AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene99294

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99294.t1 MTR_1g048880 81.699 153 13 1 1 138 1 153 5.54e-88 253
MS.gene99294.t1 MTR_1g041455 53.892 167 48 4 1 138 1 167 1.12e-47 151
MS.gene99294.t1 MTR_5g056450 44.118 170 51 7 1 138 1 158 1.37e-27 100
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAAACATGTGACGGAATT+TGG 0.152253 1.3:+31030810 None:intergenic
ACCCTCAAGGACAATTTCTT+TGG 0.288680 1.3:-31030943 MS.gene99294:CDS
CGAGAAACCTATCAAGAAAA+AGG 0.292133 1.3:-31030753 MS.gene99294:CDS
TTCTCGAGTTGCATGATATA+TGG 0.301047 1.3:+31030770 None:intergenic
CATGATTGCTTCTGAAAACT+TGG 0.342531 1.3:+31031032 None:intergenic
TTCATGTTTCGAGTATCATT+TGG 0.349932 1.3:+31030893 None:intergenic
TATGGCTTGGTGCCATCATT+TGG 0.403211 1.3:+31030788 None:intergenic
ACCAAAGAAATTGTCCTTGA+GGG 0.436733 1.3:+31030942 None:intergenic
GACGGAATTTGGTTTCTTGT+TGG 0.441716 1.3:+31030821 None:intergenic
AATTGTCCTTGAGGGTTGAC+AGG 0.443467 1.3:+31030950 None:intergenic
GTTGGCTGAAACATCGTCAT+AGG 0.450574 1.3:+31030839 None:intergenic
TGCAATACTCGGTCGCATGC+AGG 0.453126 1.3:-31031063 MS.gene99294:CDS
TGAATAGAATCTTCTAATTG+AGG 0.475140 1.3:+31030976 None:intergenic
CTTTGGTATAGTTCCCCACC+AGG 0.476657 1.3:-31030926 MS.gene99294:CDS
CAACTCAGCTGTTCCTACAT+TGG 0.498861 1.3:-31030723 MS.gene99294:CDS
GTTACTAAAGTCGTTGGCCA+TGG 0.504250 1.3:+31031099 None:intergenic
TTGAGTGTTAAATCCAATGT+AGG 0.524429 1.3:+31030710 None:intergenic
GATACTCGAAACATGAATGA+TGG 0.528985 1.3:-31030887 MS.gene99294:CDS
CCTCTTGTTACTAAAGTCGT+TGG 0.543235 1.3:+31031093 None:intergenic
TACCAAAGAAATTGTCCTTG+AGG 0.579677 1.3:+31030941 None:intergenic
GCAATACTCGGTCGCATGCA+GGG 0.585277 1.3:-31031062 MS.gene99294:CDS
TCAGAACCTGTCAACCCTCA+AGG 0.588149 1.3:-31030956 MS.gene99294:CDS
GAGGCATGATGTGCAATACT+CGG 0.590219 1.3:-31031074 MS.gene99294:CDS
TTGGAACATGAAAACCTGGT+GGG 0.591198 1.3:+31030912 None:intergenic
TCATTTGGCAAAACATGTGA+CGG 0.602209 1.3:+31030803 None:intergenic
TCATTTGGAACATGAAAACC+TGG 0.608295 1.3:+31030908 None:intergenic
ATCGTCATAGGATGTGGTTG+AGG 0.614070 1.3:+31030851 None:intergenic
CTCGAAACATGAATGATGGT+AGG 0.629894 1.3:-31030883 MS.gene99294:CDS
TGAAACATCGTCATAGGATG+TGG 0.632597 1.3:+31030845 None:intergenic
CTCACATGGAGTCTCACGAA+GGG 0.634625 1.3:-31031000 MS.gene99294:CDS
TGGAACATGAAAACCTGGTG+GGG 0.648382 1.3:+31030913 None:intergenic
TCATGCATTAGTAACTCACA+TGG 0.657144 1.3:-31031014 MS.gene99294:CDS
CCAACGACTTTAGTAACAAG+AGG 0.660073 1.3:-31031093 MS.gene99294:CDS
GAGTTGCATGATATATGGCT+TGG 0.666515 1.3:+31030775 None:intergenic
TCACATGGAGTCTCACGAAG+GGG 0.674235 1.3:-31030999 MS.gene99294:CDS
ACTCACATGGAGTCTCACGA+AGG 0.681368 1.3:-31031001 MS.gene99294:CDS
TTTGGAACATGAAAACCTGG+TGG 0.685806 1.3:+31030911 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGAATAGAATCTTCTAATTG+AGG + chr1.3:31030827-31030846 None:intergenic 25.0%
TTGAGTGTTAAATCCAATGT+AGG + chr1.3:31031093-31031112 None:intergenic 30.0%
! TCATCATCCTTTTTCTTGAT+AGG + chr1.3:31031057-31031076 None:intergenic 30.0%
! TTCATGTTTCGAGTATCATT+TGG + chr1.3:31030910-31030929 None:intergenic 30.0%
ACCAAAGAAATTGTCCTTGA+GGG + chr1.3:31030861-31030880 None:intergenic 35.0%
CGAGAAACCTATCAAGAAAA+AGG - chr1.3:31031047-31031066 MS.gene99294:CDS 35.0%
GATACTCGAAACATGAATGA+TGG - chr1.3:31030913-31030932 MS.gene99294:CDS 35.0%
TACCAAAGAAATTGTCCTTG+AGG + chr1.3:31030862-31030881 None:intergenic 35.0%
TCATGCATTAGTAACTCACA+TGG - chr1.3:31030786-31030805 MS.gene99294:CDS 35.0%
TCATTTGGCAAAACATGTGA+CGG + chr1.3:31031000-31031019 None:intergenic 35.0%
! CATGATTGCTTCTGAAAACT+TGG + chr1.3:31030771-31030790 None:intergenic 35.0%
! TCACATGTTTTGCCAAATGA+TGG - chr1.3:31031000-31031019 MS.gene99294:CDS 35.0%
! TCATTTGGAACATGAAAACC+TGG + chr1.3:31030895-31030914 None:intergenic 35.0%
! TTCTCGAGTTGCATGATATA+TGG + chr1.3:31031033-31031052 None:intergenic 35.0%
ACCCTCAAGGACAATTTCTT+TGG - chr1.3:31030857-31030876 MS.gene99294:CDS 40.0%
CCAACGACTTTAGTAACAAG+AGG - chr1.3:31030707-31030726 MS.gene99294:CDS 40.0%
CCTCTTGTTACTAAAGTCGT+TGG + chr1.3:31030710-31030729 None:intergenic 40.0%
CTCGAAACATGAATGATGGT+AGG - chr1.3:31030917-31030936 MS.gene99294:CDS 40.0%
GAGTTGCATGATATATGGCT+TGG + chr1.3:31031028-31031047 None:intergenic 40.0%
TGAAACATCGTCATAGGATG+TGG + chr1.3:31030958-31030977 None:intergenic 40.0%
TTGGAACATGAAAACCTGGT+GGG + chr1.3:31030891-31030910 None:intergenic 40.0%
! GACGGAATTTGGTTTCTTGT+TGG + chr1.3:31030982-31031001 None:intergenic 40.0%
! GCAAAACATGTGACGGAATT+TGG + chr1.3:31030993-31031012 None:intergenic 40.0%
! TTTGGAACATGAAAACCTGG+TGG + chr1.3:31030892-31030911 None:intergenic 40.0%
AATTGTCCTTGAGGGTTGAC+AGG + chr1.3:31030853-31030872 None:intergenic 45.0%
ATCGTCATAGGATGTGGTTG+AGG + chr1.3:31030952-31030971 None:intergenic 45.0%
CAACTCAGCTGTTCCTACAT+TGG - chr1.3:31031077-31031096 MS.gene99294:CDS 45.0%
GAGGCATGATGTGCAATACT+CGG - chr1.3:31030726-31030745 MS.gene99294:CDS 45.0%
GTTGGCTGAAACATCGTCAT+AGG + chr1.3:31030964-31030983 None:intergenic 45.0%
TGGAACATGAAAACCTGGTG+GGG + chr1.3:31030890-31030909 None:intergenic 45.0%
!! TATGGCTTGGTGCCATCATT+TGG + chr1.3:31031015-31031034 None:intergenic 45.0%
ACTCACATGGAGTCTCACGA+AGG - chr1.3:31030799-31030818 MS.gene99294:CDS 50.0%
CTCACATGGAGTCTCACGAA+GGG - chr1.3:31030800-31030819 MS.gene99294:CDS 50.0%
CTTTGGTATAGTTCCCCACC+AGG - chr1.3:31030874-31030893 MS.gene99294:CDS 50.0%
TCACATGGAGTCTCACGAAG+GGG - chr1.3:31030801-31030820 MS.gene99294:CDS 50.0%
TCAGAACCTGTCAACCCTCA+AGG - chr1.3:31030844-31030863 MS.gene99294:CDS 50.0%
GCAATACTCGGTCGCATGCA+GGG - chr1.3:31030738-31030757 MS.gene99294:CDS 55.0%
TGCAATACTCGGTCGCATGC+AGG - chr1.3:31030737-31030756 MS.gene99294:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 31030703 31031119 31030703 ID=MS.gene99294
chr1.3 mRNA 31030703 31031119 31030703 ID=MS.gene99294.t1;Parent=MS.gene99294
chr1.3 exon 31030703 31031119 31030703 ID=MS.gene99294.t1.exon1;Parent=MS.gene99294.t1
chr1.3 CDS 31030703 31031119 31030703 ID=cds.MS.gene99294.t1;Parent=MS.gene99294.t1
Gene Sequence

>MS.gene99294

ATGGCCAACGACTTTAGTAACAAGAGGCATGATGTGCAATACTCGGTCGCATGCAGGGTTTGCAACCAAGTTTTCAGAAGCAATCATGCATTAGTAACTCACATGGAGTCTCACGAAGGGGCCTCAATTAGAAGATTCTATTCAGAACCTGTCAACCCTCAAGGACAATTTCTTTGGTATAGTTCCCCACCAGGTTTTCATGTTCCAAATGATACTCGAAACATGAATGATGGTAGGATTTTTCAACCTCAACCACATCCTATGACGATGTTTCAGCCAACAAGAAACCAAATTCCGTCACATGTTTTGCCAAATGATGGCACCAAGCCATATATCATGCAACTCGAGAAACCTATCAAGAAAAAGGATGATGACAACTCAGCTGTTCCTACATTGGATTTAACACTCAAGCTTTAG
Protein sequence

>MS.gene99294.t1

MANDFSNKRHDVQYSVACRVCNQVFRSNHALVTHMESHEGASIRRFYSEPVNPQGQFLWYSSPPGFHVPNDTRNMNDGRIFQPQPHPMTMFQPTRNQIPSHVLPNDGTKPYIMQLEKPIKKKDDDNSAVPTLDLTLKL