AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene57030

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 39 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACAAGTGCAGCAGTGTTAA+AGG 0.223332 5.2:-8741740 MS.gene57030:CDS
ATTTCACTTCTGAATCAAAA+TGG 0.248058 5.2:-8742915 MS.gene57030:CDS
GGATGAGGTGATCCTTTAAT+AGG 0.293488 5.2:+8742412 None:intergenic
AAGTGTAGCTCTGAGAATTT+TGG 0.302152 5.2:-8742675 MS.gene57030:CDS
TTCCAACTGATGAATATTCT+TGG 0.308006 5.2:-8742453 MS.gene57030:CDS
TCTCAGGTTTCTTCTTCGTT+TGG 0.320070 5.2:-8742732 MS.gene57030:intron
TATGGTCAGAAACCTATTAA+AGG 0.332994 5.2:-8742424 MS.gene57030:CDS
ACATCATTGTTGGGGATTAG+AGG 0.351620 5.2:+8742789 None:intergenic
TTATCAATAACATCATTGTT+GGG 0.369596 5.2:+8742780 None:intergenic
CCACAATCACTCCCTCTCTA+TGG 0.372520 5.2:-8741645 MS.gene57030:CDS
CTTATCAATAACATCATTGT+TGG 0.377214 5.2:+8742779 None:intergenic
GAATATTCTTGGAGGAAGTA+TGG 0.385581 5.2:-8742442 MS.gene57030:CDS
TGAGGTTGAAAAGAGTGGTT+AGG 0.422019 5.2:-8742507 MS.gene57030:CDS
AAAACATGTAGAAAGAGCTT+TGG 0.435280 5.2:-8741705 MS.gene57030:CDS
AATCAAAATGGAACAAGAAC+TGG 0.440484 5.2:-8742903 MS.gene57030:CDS
TAAGTAACTACCAACATAGA+TGG 0.441381 5.2:+8741677 None:intergenic
CTCCAAGAATATTCATCAGT+TGG 0.460948 5.2:+8742451 None:intergenic
TGAATTCAATTCAGTTCAAG+AGG 0.508819 5.2:+8741595 None:intergenic
ATGTTGGTAGTTACTTATGA+AGG 0.517787 5.2:-8741671 MS.gene57030:CDS
CTAGTTTCAGAAGTGGAAGT+AGG 0.526285 5.2:+8742846 None:intergenic
GAAAAGAGTGGTTAGGGTAG+CGG 0.527347 5.2:-8742500 MS.gene57030:CDS
TCAGAAGTGGAAGTAGGAGA+AGG 0.528280 5.2:+8742852 None:intergenic
GAGGTTGAAAAGAGTGGTTA+GGG 0.534113 5.2:-8742506 MS.gene57030:CDS
TATCAATAACATCATTGTTG+GGG 0.534993 5.2:+8742781 None:intergenic
CAACTGATGAATATTCTTGG+AGG 0.535323 5.2:-8742450 MS.gene57030:CDS
CCATAGAGAGGGAGTGATTG+TGG 0.545149 5.2:+8741645 None:intergenic
ACTGTCATTGTTCAAAGAAG+AGG 0.551193 5.2:-8742623 MS.gene57030:intron
TTTGGATGATCCATCTATGT+TGG 0.552858 5.2:-8741687 MS.gene57030:CDS
AGCGGCAATAAGCTTGAAGA+TGG 0.558574 5.2:-8742482 MS.gene57030:CDS
ATAATCAAGTACCTTGGATG+AGG 0.580943 5.2:+8742397 None:intergenic
GTGGAAGTAGGAGAAGGTAA+AGG 0.586033 5.2:+8742858 None:intergenic
GTAGACTCTAGTTTCAGAAG+TGG 0.596356 5.2:+8742839 None:intergenic
TTAAAGGATCACCTCATCCA+AGG 0.601665 5.2:-8742408 MS.gene57030:intron
ATTAGCTTCAACCATAGAGA+GGG 0.604376 5.2:+8741634 None:intergenic
AGAGGAGGAATCTGCTGCAA+CGG 0.605875 5.2:+8742807 None:intergenic
TATTAGCTTCAACCATAGAG+AGG 0.607872 5.2:+8741633 None:intergenic
TCATTGTTGGGGATTAGAGG+AGG 0.627905 5.2:+8742792 None:intergenic
TCTGCTGCAACGGAGTAGCA+TGG 0.640412 5.2:+8742817 None:intergenic
TCTTCTTTGAACAATGACAG+TGG 0.712784 5.2:+8742625 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATAAATTACTTAAGTTTTA+AGG + chr5.2:8742503-8742522 None:intergenic 10.0%
!!! TTAGTGATTTTTTTAATTAT+TGG - chr5.2:8742637-8742656 MS.gene57030:CDS 10.0%
!! ACTCAATTAAAATATTACTA+AGG + chr5.2:8742199-8742218 None:intergenic 15.0%
!!! AACACATATAAGAAATTTTT+TGG + chr5.2:8742240-8742259 None:intergenic 15.0%
!! ATCTTAAAAGTAGAAGTTTA+TGG + chr5.2:8742589-8742608 None:intergenic 20.0%
!! ATTTAGTACTCAATCTTAAT+AGG + chr5.2:8742677-8742696 None:intergenic 20.0%
!! GGAAATGATTCAAAATTAAA+CGG + chr5.2:8742282-8742301 None:intergenic 20.0%
!! TTAATTACTGTAGAAAAATG+AGG - chr5.2:8742032-8742051 MS.gene57030:intron 20.0%
!! TTATCAATAACATCATTGTT+GGG + chr5.2:8741780-8741799 None:intergenic 20.0%
!!! TTCAAACAATTTTCAAATAC+TGG + chr5.2:8742356-8742375 None:intergenic 20.0%
!!! TTTTTTTAATTATTGGTCCA+CGG - chr5.2:8742644-8742663 MS.gene57030:CDS 20.0%
! ACTATGTGCATAAAGAAAAA+GGG + chr5.2:8742303-8742322 None:intergenic 25.0%
! ATACTAATAATCAAGTACCT+TGG + chr5.2:8742169-8742188 None:intergenic 25.0%
! ATTTCACTTCTGAATCAAAA+TGG - chr5.2:8741642-8741661 MS.gene57030:CDS 25.0%
! CTTATCAATAACATCATTGT+TGG + chr5.2:8741781-8741800 None:intergenic 25.0%
! TATCAATAACATCATTGTTG+GGG + chr5.2:8741779-8741798 None:intergenic 25.0%
! TGGTAAATTACAAATCAAGA+TGG + chr5.2:8742329-8742348 None:intergenic 25.0%
!!! AATTTTCAAATACTGGCTTT+TGG + chr5.2:8742349-8742368 None:intergenic 25.0%
!!! AATTTTGGTAATGAAAAGTG+TGG - chr5.2:8741897-8741916 MS.gene57030:intron 25.0%
AAAAATGAGGTTGAAAAGAG+TGG - chr5.2:8742045-8742064 MS.gene57030:intron 30.0%
AAAACATGTAGAAAGAGCTT+TGG - chr5.2:8742852-8742871 MS.gene57030:CDS 30.0%
AATCAAAATGGAACAAGAAC+TGG - chr5.2:8741654-8741673 MS.gene57030:CDS 30.0%
CACTATGTGCATAAAGAAAA+AGG + chr5.2:8742304-8742323 None:intergenic 30.0%
TAAGATACGCAAATAACGTT+AGG - chr5.2:8742603-8742622 MS.gene57030:intron 30.0%
TAAGTAACTACCAACATAGA+TGG + chr5.2:8742883-8742902 None:intergenic 30.0%
TAGTACTCAATCTTAATAGG+TGG + chr5.2:8742674-8742693 None:intergenic 30.0%
TATGGTCAGAAACCTATTAA+AGG - chr5.2:8742133-8742152 MS.gene57030:intron 30.0%
TTCCAACTGATGAATATTCT+TGG - chr5.2:8742104-8742123 MS.gene57030:intron 30.0%
TTGAGTTATCACTTACTGTA+AGG - chr5.2:8742213-8742232 MS.gene57030:intron 30.0%
TTGTGTTTGTCGTTAGTATA+AGG + chr5.2:8742429-8742448 None:intergenic 30.0%
! CTTTTTCTTTATGCACATAG+TGG - chr5.2:8742302-8742321 MS.gene57030:intron 30.0%
! TGATTTTTCTTATTCCTCTC+AGG - chr5.2:8741809-8741828 MS.gene57030:intron 30.0%
!! ATGTTGGTAGTTACTTATGA+AGG - chr5.2:8742886-8742905 MS.gene57030:CDS 30.0%
ACGATGATTATTACTACTGC+AGG - chr5.2:8742788-8742807 MS.gene57030:intron 35.0%
ACTGTCATTGTTCAAAGAAG+AGG - chr5.2:8741934-8741953 MS.gene57030:intron 35.0%
ATAATCAAGTACCTTGGATG+AGG + chr5.2:8742163-8742182 None:intergenic 35.0%
ATCCAAGACAATGACCTAAT+TGG + chr5.2:8742550-8742569 None:intergenic 35.0%
CAACTGATGAATATTCTTGG+AGG - chr5.2:8742107-8742126 MS.gene57030:intron 35.0%
CGATGATTATTACTACTGCA+GGG - chr5.2:8742789-8742808 MS.gene57030:intron 35.0%
CTCCAAGAATATTCATCAGT+TGG + chr5.2:8742109-8742128 None:intergenic 35.0%
CTCGAAGAAAATGTCTATTG+TGG + chr5.2:8742386-8742405 None:intergenic 35.0%
GAATATTCTTGGAGGAAGTA+TGG - chr5.2:8742115-8742134 MS.gene57030:intron 35.0%
GATGATTATTACTACTGCAG+GGG - chr5.2:8742790-8742809 MS.gene57030:intron 35.0%
TCTTCTTTGAACAATGACAG+TGG + chr5.2:8741935-8741954 None:intergenic 35.0%
TTTGGATGATCCATCTATGT+TGG - chr5.2:8742870-8742889 MS.gene57030:CDS 35.0%
! ATTAGCTTCAACCATAGAGA+GGG + chr5.2:8742926-8742945 None:intergenic 35.0%
! TATTAGCTTCAACCATAGAG+AGG + chr5.2:8742927-8742946 None:intergenic 35.0%
!! TTTTAATTATTGGTCCACGG+TGG - chr5.2:8742647-8742666 MS.gene57030:CDS 35.0%
!!! AAGTGTAGCTCTGAGAATTT+TGG - chr5.2:8741882-8741901 MS.gene57030:intron 35.0%
AAACGAAGAAGAAACCTGAG+AGG + chr5.2:8741826-8741845 None:intergenic 40.0%
ACATCATTGTTGGGGATTAG+AGG + chr5.2:8741771-8741790 None:intergenic 40.0%
CACCAATTAGGTCATTGTCT+TGG - chr5.2:8742545-8742564 MS.gene57030:intron 40.0%
CTAGTTTCAGAAGTGGAAGT+AGG + chr5.2:8741714-8741733 None:intergenic 40.0%
GACAATGACCTAATTGGTGT+CGG + chr5.2:8742544-8742563 None:intergenic 40.0%
GAGGTTGAAAAGAGTGGTTA+GGG - chr5.2:8742051-8742070 MS.gene57030:intron 40.0%
GGATGAGGTGATCCTTTAAT+AGG + chr5.2:8742148-8742167 None:intergenic 40.0%
TACAAGTGCAGCAGTGTTAA+AGG - chr5.2:8742817-8742836 MS.gene57030:CDS 40.0%
TCTCAGGTTTCTTCTTCGTT+TGG - chr5.2:8741825-8741844 MS.gene57030:intron 40.0%
TGAGGTTGAAAAGAGTGGTT+AGG - chr5.2:8742050-8742069 MS.gene57030:intron 40.0%
TTAAAGGATCACCTCATCCA+AGG - chr5.2:8742149-8742168 MS.gene57030:intron 40.0%
! CTTTCTACATGTTTTCGTGC+TGG + chr5.2:8742847-8742866 None:intergenic 40.0%
! GTAGACTCTAGTTTCAGAAG+TGG + chr5.2:8741721-8741740 None:intergenic 40.0%
AGCGGCAATAAGCTTGAAGA+TGG - chr5.2:8742075-8742094 MS.gene57030:intron 45.0%
GAAAAGAGTGGTTAGGGTAG+CGG - chr5.2:8742057-8742076 MS.gene57030:intron 45.0%
GTGGAAGTAGGAGAAGGTAA+AGG + chr5.2:8741702-8741721 None:intergenic 45.0%
TCAGAAGTGGAAGTAGGAGA+AGG + chr5.2:8741708-8741727 None:intergenic 45.0%
TCATTGTTGGGGATTAGAGG+AGG + chr5.2:8741768-8741787 None:intergenic 45.0%
!!! GTAATTTATTTTTATTATTT+TGG - chr5.2:8742513-8742532 MS.gene57030:CDS 5.0%
AGAGGAGGAATCTGCTGCAA+CGG + chr5.2:8741753-8741772 None:intergenic 50.0%
CCACAATCACTCCCTCTCTA+TGG - chr5.2:8742912-8742931 MS.gene57030:CDS 50.0%
CCATAGAGAGGGAGTGATTG+TGG + chr5.2:8742915-8742934 None:intergenic 50.0%
TCTTAATAGGTGGTCCACCG+TGG + chr5.2:8742664-8742683 None:intergenic 50.0%
TGGTCGAACCGACACCAATT+AGG - chr5.2:8742533-8742552 MS.gene57030:intron 50.0%
TCTGCTGCAACGGAGTAGCA+TGG + chr5.2:8741743-8741762 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 8741610 8742969 8741610 ID=MS.gene57030
chr5.2 mRNA 8741610 8742969 8741610 ID=MS.gene57030.t1;Parent=MS.gene57030
chr5.2 exon 8742791 8742969 8742791 ID=MS.gene57030.t1.exon1;Parent=MS.gene57030.t1
chr5.2 CDS 8742791 8742969 8742791 ID=cds.MS.gene57030.t1;Parent=MS.gene57030.t1
chr5.2 exon 8742624 8742748 8742624 ID=MS.gene57030.t1.exon2;Parent=MS.gene57030.t1
chr5.2 CDS 8742624 8742748 8742624 ID=cds.MS.gene57030.t1;Parent=MS.gene57030.t1
chr5.2 exon 8742409 8742534 8742409 ID=MS.gene57030.t1.exon3;Parent=MS.gene57030.t1
chr5.2 CDS 8742409 8742534 8742409 ID=cds.MS.gene57030.t1;Parent=MS.gene57030.t1
chr5.2 exon 8741610 8741769 8741610 ID=MS.gene57030.t1.exon4;Parent=MS.gene57030.t1
chr5.2 CDS 8741610 8741769 8741610 ID=cds.MS.gene57030.t1;Parent=MS.gene57030.t1
Gene Sequence

>MS.gene57030

CTGATGTTGCTGTTTCAAAGTTTAAGAATGTTATTTCACTTCTGAATCAAAATGGAACAAGAACTGGTCATGCACGTTTCAGAAGAGCACCTTTACCTTCTCCTACTTCCACTTCTGAAACTAGAGTCTACCATGCTACTCCGTTGCAGCAGATTCCTCCTCTAATCCCCAACAATGATGTTATTGATAAGAATATCATTGATTTTTCTTATTCCTCTCAGGTTTCTTCTTCGTTTGGAAAGTCTTGTGTTTCTTCATGTTCGTTGAAGAGAAAGTGTAGCTCTGAGAATTTTGGTAATGAAAAGTGTGGTAGTTCATCTAGCCACTGTCATTGTTCAAAGAAGAGGTATATATGTAGCTCTCAAAATTCGTTTTATTTTTGTTCTTCTTTTTTGAGTTAATTACTTTATGTTAATTTGTTGTTAATTACTGTAGAAAAATGAGGTTGAAAAGAGTGGTTAGGGTAGCGGCAATAAGCTTGAAGATGGCTGATATTCCAACTGATGAATATTCTTGGAGGAAGTATGGTCAGAAACCTATTAAAGGATCACCTCATCCAAGGTACTTGATTATTAGTATTAAGCAACCTTAGTAATATTTTAATTGAGTTATCACTTACTGTAAGGACCAAAAAATTTCTTATATGTGTTACACTAGATTGCTCACTGACCGTTTAATTTTGAATCATTTCCCTTTTTCTTTATGCACATAGTGGACCATCTTGATTTGTAATTTACCAAAAGCCAGTATTTGAAAATTGTTTGAAACTTAAACCACAATAGACATTTTCTTCGAGAAGTAGAAGTTCACGATTGTCCTTATACTAACGACAAACACAAATGACTTGATTGATGCAAGTTCGTCAAAAACAAGAGAAATGAATTTATGTACCTTAAAACTTAAGTAATTTATTTTTATTATTTTGGTCGAACCGACACCAATTAGGTCATTGTCTTGGATGTAAGAATGAGAAAGACCATAAACTTCTACTTTTAAGATACGCAAATAACGTTAGGTGTTATAATGTTTAGTGATTTTTTTAATTATTGGTCCACGGTGGACCACCTATTAAGATTGAGTACTAAATTTAGAAAAAAAAAAATCATTATTATGCAGTGTTATTGAGTTAAGTTGATTTTGAATTGAGTAGTAATGAATACTAAGTTATCAATTTGTGAACGATGATTATTACTACTGCAGGGGTTATTACAAGTGCAGCAGTGTTAAAGGTTGTCCAGCACGAAAACATGTAGAAAGAGCTTTGGATGATCCATCTATGTTGGTAGTTACTTATGAAGGCGACCACAATCACTCCCTCTCTATGGTTGAAGCTAATAATCTCATCTTAGAATCCTCTTGA
Protein sequence

>MS.gene57030.t1

LMLLFQSLRMLFHFUIKMEQELVMHVSEEHLYLLLLPLLKLESTMLLRCSRFLLUSPTMMFLLRLESLVFLHVRURESVALRILVMKSVVVHLATVIVQRREKUGUKEWLGURQUAURWLIFQLMNILGGSMVRNLLKDHLIQGVITSAAVLKVVQHENMUKELWMIHLCWULLMKATTITPSLWLKLIISSUNPL