AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene24567

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene24567.t1 MTR_1g016200 51.351 111 35 4 9 108 2 104 7.74e-21 81.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 28 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTCTTTGTGGCTGGAAC+TGG 0.239072 1.2:-6302789 None:intergenic
AGTATTCGCCATTGCCCTTT+TGG 0.253039 1.2:-6302900 None:intergenic
ATGAGTATCAAGACCCTTAT+CGG 0.303482 1.2:-6303191 None:intergenic
ATACAAACACTACTCCTCTT+TGG 0.387924 1.2:+6302952 MS.gene24567:CDS
GGAAGAGACAAAAGCCGATA+AGG 0.446474 1.2:+6303177 MS.gene24567:CDS
CAATCGAAACAAACCCTAGT+TGG 0.460017 1.2:-6302927 None:intergenic
TCTTGATACTCATAAGGAAA+AGG 0.465163 1.2:+6303201 MS.gene24567:CDS
TTGTCTCTTCCCTTCTTCGT+CGG 0.477939 1.2:-6303165 None:intergenic
CTTGATACTCATAAGGAAAA+GGG 0.489428 1.2:+6303202 MS.gene24567:CDS
TAAGGGTCTTGATACTCATA+AGG 0.492473 1.2:+6303195 MS.gene24567:CDS
CACATGCATTGCACAACGAC+TGG 0.503362 1.2:-6303138 None:intergenic
GAAGAGACAAAAGCCGATAA+GGG 0.509802 1.2:+6303178 MS.gene24567:CDS
ACTGAATACGAATACCCAAA+AGG 0.516751 1.2:+6302885 MS.gene24567:CDS
CTGAATACGAATACCCAAAA+GGG 0.528839 1.2:+6302886 MS.gene24567:CDS
ATGTGGACTCCGACGAAGAA+GGG 0.540307 1.2:+6303156 MS.gene24567:CDS
CTTTGGAGGAGTGATCCTAC+AGG 0.546346 1.2:+6302969 MS.gene24567:CDS
GGCGAATACTATATCCAACT+AGG 0.572160 1.2:+6302913 MS.gene24567:CDS
CATGTGGACTCCGACGAAGA+AGG 0.573346 1.2:+6303155 MS.gene24567:CDS
ATAGTTAACAAGAAATATGT+TGG 0.573507 1.2:+6303114 MS.gene24567:intron
GAGTGATCCTACAGGTTCCA+AGG 0.583772 1.2:+6302977 MS.gene24567:CDS
CAAACACTACTCCTCTTTGG+AGG 0.592172 1.2:+6302955 MS.gene24567:CDS
GCGAATACTATATCCAACTA+GGG 0.606852 1.2:+6302914 MS.gene24567:CDS
CAGTCGTTGTGCAATGCATG+TGG 0.610062 1.2:+6303139 MS.gene24567:CDS
ACGAATACCCAAAAGGGCAA+TGG 0.610371 1.2:+6302892 MS.gene24567:CDS
ACTCATAAGGAAAAGGGCAA+TGG 0.616678 1.2:+6303208 MS.gene24567:CDS
CTAATTACCTTGGAACCTGT+AGG 0.621221 1.2:-6302984 None:intergenic
TGGCGAAAGCTCATCATCTG+AGG 0.622295 1.2:+6303228 MS.gene24567:CDS
GTAGGATCACTCCTCCAAAG+AGG 0.666474 1.2:-6302966 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGTTAACAAGAAATATGT+TGG + chr1.2:6303114-6303133 MS.gene24567:intron 20.0%
!!! TCCAGTTTTTATTTTCTTTT+TGG - chr1.2:6302865-6302884 None:intergenic 20.0%
! GCCAAAAAGAAAATAAAAAC+TGG + chr1.2:6302861-6302880 MS.gene24567:CDS 25.0%
! TAGAGATTAACTAATTACCT+TGG - chr1.2:6302997-6303016 None:intergenic 25.0%
CTTGATACTCATAAGGAAAA+GGG + chr1.2:6303202-6303221 MS.gene24567:CDS 30.0%
TCTTGATACTCATAAGGAAA+AGG + chr1.2:6303201-6303220 MS.gene24567:CDS 30.0%
ACTGAATACGAATACCCAAA+AGG + chr1.2:6302885-6302904 MS.gene24567:CDS 35.0%
ATACAAACACTACTCCTCTT+TGG + chr1.2:6302952-6302971 MS.gene24567:CDS 35.0%
ATGAACCAAGAGTGAAAGTT+GGG - chr1.2:6303025-6303044 None:intergenic 35.0%
ATGAGTATCAAGACCCTTAT+CGG - chr1.2:6303194-6303213 None:intergenic 35.0%
CTGAATACGAATACCCAAAA+GGG + chr1.2:6302886-6302905 MS.gene24567:CDS 35.0%
GCGAATACTATATCCAACTA+GGG + chr1.2:6302914-6302933 MS.gene24567:CDS 35.0%
TAAGGGTCTTGATACTCATA+AGG + chr1.2:6303195-6303214 MS.gene24567:CDS 35.0%
!!! AGCAGCTTTTTTCTTCTTTG+TGG - chr1.2:6302802-6302821 None:intergenic 35.0%
ACTCATAAGGAAAAGGGCAA+TGG + chr1.2:6303208-6303227 MS.gene24567:CDS 40.0%
ACTCTTGGTTCATGCAAAAG+TGG + chr1.2:6303032-6303051 MS.gene24567:intron 40.0%
AGAAGAAAAAAGCTGCTGCT+AGG + chr1.2:6302805-6302824 MS.gene24567:CDS 40.0%
CAATCGAAACAAACCCTAGT+TGG - chr1.2:6302930-6302949 None:intergenic 40.0%
CATGAACCAAGAGTGAAAGT+TGG - chr1.2:6303026-6303045 None:intergenic 40.0%
CTAATTACCTTGGAACCTGT+AGG - chr1.2:6302987-6303006 None:intergenic 40.0%
GAAGAAAAAAGCTGCTGCTA+GGG + chr1.2:6302806-6302825 MS.gene24567:CDS 40.0%
GAAGAGACAAAAGCCGATAA+GGG + chr1.2:6303178-6303197 MS.gene24567:CDS 40.0%
GGCGAATACTATATCCAACT+AGG + chr1.2:6302913-6302932 MS.gene24567:CDS 40.0%
TGAACCAAGAGTGAAAGTTG+GGG - chr1.2:6303024-6303043 None:intergenic 40.0%
!!! GCTTTTTTCTTCTTTGTGGC+TGG - chr1.2:6302798-6302817 None:intergenic 40.0%
ACGAATACCCAAAAGGGCAA+TGG + chr1.2:6302892-6302911 MS.gene24567:CDS 45.0%
CAAACACTACTCCTCTTTGG+AGG + chr1.2:6302955-6302974 MS.gene24567:CDS 45.0%
GGAAGAGACAAAAGCCGATA+AGG + chr1.2:6303177-6303196 MS.gene24567:CDS 45.0%
TTCTCCCCAACTTTCACTCT+TGG + chr1.2:6303017-6303036 MS.gene24567:intron 45.0%
TTCTTCTTTGTGGCTGGAAC+TGG - chr1.2:6302792-6302811 None:intergenic 45.0%
TTGTCTCTTCCCTTCTTCGT+CGG - chr1.2:6303168-6303187 None:intergenic 45.0%
! AGTATTCGCCATTGCCCTTT+TGG - chr1.2:6302903-6302922 None:intergenic 45.0%
! GTATTCGCCATTGCCCTTTT+GGG - chr1.2:6302902-6302921 None:intergenic 45.0%
ATGTGGACTCCGACGAAGAA+GGG + chr1.2:6303156-6303175 MS.gene24567:CDS 50.0%
CACATGCATTGCACAACGAC+TGG - chr1.2:6303141-6303160 None:intergenic 50.0%
CAGTCGTTGTGCAATGCATG+TGG + chr1.2:6303139-6303158 MS.gene24567:CDS 50.0%
GAGTGATCCTACAGGTTCCA+AGG + chr1.2:6302977-6302996 MS.gene24567:CDS 50.0%
GTAGGATCACTCCTCCAAAG+AGG - chr1.2:6302969-6302988 None:intergenic 50.0%
TGGCGAAAGCTCATCATCTG+AGG + chr1.2:6303228-6303247 MS.gene24567:CDS 50.0%
! CTTTGGAGGAGTGATCCTAC+AGG + chr1.2:6302969-6302988 MS.gene24567:CDS 50.0%
CATGTGGACTCCGACGAAGA+AGG + chr1.2:6303155-6303174 MS.gene24567:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 6302768 6303279 6302768 ID=MS.gene24567
chr1.2 mRNA 6302768 6303279 6302768 ID=MS.gene24567.t1;Parent=MS.gene24567
chr1.2 exon 6302768 6302998 6302768 ID=MS.gene24567.t1.exon1;Parent=MS.gene24567.t1
chr1.2 CDS 6302768 6302998 6302768 ID=cds.MS.gene24567.t1;Parent=MS.gene24567.t1
chr1.2 exon 6303118 6303279 6303118 ID=MS.gene24567.t1.exon2;Parent=MS.gene24567.t1
chr1.2 CDS 6303118 6303279 6303118 ID=cds.MS.gene24567.t1;Parent=MS.gene24567.t1
Gene Sequence

>MS.gene24567

ATGAGAGTAAGTAACGATGATCCAGTTCCAGCCACAAAGAAGAAAAAAGCTGCTGCTAGGGCTACAAAAAAGAAGAAAACAGCTGCTAGTGCTGCCAAAAAGAAAATAAAAACTGGAACTGAATACGAATACCCAAAAGGGCAATGGCGAATACTATATCCAACTAGGGTTTGTTTCGATTGCAATACAAACACTACTCCTCTTTGGAGGAGTGATCCTACAGGTTCCAAGGTAATTAGTTAATCTCTATTCTCCCCAACTTTCACTCTTGGTTCATGCAAAAGTGGTATTCTATACTTATACAATATTAATGATTAATAATTTGAATATCTAGTTATATATATATATAGTTAACAAGAAATATGTTGGTCCAGTCGTTGTGCAATGCATGTGGACTCCGACGAAGAAGGGAAGAGACAAAAGCCGATAAGGGTCTTGATACTCATAAGGAAAAGGGCAATGGCGAAAGCTCATCATCTGAGGATGTGAAGAATGTTTTATTGTTCATTTGA
Protein sequence

>MS.gene24567.t1

MRVSNDDPVPATKKKKAAARATKKKKTAASAAKKKIKTGTEYEYPKGQWRILYPTRVCFDCNTNTTPLWRSDPTGSKLTRNMLVQSLCNACGLRRRREETKADKGLDTHKEKGNGESSSSEDVKNVLLFI