AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene006276

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene006276.t1 MTR_1g100960 100.000 111 0 0 1 111 1 111 7.15e-75 217
MS.gene006276.t1 MTR_6g053730 96.396 111 4 0 1 111 1 111 3.38e-72 210
MS.gene006276.t1 MTR_1g100960 100.000 101 0 0 1 101 1 101 6.71e-68 199
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene006276.t1 AT3G53740 80.180 111 22 0 1 111 1 111 1.86e-58 176
MS.gene006276.t1 AT3G53740 80.180 111 22 0 1 111 1 111 1.86e-58 176
MS.gene006276.t1 AT3G53740 80.180 111 22 0 1 111 1 111 1.86e-58 176
MS.gene006276.t1 AT2G37600 82.692 104 18 0 8 111 8 111 2.05e-56 171
MS.gene006276.t1 AT2G37600 82.692 104 18 0 8 111 8 111 2.05e-56 171
MS.gene006276.t1 AT5G02450 83.019 106 17 1 7 111 3 108 8.05e-56 169
MS.gene006276.t1 AT3G53740 72.072 111 22 1 1 111 1 102 3.04e-49 152

Find 36 sgRNAs with CRISPR-Local

Find 68 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAACCAGTACTTGGTTGTTT+AGG 0.306770 1.1:-72201095 None:intergenic
CTTCTTCTTTGCACGTTTGT+GGG 0.313110 1.1:-72201761 None:intergenic
TCTTCTTCTTTGCACGTTTG+TGG 0.365751 1.1:-72201762 None:intergenic
AAAAGACAAGAGGGCACTTA+AGG 0.398330 1.1:+72201717 MS.gene006276:CDS
TCCACGTCCTTCAGCTCGCA+AGG 0.427898 1.1:+72201166 MS.gene006276:CDS
TGCAGGGCTGGTGGTGGAGC+AGG 0.430321 1.1:+72201932 MS.gene006276:intron
AGCAGGAGATAAGAAGAAAT+AGG 0.434078 1.1:+72201949 MS.gene006276:CDS
CATCGTCACAAAGAAGGAAT+TGG 0.434230 1.1:+72201142 MS.gene006276:CDS
CCAAGTACTGGTTTGTTCGT+TGG 0.458873 1.1:+72201104 MS.gene006276:CDS
AAGGTTGCAAAGAGAAAGCT+TGG 0.461674 1.1:+72201736 MS.gene006276:CDS
CCAACGAACAAACCAGTACT+TGG 0.464574 1.1:-72201104 None:intergenic
AACCTCATTAGAGAGGTTGC+TGG 0.487721 1.1:+72201649 MS.gene006276:CDS
ATCACTGAGTTGCTCAAGGT+TGG 0.503868 1.1:+72201694 MS.gene006276:CDS
TCAATGTGCAGGGCTGGTGG+TGG 0.508415 1.1:+72201926 MS.gene006276:intron
AGGAGATGTCTAATGTCCTC+AGG 0.510350 1.1:+72201788 MS.gene006276:CDS
ACCTCATTAGAGAGGTTGCT+GGG 0.511316 1.1:+72201650 MS.gene006276:CDS
CCCTTGCGAGCTGAAGGACG+TGG 0.511446 1.1:-72201167 None:intergenic
CCACGTCCTTCAGCTCGCAA+GGG 0.521414 1.1:+72201167 MS.gene006276:CDS
AGGCCACATCGTCACAAAGA+AGG 0.551215 1.1:+72201136 MS.gene006276:CDS
GCTCCTAAACAACCAAGTAC+TGG 0.551611 1.1:+72201092 MS.gene006276:CDS
CACGTCCTTCAGCTCGCAAG+GGG 0.561496 1.1:+72201168 MS.gene006276:CDS
ATTCCTTCTTTGTGACGATG+TGG 0.577252 1.1:-72201139 None:intergenic
TTGTTCGTTGGATTGAACAA+AGG 0.583526 1.1:+72201116 MS.gene006276:CDS
TCAGTGATACGCTTCTCGTA+AGG 0.584616 1.1:-72201679 None:intergenic
ACCCAGCAACCTCTCTAATG+AGG 0.601885 1.1:-72201651 None:intergenic
TGTGAGGAACCTCATTAGAG+AGG 0.602916 1.1:+72201642 MS.gene006276:CDS
TCGTTCAGAAAACAAGCAAG+AGG 0.606732 1.1:+72201611 MS.gene006276:intron
ACGTGCAAAGAAGAAGAGAG+AGG 0.618868 1.1:+72201768 MS.gene006276:CDS
GCAAGAGGGTGCACTTTGTG+AGG 0.622900 1.1:+72201626 MS.gene006276:CDS
CTAATGTCCTCAGGAAGATG+AGG 0.627117 1.1:+72201797 MS.gene006276:CDS
CAAGGTTGGAAAAGACAAGA+GGG 0.628294 1.1:+72201708 MS.gene006276:CDS
GCGTATCACTGAGTTGCTCA+AGG 0.629950 1.1:+72201690 MS.gene006276:CDS
CGTTCAGAAAACAAGCAAGA+GGG 0.632672 1.1:+72201612 MS.gene006276:intron
TCAAGGTTGGAAAAGACAAG+AGG 0.663036 1.1:+72201707 MS.gene006276:CDS
GAACAAACCTCATCTTCCTG+AGG 0.694769 1.1:-72201804 None:intergenic
ACGTCCTTCAGCTCGCAAGG+GGG 0.706112 1.1:+72201169 MS.gene006276:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTTAAATCTAACATAAAA+TGG - chr1.1:72201237-72201256 None:intergenic 10.0%
!!! ATTTTATGTTAGATTTAAAT+TGG + chr1.1:72201236-72201255 MS.gene006276:intron 10.0%
!! AACGAATAAAAACAATCTTT+AGG - chr1.1:72201596-72201615 None:intergenic 20.0%
!! ACGAATAAAAACAATCTTTA+GGG - chr1.1:72201595-72201614 None:intergenic 20.0%
!!! AAATTGGAATTATTAGCTTA+AGG + chr1.1:72201252-72201271 MS.gene006276:intron 20.0%
!!! TTTGTTATTATTGTTATGCT+TGG + chr1.1:72201834-72201853 MS.gene006276:intron 20.0%
! AATAGAAGGAGAAATAATGT+TGG + chr1.1:72201477-72201496 MS.gene006276:intron 25.0%
! ATAGAAGGAGAAATAATGTT+GGG + chr1.1:72201478-72201497 MS.gene006276:intron 25.0%
! ATTAATTCATAAGCTTGTCA+AGG + chr1.1:72201385-72201404 MS.gene006276:intron 25.0%
! CATTATTTCATTCATTCCTA+TGG - chr1.1:72201526-72201545 None:intergenic 25.0%
! CGAATAAAAACAATCTTTAG+GGG - chr1.1:72201594-72201613 None:intergenic 25.0%
! GTTATTATGATAAACATTCC+CGG + chr1.1:72201863-72201882 MS.gene006276:intron 25.0%
! TTAAGAAAAAACTGCTTATG+AGG + chr1.1:72201412-72201431 MS.gene006276:intron 25.0%
! TTATGAGGATGATATTTATG+AGG + chr1.1:72201427-72201446 MS.gene006276:intron 25.0%
! TTATTGTTATGCTTGGTATT+TGG + chr1.1:72201841-72201860 MS.gene006276:intron 25.0%
!! TTAGATATTTTCAATGTGCA+GGG + chr1.1:72201916-72201935 MS.gene006276:intron 25.0%
!! TTTAGATATTTTCAATGTGC+AGG + chr1.1:72201915-72201934 MS.gene006276:intron 25.0%
CTTTGTATTAAGGATCTGTT+TGG + chr1.1:72201311-72201330 MS.gene006276:intron 30.0%
TAGGGAGATATATGAATAGA+AGG + chr1.1:72201463-72201482 MS.gene006276:intron 30.0%
TATGCTCGTACTTTGTATTA+AGG + chr1.1:72201301-72201320 MS.gene006276:intron 30.0%
TATTAAGGATCTGTTTGGAT+TGG + chr1.1:72201316-72201335 MS.gene006276:intron 30.0%
TATTTCATTCATTCCTATGG+TGG - chr1.1:72201523-72201542 None:intergenic 30.0%
! ATGAGGATGACATTTTTGTT+AGG + chr1.1:72201444-72201463 MS.gene006276:intron 30.0%
! TGAGGATGACATTTTTGTTA+GGG + chr1.1:72201445-72201464 MS.gene006276:intron 30.0%
! TTTTTGCATTCTGTTCATCT+TGG + chr1.1:72201562-72201581 MS.gene006276:intron 30.0%
AAACCAGTACTTGGTTGTTT+AGG - chr1.1:72201098-72201117 None:intergenic 35.0%
ATACACTATCTATCCACCAT+AGG + chr1.1:72201507-72201526 MS.gene006276:intron 35.0%
CAATAACAAGAACATGTTCC+GGG - chr1.1:72201884-72201903 None:intergenic 35.0%
CCAATAACAAGAACATGTTC+CGG - chr1.1:72201885-72201904 None:intergenic 35.0%
TTGTTCGTTGGATTGAACAA+AGG + chr1.1:72201116-72201135 MS.gene006276:CDS 35.0%
AAGGTTGCAAAGAGAAAGCT+TGG + chr1.1:72201736-72201755 MS.gene006276:CDS 40.0%
ATTCCTTCTTTGTGACGATG+TGG - chr1.1:72201142-72201161 None:intergenic 40.0%
CAAGGTTGGAAAAGACAAGA+GGG + chr1.1:72201708-72201727 MS.gene006276:CDS 40.0%
CATCGTCACAAAGAAGGAAT+TGG + chr1.1:72201142-72201161 MS.gene006276:CDS 40.0%
CATTCTGTTCATCTTGGATG+TGG + chr1.1:72201568-72201587 MS.gene006276:intron 40.0%
CGTTCAGAAAACAAGCAAGA+GGG + chr1.1:72201612-72201631 MS.gene006276:intron 40.0%
CTTCTTCTTTGCACGTTTGT+GGG - chr1.1:72201764-72201783 None:intergenic 40.0%
TCAAGGTTGGAAAAGACAAG+AGG + chr1.1:72201707-72201726 MS.gene006276:CDS 40.0%
TCGTTCAGAAAACAAGCAAG+AGG + chr1.1:72201611-72201630 MS.gene006276:intron 40.0%
TCTTCTTCTTTGCACGTTTG+TGG - chr1.1:72201765-72201784 None:intergenic 40.0%
! ATATTTTCAATGTGCAGGGC+TGG + chr1.1:72201920-72201939 MS.gene006276:intron 40.0%
! CCGGAACATGTTCTTGTTAT+TGG + chr1.1:72201882-72201901 MS.gene006276:intron 40.0%
!! AAAAGACAAGAGGGCACTTA+AGG + chr1.1:72201717-72201736 MS.gene006276:CDS 40.0%
AACCTCATTAGAGAGGTTGC+TGG + chr1.1:72201649-72201668 MS.gene006276:CDS 45.0%
ACCTCATTAGAGAGGTTGCT+GGG + chr1.1:72201650-72201669 MS.gene006276:CDS 45.0%
ACGTGCAAAGAAGAAGAGAG+AGG + chr1.1:72201768-72201787 MS.gene006276:CDS 45.0%
AGGAGATGTCTAATGTCCTC+AGG + chr1.1:72201788-72201807 MS.gene006276:CDS 45.0%
ATCACTGAGTTGCTCAAGGT+TGG + chr1.1:72201694-72201713 MS.gene006276:CDS 45.0%
CCAACGAACAAACCAGTACT+TGG - chr1.1:72201107-72201126 None:intergenic 45.0%
CTAATGTCCTCAGGAAGATG+AGG + chr1.1:72201797-72201816 MS.gene006276:CDS 45.0%
GAACAAACCTCATCTTCCTG+AGG - chr1.1:72201807-72201826 None:intergenic 45.0%
GCTCCTAAACAACCAAGTAC+TGG + chr1.1:72201092-72201111 MS.gene006276:CDS 45.0%
TCAGTGATACGCTTCTCGTA+AGG - chr1.1:72201682-72201701 None:intergenic 45.0%
TGTGAGGAACCTCATTAGAG+AGG + chr1.1:72201642-72201661 MS.gene006276:CDS 45.0%
!! CCAAGTACTGGTTTGTTCGT+TGG + chr1.1:72201104-72201123 MS.gene006276:CDS 45.0%
ACCCAGCAACCTCTCTAATG+AGG - chr1.1:72201654-72201673 None:intergenic 50.0%
AGGCCACATCGTCACAAAGA+AGG + chr1.1:72201136-72201155 MS.gene006276:CDS 50.0%
GCGTATCACTGAGTTGCTCA+AGG + chr1.1:72201690-72201709 MS.gene006276:CDS 50.0%
! TTTTCAATGTGCAGGGCTGG+TGG + chr1.1:72201923-72201942 MS.gene006276:intron 50.0%
! GCAAGAGGGTGCACTTTGTG+AGG + chr1.1:72201626-72201645 MS.gene006276:CDS 55.0%
ACGTCCTTCAGCTCGCAAGG+GGG + chr1.1:72201169-72201188 MS.gene006276:CDS 60.0%
CACGTCCTTCAGCTCGCAAG+GGG + chr1.1:72201168-72201187 MS.gene006276:CDS 60.0%
CCACGTCCTTCAGCTCGCAA+GGG + chr1.1:72201167-72201186 MS.gene006276:CDS 60.0%
TCCACGTCCTTCAGCTCGCA+AGG + chr1.1:72201166-72201185 MS.gene006276:CDS 60.0%
! TCAATGTGCAGGGCTGGTGG+TGG + chr1.1:72201926-72201945 MS.gene006276:intron 60.0%
CCCTTGCGAGCTGAAGGACG+TGG - chr1.1:72201170-72201189 None:intergenic 65.0%
CTGACCCCCTTGCGAGCTGA+AGG - chr1.1:72201176-72201195 None:intergenic 65.0%
!! TGCAGGGCTGGTGGTGGAGC+AGG + chr1.1:72201932-72201951 MS.gene006276:intron 70.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 72201089 72201970 72201089 ID=MS.gene006276
chr1.1 mRNA 72201089 72201970 72201089 ID=MS.gene006276.t1;Parent=MS.gene006276
chr1.1 exon 72201089 72201190 72201089 ID=MS.gene006276.t1.exon1;Parent=MS.gene006276.t1
chr1.1 CDS 72201089 72201190 72201089 ID=cds.MS.gene006276.t1;Parent=MS.gene006276.t1
chr1.1 exon 72201619 72201818 72201619 ID=MS.gene006276.t1.exon2;Parent=MS.gene006276.t1
chr1.1 CDS 72201619 72201818 72201619 ID=cds.MS.gene006276.t1;Parent=MS.gene006276.t1
chr1.1 exon 72201937 72201970 72201937 ID=MS.gene006276.t1.exon3;Parent=MS.gene006276.t1
chr1.1 CDS 72201937 72201970 72201937 ID=cds.MS.gene006276.t1;Parent=MS.gene006276.t1
Gene Sequence

>MS.gene006276

ATGGCTCCTAAACAACCAAGTACTGGTTTGTTCGTTGGATTGAACAAAGGCCACATCGTCACAAAGAAGGAATTGGCTCCACGTCCTTCAGCTCGCAAGGGGGTCAGTCTCATTTTTTTCTCTTTTTTTTTTTTTTTTTTCAGATCCATTTTATGTTAGATTTAAATTGGAATTATTAGCTTAAGGTTTTAAGTAGTATCTGTTAAGCTTGTTATGCTCGTACTTTGTATTAAGGATCTGTTTGGATTGGCTTATTTTTTAGCTTATGCAAGTAAATAAGTTTTTTTGTACTATGTATTAATTCATAAGCTTGTCAAGGTAGTTTAAGAAAAAACTGCTTATGAGGATGATATTTATGAGGATGACATTTTTGTTAGGGAGATATATGAATAGAAGGAGAAATAATGTTGGGCAAATTATACACTATCTATCCACCATAGGAATGAATGAAATAATGTTGTAAGACGAAATGATTTTTGCATTCTGTTCATCTTGGATGTGGCCCCTAAAGATTGTTTTTATTCGTTCAGAAAACAAGCAAGAGGGTGCACTTTGTGAGGAACCTCATTAGAGAGGTTGCTGGGTTTGCTCCTTACGAGAAGCGTATCACTGAGTTGCTCAAGGTTGGAAAAGACAAGAGGGCACTTAAGGTTGCAAAGAGAAAGCTTGGAACCCACAAACGTGCAAAGAAGAAGAGAGAGGAGATGTCTAATGTCCTCAGGAAGATGAGGTTTGTTCTATGTTCTTTGTTATTATTGTTATGCTTGGTATTTGGTTATTATGATAAACATTCCCGGAACATGTTCTTGTTATTGGTTTTTGCTTATTTAGATATTTTCAATGTGCAGGGCTGGTGGTGGAGCAGGAGATAAGAAGAAATAG
Protein sequence

>MS.gene006276.t1

MAPKQPSTGLFVGLNKGHIVTKKELAPRPSARKGKTSKRVHFVRNLIREVAGFAPYEKRITELLKVGKDKRALKVAKRKLGTHKRAKKKREEMSNVLRKMRAGGGAGDKKK