AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene25658

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAGTTCCTCAATCTTCTCT+TGG 0.329948 8.2:-7958932 None:intergenic
CAAAGTGAAAGAGGAGGAAA+TGG 0.338863 8.2:+7958852 MS.gene25658:CDS
GATTCAGGTAACAAATAATA+AGG 0.348275 8.2:-7959251 None:intergenic
AATGAGTAAATCCTTGATTC+AGG 0.352373 8.2:-7959266 None:intergenic
AGGAGGGAGCAAAGTGAAAG+AGG 0.406040 8.2:+7958843 None:intergenic
TTACCAATGGAATGACTTCA+TGG 0.420824 8.2:-7958991 None:intergenic
ATTATTTGTTACCTGAATCA+AGG 0.432767 8.2:+7959255 MS.gene25658:CDS
AAAGTTGCTCGTTCCTTGCT+TGG 0.439365 8.2:+7959362 MS.gene25658:CDS
GAGTTCCTCAATCTTCTCTT+GGG 0.443255 8.2:-7958931 None:intergenic
GTAGTGAAGAACATAGTGAT+TGG 0.457715 8.2:+7958889 MS.gene25658:CDS
AGTGAAAGAGGAGGAAATGG+AGG 0.502250 8.2:+7958855 MS.gene25658:CDS
GAGGAAATGGAGGAAGCAAA+AGG 0.502851 8.2:+7958865 MS.gene25658:CDS
TGGGATGAGATTGACGAGAT+TGG 0.516286 8.2:-7958967 None:intergenic
ATTCAAAGGTTAACGATGGT+GGG 0.545431 8.2:-7959411 None:intergenic
TCCTTGCTTGGAGAAAGTGC+TGG 0.548785 8.2:+7959374 MS.gene25658:CDS
CACCCATGAAGTCATTCCAT+TGG 0.553232 8.2:+7958988 MS.gene25658:CDS
TGAATCAACATTTGAGAGTG+TGG 0.555452 8.2:+7959293 MS.gene25658:CDS
TTTGCATACTCAACATGAGC+AGG 0.558557 8.2:-7959342 None:intergenic
GAAGATTGAGGAACTCATCA+AGG 0.571882 8.2:+7958938 MS.gene25658:CDS
GCCAGCACTTTCTCCAAGCA+AGG 0.576667 8.2:-7959375 None:intergenic
GATTCAAAGGTTAACGATGG+TGG 0.578082 8.2:-7959412 None:intergenic
GAGATTGACGAGATTGGCAA+AGG 0.580515 8.2:-7958961 None:intergenic
AGGGAGCAAAGTGAAAGAGG+AGG 0.582719 8.2:+7958846 MS.gene25658:CDS
CAATGGAATGACTTCATGGG+TGG 0.583790 8.2:-7958987 None:intergenic
AATCTCCCAAGAGAAGATTG+AGG 0.597731 8.2:+7958926 MS.gene25658:CDS
ATGAGCTACATACTCTGCAA+TGG 0.614733 8.2:-7959319 None:intergenic
TACCAATGGAATGACTTCAT+GGG 0.631729 8.2:-7958990 None:intergenic
AATGGAATGACTTCATGGGT+GGG 0.706119 8.2:-7958986 None:intergenic
ACGGATTCAAAGGTTAACGA+TGG 0.711712 8.2:-7959415 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTAAGTTTTTTAAGTTT+TGG - chr8.2:7959093-7959112 None:intergenic 10.0%
!!! ATACATGTCTTATTTTTTTT+AGG + chr8.2:7959211-7959230 MS.gene25658:intron 15.0%
! GATTCAGGTAACAAATAATA+AGG - chr8.2:7959254-7959273 None:intergenic 25.0%
!! ATTATTTGTTACCTGAATCA+AGG + chr8.2:7959255-7959274 MS.gene25658:CDS 25.0%
!! TTTAAGTTTCATCTTACCAA+TGG - chr8.2:7959007-7959026 None:intergenic 25.0%
AATGAGTAAATCCTTGATTC+AGG - chr8.2:7959269-7959288 None:intergenic 30.0%
GTAGTGAAGAACATAGTGAT+TGG + chr8.2:7958889-7958908 MS.gene25658:CDS 35.0%
TACCAATGGAATGACTTCAT+GGG - chr8.2:7958993-7959012 None:intergenic 35.0%
TGAATCAACATTTGAGAGTG+TGG + chr8.2:7959293-7959312 MS.gene25658:CDS 35.0%
TTACCAATGGAATGACTTCA+TGG - chr8.2:7958994-7959013 None:intergenic 35.0%
!! ATAGTCTAGACTGCTTTTGT+CGG - chr8.2:7959043-7959062 None:intergenic 35.0%
AATCTCCCAAGAGAAGATTG+AGG + chr8.2:7958926-7958945 MS.gene25658:CDS 40.0%
AATGGAATGACTTCATGGGT+GGG - chr8.2:7958989-7959008 None:intergenic 40.0%
ATGAGCTACATACTCTGCAA+TGG - chr8.2:7959322-7959341 None:intergenic 40.0%
CAAAGTGAAAGAGGAGGAAA+TGG + chr8.2:7958852-7958871 MS.gene25658:CDS 40.0%
GAAGATTGAGGAACTCATCA+AGG + chr8.2:7958938-7958957 MS.gene25658:CDS 40.0%
GAGTTCCTCAATCTTCTCTT+GGG - chr8.2:7958934-7958953 None:intergenic 40.0%
TGAGTTCCTCAATCTTCTCT+TGG - chr8.2:7958935-7958954 None:intergenic 40.0%
TTTGCATACTCAACATGAGC+AGG - chr8.2:7959345-7959364 None:intergenic 40.0%
AAAGTTGCTCGTTCCTTGCT+TGG + chr8.2:7959362-7959381 MS.gene25658:CDS 45.0%
AGTGAAAGAGGAGGAAATGG+AGG + chr8.2:7958855-7958874 MS.gene25658:CDS 45.0%
CAATGGAATGACTTCATGGG+TGG - chr8.2:7958990-7959009 None:intergenic 45.0%
CACCCATGAAGTCATTCCAT+TGG + chr8.2:7958988-7959007 MS.gene25658:CDS 45.0%
GAGATTGACGAGATTGGCAA+AGG - chr8.2:7958964-7958983 None:intergenic 45.0%
GAGGAAATGGAGGAAGCAAA+AGG + chr8.2:7958865-7958884 MS.gene25658:CDS 45.0%
TGGGATGAGATTGACGAGAT+TGG - chr8.2:7958970-7958989 None:intergenic 45.0%
! GATTTTCGCTAAGTGGACGA+GGG - chr8.2:7959129-7959148 None:intergenic 45.0%
! TACCAGCGATTTTCGCTAAG+TGG - chr8.2:7959136-7959155 None:intergenic 45.0%
AGGGAGCAAAGTGAAAGAGG+AGG + chr8.2:7958846-7958865 MS.gene25658:CDS 50.0%
GTCCACTTAGCGAAAATCGC+TGG + chr8.2:7959131-7959150 MS.gene25658:intron 50.0%
! CGATTTTCGCTAAGTGGACG+AGG - chr8.2:7959130-7959149 None:intergenic 50.0%
! TCCTTGCTTGGAGAAAGTGC+TGG + chr8.2:7959374-7959393 MS.gene25658:CDS 50.0%
GCCAGCACTTTCTCCAAGCA+AGG - chr8.2:7959378-7959397 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr8.2 gene 7958845 7959431 7958845 ID=MS.gene25658
chr8.2 mRNA 7958845 7959431 7958845 ID=MS.gene25658.t1;Parent=MS.gene25658
chr8.2 exon 7958845 7959009 7958845 ID=MS.gene25658.t1.exon1;Parent=MS.gene25658.t1
chr8.2 CDS 7958845 7959009 7958845 ID=cds.MS.gene25658.t1;Parent=MS.gene25658.t1
chr8.2 exon 7959233 7959431 7959233 ID=MS.gene25658.t1.exon2;Parent=MS.gene25658.t1
chr8.2 CDS 7959233 7959431 7959233 ID=cds.MS.gene25658.t1;Parent=MS.gene25658.t1
Gene Sequence

>MS.gene25658

GAGGGAGCAAAGTGAAAGAGGAGGAAATGGAGGAAGCAAAAGGAGTAGTGAAGAACATAGTGATTGGAAAGTTCAAGATGAAATCTCCCAAGAGAAGATTGAGGAACTCATCAAGGCCTTTGCCAATCTCGTCAATCTCATCCCACCCATGAAGTCATTCCATTGGTAAGATGAAACTTAAACTTAAATAAGTTACCGACAAAAGCAGTCTAGACTATGATTTTAAGTCTAATTTTTTGTCTAAACCAAAACTTAAAAAACTTAATTTAGTTATAAATACTCCCTCGTCCACTTAGCGAAAATCGCTGGTATTAAAACAAATTATTTGAAAAACAAATTTGTCTGAAATATGTTTCAATTTTATATATACATGTCTTATTTTTTTTAGGAATTGTTGTTATACTTTCCTTATTATTTGTTACCTGAATCAAGGATTTACTCATTTCTTTGAATCAACATTTGAGAGTGTGGAAGCCATTGCAGAGTATGTAGCTCATCCTGCTCATGTTGAGTATGCAAAGTTGCTCGTTCCTTGCTTGGAGAAAGTGCTGGCATTTGATTATAAGCCCACCATCGTTAACCTTTGA
Protein sequence

>MS.gene25658.t1

EGAKUKRRKWRKQKEUURTUULESSRUNLPREDUGTHQGLCQSRQSHPTHEVIPLELLLYFPYYLLPESRIYSFLUINIUECGSHCRVCSSSCSCUVCKVARSLLGESAGIULUAHHRUPL