AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene020926

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene020926.t1 MTR_7g083950 57.895 76 32 0 4 79 4 79 4.04e-24 94.4
MS.gene020926.t1 MTR_5g073430 53.846 78 36 0 4 81 3 80 3.55e-23 85.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 17 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCATGTCAGTACGATAAC+AGG 0.348327 5.4:+77209946 MS.gene020926:CDS
ATATGCATGGCTATCGCTTC+CGG 0.369191 5.4:-77209892 None:intergenic
TATGCATGGCTATCGCTTCC+GGG 0.369985 5.4:-77209891 None:intergenic
TCCTCTCTGATCTTTCCAAC+TGG 0.408414 5.4:+77210095 MS.gene020926:CDS
CTCAGAAGAGATTTCAATGC+TGG 0.438133 5.4:+77209993 MS.gene020926:CDS
GAGTGCGGAGGTTGCTTCAA+GGG 0.485352 5.4:+77210045 MS.gene020926:CDS
TTGAATACGTATATTAAACT+TGG 0.501110 5.4:-77210071 None:intergenic
AGAGTGCGGAGGTTGCTTCA+AGG 0.575208 5.4:+77210044 MS.gene020926:CDS
TGCACTAGTCAAGCTTCTCA+AGG 0.575364 5.4:+77209914 MS.gene020926:CDS
ATAAAGATGCACATCCTCCC+CGG 0.586546 5.4:+77209873 None:intergenic
ATTTAGAGACTACTTTGATG+AGG 0.601912 5.4:+77210213 MS.gene020926:intron
ATGCATGGCTATCGCTTCCG+GGG 0.620717 5.4:-77209890 None:intergenic
CATGGCTATCGCTTCCGGGG+AGG 0.623061 5.4:-77209887 None:intergenic
GCTTGACTAGTGCATATGCA+TGG 0.638715 5.4:-77209905 None:intergenic
AAGGTGTCAAATCAAGAGTG+CGG 0.694012 5.4:+77210030 MS.gene020926:CDS
GTGTCAAATCAAGAGTGCGG+AGG 0.698517 5.4:+77210033 MS.gene020926:CDS
ACCAGTTGGAAAGATCAGAG+AGG 0.735926 5.4:-77210096 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGATAAATATAGTAAAAAAA+GGG - chr5.4:77210166-77210185 None:intergenic 10.0%
!! CAGATAAATATAGTAAAAAA+AGG - chr5.4:77210167-77210186 None:intergenic 15.0%
!! TTGAATACGTATATTAAACT+TGG - chr5.4:77210074-77210093 None:intergenic 20.0%
! ATCAAAGTAGTCTCTAAATT+AGG - chr5.4:77210212-77210231 None:intergenic 25.0%
! GCTGGAAAAATTGATATAAA+AGG + chr5.4:77210011-77210030 MS.gene020926:CDS 25.0%
! TCAAAGTAGTCTCTAAATTA+GGG - chr5.4:77210211-77210230 None:intergenic 25.0%
ATTTAGAGACTACTTTGATG+AGG + chr5.4:77210213-77210232 MS.gene020926:intron 30.0%
GGTTCCATATAGTAGAAACA+TGG - chr5.4:77210190-77210209 None:intergenic 35.0%
TTTCATGTCAGTACGATAAC+AGG + chr5.4:77209946-77209965 MS.gene020926:CDS 35.0%
! TAGAAAAAGTACGAACCAGT+TGG - chr5.4:77210113-77210132 None:intergenic 35.0%
! TCTGCCATGTTTCTACTATA+TGG + chr5.4:77210183-77210202 MS.gene020926:intron 35.0%
CTCAGAAGAGATTTCAATGC+TGG + chr5.4:77209993-77210012 MS.gene020926:CDS 40.0%
! AAGGTGTCAAATCAAGAGTG+CGG + chr5.4:77210030-77210049 MS.gene020926:CDS 40.0%
ACCAGTTGGAAAGATCAGAG+AGG - chr5.4:77210099-77210118 None:intergenic 45.0%
ATATGCATGGCTATCGCTTC+CGG - chr5.4:77209895-77209914 None:intergenic 45.0%
GCTTGACTAGTGCATATGCA+TGG - chr5.4:77209908-77209927 None:intergenic 45.0%
TCCTCTCTGATCTTTCCAAC+TGG + chr5.4:77210095-77210114 MS.gene020926:CDS 45.0%
TGCACTAGTCAAGCTTCTCA+AGG + chr5.4:77209914-77209933 MS.gene020926:CDS 45.0%
TATGCATGGCTATCGCTTCC+GGG - chr5.4:77209894-77209913 None:intergenic 50.0%
! GTGTCAAATCAAGAGTGCGG+AGG + chr5.4:77210033-77210052 MS.gene020926:CDS 50.0%
AGAGTGCGGAGGTTGCTTCA+AGG + chr5.4:77210044-77210063 MS.gene020926:CDS 55.0%
ATGCATGGCTATCGCTTCCG+GGG - chr5.4:77209893-77209912 None:intergenic 55.0%
GAGTGCGGAGGTTGCTTCAA+GGG + chr5.4:77210045-77210064 MS.gene020926:CDS 55.0%
CATGGCTATCGCTTCCGGGG+AGG - chr5.4:77209890-77209909 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 77209879 77210253 77209879 ID=MS.gene020926
chr5.4 mRNA 77209879 77210253 77209879 ID=MS.gene020926.t1;Parent=MS.gene020926
chr5.4 exon 77209879 77210116 77209879 ID=MS.gene020926.t1.exon1;Parent=MS.gene020926.t1
chr5.4 CDS 77209879 77210116 77209879 ID=cds.MS.gene020926.t1;Parent=MS.gene020926.t1
chr5.4 exon 77210219 77210253 77210219 ID=MS.gene020926.t1.exon2;Parent=MS.gene020926.t1
chr5.4 CDS 77210219 77210253 77210219 ID=cds.MS.gene020926.t1;Parent=MS.gene020926.t1
Gene Sequence

>MS.gene020926

ATGCACATCCTCCCCGGAAGCGATAGCCATGCATATGCACTAGTCAAGCTTCTCAAGGCAGTCAAATTTTCATGTCAGTACGATAACAGGATAAAGTATGATGAATTTGTAAAACTCAGAAGAGATTTCAATGCTGGAAAAATTGATATAAAAGGTGTCAAATCAAGAGTGCGGAGGTTGCTTCAAGGGCATCCAAGTTTAATATACGTATTCAACTCCTCTCTGATCTTTCCAACTGGTTCGTACTTTTTCTATTACAATTCACATATCTTGATAGTTTTCTGCCCTTTTTTTACTATATTTATCTGCCATGTTTCTACTATATGGAACCCTAATTTAGAGACTACTTTGATGAGGTTTTACGCAATTAATTGA
Protein sequence

>MS.gene020926.t1

MHILPGSDSHAYALVKLLKAVKFSCQYDNRIKYDEFVKLRRDFNAGKIDIKGVKSRVRRLLQGHPSLIYVFNSSLIFPTETTLMRFYAIN