AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0560420

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0560420 MtrunA17_Chr4g0050461 100.000 147 0 0 1 147 1 147 8.09e-102 288
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0560420 AT5G64180.2 79.286 140 29 0 8 147 10 149 1.43e-69 207
Msa0560420 AT5G64180.1 79.286 140 29 0 8 147 10 149 1.43e-69 207

Find 33 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGCTTCGGCTTGTCGTTTCT+CGG 0.286319 4_1:+59717198 None:intergenic
TGATAATGATATTAAGCTTT+TGG 0.294840 4_1:-59716952 Msa0560420:CDS
ACGACTTCAACAACCTTTCT+CGG 0.324261 4_1:+59717471 None:intergenic
TTCTGTGTTAGTTAGTTCTC+TGG 0.381625 4_1:-59716757 Msa0560420:three_prime_UTR
AGCGCGAGCGGCGGCGGTGA+TGG 0.397256 4_1:+59717225 None:intergenic
GGAACGAGCGCGAGCGGCGG+CGG 0.415630 4_1:+59717219 None:intergenic
CGAAAGAAACTAAGAACAAC+AGG 0.416969 4_1:+59716865 None:intergenic
AGAGGTGTTTGAGTTGCATA+TGG 0.431731 4_1:-59717012 Msa0560420:CDS
AAAAGCAAAAGCAACGAGTA+TGG 0.443902 4_1:-59717512 Msa0560420:five_prime_UTR
GGCGTCGAGTTCTCGTTCTA+AGG 0.445222 4_1:+59717249 None:intergenic
TTTGATAGTGCGGGCTTGAT+CGG 0.446495 4_1:+59717294 None:intergenic
AAGTCGTTGAGAGATGGATT+CGG 0.469234 4_1:-59717455 Msa0560420:exon
AGCGGCTTTCTGTGACGCTT+CGG 0.485423 4_1:+59717183 None:intergenic
GCTATTATCCAAACGCTTGG+TGG 0.487329 4_1:-59716927 Msa0560420:CDS
GGCTTGATCGGCGGCGAGAG+AGG 0.490699 4_1:+59717306 None:intergenic
TTAGTTAGTTCTCTGGTGCA+AGG 0.496131 4_1:-59716750 Msa0560420:three_prime_UTR
ATCGAGGAGTTTGATAGTGC+GGG 0.500242 4_1:+59717285 None:intergenic
TTGTTGAAGTCGTTGAGAGA+TGG 0.503310 4_1:-59717461 Msa0560420:exon
CTCGGAACGAGCGCGAGCGG+CGG 0.505434 4_1:+59717216 None:intergenic
GCGAGCGGCGGCGGTGATGG+CGG 0.515286 4_1:+59717228 None:intergenic
GTCGTCGACGAAAACAGCTT+TGG 0.515580 4_1:+59717345 None:intergenic
CGGATTCGAAAGGAGAAAGA+TGG 0.528818 4_1:-59717435 Msa0560420:CDS
GAAGCTATTATCCAAACGCT+TGG 0.530020 4_1:-59716930 Msa0560420:CDS
AATTTGTGAGTGTGAAATGA+AGG 0.560801 4_1:-59716723 Msa0560420:three_prime_UTR
CGAGTTCTCGTTCTAAGGTG+TGG 0.570651 4_1:+59717254 None:intergenic
TTTCTCGGAACGAGCGCGAG+CGG 0.570899 4_1:+59717213 None:intergenic
AGGTGTGGACGCGTTGATCG+AGG 0.581765 4_1:+59717269 None:intergenic
TTCAAGAGCGCGTAATTCAG+CGG 0.601000 4_1:+59717165 None:intergenic
GATAGTGCGGGCTTGATCGG+CGG 0.606803 4_1:+59717297 None:intergenic
AATGAGAGAGAAACCGAGAA+AGG 0.626915 4_1:-59717484 Msa0560420:five_prime_UTR
GATCGAGGAGTTTGATAGTG+CGG 0.631084 4_1:+59717284 None:intergenic
TCGAAAGGAGAAAGATGGAG+CGG 0.658226 4_1:-59717430 Msa0560420:CDS
GAGATGGATTCGGATTCGAA+AGG 0.675806 4_1:-59717445 Msa0560420:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CGAAATTAGGATTAATAATT+AGG + chr4_1:59717131-59717150 None:intergenic 20.0%
!!! GGTTTCTGATTTTTTTAATA+CGG - chr4_1:59717192-59717211 Msa0560420:CDS 20.0%
!!! TGATAATGATATTAAGCTTT+TGG - chr4_1:59717276-59717295 Msa0560420:CDS 20.0%
!! CGAAATTAGGATTAATAATT+AGG + chr4_1:59717131-59717150 None:intergenic 20.0%
!!! GGTTTCTGATTTTTTTAATA+CGG - chr4_1:59717192-59717211 Msa0560420:CDS 20.0%
!!! TGATAATGATATTAAGCTTT+TGG - chr4_1:59717276-59717295 Msa0560420:CDS 20.0%
! CAATAACTCAATTCGAAATT+AGG + chr4_1:59717144-59717163 None:intergenic 25.0%
!!! TGATTTTTTTAATACGGTAG+AGG - chr4_1:59717198-59717217 Msa0560420:CDS 25.0%
! CAATAACTCAATTCGAAATT+AGG + chr4_1:59717144-59717163 None:intergenic 25.0%
!!! TGATTTTTTTAATACGGTAG+AGG - chr4_1:59717198-59717217 Msa0560420:CDS 25.0%
AGGTTAATAGTACTTACTTG+TGG + chr4_1:59717111-59717130 None:intergenic 30.0%
TGATTGGAGAAGTTAATTGA+TGG - chr4_1:59717171-59717190 Msa0560420:CDS 30.0%
!! AACAGGTTTTAGTGTTTTAC+AGG + chr4_1:59717349-59717368 None:intergenic 30.0%
AATTTGTGAGTGTGAAATGA+AGG - chr4_1:59717505-59717524 Msa0560420:five_prime_UTR 30.0%
AGGTTAATAGTACTTACTTG+TGG + chr4_1:59717111-59717130 None:intergenic 30.0%
TGATTGGAGAAGTTAATTGA+TGG - chr4_1:59717171-59717190 Msa0560420:CDS 30.0%
!! AACAGGTTTTAGTGTTTTAC+AGG + chr4_1:59717349-59717368 None:intergenic 30.0%
AATTTGTGAGTGTGAAATGA+AGG - chr4_1:59717505-59717524 Msa0560420:five_prime_UTR 30.0%
AAAAGCAAAAGCAACGAGTA+TGG - chr4_1:59716716-59716735 Msa0560420:three_prime_UTR 35.0%
GAGTTATTGTGATCTGTGAT+TGG - chr4_1:59717155-59717174 Msa0560420:CDS 35.0%
! TTAGTGTTTTACAGGAGATG+TGG + chr4_1:59717341-59717360 None:intergenic 35.0%
CGAAAGAAACTAAGAACAAC+AGG + chr4_1:59717366-59717385 None:intergenic 35.0%
! TTCTGTGTTAGTTAGTTCTC+TGG - chr4_1:59717471-59717490 Msa0560420:five_prime_UTR 35.0%
AAAAGCAAAAGCAACGAGTA+TGG - chr4_1:59716716-59716735 Msa0560420:three_prime_UTR 35.0%
GAGTTATTGTGATCTGTGAT+TGG - chr4_1:59717155-59717174 Msa0560420:CDS 35.0%
! TTAGTGTTTTACAGGAGATG+TGG + chr4_1:59717341-59717360 None:intergenic 35.0%
CGAAAGAAACTAAGAACAAC+AGG + chr4_1:59717366-59717385 None:intergenic 35.0%
! TTCTGTGTTAGTTAGTTCTC+TGG - chr4_1:59717471-59717490 Msa0560420:five_prime_UTR 35.0%
AATGAGAGAGAAACCGAGAA+AGG - chr4_1:59716744-59716763 Msa0560420:three_prime_UTR 40.0%
ACGACTTCAACAACCTTTCT+CGG + chr4_1:59716760-59716779 None:intergenic 40.0%
TTGTTGAAGTCGTTGAGAGA+TGG - chr4_1:59716767-59716786 Msa0560420:three_prime_UTR 40.0%
! AAGTCGTTGAGAGATGGATT+CGG - chr4_1:59716773-59716792 Msa0560420:three_prime_UTR 40.0%
!!! TGTGGTGTTTTCGAGTTCTT+TGG + chr4_1:59717093-59717112 None:intergenic 40.0%
!! AGAGGTGTTTGAGTTGCATA+TGG - chr4_1:59717216-59717235 Msa0560420:CDS 40.0%
GAAGCTATTATCCAAACGCT+TGG - chr4_1:59717298-59717317 Msa0560420:CDS 40.0%
! ATTCTTTTCCACCAAGCGTT+TGG + chr4_1:59717312-59717331 None:intergenic 40.0%
! TTAGTTAGTTCTCTGGTGCA+AGG - chr4_1:59717478-59717497 Msa0560420:five_prime_UTR 40.0%
AATGAGAGAGAAACCGAGAA+AGG - chr4_1:59716744-59716763 Msa0560420:three_prime_UTR 40.0%
ACGACTTCAACAACCTTTCT+CGG + chr4_1:59716760-59716779 None:intergenic 40.0%
TTGTTGAAGTCGTTGAGAGA+TGG - chr4_1:59716767-59716786 Msa0560420:three_prime_UTR 40.0%
! AAGTCGTTGAGAGATGGATT+CGG - chr4_1:59716773-59716792 Msa0560420:three_prime_UTR 40.0%
!!! TGTGGTGTTTTCGAGTTCTT+TGG + chr4_1:59717093-59717112 None:intergenic 40.0%
!! AGAGGTGTTTGAGTTGCATA+TGG - chr4_1:59717216-59717235 Msa0560420:CDS 40.0%
GAAGCTATTATCCAAACGCT+TGG - chr4_1:59717298-59717317 Msa0560420:CDS 40.0%
! ATTCTTTTCCACCAAGCGTT+TGG + chr4_1:59717312-59717331 None:intergenic 40.0%
! TTAGTTAGTTCTCTGGTGCA+AGG - chr4_1:59717478-59717497 Msa0560420:five_prime_UTR 40.0%
! GAGATGGATTCGGATTCGAA+AGG - chr4_1:59716783-59716802 Msa0560420:three_prime_UTR 45.0%
CGGATTCGAAAGGAGAAAGA+TGG - chr4_1:59716793-59716812 Msa0560420:three_prime_UTR 45.0%
TCGAAAGGAGAAAGATGGAG+CGG - chr4_1:59716798-59716817 Msa0560420:three_prime_UTR 45.0%
!! TTTGATAGTGCGGGCTTGAT+CGG + chr4_1:59716937-59716956 None:intergenic 45.0%
!! ATCGAGGAGTTTGATAGTGC+GGG + chr4_1:59716946-59716965 None:intergenic 45.0%
!! GATCGAGGAGTTTGATAGTG+CGG + chr4_1:59716947-59716966 None:intergenic 45.0%
! TTCAAGAGCGCGTAATTCAG+CGG + chr4_1:59717066-59717085 None:intergenic 45.0%
GCTATTATCCAAACGCTTGG+TGG - chr4_1:59717301-59717320 Msa0560420:CDS 45.0%
! GAGATGGATTCGGATTCGAA+AGG - chr4_1:59716783-59716802 Msa0560420:three_prime_UTR 45.0%
CGGATTCGAAAGGAGAAAGA+TGG - chr4_1:59716793-59716812 Msa0560420:three_prime_UTR 45.0%
TCGAAAGGAGAAAGATGGAG+CGG - chr4_1:59716798-59716817 Msa0560420:three_prime_UTR 45.0%
!! TTTGATAGTGCGGGCTTGAT+CGG + chr4_1:59716937-59716956 None:intergenic 45.0%
!! ATCGAGGAGTTTGATAGTGC+GGG + chr4_1:59716946-59716965 None:intergenic 45.0%
!! GATCGAGGAGTTTGATAGTG+CGG + chr4_1:59716947-59716966 None:intergenic 45.0%
! TTCAAGAGCGCGTAATTCAG+CGG + chr4_1:59717066-59717085 None:intergenic 45.0%
GCTATTATCCAAACGCTTGG+TGG - chr4_1:59717301-59717320 Msa0560420:CDS 45.0%
GTCGTCGACGAAAACAGCTT+TGG + chr4_1:59716886-59716905 None:intergenic 50.0%
!! CGAGTTCTCGTTCTAAGGTG+TGG + chr4_1:59716977-59716996 None:intergenic 50.0%
GTCGTCGACGAAAACAGCTT+TGG + chr4_1:59716886-59716905 None:intergenic 50.0%
!! CGAGTTCTCGTTCTAAGGTG+TGG + chr4_1:59716977-59716996 None:intergenic 50.0%
! GGCGTCGAGTTCTCGTTCTA+AGG + chr4_1:59716982-59717001 None:intergenic 55.0%
! CGCTTCGGCTTGTCGTTTCT+CGG + chr4_1:59717033-59717052 None:intergenic 55.0%
AGCGGCTTTCTGTGACGCTT+CGG + chr4_1:59717048-59717067 None:intergenic 55.0%
! GGCGTCGAGTTCTCGTTCTA+AGG + chr4_1:59716982-59717001 None:intergenic 55.0%
! CGCTTCGGCTTGTCGTTTCT+CGG + chr4_1:59717033-59717052 None:intergenic 55.0%
AGCGGCTTTCTGTGACGCTT+CGG + chr4_1:59717048-59717067 None:intergenic 55.0%
GATAGTGCGGGCTTGATCGG+CGG + chr4_1:59716934-59716953 None:intergenic 60.0%
! AGGTGTGGACGCGTTGATCG+AGG + chr4_1:59716962-59716981 None:intergenic 60.0%
TTTCTCGGAACGAGCGCGAG+CGG + chr4_1:59717018-59717037 None:intergenic 60.0%
GATAGTGCGGGCTTGATCGG+CGG + chr4_1:59716934-59716953 None:intergenic 60.0%
! AGGTGTGGACGCGTTGATCG+AGG + chr4_1:59716962-59716981 None:intergenic 60.0%
TTTCTCGGAACGAGCGCGAG+CGG + chr4_1:59717018-59717037 None:intergenic 60.0%
GGCTTGATCGGCGGCGAGAG+AGG + chr4_1:59716925-59716944 None:intergenic 70.0%
GGCTTGATCGGCGGCGAGAG+AGG + chr4_1:59716925-59716944 None:intergenic 70.0%
CTCGGAACGAGCGCGAGCGG+CGG + chr4_1:59717015-59717034 None:intergenic 75.0%
CTCGGAACGAGCGCGAGCGG+CGG + chr4_1:59717015-59717034 None:intergenic 75.0%
!! GCGAGCGGCGGCGGTGATGG+CGG + chr4_1:59717003-59717022 None:intergenic 80.0%
! AGCGCGAGCGGCGGCGGTGA+TGG + chr4_1:59717006-59717025 None:intergenic 80.0%
! GGAACGAGCGCGAGCGGCGG+CGG + chr4_1:59717012-59717031 None:intergenic 80.0%
!! GCGAGCGGCGGCGGTGATGG+CGG + chr4_1:59717003-59717022 None:intergenic 80.0%
! AGCGCGAGCGGCGGCGGTGA+TGG + chr4_1:59717006-59717025 None:intergenic 80.0%
! GGAACGAGCGCGAGCGGCGG+CGG + chr4_1:59717012-59717031 None:intergenic 80.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 59716705 59717545 59716705 ID=Msa0560420;Name=Msa0560420
chr4_1 mRNA 59716705 59717545 59716705 ID=Msa0560420-mRNA-1;Parent=Msa0560420;Name=Msa0560420-mRNA-1;_AED=0.01;_eAED=0.01;_QI=81|1|1|1|1|1|2|212|147
chr4_1 exon 59716705 59717032 59716705 ID=Msa0560420-mRNA-1:exon:18550;Parent=Msa0560420-mRNA-1
chr4_1 exon 59717137 59717545 59717137 ID=Msa0560420-mRNA-1:exon:18549;Parent=Msa0560420-mRNA-1
chr4_1 five_prime_UTR 59717465 59717545 59717465 ID=Msa0560420-mRNA-1:five_prime_utr;Parent=Msa0560420-mRNA-1
chr4_1 CDS 59717137 59717464 59717137 ID=Msa0560420-mRNA-1:cds;Parent=Msa0560420-mRNA-1
chr4_1 CDS 59716917 59717032 59716917 ID=Msa0560420-mRNA-1:cds;Parent=Msa0560420-mRNA-1
chr4_1 three_prime_UTR 59716705 59716916 59716705 ID=Msa0560420-mRNA-1:three_prime_utr;Parent=Msa0560420-mRNA-1
Gene Sequence

>Msa0560420

ATGGATTCGGATTCGAAAGGAGAAAGATGGAGCGGAGCGATGACGAATCTATCAGAAATGAGTTCAAATCTCGAATCTCTTCAGAAGCTTCTTCTCACCAAAGCTGTTTTCGTCGACGACGATACTTTCTCTAAAGCCTCTCTCGCCGCCGATCAAGCCCGCACTATCAAACTCCTCGATCAACGCGTCCACACCTTAGAACGAGAACTCGACGCCGCCATCACCGCCGCCGCTCGCGCTCGTTCCGAGAAACGACAAGCCGAAGCGTCACAGAAAGCCGCTGAATTACGCGCTCTTGAAGTCACCAAAGAACTCGAAAACACCACAAAGGTGTTTGAGTTGCATATGGAAGAACTGCGTGCAAAACAAGAAGAAATTACGAAGCGTGATAATGATATTAAGCTTTTGGAAGCTATTATCCAAACGCTTGGTGGAAAAGAATGA
Protein sequence

>Msa0560420

MDSDSKGERWSGAMTNLSEMSSNLESLQKLLLTKAVFVDDDTFSKASLAADQARTIKLLDQRVHTLERELDAAITAAARARSEKRQAEASQKAAELRALEVTKELENTTKVFELHMEELRAKQEEITKRDNDIKLLEAIIQTLGGKE*