_2:70304116-70304135 None:intergenic 35.0%
TCAAGGAAAGAACGATTGAA+GGG + chr8_2:70304123-70304142 None:intergenic 35.0%
ATCAAGGAAAGAACGATTGA+AGG + chr8_2:70304124-70304143 None:intergenic 35.0%
CTCAAGTCTAGTGAATTATC+TGG + chr8_2:70304275-70304294 None:intergenic 35.0%
TACCAGGTTTCTACTATACA+CGG - chr8_2:70304404-70304423 Msa1265770:intron 35.0%
TATGCTTACAAGGGATACAA+AGG - chr8_2:70304436-70304455 Msa1265770:intron 35.0%
TCTATACATAAGGATGCTAC+TGG + chr8_2:70304499-70304518 None:intergenic 35.0%
TATACATTAGATGCAACGCA+AGG + chr8_2:70304561-70304580 None:intergenic 35.0%
TTCCATCATCATGTCTTCAT+CGG + chr8_2:70303940-70303959 None:intergenic 35.0%
!! GATGATGGAAACATCATACA+CGG - chr8_2:70303950-70303969 Msa1265770:three_prime_UTR 35.0%
AGAACGATTGAAGGGAAAAA+GGG + chr8_2:70304115-70304134 None:intergenic 35.0%
AAGAACGATTGAAGGGAAAA+AGG + chr8_2:70304116-70304135 None:intergenic 35.0%
TCAAGGAAAGAACGATTGAA+GGG + chr8_2:70304123-70304142 None:intergenic 35.0%
ATCAAGGAAAGAACGATTGA+AGG + chr8_2:70304124-70304143 None:intergenic 35.0%
CTCAAGTCTAGTGAATTATC+TGG + chr8_2:70304275-70304294 None:intergenic 35.0%
TACCAGGTTTCTACTATACA+CGG - chr8_2:70304404-70304423 Msa1265770:intron 35.0%
TATGCTTACAAGGGATACAA+AGG - chr8_2:70304436-70304455 Msa1265770:intron 35.0%
TCTATACATAAGGATGCTAC+TGG + chr8_2:70304499-70304518 None:intergenic 35.0%
TATACATTAGATGCAACGCA+AGG + chr8_2:70304561-70304580 None:intergenic 35.0%
TTCCGATGAAGACATGATGA+TGG - chr8_2:70303935-70303954 Msa1265770:three_prime_UTR 40.0%
GAATAACAAACCACCGATCA+AGG - chr8_2:70303974-70303993 Msa1265770:three_prime_UTR 40.0%
AGAACCGATGATGATACCTA+GGG + chr8_2:70304036-70304055 None:intergenic 40.0%
!! TATCATCATCGGTTCTCTCA+TGG - chr8_2:70304040-70304059 Msa1265770:exon 40.0%
GAACGATTGAAGGGAAAAAG+GGG + chr8_2:70304114-70304133 None:intergenic 40.0%
AGGTCTCTTCTTTGCAATAC+TGG - chr8_2:70304366-70304385 Msa1265770:intron 40.0%
GGTCTCTTCTTTGCAATACT+GGG - chr8_2:70304367-70304386 Msa1265770:intron 40.0%
GGATCAATCTTGTTCATACC+AGG - chr8_2:70304388-70304407 Msa1265770:intron 40.0%
ATCCGTGTATAGTAGAAACC+TGG + chr8_2:70304409-70304428 None:intergenic 40.0%
ACTGGAGAAAACTATACAGG+AGG + chr8_2:70304481-70304500 None:intergenic 40.0%
GCTACTGGAGAAAACTATAC+AGG + chr8_2:70304484-70304503 None:intergenic 40.0%
TTCCGATGAAGACATGATGA+TGG - chr8_2:70303935-70303954 Msa1265770:three_prime_UTR 40.0%
GAATAACAAACCACCGATCA+AGG - chr8_2:70303974-70303993 Msa1265770:three_prime_UTR 40.0%
AGAACCGATGATGATACCTA+GGG + chr8_2:70304036-70304055 None:intergenic 40.0%
!! TATCATCATCGGTTCTCTCA+TGG - chr8_2:70304040-70304059 Msa1265770:exon 40.0%
GAACGATTGAAGGGAAAAAG+GGG + chr8_2:70304114-70304133 None:intergenic 40.0%
AGGTCTCTTCTTTGCAATAC+TGG - chr8_2:70304366-70304385 Msa1265770:intron 40.0%
GGTCTCTTCTTTGCAATACT+GGG - chr8_2:70304367-70304386 Msa1265770:intron 40.0%
GGATCAATCTTGTTCATACC+AGG - chr8_2:70304388-70304407 Msa1265770:intron 40.0%
ATCCGTGTATAGTAGAAACC+TGG + chr8_2:70304409-70304428 None:intergenic 40.0%
ACTGGAGAAAACTATACAGG+AGG + chr8_2:70304481-70304500 None:intergenic 40.0%
GCTACTGGAGAAAACTATAC+AGG + chr8_2:70304484-70304503 None:intergenic 40.0%
GGAACCCTAGGTATCATCAT+CGG - chr8_2:70304029-70304048 Msa1265770:exon 45.0%
GAGAACCGATGATGATACCT+AGG + chr8_2:70304037-70304056 None:intergenic 45.0%
CTCATGGCTTACAATCACGT+CGG - chr8_2:70304056-70304075 Msa1265770:CDS 45.0%
GGAACCCTAGGTATCATCAT+CGG - chr8_2:70304029-70304048 Msa1265770:exon 45.0%
GAGAACCGATGATGATACCT+AGG + chr8_2:70304037-70304056 None:intergenic 45.0%
CTCATGGCTTACAATCACGT+CGG - chr8_2:70304056-70304075 Msa1265770:CDS 45.0%
TCCGAAAACGAGAAGAGCGA+CGG + chr8_2:70304012-70304031 None:intergenic 50.0%
! CTTCTCGTTTTCGGAACCCT+AGG - chr8_2:70304017-70304036 Msa1265770:three_prime_UTR 50.0%
ATGGCTTACAATCACGTCGG+CGG - chr8_2:70304059-70304078 Msa1265770:CDS 50.0%
CGATTGAAGGGAAAAAGGGG+TGG + chr8_2:70304111-70304130 None:intergenic 50.0%
TCCGAAAACGAGAAGAGCGA+CGG + chr8_2:70304012-70304031 None:intergenic 50.0%
! CTTCTCGTTTTCGGAACCCT+AGG - chr8_2:70304017-70304036 Msa1265770:three_prime_UTR 50.0%
ATGGCTTACAATCACGTCGG+CGG - chr8_2:70304059-70304078 Msa1265770:CDS 50.0%
CGATTGAAGGGAAAAAGGGG+TGG + chr8_2:70304111-70304130 None:intergenic 50.0%
AGAGCGATCTCCTTGATCGG+TGG + chr8_2:70303987-70304006 None:intergenic 55.0%
GCGAGAGCGATCTCCTTGAT+CGG + chr8_2:70303990-70304009 None:intergenic 55.0%
! GCCGTCGCTCTTCTCGTTTT+CGG - chr8_2:70304008-70304027 Msa1265770:three_prime_UTR 55.0%
AGAGCGATCTCCTTGATCGG+TGG + chr8_2:70303987-70304006 None:intergenic 55.0%
GCGAGAGCGATCTCCTTGAT+CGG + chr8_2:70303990-70304009 None:intergenic 55.0%
! GCCGTCGCTCTTCTCGTTTT+CGG - chr8_2:70304008-70304027 Msa1265770:three_prime_UTR 55.0%
GTCGGCGGTGACACTGCTCA+CGG - chr8_2:70304074-70304093 Msa1265770:CDS 65.0%
GTCGGCGGTGACACTGCTCA+CGG - chr8_2:70304074-70304093 Msa1265770:CDS 65.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 70303827 70304707 70303827 ID=Msa1265770;Name=Msa1265770
chr8_2 mRNA 70303827 70304707 70303827 ID=Msa1265770-mRNA-1;Parent=Msa1265770;Name=Msa1265770-mRNA-1;_AED=0.00;_eAED=0.00;_QI=82|1|1|1|1|1|2|218|102
chr8_2 exon 70303827 70304166 70303827 ID=Msa1265770-mRNA-1:exon:23364;Parent=Msa1265770-mRNA-1
chr8_2 exon 70304439 70304707 70304439 ID=Msa1265770-mRNA-1:exon:23363;Parent=Msa1265770-mRNA-1
chr8_2 five_prime_UTR 70304626 70304707 70304626 ID=Msa1265770-mRNA-1:five_prime_utr;Parent=Msa1265770-mRNA-1
chr8_2 CDS 70304439 70304625 70304439 ID=Msa1265770-mRNA-1:cds;Parent=Msa1265770-mRNA-1
chr8_2 CDS 70304045 70304166 70304045 ID=Msa1265770-mRNA-1:cds;Parent=Msa1265770-mRNA-1
chr8_2 three_prime_UTR 70303827 70304044 70303827 ID=Msa1265770-mRNA-1:three_prime_utr;Parent=Msa1265770-mRNA-1
Gene Sequence

>Msa1265770

ATGTACGTAGATCACGCATTCTCGATTTCCGATGAAGACATGATGATGGAAACATCATACACGGCGAATAACAAACCACCGATCAAGGAGATCGCTCTCGCCGTCGCTCTTCTCGTTTTCGGAACCCTAGGTATCATCATCGGTTCTCTCATGGCTTACAATCACGTCGGCGGTGACACTGCTCACGGTCTCTTCTTTGCAATACTGGGATCAATCTTGTTCATACCAGGTTTCTACTATACACGGATTGCATATTATGCTTACAAGGGATACAAAGGCTTCTCTTTCTCTAACATACCTCCTGTATAG
Protein sequence

>Msa1265770

MYVDHAFSISDEDMMMETSYTANNKPPIKEIALAVALLVFGTLGIIIGSLMAYNHVGGDTAHGLFFAILGSILFIPGFYYTRIAYYAYKGYKGFSFSNIPPV*