AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1303360

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1303360 MtrunA17_Chr4g0071441 100.000 101 0 0 1 101 1 101 3.42e-70 204
Msa1303360 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
Msa1303360 AT4G29850.1 82.178 101 18 0 2 102 3 103 3.37e-59 177
Msa1303360 AT2G19350.1 78.218 101 22 0 2 102 3 103 3.18e-56 169
Msa1303360 AT3G29170.1 40.659 91 54 0 10 100 29 119 1.09e-13 62.4
Msa1303360 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:+66445982 None:intergenic
AGGTCTCTTCTTTGCAATAC+TGG 0.262488 8_3:-66445500 Msa1303360:CDS
GTATAGATGTTGATCTTCTA+TGG 0.296101 8_3:-66445354 Msa1303360:three_prime_UTR
AGCTGTAAATGTATTTGTTC+AGG 0.421470 8_3:+66445193 None:intergenic
GAATAACAAACCACCGATCA+AGG 0.440187 8_3:-66445892 Msa1303360:CDS
AAGATCAACATCTATACATA+AGG 0.483235 8_3:+66445360 None:intergenic
TCTATACATAAGGATGCTAC+TGG 0.485278 8_3:+66445370 None:intergenic
GGTCTCTTCTTTGCAATACT+GGG 0.489973 8_3:-66445499 Msa1303360:CDS
GATTGCATATTATGCTTACA+AGG 0.497760 8_3:-66445440 Msa1303360:CDS
TTCCGATGAAGACATGATGA+TGG 0.501107 8_3:-66445931 Msa1303360:CDS
GCTACTGGAGAAAACTATAC+AGG 0.517069 8_3:+66445385 None:intergenic
TTCCATCATCATGTCTTCAT+CGG 0.520845 8_3:+66445929 None:intergenic
TATCATCATCGGTTCTCTCA+TGG 0.531321 8_3:-66445826 Msa1303360:CDS
GGATCAATCTTGTTCATACC+AGG 0.533605 8_3:-66445478 Msa1303360:CDS
GAGAACCGATGATGATACCT+AGG 0.557809 8_3:+66445832 None:intergenic
TACCAGGTTTCTACTATACA+CGG 0.584090 8_3:-66445462 Msa1303360:CDS
TATGCTTACAAGGGATACAA+AGG 0.595286 8_3:-66445430 Msa1303360:CDS
TCCGAAAACGAGAAGAGCGA+CGG 0.605899 8_3:+66445857 None:intergenic
ATCCGTGTATAGTAGAAACC+TGG 0.613139 8_3:+66445460 None:intergenic
GCGAGAGCGATCTCCTTGAT+CGG 0.617044 8_3:+66445879 None:intergenic
GGAACCCTAGGTATCATCAT+CGG 0.618807 8_3:-66445837 Msa1303360:CDS
ATTGCATATTATGCTTACAA+GGG 0.625358 8_3:-66445439 Msa1303360:CDS
AGAGCGATCTCCTTGATCGG+TGG 0.654102 8_3:+66445882 None:intergenic
AGAACCGATGATGATACCTA+GGG 0.654644 8_3:+66445833 None:intergenic
TATACATTAGATGCAACGCA+AGG 0.662693 8_3:+66445308 None:intergenic
ATGGCTTACAATCACGTCGG+CGG 0.675872 8_3:-66445807 Msa1303360:CDS
GATGATGGAAACATCATACA+CGG 0.676748 8_3:-66445916 Msa1303360:CDS
GTCGGCGGTGACACTGCTCA+CGG 0.677770 8_3:-66445792 Msa1303360:intron
ACTGGAGAAAACTATACAGG+AGG 0.682610 8_3:+66445388 None:intergenic
CTCATGGCTTACAATCACGT+CGG 0.683421 8_3:-66445810 Msa1303360:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGACTAATATTAATTATTTT+AGG - chr8_3:66445653-66445672 Msa1303360:intron 10.0%
!!! AGACTAATATTAATTATTTT+AGG - chr8_3:66445653-66445672 Msa1303360:intron 10.0%
!!! TTTGTTATTGAATGATTTAT+AGG - chr8_3:66445700-66445719 Msa1303360:intron 15.0%
!!! TTTGTTATTGAATGATTTAT+AGG - chr8_3:66445700-66445719 Msa1303360:intron 15.0%
!!! AATTGATTCAGAAAATTTCT+TGG - chr8_3:66445531-66445550 Msa1303360:intron 20.0%
!!! AATTGATTCAGAAAATTTCT+TGG - chr8_3:66445531-66445550 Msa1303360:intron 20.0%
! AGAAACTTAATTCTGAATCA+AGG + chr8_3:66445494-66445513 None:intergenic 25.0%
! ATTGCATATTATGCTTACAA+GGG - chr8_3:66445781-66445800 Msa1303360:intron 25.0%
! AAGATCAACATCTATACATA+AGG + chr8_3:66445863-66445882 None:intergenic 25.0%
! AGGCAGAACAAATAAAAAAA+AGG + chr8_3:66445895-66445914 None:intergenic 25.0%
! AGAAACTTAATTCTGAATCA+AGG + chr8_3:66445494-66445513 None:intergenic 25.0%
! ATTGCATATTATGCTTACAA+GGG - chr8_3:66445781-66445800 Msa1303360:intron 25.0%
! AAGATCAACATCTATACATA+AGG + chr8_3:66445863-66445882 None:intergenic 25.0%
! AGGCAGAACAAATAAAAAAA+AGG + chr8_3:66445895-66445914 None:intergenic 25.0%
TTTGAACTCTCTCAGATTAT+AGG + chr8_3:66445241-66445260 None:intergenic 30.0%
GATTGCATATTATGCTTACA+AGG - chr8_3:66445780-66445799 Msa1303360:intron 30.0%
GTATAGATGTTGATCTTCTA+TGG - chr8_3:66445866-66445885 Msa1303360:CDS 30.0%
AGCTGTAAATGTATTTGTTC+AGG + chr8_3:66446030-66446049 None:intergenic 30.0%
TTTGAACTCTCTCAGATTAT+AGG + chr8_3:66445241-66445260 None:intergenic 30.0%
GATTGCATATTATGCTTACA+AGG - chr8_3:66445780-66445799 Msa1303360:intron 30.0%
GTATAGATGTTGATCTTCTA+TGG - chr8_3:66445866-66445885 Msa1303360:CDS 30.0%
AGCTGTAAATGTATTTGTTC+AGG + chr8_3:66446030-66446049 None:intergenic 30.0%
TTCCATCATCATGTCTTCAT+CGG + chr8_3:66445294-66445313 None:intergenic 35.0%
!! GATGATGGAAACATCATACA+CGG - chr8_3:66445304-66445323 Msa1303360:three_prime_UTR 35.0%
AAGAACGATTGAAGGGAAAA+AGG + chr8_3:66445470-66445489 None:intergenic 35.0%
TCAAGGAAAGAACGATTGAA+GGG + chr8_3:66445477-66445496 None:intergenic 35.0%
ATCAAGGAAAGAACGATTGA+AGG + chr8_3:66445478-66445497 None:intergenic 35.0%
CTCAAGTCTAGTGAATTATC+TGG + chr8_3:66445629-66445648 None:intergenic 35.0%
TACCAGGTTTCTACTATACA+CGG - chr8_3:66445758-66445777 Msa1303360:intron 35.0%
TATGCTTACAAGGGATACAA+AGG - chr8_3:66445790-66445809 Msa1303360:intron 35.0%
TCTATACATAAGGATGCTAC+TGG + chr8_3:66445853-66445872 None:intergenic 35.0%
TATACATTAGATGCAACGCA+AGG + chr8_3:66445915-66445934 None:intergenic 35.0%
TTCCATCATCATGTCTTCAT+CGG + chr8_3:66445294-66445313 None:intergenic 35.0%
!! GATGATGGAAACATCATACA+CGG - chr8_3:66445304-66445323 Msa1303360:three_prime_UTR 35.0%
AAGAACGATTGAAGGGAAAA+AGG + chr8_3:66445470-66445489 None:intergenic 35.0%
TCAAGGAAAGAACGATTGAA+GGG + chr8_3:66445477-66445496 None:intergenic 35.0%
ATCAAGGAAAGAACGATTGA+AGG + chr8_3:66445478-66445497 None:intergenic 35.0%
CTCAAGTCTAGTGAATTATC+TGG + chr8_3:66445629-66445648 None:intergenic 35.0%
TACCAGGTTTCTACTATACA+CGG - chr8_3:66445758-66445777 Msa1303360:intron 35.0%
TATGCTTACAAGGGATACAA+AGG - chr8_3:66445790-66445809 Msa1303360:intron 35.0%
TCTATACATAAGGATGCTAC+TGG + chr8_3:66445853-66445872 None:intergenic 35.0%
TATACATTAGATGCAACGCA+AGG + chr8_3:66445915-66445934 None:intergenic 35.0%
TTCCGATGAAGACATGATGA+TGG - chr8_3:66445289-66445308 Msa1303360:three_prime_UTR 40.0%
GAATAACAAACCACCGATCA+AGG - chr8_3:66445328-66445347 Msa1303360:three_prime_UTR 40.0%
AGAACCGATGATGATACCTA+GGG + chr8_3:66445390-66445409 None:intergenic 40.0%
!! TATCATCATCGGTTCTCTCA+TGG - chr8_3:66445394-66445413 Msa1303360:exon 40.0%
AGGTCTCTTCTTTGCAATAC+TGG - chr8_3:66445720-66445739 Msa1303360:intron 40.0%
GGTCTCTTCTTTGCAATACT+GGG - chr8_3:66445721-66445740 Msa1303360:intron 40.0%
GGATCAATCTTGTTCATACC+AGG - chr8_3:66445742-66445761 Msa1303360:intron 40.0%
ATCCGTGTATAGTAGAAACC+TGG + chr8_3:66445763-66445782 None:intergenic 40.0%
ACTGGAGAAAACTATACAGG+AGG + chr8_3:66445835-66445854 None:intergenic 40.0%
GCTACTGGAGAAAACTATAC+AGG + chr8_3:66445838-66445857 None:intergenic 40.0%
TTCCGATGAAGACATGATGA+TGG - chr8_3:66445289-66445308 Msa1303360:three_prime_UTR 40.0%
GAATAACAAACCACCGATCA+AGG - chr8_3:66445328-66445347 Msa1303360:three_prime_UTR 40.0%
AGAACCGATGATGATACCTA+GGG + chr8_3:66445390-66445409 None:intergenic 40.0%
!! TATCATCATCGGTTCTCTCA+TGG - chr8_3:66445394-66445413 Msa1303360:exon 40.0%
AGGTCTCTTCTTTGCAATAC+TGG - chr8_3:66445720-66445739 Msa1303360:intron 40.0%
GGTCTCTTCTTTGCAATACT+GGG - chr8_3:66445721-66445740 Msa1303360:intron 40.0%
GGATCAATCTTGTTCATACC+AGG - chr8_3:66445742-66445761 Msa1303360:intron 40.0%
ATCCGTGTATAGTAGAAACC+TGG + chr8_3:66445763-66445782 None:intergenic 40.0%
ACTGGAGAAAACTATACAGG+AGG + chr8_3:66445835-66445854 None:intergenic 40.0%
GCTACTGGAGAAAACTATAC+AGG + chr8_3:66445838-66445857 None:intergenic 40.0%
GGAACCCTAGGTATCATCAT+CGG - chr8_3:66445383-66445402 Msa1303360:exon 45.0%
GAGAACCGATGATGATACCT+AGG + chr8_3:66445391-66445410 None:intergenic 45.0%
CTCATGGCTTACAATCACGT+CGG - chr8_3:66445410-66445429 Msa1303360:CDS 45.0%
CGATTGAAGGGAAAAAGGTG+TGG + chr8_3:66445465-66445484 None:intergenic 45.0%
GGAACCCTAGGTATCATCAT+CGG - chr8_3:66445383-66445402 Msa1303360:exon 45.0%
GAGAACCGATGATGATACCT+AGG + chr8_3:66445391-66445410 None:intergenic 45.0%
CTCATGGCTTACAATCACGT+CGG - chr8_3:66445410-66445429 Msa1303360:CDS 45.0%
CGATTGAAGGGAAAAAGGTG+TGG + chr8_3:66445465-66445484 None:intergenic 45.0%
TCCGAAAACGAGAAGAGCGA+CGG + chr8_3:66445366-66445385 None:intergenic 50.0%
! CTTCTCGTTTTCGGAACCCT+AGG - chr8_3:66445371-66445390 Msa1303360:three_prime_UTR 50.0%
ATGGCTTACAATCACGTCGG+CGG - chr8_3:66445413-66445432 Msa1303360:CDS 50.0%
TCCGAAAACGAGAAGAGCGA+CGG + chr8_3:66445366-66445385 None:intergenic 50.0%
! CTTCTCGTTTTCGGAACCCT+AGG - chr8_3:66445371-66445390 Msa1303360:three_prime_UTR 50.0%
ATGGCTTACAATCACGTCGG+CGG - chr8_3:66445413-66445432 Msa1303360:CDS 50.0%
AGAGCGATCTCCTTGATCGG+TGG + chr8_3:66445341-66445360 None:intergenic 55.0%
GCGAGAGCGATCTCCTTGAT+CGG + chr8_3:66445344-66445363 None:intergenic 55.0%
! GCCGTCGCTCTTCTCGTTTT+CGG - chr8_3:66445362-66445381 Msa1303360:three_prime_UTR 55.0%
AGAGCGATCTCCTTGATCGG+TGG + chr8_3:66445341-66445360 None:intergenic 55.0%
GCGAGAGCGATCTCCTTGAT+CGG + chr8_3:66445344-66445363 None:intergenic 55.0%
! GCCGTCGCTCTTCTCGTTTT+CGG - chr8_3:66445362-66445381 Msa1303360:three_prime_UTR 55.0%
GTCGGCGGTGACACTGCTCA+CGG - chr8_3:66445428-66445447 Msa1303360:CDS 65.0%
GTCGGCGGTGACACTGCTCA+CGG - chr8_3:66445428-66445447 Msa1303360:CDS 65.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 66445181 66446061 66445181 ID=Msa1303360;Name=Msa1303360
chr8_3 mRNA 66445181 66446061 66445181 ID=Msa1303360-mRNA-1;Parent=Msa1303360;Name=Msa1303360-mRNA-1;_AED=0.00;_eAED=0.00;_QI=82|1|1|1|1|1|2|218|102
chr8_3 exon 66445181 66445520 66445181 ID=Msa1303360-mRNA-1:exon:20197;Parent=Msa1303360-mRNA-1
chr8_3 exon 66445793 66446061 66445793 ID=Msa1303360-mRNA-1:exon:20196;Parent=Msa1303360-mRNA-1
chr8_3 five_prime_UTR 66445980 66446061 66445980 ID=Msa1303360-mRNA-1:five_prime_utr;Parent=Msa1303360-mRNA-1
chr8_3 CDS 66445793 66445979 66445793 ID=Msa1303360-mRNA-1:cds;Parent=Msa1303360-mRNA-1
chr8_3 CDS 66445399 66445520 66445399 ID=Msa1303360-mRNA-1:cds;Parent=Msa1303360-mRNA-1
chr8_3 three_prime_UTR 66445181 66445398 66445181 ID=Msa1303360-mRNA-1:three_prime_utr;Parent=Msa1303360-mRNA-1
Gene Sequence

>Msa1303360

ATGTACGTAGATCACGCATTCTCGATTTCCGATGAAGACATGATGATGGAAACATCATACACGGCGAATAACAAACCACCGATCAAGGAGATCGCTCTCGCCGTCGCTCTTCTCGTTTTCGGAACCCTAGGTATCATCATCGGTTCTCTCATGGCTTACAATCACGTCGGCGGTGACACTGCTCACGGTCTCTTCTTTGCAATACTGGGATCAATCTTGTTCATACCAGGTTTCTACTATACACGGATTGCATATTATGCTTACAAGGGATACAAAGGCTTCTCTTTCTCTAACATACCTCCTGTATAG
Protein sequence

>Msa1303360

MYVDHAFSISDEDMMMETSYTANNKPPIKEIALAVALLVFGTLGIIIGSLMAYNHVGGDTAHGLFFAILGSILFIPGFYYTRIAYYAYKGYKGFSFSNIPPV*