AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene028177

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028177.t1 MTR_1g058250 93.103 116 8 0 1 116 1 116 3.76e-75 220
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene028177.t1 AT5G04800 73.239 142 35 2 1 140 1 141 1.26e-69 206
MS.gene028177.t1 AT5G04800 73.239 142 35 2 1 140 1 141 1.26e-69 206
MS.gene028177.t1 AT5G04800 73.239 142 35 2 1 140 1 141 1.26e-69 206
MS.gene028177.t1 AT5G04800 73.239 142 35 2 1 140 1 141 1.26e-69 206
MS.gene028177.t1 AT3G10610 73.571 140 36 1 1 139 1 140 5.11e-69 204
MS.gene028177.t1 AT2G04390 73.759 141 36 1 1 140 1 141 1.10e-68 204
MS.gene028177.t1 AT2G05220 72.857 140 38 0 1 140 1 140 4.15e-68 202
MS.gene028177.t1 AT2G05220 72.857 140 38 0 1 140 1 140 4.15e-68 202

Find 35 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAGGATTTCTTCACGGTTT+TGG 0.259892 4.2:-16001745 None:intergenic
TTCCTGATGTTTCTGCTATT+AGG 0.341443 4.2:+16001982 MS.gene028177:CDS
GAAGATTCCTGGTGTTGTTC+AGG 0.347999 4.2:+16002064 MS.gene028177:CDS
CGTCTTCGTAACAAGATTGC+TGG 0.356034 4.2:+16001861 MS.gene028177:CDS
CAAGAGCAGCAAGCATATCT+AGG 0.361317 4.2:-16002034 None:intergenic
CTTGGCATGTCGAAGATTCC+TGG 0.368757 4.2:+16002053 MS.gene028177:CDS
TTCTTCAAGGATCTTCTTGT+TGG 0.377402 4.2:-16001817 None:intergenic
CTAGATATGCTTGCTGCTCT+TGG 0.395976 4.2:+16002035 MS.gene028177:CDS
GCACCAGCACCACGACCATA+TGG 0.428749 4.2:-16002113 None:intergenic
ATCCCATATGGTCGTGGTGC+TGG 0.431174 4.2:+16002110 MS.gene028177:CDS
TATGGTCGTGGTGCTGGTGC+TGG 0.432732 4.2:+16002116 MS.gene028177:CDS
TTCAATGAAATTCCACGAAC+AGG 0.443778 4.2:-16001921 None:intergenic
TTGTTACGAAGACGCTTTGA+AGG 0.464587 4.2:-16001852 None:intergenic
GGATCAAAGCGACTTCTTCA+AGG 0.477079 4.2:-16001830 None:intergenic
CTTGTTCAGCAGATCCCATA+TGG 0.480117 4.2:+16002098 MS.gene028177:CDS
ATTCGAAAGGGACCTGTTCG+TGG 0.480777 4.2:+16001909 MS.gene028177:CDS
TGATCATATTGAGGTTGATA+AGG 0.481558 4.2:+16002007 MS.gene028177:CDS
GTCCTAATAGCAGAAACATC+AGG 0.505221 4.2:-16001984 None:intergenic
TTTGGTTCGGACTCGTCCCA+TGG 0.523667 4.2:-16001727 None:intergenic
TTGACGAGAGGATTTCTTCA+CGG 0.524605 4.2:-16001751 None:intergenic
GGAGGAGCGTGATCGTCGTA+TGG 0.525336 4.2:+16001953 MS.gene028177:CDS
TATTAGGACTGATCATATTG+AGG 0.542204 4.2:+16001998 MS.gene028177:CDS
GTGGTGCTGGTGCTGGAAGG+AGG 0.550588 4.2:+16002123 MS.gene028177:CDS
CACCAGCACCACGACCATAT+GGG 0.556729 4.2:-16002112 None:intergenic
CTCATGCAGCGTATTCGAAA+GGG 0.564195 4.2:+16001897 MS.gene028177:CDS
GTCGTGGTGCTGGTGCTGGA+AGG 0.566651 4.2:+16002120 MS.gene028177:CDS
TTCATTGAAGCTGCAAGAGG+AGG 0.567846 4.2:+16001935 MS.gene028177:CDS
CGATTAACCTGAACAACACC+AGG 0.574528 4.2:-16002071 None:intergenic
CAGCAGATCCCATATGGTCG+TGG 0.574554 4.2:+16002104 MS.gene028177:CDS
AAGAGCAGCAAGCATATCTA+GGG 0.580550 4.2:-16002033 None:intergenic
TCTCATGCAGCGTATTCGAA+AGG 0.588377 4.2:+16001896 MS.gene028177:CDS
TGTTACGAAGACGCTTTGAA+GGG 0.597110 4.2:-16001851 None:intergenic
ACGCTCGATGATTTGACGAG+AGG 0.611995 4.2:-16001763 None:intergenic
TAACCACCCTAAAATGACAC+TGG 0.617615 4.2:+16001785 MS.gene028177:CDS
AATTTCATTGAAGCTGCAAG+AGG 0.634258 4.2:+16001932 MS.gene028177:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TATTAGGACTGATCATATTG+AGG + chr4.2:16001998-16002017 MS.gene028177:CDS 30.0%
!! TGATCATATTGAGGTTGATA+AGG + chr4.2:16002007-16002026 MS.gene028177:CDS 30.0%
!!! GAAAATCCAGTGTCATTTTA+GGG - chr4.2:16001794-16001813 None:intergenic 30.0%
!!! TGAAAATCCAGTGTCATTTT+AGG - chr4.2:16001795-16001814 None:intergenic 30.0%
AATTTCATTGAAGCTGCAAG+AGG + chr4.2:16001932-16001951 MS.gene028177:CDS 35.0%
TTCAATGAAATTCCACGAAC+AGG - chr4.2:16001924-16001943 None:intergenic 35.0%
TTCTTCAAGGATCTTCTTGT+TGG - chr4.2:16001820-16001839 None:intergenic 35.0%
! TTCCTGATGTTTCTGCTATT+AGG + chr4.2:16001982-16002001 MS.gene028177:CDS 35.0%
!!! ATTTCTTCACGGTTTTGGTT+CGG - chr4.2:16001743-16001762 None:intergenic 35.0%
AAGAGCAGCAAGCATATCTA+GGG - chr4.2:16002036-16002055 None:intergenic 40.0%
GTCCTAATAGCAGAAACATC+AGG - chr4.2:16001987-16002006 None:intergenic 40.0%
TAACCACCCTAAAATGACAC+TGG + chr4.2:16001785-16001804 MS.gene028177:CDS 40.0%
TTGACGAGAGGATTTCTTCA+CGG - chr4.2:16001754-16001773 None:intergenic 40.0%
TTGTTACGAAGACGCTTTGA+AGG - chr4.2:16001855-16001874 None:intergenic 40.0%
! AGAGGATTTCTTCACGGTTT+TGG - chr4.2:16001748-16001767 None:intergenic 40.0%
! TGTTACGAAGACGCTTTGAA+GGG - chr4.2:16001854-16001873 None:intergenic 40.0%
!!! AATCCAGTGTCATTTTAGGG+TGG - chr4.2:16001791-16001810 None:intergenic 40.0%
CAAGAGCAGCAAGCATATCT+AGG - chr4.2:16002037-16002056 None:intergenic 45.0%
CGATTAACCTGAACAACACC+AGG - chr4.2:16002074-16002093 None:intergenic 45.0%
CGTCTTCGTAACAAGATTGC+TGG + chr4.2:16001861-16001880 MS.gene028177:CDS 45.0%
CTCATGCAGCGTATTCGAAA+GGG + chr4.2:16001897-16001916 MS.gene028177:CDS 45.0%
CTTGTTCAGCAGATCCCATA+TGG + chr4.2:16002098-16002117 MS.gene028177:CDS 45.0%
GGATCAAAGCGACTTCTTCA+AGG - chr4.2:16001833-16001852 None:intergenic 45.0%
TCTCATGCAGCGTATTCGAA+AGG + chr4.2:16001896-16001915 MS.gene028177:CDS 45.0%
TTCATTGAAGCTGCAAGAGG+AGG + chr4.2:16001935-16001954 MS.gene028177:CDS 45.0%
! CTAGATATGCTTGCTGCTCT+TGG + chr4.2:16002035-16002054 MS.gene028177:CDS 45.0%
!! GAAGATTCCTGGTGTTGTTC+AGG + chr4.2:16002064-16002083 MS.gene028177:CDS 45.0%
ACGCTCGATGATTTGACGAG+AGG - chr4.2:16001766-16001785 None:intergenic 50.0%
ATTCGAAAGGGACCTGTTCG+TGG + chr4.2:16001909-16001928 MS.gene028177:CDS 50.0%
CTTGGCATGTCGAAGATTCC+TGG + chr4.2:16002053-16002072 MS.gene028177:CDS 50.0%
ATCCCATATGGTCGTGGTGC+TGG + chr4.2:16002110-16002129 MS.gene028177:CDS 55.0%
CACCAGCACCACGACCATAT+GGG - chr4.2:16002115-16002134 None:intergenic 55.0%
CAGCAGATCCCATATGGTCG+TGG + chr4.2:16002104-16002123 MS.gene028177:CDS 55.0%
GCACCAGCACCACGACCATA+TGG - chr4.2:16002116-16002135 None:intergenic 60.0%
! GGAGGAGCGTGATCGTCGTA+TGG + chr4.2:16001953-16001972 MS.gene028177:CDS 60.0%
!! TATGGTCGTGGTGCTGGTGC+TGG + chr4.2:16002116-16002135 MS.gene028177:CDS 60.0%
!! GTCGTGGTGCTGGTGCTGGA+AGG + chr4.2:16002120-16002139 MS.gene028177:CDS 65.0%
!! GTGGTGCTGGTGCTGGAAGG+AGG + chr4.2:16002123-16002142 MS.gene028177:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 16001729 16002151 16001729 ID=MS.gene028177
chr4.2 mRNA 16001729 16002151 16001729 ID=MS.gene028177.t1;Parent=MS.gene028177
chr4.2 exon 16001729 16002151 16001729 ID=MS.gene028177.t1.exon1;Parent=MS.gene028177.t1
chr4.2 CDS 16001729 16002151 16001729 ID=cds.MS.gene028177.t1;Parent=MS.gene028177.t1
Gene Sequence

>MS.gene028177

ATGGGACGAGTCCGAACCAAAACCGTGAAGAAATCCTCTCGTCAAATCATCGAGCGTAACCACCCTAAAATGACACTGGATTTTCACACCAACAAGAAGATCCTTGAAGAAGTCGCTTTGATCCCTTCAAAGCGTCTTCGTAACAAGATTGCTGGTTTCTCTACGCATCTCATGCAGCGTATTCGAAAGGGACCTGTTCGTGGAATTTCATTGAAGCTGCAAGAGGAGGAGCGTGATCGTCGTATGGATTTCGTTCCTGATGTTTCTGCTATTAGGACTGATCATATTGAGGTTGATAAGGAAACCCTAGATATGCTTGCTGCTCTTGGCATGTCGAAGATTCCTGGTGTTGTTCAGGTTAATCGTGTTCTTGTTCAGCAGATCCCATATGGTCGTGGTGCTGGTGCTGGAAGGAGGTTTTAA
Protein sequence

>MS.gene028177.t1

MGRVRTKTVKKSSRQIIERNHPKMTLDFHTNKKILEEVALIPSKRLRNKIAGFSTHLMQRIRKGPVRGISLKLQEEERDRRMDFVPDVSAIRTDHIEVDKETLDMLAALGMSKIPGVVQVNRVLVQQIPYGRGAGAGRRF