AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1334710

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1334710 MtrunA17_Chr4g0060821 82.222 90 15 1 1 89 1 90 5.67e-45 139
Msa1334710 MtrunA17_Chr3g0092121 55.435 92 36 2 1 89 1 90 9.53e-29 99.0
Msa1334710 MtrunA17_Chr6g0460751 38.889 90 49 3 1 89 1 85 2.11e-12 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 43 sgRNAs with CRISPR-Local

Find 131 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTTTATTCGTGATTCTTCT+TGG 0.169086 8_4:-55218917 Msa1334710:CDS
ATTAAGCACAAAACTGAAAA+AGG 0.192325 8_4:-55218009 Msa1334710:three_prime_UTR
TTGTTTATGTATGGGATCTT+AGG 0.200401 8_4:-55218179 Msa1334710:three_prime_UTR
TCCATCCTCTCATTAATTCT+TGG 0.236814 8_4:+55218396 None:intergenic
CTCTCATTAATTCTTGGCTT+TGG 0.277804 8_4:+55218402 None:intergenic
TAGAAGAATTTACTTGTAAC+TGG 0.288724 8_4:+55218863 None:intergenic
AATTAATGAGAGGATGGATT+TGG 0.333806 8_4:-55218391 Msa1334710:CDS
AAATCCCCATTGTTTATGTA+TGG 0.334660 8_4:-55218188 Msa1334710:three_prime_UTR
CTCAATGATTATGCACCATC+TGG 0.362640 8_4:-55218366 Msa1334710:CDS
AGAGGAACTAACATTTAATC+AGG 0.392881 8_4:+55218299 None:intergenic
AAAAGGGTCCATATTCATAT+TGG 0.393272 8_4:-55217992 Msa1334710:three_prime_UTR
CAACTTGGACATCTTGCATA+AGG 0.415467 8_4:+55218592 None:intergenic
AATCAGGTTACACACCATTA+CGG 0.442297 8_4:+55218315 None:intergenic
ATAAATTGAGAACTAGCATA+TGG 0.454361 8_4:-55219010 Msa1334710:five_prime_UTR
AGATCCCATACATAAACAAT+GGG 0.456560 8_4:+55218183 None:intergenic
AATATATAGGTGGACGGTAG+AGG 0.459504 8_4:+55217959 None:intergenic
ACACACCATTACGGTGCTCT+TGG 0.466740 8_4:+55218324 None:intergenic
TATGCACCATCTGGGGCAAA+TGG 0.473723 8_4:-55218357 Msa1334710:CDS
GAGAAGGGTCATTGCAGTGC+AGG 0.473866 8_4:-55218959 Msa1334710:five_prime_UTR
CATTGCAGTGCAGGAATGGC+AGG 0.490014 8_4:-55218950 Msa1334710:exon
GGGTCATTGCAGTGCAGGAA+TGG 0.499077 8_4:-55218954 Msa1334710:exon
ATCATTGAAATTCTAGTACA+TGG 0.502495 8_4:+55218121 None:intergenic
ATAAAATAAGACAAAATCAA+TGG 0.507774 8_4:+55218067 None:intergenic
AATCCCCATTGTTTATGTAT+GGG 0.510722 8_4:-55218187 Msa1334710:three_prime_UTR
AAGACAAAATCAATGGCTGT+TGG 0.520940 8_4:+55218074 None:intergenic
TCAATGATTATGCACCATCT+GGG 0.530735 8_4:-55218365 Msa1334710:CDS
ATTTATGTATGATGAAAGAA+AGG 0.544291 8_4:-55218231 Msa1334710:three_prime_UTR
GCCAAGAATTAATGAGAGGA+TGG 0.546052 8_4:-55218397 Msa1334710:CDS
AAGATCCCATACATAAACAA+TGG 0.554557 8_4:+55218182 None:intergenic
ATATATAGGTGGACGGTAGA+GGG 0.556953 8_4:+55217960 None:intergenic
GTGTTACATGCAGGTTAAAG+TGG 0.557750 8_4:+55218036 None:intergenic
TAAATTGAGAACTAGCATAT+GGG 0.561490 8_4:-55219009 Msa1334710:five_prime_UTR
TACTCCGGAAAATACCCCTC+AGG 0.579089 8_4:-55218562 Msa1334710:intron
ACACTCCAAGAGCACCGTAA+TGG 0.580515 8_4:-55218329 Msa1334710:exon
TTAATGCTTGTGTTACATGC+AGG 0.582300 8_4:+55218027 None:intergenic
CCAAGTTGACCTAATTACTC+CGG 0.594810 8_4:-55218577 Msa1334710:CDS
CAAAGCCAAGAATTAATGAG+AGG 0.628754 8_4:-55218401 Msa1334710:CDS
TGACGACCATTTGCCCCAGA+TGG 0.633835 8_4:+55218351 None:intergenic
CAATGATTATGCACCATCTG+GGG 0.636327 8_4:-55218364 Msa1334710:CDS
TTAAGCATAGAAGATGTGAA+AGG 0.652061 8_4:+55218894 None:intergenic
ATTGAGAACTAGCATATGGG+AGG 0.656265 8_4:-55219006 Msa1334710:five_prime_UTR
GATCCCATACATAAACAATG+GGG 0.744720 8_4:+55218184 None:intergenic
AGTATCAAACTGTACCTGAG+GGG 0.746962 8_4:+55218548 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAAATAAGACAAAATCAA+TGG + chr8_4:55218963-55218982 None:intergenic 15.0%
!! ATAAAATAAGACAAAATCAA+TGG + chr8_4:55218963-55218982 None:intergenic 15.0%
!!! TTTGTGATGTTTTTTTAACA+TGG + chr8_4:55217981-55218000 None:intergenic 20.0%
!! AACAAGATTATATATGTTAC+AGG - chr8_4:55218570-55218589 Msa1334710:CDS 20.0%
!!! CTTAATATTGTTTTACATAG+AGG + chr8_4:55218749-55218768 None:intergenic 20.0%
!!! ATATATGAGTTTTATTGTAG+AGG - chr8_4:55218772-55218791 Msa1334710:intron 20.0%
!! ATTTATGTATGATGAAAGAA+AGG - chr8_4:55218796-55218815 Msa1334710:intron 20.0%
!!! TTTGTGATGTTTTTTTAACA+TGG + chr8_4:55217981-55218000 None:intergenic 20.0%
!! AACAAGATTATATATGTTAC+AGG - chr8_4:55218570-55218589 Msa1334710:CDS 20.0%
!!! CTTAATATTGTTTTACATAG+AGG + chr8_4:55218749-55218768 None:intergenic 20.0%
!!! ATATATGAGTTTTATTGTAG+AGG - chr8_4:55218772-55218791 Msa1334710:intron 20.0%
!! ATTTATGTATGATGAAAGAA+AGG - chr8_4:55218796-55218815 Msa1334710:intron 20.0%
! ATAAATTGAGAACTAGCATA+TGG - chr8_4:55218017-55218036 Msa1334710:three_prime_UTR 25.0%
! TAAATTGAGAACTAGCATAT+GGG - chr8_4:55218018-55218037 Msa1334710:three_prime_UTR 25.0%
! TAGAAGAATTTACTTGTAAC+TGG + chr8_4:55218167-55218186 None:intergenic 25.0%
! TACGTCTATATTTGAATTGA+CGG - chr8_4:55218219-55218238 Msa1334710:three_prime_UTR 25.0%
!! AGTCTTAGTCTTCTTATATA+TGG - chr8_4:55218384-55218403 Msa1334710:CDS 25.0%
! ATCATTGAAATTCTAGTACA+TGG + chr8_4:55218909-55218928 None:intergenic 25.0%
! ATTAAGCACAAAACTGAAAA+AGG - chr8_4:55219018-55219037 Msa1334710:five_prime_UTR 25.0%
! TTAAGCACAAAACTGAAAAA+GGG - chr8_4:55219019-55219038 Msa1334710:five_prime_UTR 25.0%
!! TTTTTGCACCAATATGAATA+TGG + chr8_4:55219046-55219065 None:intergenic 25.0%
! ATAAATTGAGAACTAGCATA+TGG - chr8_4:55218017-55218036 Msa1334710:three_prime_UTR 25.0%
! TAAATTGAGAACTAGCATAT+GGG - chr8_4:55218018-55218037 Msa1334710:three_prime_UTR 25.0%
! TAGAAGAATTTACTTGTAAC+TGG + chr8_4:55218167-55218186 None:intergenic 25.0%
! TACGTCTATATTTGAATTGA+CGG - chr8_4:55218219-55218238 Msa1334710:three_prime_UTR 25.0%
!! AGTCTTAGTCTTCTTATATA+TGG - chr8_4:55218384-55218403 Msa1334710:CDS 25.0%
! ATCATTGAAATTCTAGTACA+TGG + chr8_4:55218909-55218928 None:intergenic 25.0%
! ATTAAGCACAAAACTGAAAA+AGG - chr8_4:55219018-55219037 Msa1334710:five_prime_UTR 25.0%
! TTAAGCACAAAACTGAAAAA+GGG - chr8_4:55219019-55219038 Msa1334710:five_prime_UTR 25.0%
!! TTTTTGCACCAATATGAATA+TGG + chr8_4:55219046-55219065 None:intergenic 25.0%
TTAAGCATAGAAGATGTGAA+AGG + chr8_4:55218136-55218155 None:intergenic 30.0%
ATTTGAATTGACGGTGAATT+TGG - chr8_4:55218228-55218247 Msa1334710:three_prime_UTR 30.0%
TGTATTTCATGAAATCATGG+TGG + chr8_4:55218323-55218342 None:intergenic 30.0%
CGATGTATTTCATGAAATCA+TGG + chr8_4:55218326-55218345 None:intergenic 30.0%
GGAAAATTACATGCATGTTT+CGG + chr8_4:55218353-55218372 None:intergenic 30.0%
ATGGTATGTTTGTATTAAGC+AGG - chr8_4:55218403-55218422 Msa1334710:CDS 30.0%
TATTGAGAAAAACTTGCACT+TGG - chr8_4:55218597-55218616 Msa1334710:CDS 30.0%
! AATTAATGAGAGGATGGATT+TGG - chr8_4:55218636-55218655 Msa1334710:intron 30.0%
AGAGGAACTAACATTTAATC+AGG + chr8_4:55218731-55218750 None:intergenic 30.0%
AAATCCCCATTGTTTATGTA+TGG - chr8_4:55218839-55218858 Msa1334710:intron 30.0%
AATCCCCATTGTTTATGTAT+GGG - chr8_4:55218840-55218859 Msa1334710:intron 30.0%
AGATCCCATACATAAACAAT+GGG + chr8_4:55218847-55218866 None:intergenic 30.0%
AAGATCCCATACATAAACAA+TGG + chr8_4:55218848-55218867 None:intergenic 30.0%
TTGTTTATGTATGGGATCTT+AGG - chr8_4:55218848-55218867 Msa1334710:intron 30.0%
AAAAGGGTCCATATTCATAT+TGG - chr8_4:55219035-55219054 Msa1334710:five_prime_UTR 30.0%
! TTTTAACATGGAATGTCGAT+TGG + chr8_4:55217969-55217988 None:intergenic 30.0%
TTAAGCATAGAAGATGTGAA+AGG + chr8_4:55218136-55218155 None:intergenic 30.0%
ATTTGAATTGACGGTGAATT+TGG - chr8_4:55218228-55218247 Msa1334710:three_prime_UTR 30.0%
TGTATTTCATGAAATCATGG+TGG + chr8_4:55218323-55218342 None:intergenic 30.0%
CGATGTATTTCATGAAATCA+TGG + chr8_4:55218326-55218345 None:intergenic 30.0%
GGAAAATTACATGCATGTTT+CGG + chr8_4:55218353-55218372 None:intergenic 30.0%
ATGGTATGTTTGTATTAAGC+AGG - chr8_4:55218403-55218422 Msa1334710:CDS 30.0%
TATTGAGAAAAACTTGCACT+TGG - chr8_4:55218597-55218616 Msa1334710:CDS 30.0%
! AATTAATGAGAGGATGGATT+TGG - chr8_4:55218636-55218655 Msa1334710:intron 30.0%
AGAGGAACTAACATTTAATC+AGG + chr8_4:55218731-55218750 None:intergenic 30.0%
AAATCCCCATTGTTTATGTA+TGG - chr8_4:55218839-55218858 Msa1334710:intron 30.0%
AATCCCCATTGTTTATGTAT+GGG - chr8_4:55218840-55218859 Msa1334710:intron 30.0%
AGATCCCATACATAAACAAT+GGG + chr8_4:55218847-55218866 None:intergenic 30.0%
AAGATCCCATACATAAACAA+TGG + chr8_4:55218848-55218867 None:intergenic 30.0%
TTGTTTATGTATGGGATCTT+AGG - chr8_4:55218848-55218867 Msa1334710:intron 30.0%
AAAAGGGTCCATATTCATAT+TGG - chr8_4:55219035-55219054 Msa1334710:five_prime_UTR 30.0%
!!! CTAGAGCTTGTTTTTGAGAA+GGG - chr8_4:55218053-55218072 Msa1334710:three_prime_UTR 35.0%
CGTTTATTCGTGATTCTTCT+TGG - chr8_4:55218110-55218129 Msa1334710:three_prime_UTR 35.0%
GACTAAGACTAAGAAGATGA+AGG + chr8_4:55218374-55218393 None:intergenic 35.0%
CTCTCATTAATTCTTGGCTT+TGG + chr8_4:55218628-55218647 None:intergenic 35.0%
CAAAGCCAAGAATTAATGAG+AGG - chr8_4:55218626-55218645 Msa1334710:intron 35.0%
TCCATCCTCTCATTAATTCT+TGG + chr8_4:55218634-55218653 None:intergenic 35.0%
TCAATGATTATGCACCATCT+GGG - chr8_4:55218662-55218681 Msa1334710:intron 35.0%
AATCAGGTTACACACCATTA+CGG + chr8_4:55218715-55218734 None:intergenic 35.0%
GATCCCATACATAAACAATG+GGG + chr8_4:55218846-55218865 None:intergenic 35.0%
AAGACAAAATCAATGGCTGT+TGG + chr8_4:55218956-55218975 None:intergenic 35.0%
TTAATGCTTGTGTTACATGC+AGG + chr8_4:55219003-55219022 None:intergenic 35.0%
!!! CTAGAGCTTGTTTTTGAGAA+GGG - chr8_4:55218053-55218072 Msa1334710:three_prime_UTR 35.0%
CGTTTATTCGTGATTCTTCT+TGG - chr8_4:55218110-55218129 Msa1334710:three_prime_UTR 35.0%
GACTAAGACTAAGAAGATGA+AGG + chr8_4:55218374-55218393 None:intergenic 35.0%
CTCTCATTAATTCTTGGCTT+TGG + chr8_4:55218628-55218647 None:intergenic 35.0%
CAAAGCCAAGAATTAATGAG+AGG - chr8_4:55218626-55218645 Msa1334710:intron 35.0%
TCCATCCTCTCATTAATTCT+TGG + chr8_4:55218634-55218653 None:intergenic 35.0%
TCAATGATTATGCACCATCT+GGG - chr8_4:55218662-55218681 Msa1334710:intron 35.0%
AATCAGGTTACACACCATTA+CGG + chr8_4:55218715-55218734 None:intergenic 35.0%
GATCCCATACATAAACAATG+GGG + chr8_4:55218846-55218865 None:intergenic 35.0%
AAGACAAAATCAATGGCTGT+TGG + chr8_4:55218956-55218975 None:intergenic 35.0%
TTAATGCTTGTGTTACATGC+AGG + chr8_4:55219003-55219022 None:intergenic 35.0%
ATTGAGAACTAGCATATGGG+AGG - chr8_4:55218021-55218040 Msa1334710:three_prime_UTR 40.0%
CCTTCTCAAAAACAAGCTCT+AGG + chr8_4:55218055-55218074 None:intergenic 40.0%
!!! CCTAGAGCTTGTTTTTGAGA+AGG - chr8_4:55218052-55218071 Msa1334710:three_prime_UTR 40.0%
TGAATTGACGGTGAATTTGG+TGG - chr8_4:55218231-55218250 Msa1334710:three_prime_UTR 40.0%
CAACTTGGACATCTTGCATA+AGG + chr8_4:55218438-55218457 None:intergenic 40.0%
! CCAAGTTGACCTAATTACTC+CGG - chr8_4:55218450-55218469 Msa1334710:intron 40.0%
! GGGTATTTTCCGGAGTAATT+AGG + chr8_4:55218462-55218481 None:intergenic 40.0%
AGTATCAAACTGTACCTGAG+GGG + chr8_4:55218482-55218501 None:intergenic 40.0%
GAGTATCAAACTGTACCTGA+GGG + chr8_4:55218483-55218502 None:intergenic 40.0%
! AGAGTATCAAACTGTACCTG+AGG + chr8_4:55218484-55218503 None:intergenic 40.0%
GCCAAGAATTAATGAGAGGA+TGG - chr8_4:55218630-55218649 Msa1334710:intron 40.0%
CTCAATGATTATGCACCATC+TGG - chr8_4:55218661-55218680 Msa1334710:intron 40.0%
CAATGATTATGCACCATCTG+GGG - chr8_4:55218663-55218682 Msa1334710:intron 40.0%
GTGTTACATGCAGGTTAAAG+TGG + chr8_4:55218994-55219013 None:intergenic 40.0%
ATTGAGAACTAGCATATGGG+AGG - chr8_4:55218021-55218040 Msa1334710:three_prime_UTR 40.0%
CCTTCTCAAAAACAAGCTCT+AGG + chr8_4:55218055-55218074 None:intergenic 40.0%
!!! CCTAGAGCTTGTTTTTGAGA+AGG - chr8_4:55218052-55218071 Msa1334710:three_prime_UTR 40.0%
TGAATTGACGGTGAATTTGG+TGG - chr8_4:55218231-55218250 Msa1334710:three_prime_UTR 40.0%
CAACTTGGACATCTTGCATA+AGG + chr8_4:55218438-55218457 None:intergenic 40.0%
! CCAAGTTGACCTAATTACTC+CGG - chr8_4:55218450-55218469 Msa1334710:intron 40.0%
! GGGTATTTTCCGGAGTAATT+AGG + chr8_4:55218462-55218481 None:intergenic 40.0%
AGTATCAAACTGTACCTGAG+GGG + chr8_4:55218482-55218501 None:intergenic 40.0%
GAGTATCAAACTGTACCTGA+GGG + chr8_4:55218483-55218502 None:intergenic 40.0%
! AGAGTATCAAACTGTACCTG+AGG + chr8_4:55218484-55218503 None:intergenic 40.0%
GCCAAGAATTAATGAGAGGA+TGG - chr8_4:55218630-55218649 Msa1334710:intron 40.0%
CTCAATGATTATGCACCATC+TGG - chr8_4:55218661-55218680 Msa1334710:intron 40.0%
CAATGATTATGCACCATCTG+GGG - chr8_4:55218663-55218682 Msa1334710:intron 40.0%
GTGTTACATGCAGGTTAAAG+TGG + chr8_4:55218994-55219013 None:intergenic 40.0%
CCGGAGTAATTAGGTCAACT+TGG + chr8_4:55218453-55218472 None:intergenic 45.0%
!!! TGTACCTGAGGGGTATTTTC+CGG + chr8_4:55218472-55218491 None:intergenic 45.0%
CCGGAGTAATTAGGTCAACT+TGG + chr8_4:55218453-55218472 None:intergenic 45.0%
!!! TGTACCTGAGGGGTATTTTC+CGG + chr8_4:55218472-55218491 None:intergenic 45.0%
TACTCCGGAAAATACCCCTC+AGG - chr8_4:55218465-55218484 Msa1334710:intron 50.0%
! TATGCACCATCTGGGGCAAA+TGG - chr8_4:55218670-55218689 Msa1334710:intron 50.0%
!! ACACTCCAAGAGCACCGTAA+TGG - chr8_4:55218698-55218717 Msa1334710:intron 50.0%
ACACACCATTACGGTGCTCT+TGG + chr8_4:55218706-55218725 None:intergenic 50.0%
TACTCCGGAAAATACCCCTC+AGG - chr8_4:55218465-55218484 Msa1334710:intron 50.0%
! TATGCACCATCTGGGGCAAA+TGG - chr8_4:55218670-55218689 Msa1334710:intron 50.0%
!! ACACTCCAAGAGCACCGTAA+TGG - chr8_4:55218698-55218717 Msa1334710:intron 50.0%
ACACACCATTACGGTGCTCT+TGG + chr8_4:55218706-55218725 None:intergenic 50.0%
GAGAAGGGTCATTGCAGTGC+AGG - chr8_4:55218068-55218087 Msa1334710:three_prime_UTR 55.0%
GGGTCATTGCAGTGCAGGAA+TGG - chr8_4:55218073-55218092 Msa1334710:three_prime_UTR 55.0%
CATTGCAGTGCAGGAATGGC+AGG - chr8_4:55218077-55218096 Msa1334710:three_prime_UTR 55.0%
TGACGACCATTTGCCCCAGA+TGG + chr8_4:55218679-55218698 None:intergenic 55.0%
GAGAAGGGTCATTGCAGTGC+AGG - chr8_4:55218068-55218087 Msa1334710:three_prime_UTR 55.0%
GGGTCATTGCAGTGCAGGAA+TGG - chr8_4:55218073-55218092 Msa1334710:three_prime_UTR 55.0%
CATTGCAGTGCAGGAATGGC+AGG - chr8_4:55218077-55218096 Msa1334710:three_prime_UTR 55.0%
TGACGACCATTTGCCCCAGA+TGG + chr8_4:55218679-55218698 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_4 gene 55217969 55219080 55217969 ID=Msa1334710;Name=Msa1334710
chr8_4 mRNA 55217969 55219080 55217969 ID=Msa1334710-mRNA-1;Parent=Msa1334710;Name=Msa1334710-mRNA-1;_AED=0.08;_eAED=0.08;_QI=123|1|1|1|1|1|3|363|89
chr8_4 exon 55217969 55218457 55217969 ID=Msa1334710-mRNA-1:exon:17283;Parent=Msa1334710-mRNA-1
chr8_4 exon 55218563 55218624 55218563 ID=Msa1334710-mRNA-1:exon:17282;Parent=Msa1334710-mRNA-1
chr8_4 exon 55218876 55219080 55218876 ID=Msa1334710-mRNA-1:exon:17281;Parent=Msa1334710-mRNA-1
chr8_4 five_prime_UTR 55218958 55219080 55218958 ID=Msa1334710-mRNA-1:five_prime_utr;Parent=Msa1334710-mRNA-1
chr8_4 CDS 55218876 55218957 55218876 ID=Msa1334710-mRNA-1:cds;Parent=Msa1334710-mRNA-1
chr8_4 CDS 55218563 55218624 55218563 ID=Msa1334710-mRNA-1:cds;Parent=Msa1334710-mRNA-1
chr8_4 CDS 55218332 55218457 55218332 ID=Msa1334710-mRNA-1:cds;Parent=Msa1334710-mRNA-1
chr8_4 three_prime_UTR 55217969 55218331 55217969 ID=Msa1334710-mRNA-1:three_prime_utr;Parent=Msa1334710-mRNA-1
Gene Sequence

>Msa1334710

ATGGCAGGAACTTTCTTTCGTTTATTCGTGATTCTTCTTGGCCTTTCACATCTTCTATGCTTAACAGCAGTTCCAGTTACAAGAACTGAAAACCTTATGCAAGATGTCCAAGTTGACCTAATTACTCCGGAAAATACCCCTCAGGTTATTATTGAGAAAAACTTGCACTTGGAAGAGCCAAAGCCAAGAATTAATGAGAGGATGGATTTGGAACTCAATGATTATGCACCATCTGGGGCAAATGGTCGTCACACTCCAAGAGCACCGTAA
Protein sequence

>Msa1334710

MAGTFFRLFVILLGLSHLLCLTAVPVTRTENLMQDVQVDLITPENTPQVIIEKNLHLEEPKPRINERMDLELNDYAPSGANGRHTPRAP*