AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1229730

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1229730 MtrunA17_Chr8g0337271 80.838 167 32 0 1 167 1 167 3.69e-101 289
Msa1229730 MtrunA17_Chr8g0358731 36.134 119 72 1 1 119 1 115 3.39e-21 85.1
Msa1229730 MtrunA17_Chr6g0452691 27.211 147 100 2 10 149 9 155 1.45e-12 62.4
Msa1229730 MtrunA17_Chr5g0439111 27.660 141 96 4 10 148 9 145 1.05e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1229730 AT3G50510.1 28.696 115 81 1 1 114 3 117 2.04e-14 68.2
Msa1229730 AT3G50510.2 28.696 115 81 1 1 114 3 117 2.04e-14 68.2
Msa1229730 AT2G19820.1 30.108 93 64 1 5 96 7 99 6.87e-13 62.4
Msa1229730 AT3G27650.1 32.184 87 59 0 1 87 30 116 2.20e-11 59.3

Find 37 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCCAAGGATGTGCTTATT+TGG 0.063042 8_2:+5662998 None:intergenic
TCAGTGTGTCATTCAAATTT+TGG 0.142179 8_2:-5663163 Msa1229730:CDS
CTGACTTAAACTTGAGTATA+TGG 0.197296 8_2:-5662882 Msa1229730:CDS
CATGACACTGATTGTGAATT+TGG 0.306396 8_2:-5663219 Msa1229730:CDS
ATCCAAGGATGTGCTTATTT+GGG 0.326625 8_2:+5662999 None:intergenic
TCTTGGACACCAATTGGAGC+TGG 0.391570 8_2:-5663025 Msa1229730:CDS
TGTCCAAGAAAACCCTGATC+TGG 0.420917 8_2:+5663039 None:intergenic
TTTGGGCACCCAGCTCCAAT+TGG 0.428496 8_2:+5663016 None:intergenic
TTGGCGAAGTAACCCAGATC+AGG 0.429999 8_2:-5663052 Msa1229730:CDS
TTAATTGCATAATTCTCATC+AGG 0.430232 8_2:+5663130 None:intergenic
TGACTTAAACTTGAGTATAT+GGG 0.443514 8_2:-5662881 Msa1229730:intron
CTTGGACACCAATTGGAGCT+GGG 0.456606 8_2:-5663024 Msa1229730:CDS
TGCCCAAATAAGCACATCCT+TGG 0.475102 8_2:-5663001 Msa1229730:CDS
AGCAATTTCAATTTCATCCA+AGG 0.478006 8_2:+5662984 None:intergenic
CATATACTCAAGTTTAAGTC+AGG 0.479889 8_2:+5662883 None:intergenic
TCTCCTCTTTCACAAGTACA+TGG 0.497829 8_2:+5662632 None:intergenic
TCCTTCTGTGAGAAGCGAAT+CGG 0.511515 8_2:+5663080 None:intergenic
TACTGAACACATGGGTGACA+TGG 0.514848 8_2:-5662684 Msa1229730:CDS
GCCGATTCGCTTCTCACAGA+AGG 0.517177 8_2:-5663081 Msa1229730:CDS
ATTCCATGTACTTGTGAAAG+AGG 0.523001 8_2:-5662635 Msa1229730:CDS
CTGAAAGTCAGCATGCCTAC+TGG 0.528158 8_2:+5663182 None:intergenic
TGTGCCGACATATGAGAAGA+AGG 0.531308 8_2:-5663242 Msa1229730:CDS
GTCCAAGAAAACCCTGATCT+GGG 0.532763 8_2:+5663040 None:intergenic
CATGCCTTCTTCTCATATGT+CGG 0.541385 8_2:+5663238 None:intergenic
GCAACAATTTGTCTTTGATG+TGG 0.547669 8_2:+5663102 None:intergenic
TTCTCACAGAAGGAGAAGCT+TGG 0.549947 8_2:-5663071 Msa1229730:CDS
GTGCAAGAAGGCATGGAAGA+AGG 0.556829 8_2:+5662913 None:intergenic
AATTTGAGTGCAAGAAGGCA+TGG 0.581783 8_2:+5662906 None:intergenic
AAATGCATCAGAGAAATACA+AGG 0.593981 8_2:-5663281 Msa1229730:CDS
TGGCGAAGTAACCCAGATCA+GGG 0.596047 8_2:-5663051 Msa1229730:CDS
CTTGTGAAAGAGGAGAATCA+AGG 0.617523 8_2:-5662625 None:intergenic
CATGGGTGACATGGACATCA+CGG 0.621521 8_2:-5662675 Msa1229730:CDS
TCAGGAATTTGAGTGCAAGA+AGG 0.621914 8_2:+5662901 None:intergenic
TTAATAGAGTACTGAACACA+TGG 0.626411 8_2:-5662693 Msa1229730:intron
ATCACGGAACAAGACATGCA+AGG 0.684891 8_2:-5662659 Msa1229730:CDS
AATGCATCAGAGAAATACAA+GGG 0.687321 8_2:-5663280 Msa1229730:CDS
TAATAGAGTACTGAACACAT+GGG 0.740993 8_2:-5662692 Msa1229730:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTAATTGCATAATTCTCATC+AGG + chr8_2:5662780-5662799 None:intergenic 25.0%
! TGACTTAAACTTGAGTATAT+GGG - chr8_2:5663026-5663045 Msa1229730:CDS 25.0%
! TTGAAAAGAATGATAGATCT+TGG + chr8_2:5663170-5663189 None:intergenic 25.0%
!! TCAGTGTGTCATTCAAATTT+TGG - chr8_2:5662744-5662763 Msa1229730:intron 30.0%
!! CAGTGTGTCATTCAAATTTT+GGG - chr8_2:5662745-5662764 Msa1229730:intron 30.0%
!! AGTGTGTCATTCAAATTTTG+GGG - chr8_2:5662746-5662765 Msa1229730:intron 30.0%
AGCAATTTCAATTTCATCCA+AGG + chr8_2:5662926-5662945 None:intergenic 30.0%
CATATACTCAAGTTTAAGTC+AGG + chr8_2:5663027-5663046 None:intergenic 30.0%
CTGACTTAAACTTGAGTATA+TGG - chr8_2:5663025-5663044 Msa1229730:CDS 30.0%
ATGTGTTCAGTACTCTATTA+AGG + chr8_2:5663215-5663234 None:intergenic 30.0%
!! TTAATAGAGTACTGAACACA+TGG - chr8_2:5663214-5663233 Msa1229730:CDS 30.0%
!! TAATAGAGTACTGAACACAT+GGG - chr8_2:5663215-5663234 Msa1229730:CDS 30.0%
! CATGACACTGATTGTGAATT+TGG - chr8_2:5662688-5662707 Msa1229730:CDS 35.0%
GCAACAATTTGTCTTTGATG+TGG + chr8_2:5662808-5662827 None:intergenic 35.0%
ATCCAAGGATGTGCTTATTT+GGG + chr8_2:5662911-5662930 None:intergenic 35.0%
ATTCCATGTACTTGTGAAAG+AGG - chr8_2:5663272-5663291 Msa1229730:CDS 35.0%
CATGCCTTCTTCTCATATGT+CGG + chr8_2:5662672-5662691 None:intergenic 40.0%
! GTCAATACTTTTCGACCAGT+AGG - chr8_2:5662710-5662729 Msa1229730:intron 40.0%
CATCCAAGGATGTGCTTATT+TGG + chr8_2:5662912-5662931 None:intergenic 40.0%
AATTTGAGTGCAAGAAGGCA+TGG + chr8_2:5663004-5663023 None:intergenic 40.0%
TCAGGAATTTGAGTGCAAGA+AGG + chr8_2:5663009-5663028 None:intergenic 40.0%
TCTCCTCTTTCACAAGTACA+TGG + chr8_2:5663278-5663297 None:intergenic 40.0%
! TGTGCCGACATATGAGAAGA+AGG - chr8_2:5662665-5662684 Msa1229730:CDS 45.0%
TCCTTCTGTGAGAAGCGAAT+CGG + chr8_2:5662830-5662849 None:intergenic 45.0%
TTCTCACAGAAGGAGAAGCT+TGG - chr8_2:5662836-5662855 Msa1229730:intron 45.0%
! AACCCAGATCAGGGTTTTCT+TGG - chr8_2:5662865-5662884 Msa1229730:intron 45.0%
GTCCAAGAAAACCCTGATCT+GGG + chr8_2:5662870-5662889 None:intergenic 45.0%
TGTCCAAGAAAACCCTGATC+TGG + chr8_2:5662871-5662890 None:intergenic 45.0%
! GGGTTTTCTTGGACACCAAT+TGG - chr8_2:5662876-5662895 Msa1229730:intron 45.0%
TGCCCAAATAAGCACATCCT+TGG - chr8_2:5662906-5662925 Msa1229730:CDS 45.0%
TACTGAACACATGGGTGACA+TGG - chr8_2:5663223-5663242 Msa1229730:CDS 45.0%
ATCACGGAACAAGACATGCA+AGG - chr8_2:5663248-5663267 Msa1229730:CDS 45.0%
CTGAAAGTCAGCATGCCTAC+TGG + chr8_2:5662728-5662747 None:intergenic 50.0%
TTGGCGAAGTAACCCAGATC+AGG - chr8_2:5662855-5662874 Msa1229730:intron 50.0%
TGGCGAAGTAACCCAGATCA+GGG - chr8_2:5662856-5662875 Msa1229730:intron 50.0%
TCTTGGACACCAATTGGAGC+TGG - chr8_2:5662882-5662901 Msa1229730:CDS 50.0%
CTTGGACACCAATTGGAGCT+GGG - chr8_2:5662883-5662902 Msa1229730:CDS 50.0%
! GTGCAAGAAGGCATGGAAGA+AGG + chr8_2:5662997-5663016 None:intergenic 50.0%
CATGGGTGACATGGACATCA+CGG - chr8_2:5663232-5663251 Msa1229730:CDS 50.0%
!! GCCGATTCGCTTCTCACAGA+AGG - chr8_2:5662826-5662845 Msa1229730:intron 55.0%
TTTGGGCACCCAGCTCCAAT+TGG + chr8_2:5662894-5662913 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 5662628 5663301 5662628 ID=Msa1229730;Name=Msa1229730
chr8_2 mRNA 5662628 5663301 5662628 ID=Msa1229730-mRNA-1;Parent=Msa1229730;Name=Msa1229730-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|0|0|1|1|1|2|0|167
chr8_2 exon 5662882 5663301 5662882 ID=Msa1229730-mRNA-1:exon:1937;Parent=Msa1229730-mRNA-1
chr8_2 exon 5662628 5662708 5662628 ID=Msa1229730-mRNA-1:exon:1936;Parent=Msa1229730-mRNA-1
chr8_2 CDS 5662882 5663301 5662882 ID=Msa1229730-mRNA-1:cds;Parent=Msa1229730-mRNA-1
chr8_2 CDS 5662628 5662708 5662628 ID=Msa1229730-mRNA-1:cds;Parent=Msa1229730-mRNA-1
Gene Sequence

>Msa1229730

ATGCATCAGAGAAATACAAGGGCTATTACATGTCTTTTGTGCCGACATATGAGAAGAAGGCATGACACTGATTGTGAATTTGGTCAATACTTTTCGACCAGTAGGCATGCTGACTTTCAGTGTGTCATTCAAATTTTGGGGTTAAGTCGCCTGATGAGAATTATGCAATTAATAGAACCACATCAAAGACAAATTGTTGCCGATTCGCTTCTCACAGAAGGAGAAGCTTGGCGAAGTAACCCAGATCAGGGTTTTCTTGGACACCAATTGGAGCTGGGTGCCCAAATAAGCACATCCTTGGATGAAATTGAAATTGCTAGAAGACTTTTAGCTTTTTGCATTGATAATGCAAATTCAAACAATGCACCTTCTTCCATGCCTTCTTGCACTCAAATTCCTGACTTAAACTTGAGTATATGGAGTACTGAACACATGGGTGACATGGACATCACGGAACAAGACATGCAAGGTATTCCATGTACTTGTGAAAGAGGAGAATCA
Protein sequence

>Msa1229730

MHQRNTRAITCLLCRHMRRRHDTDCEFGQYFSTSRHADFQCVIQILGLSRLMRIMQLIEPHQRQIVADSLLTEGEAWRSNPDQGFLGHQLELGAQISTSLDEIEIARRLLAFCIDNANSNNAPSSMPSCTQIPDLNLSIWSTEHMGDMDITEQDMQGIPCTCERGES