AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0380015919.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015919.01.T01 MTR_3g079783 79.091 110 12 2 49 151 191 296 4.04e-52 167
MsG0380015919.01.T01 MTR_3g079783 57.746 71 28 1 1 69 50 120 3.57e-17 76.6
MsG0380015919.01.T01 MTR_3g079820 68.868 106 21 4 53 151 28 128 3.31e-37 124
MsG0380015919.01.T01 MTR_3g079780 47.945 73 36 1 1 71 54 126 9.12e-14 67.8
MsG0380015919.01.T01 MTR_2g037150 64.583 48 17 0 1 48 54 101 1.92e-13 63.9
MsG0380015919.01.T01 MTR_4g036080 64.583 48 17 0 1 48 52 99 6.27e-13 65.5
MsG0380015919.01.T01 MTR_3g079790 44.828 87 41 2 1 85 114 195 1.12e-12 64.7
MsG0380015919.01.T01 MTR_2g037140 64.583 48 17 0 1 48 156 203 1.36e-12 64.7
MsG0380015919.01.T01 MTR_3g079787 84.211 38 6 0 1 38 54 91 1.44e-12 60.1
MsG0380015919.01.T01 MTR_0570s0040 70.000 40 12 0 1 40 51 90 4.48e-12 60.8
MsG0380015919.01.T01 MTR_6g015775 34.444 90 57 1 1 88 52 141 6.38e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0380015919.01.T01 AT5G20935 60.000 85 27 3 67 149 38 117 3.24e-24 91.3

Find 6 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGAAGGTTATAACATTTA+TGG 0.184412 3:-76641305 MsG0380015919.01.T01:exon
AAGACTATGCTTCTTCAAAA+TGG 0.305839 3:-76641192 MsG0380015919.01.T01:intron
GACGACAGTGATCTTGAAAA+AGG 0.350587 3:-76641283 MsG0380015919.01.T01:exon
ATCACTAAACAAAGCCATTG+AGG 0.543331 3:-76641245 MsG0380015919.01.T01:exon
AGATGTGTATGACTCCTCAA+TGG 0.569825 3:+76641231 None:intergenic
CTACGATGCTCTGAGCAAGA+AGG 0.590455 3:-76641320 MsG0380015920.01.T01:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAGTAATCAAATAAAATTTA+TGG + Chr3:76640421-76640440 None:intergenic 10.0%
!! TTGTCTAAAGATTAATTAAT+TGG + Chr3:76641004-76641023 None:intergenic 15.0%
!! ATGACATGAATATATACATT+GGG + Chr3:76640316-76640335 None:intergenic 20.0%
!! ATTGGAACTTATATTATTGA+TGG - Chr3:76641160-76641179 MsG0380015919.01.T01:intron 20.0%
! CAAGAAGGTTATAACATTTA+TGG - Chr3:76639845-76639864 MsG0380015919.01.T01:exon 25.0%
! CAATGTATATATTCATGTCA+TGG - Chr3:76640315-76640334 MsG0380015919.01.T01:CDS 25.0%
! CATGACATGAATATATACAT+TGG + Chr3:76640317-76640336 None:intergenic 25.0%
! GAATAACCATACATAAATTG+TGG - Chr3:76641231-76641250 MsG0380015919.01.T01:exon 25.0%
! GATAAAGTTATAAACAGTGT+AGG - Chr3:76640608-76640627 MsG0380015919.01.T01:intron 25.0%
! TGATGAAAAATTAAGAGATG+AGG + Chr3:76640909-76640928 None:intergenic 25.0%
!! CATTATCTTCACTATGTTTT+TGG - Chr3:76640343-76640362 MsG0380015919.01.T01:CDS 25.0%
AAAAAAGCAAGAAGATGTGT+GGG - Chr3:76641123-76641142 MsG0380015919.01.T01:intron 30.0%
AAACGTTCAAAGTTGGATAA+AGG - Chr3:76640773-76640792 MsG0380015919.01.T01:intron 30.0%
AACGTTCAAAGTTGGATAAA+GGG - Chr3:76640774-76640793 MsG0380015919.01.T01:intron 30.0%
AAGACTATGCTTCTTCAAAA+TGG - Chr3:76639958-76639977 MsG0380015919.01.T01:CDS 30.0%
AATCCTATCATATGAATGAG+GGG + Chr3:76640474-76640493 None:intergenic 30.0%
AGCAAATCAACTGGAATATT+TGG + Chr3:76640722-76640741 None:intergenic 30.0%
ATATTTCAAGCCCTTAGATA+TGG - Chr3:76641186-76641205 MsG0380015919.01.T01:intron 30.0%
ATCTGATATTTCACTTCTGA+TGG + Chr3:76640065-76640084 None:intergenic 30.0%
CAAAGTCCACAATTTATGTA+TGG + Chr3:76641240-76641259 None:intergenic 30.0%
CAATCCTATCATATGAATGA+GGG + Chr3:76640475-76640494 None:intergenic 30.0%
CAGAAGTGAAATATCAGATT+GGG - Chr3:76640066-76640085 MsG0380015919.01.T01:intron 30.0%
CTAGAATGCAAAAAAGAGTT+GGG - Chr3:76640005-76640024 MsG0380015919.01.T01:CDS 30.0%
GGAGCTTCAATGATAATAAT+GGG + Chr3:76640803-76640822 None:intergenic 30.0%
GTAAAGACAAGTTGCAAAAA+TGG - Chr3:76640213-76640232 MsG0380015919.01.T01:intron 30.0%
TAGAATGCAAAAAAGAGTTG+GGG - Chr3:76640006-76640025 MsG0380015919.01.T01:CDS 30.0%
TCAATCCTATCATATGAATG+AGG + Chr3:76640476-76640495 None:intergenic 30.0%
TCAGAAGTGAAATATCAGAT+TGG - Chr3:76640065-76640084 MsG0380015919.01.T01:intron 30.0%
TGGAGCTTCAATGATAATAA+TGG + Chr3:76640804-76640823 None:intergenic 30.0%
! AAATATCAGATTGGGAGTTT+TGG - Chr3:76640074-76640093 MsG0380015919.01.T01:intron 30.0%
! AATATCAGATTGGGAGTTTT+GGG - Chr3:76640075-76640094 MsG0380015919.01.T01:intron 30.0%
! ATTGTGATACCTGTTTTCTA+CGG - Chr3:76640032-76640051 MsG0380015919.01.T01:CDS 30.0%
! CTGGGCAAGATTTTATAAAA+CGG - Chr3:76640171-76640190 MsG0380015919.01.T01:intron 30.0%
! TCTAGAATGCAAAAAAGAGT+TGG - Chr3:76640004-76640023 MsG0380015919.01.T01:CDS 30.0%
! TGGGCAAGATTTTATAAAAC+GGG - Chr3:76640172-76640191 MsG0380015919.01.T01:intron 30.0%
AAAAGGAAAGATGCTCTAAC+TGG - Chr3:76640152-76640171 MsG0380015919.01.T01:intron 35.0%
AAAGGAAAGATGCTCTAACT+GGG - Chr3:76640153-76640172 MsG0380015919.01.T01:intron 35.0%
ACGTTTGTACAAGCCAAAAT+TGG + Chr3:76640864-76640883 None:intergenic 35.0%
ATAGTAGAGCAAGAAGAACA+AGG + Chr3:76640393-76640412 None:intergenic 35.0%
ATCACTAAACAAAGCCATTG+AGG - Chr3:76639905-76639924 MsG0380015919.01.T01:exon 35.0%
ATCCTATCATATGAATGAGG+GGG + Chr3:76640473-76640492 None:intergenic 35.0%
ATTGTTTGCCAACAACTAGA+TGG - Chr3:76641264-76641283 MsG0380015919.01.T01:exon 35.0%
CAAAAAAGCAAGAAGATGTG+TGG - Chr3:76641122-76641141 MsG0380015919.01.T01:intron 35.0%
CGTTTGTACAAGCCAAAATT+GGG + Chr3:76640863-76640882 None:intergenic 35.0%
CTATACTCAGCCATATCTAA+GGG + Chr3:76641199-76641218 None:intergenic 35.0%
GACAAGTTGCAAAAATGGAA+AGG - Chr3:76640218-76640237 MsG0380015919.01.T01:intron 35.0%
GCAAGAAAAACGTTCAAAGT+TGG - Chr3:76640766-76640785 MsG0380015919.01.T01:intron 35.0%
GCAGTAGCAACTAATTGATT+TGG - Chr3:76640960-76640979 MsG0380015919.01.T01:intron 35.0%
GGAATATTTGGTATCTGTTG+TGG + Chr3:76640710-76640729 None:intergenic 35.0%
GGATTTATTCCGTAGAAAAC+AGG + Chr3:76640044-76640063 None:intergenic 35.0%
GTTTGTACAAGCCAAAATTG+GGG + Chr3:76640862-76640881 None:intergenic 35.0%
TATCATTGAAGCTCCAAAGA+TGG - Chr3:76640808-76640827 MsG0380015919.01.T01:intron 35.0%
! ATATCAGATTGGGAGTTTTG+GGG - Chr3:76640076-76640095 MsG0380015919.01.T01:intron 35.0%
! CGTTTTTCTTGCAACTCTTT+TGG + Chr3:76640758-76640777 None:intergenic 35.0%
!! ATATTCCAGTTGATTTGCTG+AGG - Chr3:76640723-76640742 MsG0380015919.01.T01:intron 35.0%
!!! AATTTTGGCTTGTACAAACG+TGG - Chr3:76640863-76640882 MsG0380015919.01.T01:intron 35.0%
!!! CTGTTGTGGAACATTGATTT+TGG + Chr3:76640696-76640715 None:intergenic 35.0%
AATACGTGCCATCTAGTTGT+TGG + Chr3:76641275-76641294 None:intergenic 40.0%
ACCAAGCCATATTTGAAGGT+CGG - Chr3:76640668-76640687 MsG0380015919.01.T01:intron 40.0%
AGATGTGTATGACTCCTCAA+TGG + Chr3:76639922-76639941 None:intergenic 40.0%
ATATGAATGAGGGGGAAAGA+AGG + Chr3:76640465-76640484 None:intergenic 40.0%
GACGACAGTGATCTTGAAAA+AGG - Chr3:76639867-76639886 MsG0380015919.01.T01:exon 40.0%
GCTATACTCAGCCATATCTA+AGG + Chr3:76641200-76641219 None:intergenic 40.0%
GGTCAAAACTGCAGCTAATT+CGG - Chr3:76640829-76640848 MsG0380015919.01.T01:intron 40.0%
GTAGAAGCAACTTGCACAAA+AGG - Chr3:76640135-76640154 MsG0380015919.01.T01:intron 40.0%
TACCACCAAGCCATATTTGA+AGG - Chr3:76640664-76640683 MsG0380015919.01.T01:intron 40.0%
TGAAGAGAAATCGTCACTGA+AGG - Chr3:76640574-76640593 MsG0380015919.01.T01:intron 40.0%
TTCCCCCTCATTCATATGAT+AGG - Chr3:76640468-76640487 MsG0380015919.01.T01:intron 40.0%
! TCGGTTTATTGCCCCAATTT+TGG - Chr3:76640848-76640867 MsG0380015919.01.T01:intron 40.0%
! TTGTACAAACGTGGTGATGT+TGG - Chr3:76640872-76640891 MsG0380015919.01.T01:intron 40.0%
ATAGTCCCAACCAGCTAAGT+TGG + Chr3:76640261-76640280 None:intergenic 45.0%
GTTGGGACTATCGAAATTGC+AGG - Chr3:76640270-76640289 MsG0380015919.01.T01:intron 45.0%
! ACAAACGTGGTGATGTTGGA+AGG - Chr3:76640876-76640895 MsG0380015919.01.T01:intron 45.0%
! CTTGGTGGTAGAGCAAGAAA+TGG + Chr3:76640654-76640673 None:intergenic 45.0%
! GACCTTCAAATATGGCTTGG+TGG + Chr3:76640669-76640688 None:intergenic 45.0%
!! GCTGCAGTTTTGACCATCTT+TGG + Chr3:76640824-76640843 None:intergenic 45.0%
!! TTGGTGCCGACCTTCAAATA+TGG + Chr3:76640677-76640696 None:intergenic 45.0%
AAGAAGATGTGTGGGCAGTG+CGG - Chr3:76641131-76641150 MsG0380015919.01.T01:intron 50.0%
AAGCAGCCAACTTAGCTGGT+TGG - Chr3:76640252-76640271 MsG0380015919.01.T01:intron 50.0%
AGCAGCCAACTTAGCTGGTT+GGG - Chr3:76640253-76640272 MsG0380015919.01.T01:intron 50.0%
CGTGACCTCAGCAAATCAAC+TGG + Chr3:76640731-76640750 None:intergenic 50.0%
GCCGACCTTCAAATATGGCT+TGG + Chr3:76640672-76640691 None:intergenic 50.0%
TGTGAAGCAGCCAACTTAGC+TGG - Chr3:76640248-76640267 MsG0380015919.01.T01:intron 50.0%
TGGGCAGTGCGGCGCAGCAT+TGG - Chr3:76641142-76641161 MsG0380015919.01.T01:intron 70.0%
Chromosome Type Strat End Strand Name
Chr3 gene 76639839 76641333 76639839 ID=MsG0380015919.01;
Chr3 mRNA 76639839 76641333 76639839 ID=MsG0380015919.01.T01;Parent=MsG0380015919.01
Chr3 exon 76639839 76640058 76639839 ID=MsG0380015919.01.T01.exon;Parent=MsG0380015919.01.T01
Chr3 CDS 76639950 76640058 76639950 ID=MsG0380015919.01.T01.cds;Parent=MsG0380015919.01.T01
Chr3 CDS 76640141 76640152 76640141 ID=MsG0380015919.01.T01.cds;Parent=MsG0380015919.01.T01
Chr3 exon 76640141 76640152 76640141 ID=MsG0380015919.01.T01.exon;Parent=MsG0380015919.01.T01
Chr3 CDS 76640275 76640456 76640275 ID=MsG0380015919.01.T01.cds;Parent=MsG0380015919.01.T01
Chr3 exon 76640275 76640456 76640275 ID=MsG0380015919.01.T01.exon;Parent=MsG0380015919.01.T01
Chr3 CDS 76640646 76640682 76640646 ID=MsG0380015919.01.T01.cds;Parent=MsG0380015919.01.T01
Chr3 exon 76640646 76640682 76640646 ID=MsG0380015919.01.T01.exon;Parent=MsG0380015919.01.T01
Chr3 CDS 76641193 76641308 76641193 ID=MsG0380015919.01.T01.cds;Parent=MsG0380015919.01.T01
Chr3 exon 76641193 76641333 76641193 ID=MsG0380015919.01.T01.exon;Parent=MsG0380015919.01.T01
Gene Sequence

>MsG0380015919.01.T01

ATGGACGACAGTGATCTTGAAAAAGGAGATGAGATATCATCATCACTAAACAAAGCCATTGAGGAGTCATACACATCTATAGTCATCTTTTCAAAAGACTATGCTTCTTCAAAATGGATTGAATCTCACTTCATTCAGCTCATCGTCAAAGATATACCAAATATTCCAGTTGATTTGCTGAGGTCACGTGAACCAAAAGAGTTGCAAGAAAAACGTTCAAAGTTGGATAAAGGGTCTCCCATTATTATCATTGAAGCTCCAAAGATGGTCAAAACTGCAGCTAATTCGGTTTATTGCCCCAATTTTGGCTTGTACAAACGTGGTGATGTTGGAAGACAAAAAATGATAATTGTTTCAAAAAAGCAAGAAGATGTGTGGGCAGTGCGGCGCAGCATTGGAACTTATATTATTGATGGCAAATATTTCAAGCCCTTAGATATGGCTGAGTATAGCTAG

Protein sequence

>MsG0380015919.01.T01

MDDSDLEKGDEISSSLNKAIEESYTSIVIFSKDYASSKWIESHFIQLIVKDIPNIPVDLLRSREPKELQEKRSKLDKGSPIIIIEAPKMVKTAANSVYCPNFGLYKRGDVGRQKMIIVSKKQEDVWAVRRSIGTYIIDGKYFKPLDMAEYS*