AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1218000

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1218000 MtrunA17_Chr7g0268821 79.592 98 17 1 45 142 10 104 6.99e-48 165
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1218000 AT4G03200.1 56.579 76 28 1 78 148 59 134 9.89e-20 85.5

Find 34 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCGATTAAGAAAGTGCTTT+TGG 0.316747 8_1:+80540237 None:intergenic
TTGTGATTTGAGAACAATTT+GGG 0.333882 8_1:+80539810 None:intergenic
TGATGATGGGTAAGTGCTTT+TGG 0.336880 8_1:+80540201 None:intergenic
ATTGGTAAACTTATGTTGAT+TGG 0.340026 8_1:+80540094 None:intergenic
TTTGTGATTTGAGAACAATT+TGG 0.353668 8_1:+80539809 None:intergenic
ATATTTAATTCAAGGTTGAT+TGG 0.368816 8_1:-80539942 Msa1218000:intron
GAATCGAAATTTCATTGTAT+TGG 0.374114 8_1:+80540178 None:intergenic
TTTCATTGTATTGGTGATGA+TGG 0.406118 8_1:+80540187 None:intergenic
GAGCGTGTTGAAGAAGATAA+GGG 0.471192 8_1:+80540051 None:intergenic
ACTTCCCAAGGTTCTATCAA+TGG 0.472933 8_1:-80540132 Msa1218000:CDS
TCAAGGTTGATTGGTATCCA+TGG 0.473689 8_1:-80539933 Msa1218000:intron
AGAATCTCTGCGGCGAGCTT+CGG 0.478485 8_1:+80539894 None:intergenic
TTCTCAAATCACAAAGATTG+AGG 0.482862 8_1:-80539801 Msa1218000:CDS
CAAGGTTGATTGGTATCCAT+GGG 0.484519 8_1:-80539932 Msa1218000:intron
TGAGCGTGTTGAAGAAGATA+AGG 0.488731 8_1:+80540050 None:intergenic
CTCGCATGTTACACTTCCCA+AGG 0.511194 8_1:-80540144 Msa1218000:CDS
GTTGCCATTGATAGAACCTT+GGG 0.521258 8_1:+80540128 None:intergenic
GAGGAGTGAATGATACGAAC+TGG 0.521806 8_1:+80540276 None:intergenic
TTGAGAACAATTTGGGAACA+AGG 0.523186 8_1:+80539817 None:intergenic
GTAACATGCGAGAATTTGAA+AGG 0.532424 8_1:+80540155 None:intergenic
TGAGAACAATTTGGGAACAA+GGG 0.541666 8_1:+80539818 None:intergenic
TTTGTTGTAGTGGTGATGAT+GGG 0.544824 8_1:-80539868 Msa1218000:CDS
CATTTCGATTTCAAACAACA+TGG 0.546309 8_1:+80540314 None:intergenic
TTCATTGTATTGGTGATGAT+GGG 0.550472 8_1:+80540188 None:intergenic
AAGATAAGGGCTTTGTTCTG+AGG 0.551809 8_1:+80540064 None:intergenic
TTGTTCTGAGGCAAGTCGAT+TGG 0.557034 8_1:+80540076 None:intergenic
GCGAAAGCTTCTTCACCCCA+TGG 0.568249 8_1:+80539916 None:intergenic
TAACATGCGAGAATTTGAAA+GGG 0.581325 8_1:+80540156 None:intergenic
TGTTGCCATTGATAGAACCT+TGG 0.598369 8_1:+80540127 None:intergenic
TGGTTATCATAGAACAAGGG+AGG 0.614383 8_1:+80540257 None:intergenic
GAACAATTTGGGAACAAGGG+AGG 0.640779 8_1:+80539821 None:intergenic
AAATCACAAAGATTGAGGTG+AGG 0.691557 8_1:-80539796 None:intergenic
AAGGTTGATTGGTATCCATG+GGG 0.724094 8_1:-80539931 Msa1218000:CDS
TGATACGAACTGGTTCAAAG+CGG 0.738006 8_1:+80540286 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGAAAAAAATAAATGAAAT+TGG + chr8_1:80540152-80540171 None:intergenic 10.0%
!! AAAATAAATGAAATTGGTGA+AGG + chr8_1:80540146-80540165 None:intergenic 20.0%
!!! ATATTTAATTCAAGGTTGAT+TGG - chr8_1:80540212-80540231 Msa1218000:CDS 20.0%
!! AACATGATTTCGATTTTGAA+TGG + chr8_1:80539817-80539836 None:intergenic 25.0%
!!! TTTTGGTTATCATAGAACAA+GGG + chr8_1:80539903-80539922 None:intergenic 25.0%
! GAATCGAAATTTCATTGTAT+TGG + chr8_1:80539979-80539998 None:intergenic 25.0%
! ATTGGTAAACTTATGTTGAT+TGG + chr8_1:80540063-80540082 None:intergenic 25.0%
! TTGTGATTTGAGAACAATTT+GGG + chr8_1:80540347-80540366 None:intergenic 25.0%
! TTTGTGATTTGAGAACAATT+TGG + chr8_1:80540348-80540367 None:intergenic 25.0%
! TCGATTTTGAATGGAAGAAT+TGG + chr8_1:80539808-80539827 None:intergenic 30.0%
CATTTCGATTTCAAACAACA+TGG + chr8_1:80539843-80539862 None:intergenic 30.0%
!! CTTTTGGTTATCATAGAACA+AGG + chr8_1:80539904-80539923 None:intergenic 30.0%
!! TTCATTGTATTGGTGATGAT+GGG + chr8_1:80539969-80539988 None:intergenic 30.0%
!! TTTCATTGTATTGGTGATGA+TGG + chr8_1:80539970-80539989 None:intergenic 30.0%
TAACATGCGAGAATTTGAAA+GGG + chr8_1:80540001-80540020 None:intergenic 30.0%
!! AGATTCTCTTTTTGTTGTAG+TGG - chr8_1:80540276-80540295 Msa1218000:CDS 30.0%
TTCTCAAATCACAAAGATTG+AGG - chr8_1:80540353-80540372 Msa1218000:CDS 30.0%
!!! AGCGATTAAGAAAGTGCTTT+TGG + chr8_1:80539920-80539939 None:intergenic 35.0%
GTAACATGCGAGAATTTGAA+AGG + chr8_1:80540002-80540021 None:intergenic 35.0%
ATTGGTGAAGGATTAGATAC+AGG + chr8_1:80540134-80540153 None:intergenic 35.0%
CAACAAAAAGAGAATCTCTG+CGG + chr8_1:80540273-80540292 None:intergenic 35.0%
!! TTTTGTTGTAGTGGTGATGA+TGG - chr8_1:80540285-80540304 Msa1218000:CDS 35.0%
! TTTGTTGTAGTGGTGATGAT+GGG - chr8_1:80540286-80540305 Msa1218000:CDS 35.0%
TGAGAACAATTTGGGAACAA+GGG + chr8_1:80540339-80540358 None:intergenic 35.0%
TTGAGAACAATTTGGGAACA+AGG + chr8_1:80540340-80540359 None:intergenic 35.0%
! TGATACGAACTGGTTCAAAG+CGG + chr8_1:80539871-80539890 None:intergenic 40.0%
TGGTTATCATAGAACAAGGG+AGG + chr8_1:80539900-80539919 None:intergenic 40.0%
!!! TGATGATGGGTAAGTGCTTT+TGG + chr8_1:80540299-80540318 None:intergenic 40.0%
ACTTCCCAAGGTTCTATCAA+TGG - chr8_1:80540022-80540041 Msa1218000:intron 40.0%
GTTGCCATTGATAGAACCTT+GGG + chr8_1:80540029-80540048 None:intergenic 40.0%
TGTTGCCATTGATAGAACCT+TGG + chr8_1:80540030-80540049 None:intergenic 40.0%
!! AAGATAAGGGCTTTGTTCTG+AGG + chr8_1:80540093-80540112 None:intergenic 40.0%
GAGCGTGTTGAAGAAGATAA+GGG + chr8_1:80540106-80540125 None:intergenic 40.0%
TGAGCGTGTTGAAGAAGATA+AGG + chr8_1:80540107-80540126 None:intergenic 40.0%
! TCAAGGTTGATTGGTATCCA+TGG - chr8_1:80540221-80540240 Msa1218000:CDS 40.0%
! CAAGGTTGATTGGTATCCAT+GGG - chr8_1:80540222-80540241 Msa1218000:CDS 40.0%
! AAGGTTGATTGGTATCCATG+GGG - chr8_1:80540223-80540242 Msa1218000:CDS 40.0%
GAGGAGTGAATGATACGAAC+TGG + chr8_1:80539881-80539900 None:intergenic 45.0%
!! TTGTTCTGAGGCAAGTCGAT+TGG + chr8_1:80540081-80540100 None:intergenic 45.0%
GAACAATTTGGGAACAAGGG+AGG + chr8_1:80540336-80540355 None:intergenic 45.0%
!! ATTTATTTATATTTAATTCA+AGG - chr8_1:80540204-80540223 Msa1218000:CDS 5.0%
CTCGCATGTTACACTTCCCA+AGG - chr8_1:80540010-80540029 Msa1218000:intron 50.0%
GCGAAAGCTTCTTCACCCCA+TGG + chr8_1:80540241-80540260 None:intergenic 55.0%
AGAATCTCTGCGGCGAGCTT+CGG + chr8_1:80540263-80540282 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 80539798 80540378 80539798 ID=Msa1218000;Name=Msa1218000
chr8_1 mRNA 80539798 80540378 80539798 ID=Msa1218000-mRNA-1;Parent=Msa1218000;Name=Msa1218000-mRNA-1;_AED=0.22;_eAED=0.33;_QI=0|0|0|1|1|1|2|0|162
chr8_1 exon 80540043 80540378 80540043 ID=Msa1218000-mRNA-1:exon:28249;Parent=Msa1218000-mRNA-1
chr8_1 exon 80539798 80539950 80539798 ID=Msa1218000-mRNA-1:exon:28248;Parent=Msa1218000-mRNA-1
chr8_1 CDS 80540043 80540378 80540043 ID=Msa1218000-mRNA-1:cds;Parent=Msa1218000-mRNA-1
chr8_1 CDS 80539798 80539950 80539798 ID=Msa1218000-mRNA-1:cds;Parent=Msa1218000-mRNA-1
Gene Sequence

>Msa1218000

TTGAAATCCAATTCTTCCATTCAAAATCGAAATCATGTTCTTCCATGTTGTTTGAAATCGAAATGCAATTCCGCTTTGAACCAGTTCGTATCATTCACTCCTCCCTTGTTCTATGATAACCAAAAGCACTTTCTTAATCGCTTTTTCTATCATAACCAAAAGCACTTACCCATCATCACCAATACAATGAAATTTCGATTCCCTTTCAAATTCTCGCATGTTACACTTCCCAAGGTTCTATCAATGGCAACATCATCTCATTCCAATCAACATAAGTTTACCAATCGACTTGCCTCAGAACAAAGCCCTTATCTTCTTCAACACGCTCATAATCCTGTTGATTGGTATCCATGGGGTGAAGAAGCTTTCGCCGAAGCTCGCCGCAGAGATTCTCTTTTTGTTGTAGTGGTGATGATGGGTAAGTGCTTTTCGTATCATTCTCTCCTCCCTTGTTCCCAAATTGTTCTCAAATCACAAAGATTGAGGTGA
Protein sequence

>Msa1218000

LKSNSSIQNRNHVLPCCLKSKCNSALNQFVSFTPPLFYDNQKHFLNRFFYHNQKHLPIITNTMKFRFPFKFSHVTLPKVLSMATSSHSNQHKFTNRLASEQSPYLLQHAHNPVDWYPWGEEAFAEARRRDSLFVVVVMMGKCFSYHSLLPCSQIVLKSQRLR*