AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1303320

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1303320 MtrunA17_Chr4g0071441 100.000 101 0 0 1 101 1 101 3.42e-70 204
Msa1303320 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
Msa1303320 AT4G29850.1 82.178 101 18 0 2 102 3 103 3.37e-59 177
Msa1303320 AT2G19350.1 78.218 101 22 0 2 102 3 103 3.18e-56 169
Msa1303320 AT3G29170.1 40.659 91 54 0 10 100 29 119 1.09e-13 62.4
Msa1303320 AT3G29170.2 40.659 91 54 0 10 100 29 119 1.09e-13 62.4

Find 30 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGAACTCTCTCAGATTAT+AGG 0.162024 8_3:+66393135 None:intergenic
AGGTCTCTTCTTTGCAATAC+TGG 0.262488 8_3:-66392650 Msa1303320:CDS
GTATAGATGTTGATCTTCTA+TGG 0.296101 8_3:-66392504 Msa1303320:three_prime_UTR
AGCTGTAAATGTATTTGTTC+AGG 0.421470 8_3:+66392343 None:intergenic
GAATAACAAACCACCGATCA+AGG 0.440187 8_3:-66393045 Msa1303320:CDS
AAGATCAACATCTATACATA+AGG 0.483235 8_3:+66392510 None:intergenic
TCTATACATAAGGATGCTAC+TGG 0.485278 8_3:+66392520 None:intergenic
GGTCTCTTCTTTGCAATACT+GGG 0.489973 8_3:-66392649 Msa1303320:CDS
GATTGCATATTATGCTTACA+AGG 0.497760 8_3:-66392590 Msa1303320:CDS
TTCCGATGAAGACATGATGA+TGG 0.501107 8_3:-66393084 Msa1303320:CDS
GCTACTGGAGAAAACTATAC+AGG 0.517069 8_3:+66392535 None:intergenic
TTCCATCATCATGTCTTCAT+CGG 0.520845 8_3:+66393082 None:intergenic
TATCATCATCGGTTCTCTCA+TGG 0.531321 8_3:-66392979 Msa1303320:CDS
GGATCAATCTTGTTCATACC+AGG 0.533605 8_3:-66392628 Msa1303320:CDS
GAGAACCGATGATGATACCT+AGG 0.557809 8_3:+66392985 None:intergenic
TACCAGGTTTCTACTATACA+CGG 0.584090 8_3:-66392612 Msa1303320:CDS
TATGCTTACAAGGGATACAA+AGG 0.595286 8_3:-66392580 Msa1303320:CDS
TCCGAAAACGAGAAGAGCGA+CGG 0.605899 8_3:+66393010 None:intergenic
ATCCGTGTATAGTAGAAACC+TGG 0.613139 8_3:+66392610 None:intergenic
GCGAGAGCGATCTCCTTGAT+CGG 0.617044 8_3:+66393032 None:intergenic
GGAACCCTAGGTATCATCAT+CGG 0.618807 8_3:-66392990 Msa1303320:CDS
ATTGCATATTATGCTTACAA+GGG 0.625358 8_3:-66392589 Msa1303320:CDS
AGAGCGATCTCCTTGATCGG+TGG 0.654102 8_3:+66393035 None:intergenic
AGAACCGATGATGATACCTA+GGG 0.654644 8_3:+66392986 None:intergenic
TATACATTAGATGCAACGCA+AGG 0.662693 8_3:+66392458 None:intergenic
ATGGCTTACAATCACGTCGG+CGG 0.675872 8_3:-66392960 Msa1303320:CDS
GATGATGGAAACATCATACA+CGG 0.676748 8_3:-66393069 Msa1303320:CDS
GTCGGCGGTGACACTGCTCA+CGG 0.677770 8_3:-66392945 Msa1303320:intron
ACTGGAGAAAACTATACAGG+AGG 0.682610 8_3:+66392538 None:intergenic
CTCATGGCTTACAATCACGT+CGG 0.683421 8_3:-66392963 Msa1303320:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGACTAATATTAATTATTTT+AGG - chr8_3:66392806-66392825 Msa1303320:intron 10.0%
!!! AGACTAATATTAATTATTTT+AGG - chr8_3:66392806-66392825 Msa1303320:intron 10.0%
!!! TTTGTTATTGAATGATTTAT+AGG - chr8_3:66392853-66392872 Msa1303320:intron 15.0%
!!! TTTGTTATTGAATGATTTAT+AGG - chr8_3:66392853-66392872 Msa1303320:intron 15.0%
!! CAATTGATTCAGAAAATTCT+TGG - chr8_3:66392684-66392703 Msa1303320:intron 25.0%
! ATTGCATATTATGCTTACAA+GGG - chr8_3:66392934-66392953 Msa1303320:intron 25.0%
! AAGATCAACATCTATACATA+AGG + chr8_3:66393016-66393035 None:intergenic 25.0%
! AGGCAGAACAAATAAAAAAA+AGG + chr8_3:66393048-66393067 None:intergenic 25.0%
!! CAATTGATTCAGAAAATTCT+TGG - chr8_3:66392684-66392703 Msa1303320:intron 25.0%
! ATTGCATATTATGCTTACAA+GGG - chr8_3:66392934-66392953 Msa1303320:intron 25.0%
! AAGATCAACATCTATACATA+AGG + chr8_3:66393016-66393035 None:intergenic 25.0%
! AGGCAGAACAAATAAAAAAA+AGG + chr8_3:66393048-66393067 None:intergenic 25.0%
TTTGAACTCTCTCAGATTAT+AGG + chr8_3:66392391-66392410 None:intergenic 30.0%
ATTCTGAATAAGAAGAACGA+AGG + chr8_3:66392639-66392658 None:intergenic 30.0%
GATTGCATATTATGCTTACA+AGG - chr8_3:66392933-66392952 Msa1303320:intron 30.0%
GTATAGATGTTGATCTTCTA+TGG - chr8_3:66393019-66393038 Msa1303320:CDS 30.0%
AGCTGTAAATGTATTTGTTC+AGG + chr8_3:66393183-66393202 None:intergenic 30.0%
TTTGAACTCTCTCAGATTAT+AGG + chr8_3:66392391-66392410 None:intergenic 30.0%
ATTCTGAATAAGAAGAACGA+AGG + chr8_3:66392639-66392658 None:intergenic 30.0%
GATTGCATATTATGCTTACA+AGG - chr8_3:66392933-66392952 Msa1303320:intron 30.0%
GTATAGATGTTGATCTTCTA+TGG - chr8_3:66393019-66393038 Msa1303320:CDS 30.0%
AGCTGTAAATGTATTTGTTC+AGG + chr8_3:66393183-66393202 None:intergenic 30.0%
TTCCATCATCATGTCTTCAT+CGG + chr8_3:66392444-66392463 None:intergenic 35.0%
!! GATGATGGAAACATCATACA+CGG - chr8_3:66392454-66392473 Msa1303320:three_prime_UTR 35.0%
CTCAAGTCTAGTGAATTATC+TGG + chr8_3:66392782-66392801 None:intergenic 35.0%
TACCAGGTTTCTACTATACA+CGG - chr8_3:66392911-66392930 Msa1303320:intron 35.0%
TATGCTTACAAGGGATACAA+AGG - chr8_3:66392943-66392962 Msa1303320:intron 35.0%
TCTATACATAAGGATGCTAC+TGG + chr8_3:66393006-66393025 None:intergenic 35.0%
TATACATTAGATGCAACGCA+AGG + chr8_3:66393068-66393087 None:intergenic 35.0%
TTCCATCATCATGTCTTCAT+CGG + chr8_3:66392444-66392463 None:intergenic 35.0%
!! GATGATGGAAACATCATACA+CGG - chr8_3:66392454-66392473 Msa1303320:three_prime_UTR 35.0%
CTCAAGTCTAGTGAATTATC+TGG + chr8_3:66392782-66392801 None:intergenic 35.0%
TACCAGGTTTCTACTATACA+CGG - chr8_3:66392911-66392930 Msa1303320:intron 35.0%
TATGCTTACAAGGGATACAA+AGG - chr8_3:66392943-66392962 Msa1303320:intron 35.0%
TCTATACATAAGGATGCTAC+TGG + chr8_3:66393006-66393025 None:intergenic 35.0%
TATACATTAGATGCAACGCA+AGG + chr8_3:66393068-66393087 None:intergenic 35.0%
TTCCGATGAAGACATGATGA+TGG - chr8_3:66392439-66392458 Msa1303320:three_prime_UTR 40.0%
GAATAACAAACCACCGATCA+AGG - chr8_3:66392478-66392497 Msa1303320:three_prime_UTR 40.0%
AGAACCGATGATGATACCTA+GGG + chr8_3:66392540-66392559 None:intergenic 40.0%
!! TATCATCATCGGTTCTCTCA+TGG - chr8_3:66392544-66392563 Msa1303320:exon 40.0%
AAGGACGATTGAAGGGAAAA+AGG + chr8_3:66392620-66392639 None:intergenic 40.0%
AAGAACGAAGGACGATTGAA+GGG + chr8_3:66392627-66392646 None:intergenic 40.0%
AGGTCTCTTCTTTGCAATAC+TGG - chr8_3:66392873-66392892 Msa1303320:intron 40.0%
GGTCTCTTCTTTGCAATACT+GGG - chr8_3:66392874-66392893 Msa1303320:intron 40.0%
GGATCAATCTTGTTCATACC+AGG - chr8_3:66392895-66392914 Msa1303320:intron 40.0%
ATCCGTGTATAGTAGAAACC+TGG + chr8_3:66392916-66392935 None:intergenic 40.0%
ACTGGAGAAAACTATACAGG+AGG + chr8_3:66392988-66393007 None:intergenic 40.0%
GCTACTGGAGAAAACTATAC+AGG + chr8_3:66392991-66393010 None:intergenic 40.0%
TTCCGATGAAGACATGATGA+TGG - chr8_3:66392439-66392458 Msa1303320:three_prime_UTR 40.0%
GAATAACAAACCACCGATCA+AGG - chr8_3:66392478-66392497 Msa1303320:three_prime_UTR 40.0%
AGAACCGATGATGATACCTA+GGG + chr8_3:66392540-66392559 None:intergenic 40.0%
!! TATCATCATCGGTTCTCTCA+TGG - chr8_3:66392544-66392563 Msa1303320:exon 40.0%
AAGGACGATTGAAGGGAAAA+AGG + chr8_3:66392620-66392639 None:intergenic 40.0%
AAGAACGAAGGACGATTGAA+GGG + chr8_3:66392627-66392646 None:intergenic 40.0%
AGGTCTCTTCTTTGCAATAC+TGG - chr8_3:66392873-66392892 Msa1303320:intron 40.0%
GGTCTCTTCTTTGCAATACT+GGG - chr8_3:66392874-66392893 Msa1303320:intron 40.0%
GGATCAATCTTGTTCATACC+AGG - chr8_3:66392895-66392914 Msa1303320:intron 40.0%
ATCCGTGTATAGTAGAAACC+TGG + chr8_3:66392916-66392935 None:intergenic 40.0%
ACTGGAGAAAACTATACAGG+AGG + chr8_3:66392988-66393007 None:intergenic 40.0%
GCTACTGGAGAAAACTATAC+AGG + chr8_3:66392991-66393010 None:intergenic 40.0%
GGAACCCTAGGTATCATCAT+CGG - chr8_3:66392533-66392552 Msa1303320:exon 45.0%
GAGAACCGATGATGATACCT+AGG + chr8_3:66392541-66392560 None:intergenic 45.0%
CTCATGGCTTACAATCACGT+CGG - chr8_3:66392560-66392579 Msa1303320:CDS 45.0%
CGATTGAAGGGAAAAAGGTG+TGG + chr8_3:66392615-66392634 None:intergenic 45.0%
GAAGAACGAAGGACGATTGA+AGG + chr8_3:66392628-66392647 None:intergenic 45.0%
GGAACCCTAGGTATCATCAT+CGG - chr8_3:66392533-66392552 Msa1303320:exon 45.0%
GAGAACCGATGATGATACCT+AGG + chr8_3:66392541-66392560 None:intergenic 45.0%
CTCATGGCTTACAATCACGT+CGG - chr8_3:66392560-66392579 Msa1303320:CDS 45.0%
CGATTGAAGGGAAAAAGGTG+TGG + chr8_3:66392615-66392634 None:intergenic 45.0%
GAAGAACGAAGGACGATTGA+AGG + chr8_3:66392628-66392647 None:intergenic 45.0%
TCCGAAAACGAGAAGAGCGA+CGG + chr8_3:66392516-66392535 None:intergenic 50.0%
! CTTCTCGTTTTCGGAACCCT+AGG - chr8_3:66392521-66392540 Msa1303320:three_prime_UTR 50.0%
ATGGCTTACAATCACGTCGG+CGG - chr8_3:66392563-66392582 Msa1303320:CDS 50.0%
TCCGAAAACGAGAAGAGCGA+CGG + chr8_3:66392516-66392535 None:intergenic 50.0%
! CTTCTCGTTTTCGGAACCCT+AGG - chr8_3:66392521-66392540 Msa1303320:three_prime_UTR 50.0%
ATGGCTTACAATCACGTCGG+CGG - chr8_3:66392563-66392582 Msa1303320:CDS 50.0%
AGAGCGATCTCCTTGATCGG+TGG + chr8_3:66392491-66392510 None:intergenic 55.0%
GCGAGAGCGATCTCCTTGAT+CGG + chr8_3:66392494-66392513 None:intergenic 55.0%
! GCCGTCGCTCTTCTCGTTTT+CGG - chr8_3:66392512-66392531 Msa1303320:three_prime_UTR 55.0%
AGAGCGATCTCCTTGATCGG+TGG + chr8_3:66392491-66392510 None:intergenic 55.0%
GCGAGAGCGATCTCCTTGAT+CGG + chr8_3:66392494-66392513 None:intergenic 55.0%
! GCCGTCGCTCTTCTCGTTTT+CGG - chr8_3:66392512-66392531 Msa1303320:three_prime_UTR 55.0%
GTCGGCGGTGACACTGCTCA+CGG - chr8_3:66392578-66392597 Msa1303320:CDS 65.0%
GTCGGCGGTGACACTGCTCA+CGG - chr8_3:66392578-66392597 Msa1303320:CDS 65.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 66392331 66393214 66392331 ID=Msa1303320;Name=Msa1303320
chr8_3 mRNA 66392331 66393214 66392331 ID=Msa1303320-mRNA-1;Parent=Msa1303320;Name=Msa1303320-mRNA-1;_AED=0.00;_eAED=0.00;_QI=82|1|1|1|1|1|2|218|102
chr8_3 exon 66392331 66392670 66392331 ID=Msa1303320-mRNA-1:exon:20195;Parent=Msa1303320-mRNA-1
chr8_3 exon 66392946 66393214 66392946 ID=Msa1303320-mRNA-1:exon:20194;Parent=Msa1303320-mRNA-1
chr8_3 five_prime_UTR 66393133 66393214 66393133 ID=Msa1303320-mRNA-1:five_prime_utr;Parent=Msa1303320-mRNA-1
chr8_3 CDS 66392946 66393132 66392946 ID=Msa1303320-mRNA-1:cds;Parent=Msa1303320-mRNA-1
chr8_3 CDS 66392549 66392670 66392549 ID=Msa1303320-mRNA-1:cds;Parent=Msa1303320-mRNA-1
chr8_3 three_prime_UTR 66392331 66392548 66392331 ID=Msa1303320-mRNA-1:three_prime_utr;Parent=Msa1303320-mRNA-1
Gene Sequence

>Msa1303320

ATGTACGTAGATCACGCATTCTCGATTTCCGATGAAGACATGATGATGGAAACATCATACACGGCGAATAACAAACCACCGATCAAGGAGATCGCTCTCGCCGTCGCTCTTCTCGTTTTCGGAACCCTAGGTATCATCATCGGTTCTCTCATGGCTTACAATCACGTCGGCGGTGACACTGCTCACGGTCTCTTCTTTGCAATACTGGGATCAATCTTGTTCATACCAGGTTTCTACTATACACGGATTGCATATTATGCTTACAAGGGATACAAAGGCTTCTCTTTCTCTAACATACCTCCTGTATAG
Protein sequence

>Msa1303320

MYVDHAFSISDEDMMMETSYTANNKPPIKEIALAVALLVFGTLGIIIGSLMAYNHVGGDTAHGLFFAILGSILFIPGFYYTRIAYYAYKGYKGFSFSNIPPV*