AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene90872

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90872.t1 MTR_1g115230 84.483 58 9 0 3 60 51 108 5.64e-29 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene90872.t1 AT1G50380 75.000 60 15 0 1 60 56 115 1.30e-27 103
MS.gene90872.t1 AT1G50380 75.000 60 15 0 1 60 122 181 2.00e-27 102

Find 10 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGATGGATCATGGAACCTTT+TGG 0.349436 1.4:+87318135 None:intergenic
TGAGATAAGAGGAAGGATAA+AGG 0.377073 1.4:-87318264 MS.gene90872:CDS
GAACCAAGCAAATTGAAGAT+AGG 0.427218 1.4:-87318295 MS.gene90872:CDS
AAGCCTATCTTCAATTTGCT+TGG 0.435111 1.4:+87318292 None:intergenic
TACACCGATTCGGTCATGTC+AGG 0.514534 1.4:-87319092 None:intergenic
TAATACGACCCTTTGCGTAC+AGG 0.547949 1.4:+87318224 None:intergenic
CCGTATATCCGATAACCAAA+AGG 0.550075 1.4:-87318150 MS.gene90872:CDS
TAACTGCACCTGTACGCAAA+GGG 0.575768 1.4:-87318232 MS.gene90872:CDS
GATAAGAGGAAGGATAAAGG+AGG 0.605118 1.4:-87318261 MS.gene90872:CDS
ATAACTGCACCTGTACGCAA+AGG 0.628634 1.4:-87318233 MS.gene90872:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTACTATTATACGAAAAATT+TGG - chr1.4:87319015-87319034 MS.gene90872:intron 15.0%
!! TTTAGAAAAACTATAACAAA+CGG - chr1.4:87318618-87318637 MS.gene90872:intron 15.0%
!! AAACAGATTATTAAAACCAT+TGG + chr1.4:87318388-87318407 None:intergenic 20.0%
!! ATTATACGAAAAATTTGGAA+GGG - chr1.4:87319020-87319039 MS.gene90872:intron 20.0%
!! TATTATACGAAAAATTTGGA+AGG - chr1.4:87319019-87319038 MS.gene90872:intron 20.0%
!! TTAGAAAAACTATAACAAAC+GGG - chr1.4:87318619-87318638 MS.gene90872:intron 20.0%
!!! ATACACATTTTTCATTTTCT+AGG - chr1.4:87318902-87318921 MS.gene90872:intron 20.0%
! TCAAAAAAGTCGATCTAAAT+AGG - chr1.4:87318662-87318681 MS.gene90872:intron 25.0%
! TTTGAACTCATTGTACAAAT+GGG - chr1.4:87318748-87318767 MS.gene90872:intron 25.0%
AACGAAAACTAGTTACTGTT+AGG + chr1.4:87318328-87318347 None:intergenic 30.0%
CGATCTAAATAGGTTCAATA+TGG - chr1.4:87318672-87318691 MS.gene90872:intron 30.0%
GTTTGAACTCATTGTACAAA+TGG - chr1.4:87318747-87318766 MS.gene90872:intron 30.0%
!!! AGAAGGCTTTTGAAATTTGA+AGG - chr1.4:87318850-87318869 MS.gene90872:intron 30.0%
ATATATACACACGCTTCAGA+AGG - chr1.4:87318833-87318852 MS.gene90872:intron 35.0%
GAACCAAGCAAATTGAAGAT+AGG - chr1.4:87318924-87318943 MS.gene90872:intron 35.0%
GAATGTGTAATTCAATGCAC+AGG - chr1.4:87318258-87318277 MS.gene90872:CDS 35.0%
GCGTGTGTATATATAGCAAT+AGG + chr1.4:87318827-87318846 None:intergenic 35.0%
TACGAAAAATTTGGAAGGGA+AGG - chr1.4:87319024-87319043 MS.gene90872:intron 35.0%
TGAGATAAGAGGAAGGATAA+AGG - chr1.4:87318955-87318974 MS.gene90872:intron 35.0%
TGTAATTCAATGCACAGGTT+TGG - chr1.4:87318263-87318282 MS.gene90872:CDS 35.0%
! AAGCCTATCTTCAATTTGCT+TGG + chr1.4:87318930-87318949 None:intergenic 35.0%
! TTTTTGCTGAGATAAGAGGA+AGG - chr1.4:87318948-87318967 MS.gene90872:intron 35.0%
!! CCTTTTGGTTATCGGATATA+CGG + chr1.4:87319072-87319091 None:intergenic 35.0%
!! TCATGGAACCTTTTGGTTAT+CGG + chr1.4:87319080-87319099 None:intergenic 35.0%
CCGTATATCCGATAACCAAA+AGG - chr1.4:87319069-87319088 MS.gene90872:intron 40.0%
GAACGATCATGAAGAGCTTA+TGG - chr1.4:87318510-87318529 MS.gene90872:intron 40.0%
GATAAGAGGAAGGATAAAGG+AGG - chr1.4:87318958-87318977 MS.gene90872:intron 40.0%
! AGGCTTTTTGCTGAGATAAG+AGG - chr1.4:87318944-87318963 MS.gene90872:intron 40.0%
! ATGACTGTAACATGCTGACT+AGG - chr1.4:87318797-87318816 MS.gene90872:intron 40.0%
! TTCTAGAAGCTGAACCAGTT+CGG + chr1.4:87318305-87318324 None:intergenic 40.0%
AAGAGCAGTGAAAGCGAAAG+AGG + chr1.4:87318181-87318200 None:intergenic 45.0%
ATAACTGCACCTGTACGCAA+AGG - chr1.4:87318986-87319005 MS.gene90872:intron 45.0%
CTCACAAATGAACTCGCCAA+TGG - chr1.4:87318369-87318388 MS.gene90872:intron 45.0%
TAACTGCACCTGTACGCAAA+GGG - chr1.4:87318987-87319006 MS.gene90872:intron 45.0%
TAATACGACCCTTTGCGTAC+AGG + chr1.4:87318998-87319017 None:intergenic 45.0%
TCAGAATTTCCGAACCGAAC+TGG - chr1.4:87318288-87318307 MS.gene90872:CDS 45.0%
GAAGCTGAACCAGTTCGGTT+CGG + chr1.4:87318300-87318319 None:intergenic 50.0%
TCACAGTGTTGCAAGTTGCG+TGG + chr1.4:87318236-87318255 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 87318142 87319099 87318142 ID=MS.gene90872
chr1.4 mRNA 87318142 87319099 87318142 ID=MS.gene90872.t1;Parent=MS.gene90872
chr1.4 exon 87319093 87319099 87319093 ID=MS.gene90872.t1.exon1;Parent=MS.gene90872.t1
chr1.4 CDS 87319093 87319099 87319093 ID=cds.MS.gene90872.t1;Parent=MS.gene90872.t1
chr1.4 exon 87318142 87318317 87318142 ID=MS.gene90872.t1.exon2;Parent=MS.gene90872.t1
chr1.4 CDS 87318142 87318317 87318142 ID=cds.MS.gene90872.t1;Parent=MS.gene90872.t1
Gene Sequence

>MS.gene90872

ATGTCAGGTATCAATAATTCTATTTCATTATCTTATCCTCTTTCGCTTTCACTGCTCTTTCATTTATTATTAATTATTTATAAAATACGATCCACGCAACTTGCAACACTGTGAACGAATGTGTAATTCAATGCACAGGTTTGGTTTCAGAATTTCCGAACCGAACTGGTTCAGCTTCTAGAACCTAACAGTAACTAGTTTTCGTTTTAAGAACTCAACTGCTTCTACTCACAAATGAACTCGCCAATGGTTTTAATAATCTGTTTCGATTAAACAGCTTATTTTGTATAAGCGCAAGCTCTTATGCATAAGTTATTTCTATAAAATAAAGTCATATTGCTTACGTATATTCTATAAGTTGTTTTCACGAACGATCATGAAGAGCTTATGGAAATAAGCTGAAAACAGCTCATGAACGTCTCATTTGAAGCTTTCTTAAAAAATTATAGCAAAGCATGATACACTATAAAAATCTTTTTAGAAAAACTATAACAAACGGGCTGTATTTCAGTAGATAAGCTCAAAAAAGTCGATCTAAATAGGTTCAATATGGCATTGTTAAGTAAACACTATAGATTAGACACAACTAAACTGATCAAGCATATGTTTGAACTCATTGTACAAATGGGTAGAGACTCAATGACGTAGAGACTCAATGACTGTAACATGCTGACTAGGAAATCCTATTGCTATATATACACACGCTTCAGAAGGCTTTTGAAATTTGAAGGAGATTAATTCAAATCACTAGCATACTATTATACACATTTTTCATTTTCTAGGAACCAAGCAAATTGAAGATAGGCTTTTTGCTGAGATAAGAGGAAGGATAAAGGAGGAAGATATAACTGCACCTGTACGCAAAGGGTCGTATTACTATTATACGAAAAATTTGGAAGGGAAGGAGTATGTTCAACATTGTAGACGCCGTATATCCGATAACCAAAAGGTTCCATGA
Protein sequence

>MS.gene90872.t1

MSGTKQIEDRLFAEIRGRIKEEDITAPVRKGSYYYYTKNLEGKEYVQHCRRRISDNQKVP