AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene042565

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene042565.t1 MTR_3g070120 31.646 158 94 4 28 174 146 300 4.49e-13 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTGATGTTTGCTTCTTTA+AGG 0.138534 6.2:-21629811 None:intergenic
CTTAGATTTCAAATCCAATT+TGG 0.142363 6.2:+21629887 MS.gene042565:CDS
TTTACCTTTCTCACAAGATT+TGG 0.226819 6.2:+21630096 MS.gene042565:CDS
GAAGAGGGTTTCTCTTGTTT+TGG 0.245975 6.2:-21629786 None:intergenic
TCAAGATCATTATAGAATTT+AGG 0.267084 6.2:-21630062 None:intergenic
GGAGCGTGCACGGTTAATTA+AGG 0.290096 6.2:+21630205 MS.gene042565:CDS
TCAAGAGCCGGAATTGGATT+TGG 0.301896 6.2:+21630184 MS.gene042565:CDS
TTACCTTTCTCACAAGATTT+GGG 0.302378 6.2:+21630097 MS.gene042565:CDS
TTTGGGGACAAGAGTTGATT+GGG 0.351467 6.2:+21630114 MS.gene042565:CDS
GGCAGCTTAGAAAGAGGATA+TGG 0.353135 6.2:+21629985 MS.gene042565:CDS
TTAGATTTCAAATCCAATTT+GGG 0.355655 6.2:+21629888 MS.gene042565:CDS
GAAAGTTCAAGAGCCGGAAT+TGG 0.391991 6.2:+21630178 MS.gene042565:CDS
ATTTGGGGACAAGAGTTGAT+TGG 0.406484 6.2:+21630113 MS.gene042565:CDS
ACAAGAGTTGATTGGGGAAT+CGG 0.415419 6.2:+21630121 MS.gene042565:CDS
GCACGCTCCAAATCCAATTC+CGG 0.440433 6.2:-21630191 None:intergenic
GTCCCCAAATCTTGTGAGAA+AGG 0.458776 6.2:-21630100 None:intergenic
CTAAGAAGCCATTGAGAATG+AGG 0.476463 6.2:-21629869 None:intergenic
ATCCTCTTTCTAAGCTGCCC+TGG 0.495595 6.2:-21629981 None:intergenic
ATATGAGAACATGAAGAAAG+AGG 0.508111 6.2:+21630022 MS.gene042565:CDS
ATTCTATAATGATCTTGAGC+AGG 0.511151 6.2:+21630067 MS.gene042565:CDS
CTTTCTAAGCTGCCCTGGTG+TGG 0.513545 6.2:-21629976 None:intergenic
GTCATTTCTAAGTTATTGCA+AGG 0.515777 6.2:+21630239 MS.gene042565:CDS
GACGAAATCCTCATTCTCAA+TGG 0.536241 6.2:+21629861 MS.gene042565:CDS
GGATAGAGTTGGATGAAATG+TGG 0.536445 6.2:+21630147 MS.gene042565:CDS
AATTGGATTTGGAGCGTGCA+CGG 0.556576 6.2:+21630195 MS.gene042565:CDS
GGAATTGAAAGTTCAAGAGC+CGG 0.565005 6.2:+21630172 MS.gene042565:CDS
CTTACTGTGAAAACCACACC+AGG 0.566823 6.2:+21629963 MS.gene042565:CDS
TGCTTCTTTAAGGAAGAAGA+GGG 0.572401 6.2:-21629801 None:intergenic
CACCAGGGCAGCTTAGAAAG+AGG 0.573849 6.2:+21629979 MS.gene042565:CDS
TACCTTTCTCACAAGATTTG+GGG 0.576919 6.2:+21630098 MS.gene042565:CDS
TTGGGGACAAGAGTTGATTG+GGG 0.578511 6.2:+21630115 MS.gene042565:CDS
AGATCATTATAGAATTTAGG+AGG 0.583496 6.2:-21630059 None:intergenic
TTGCTTCTTTAAGGAAGAAG+AGG 0.590446 6.2:-21629802 None:intergenic
AGAGTTGGATGAAATGTGGA+AGG 0.591400 6.2:+21630151 MS.gene042565:CDS
GGAATCGGATCGGATAGAGT+TGG 0.604264 6.2:+21630136 MS.gene042565:CDS
GATTTCGTCATCGAAAGTGA+AGG 0.605806 6.2:-21629847 None:intergenic
AGTTGATTGGGGAATCGGAT+CGG 0.606498 6.2:+21630126 MS.gene042565:CDS
TTACTGTGAAAACCACACCA+GGG 0.799910 6.2:+21629964 MS.gene042565:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TCAAGATCATTATAGAATTT+AGG - chr6.2:21630065-21630084 None:intergenic 20.0%
!! TTAGATTTCAAATCCAATTT+GGG + chr6.2:21629888-21629907 MS.gene042565:CDS 20.0%
! AGATCATTATAGAATTTAGG+AGG - chr6.2:21630062-21630081 None:intergenic 25.0%
! CTTAGATTTCAAATCCAATT+TGG + chr6.2:21629887-21629906 MS.gene042565:CDS 25.0%
!! AGAATTTAGGAGGAAATTTT+TGG - chr6.2:21630052-21630071 None:intergenic 25.0%
!!! TTTCTCTTGTTTTGGATTTT+GGG - chr6.2:21629781-21629800 None:intergenic 25.0%
ATATGAGAACATGAAGAAAG+AGG + chr6.2:21630022-21630041 MS.gene042565:CDS 30.0%
ATTCTATAATGATCTTGAGC+AGG + chr6.2:21630067-21630086 MS.gene042565:CDS 30.0%
GTCATTTCTAAGTTATTGCA+AGG + chr6.2:21630239-21630258 MS.gene042565:CDS 30.0%
GTTTGATGTTTGCTTCTTTA+AGG - chr6.2:21629814-21629833 None:intergenic 30.0%
TTACCTTTCTCACAAGATTT+GGG + chr6.2:21630097-21630116 MS.gene042565:CDS 30.0%
TTTACCTTTCTCACAAGATT+TGG + chr6.2:21630096-21630115 MS.gene042565:CDS 30.0%
!!! GTTTCTCTTGTTTTGGATTT+TGG - chr6.2:21629782-21629801 None:intergenic 30.0%
TACCTTTCTCACAAGATTTG+GGG + chr6.2:21630098-21630117 MS.gene042565:CDS 35.0%
! TGCTTCTTTAAGGAAGAAGA+GGG - chr6.2:21629804-21629823 None:intergenic 35.0%
! TTGCTTCTTTAAGGAAGAAG+AGG - chr6.2:21629805-21629824 None:intergenic 35.0%
!! CATTGCATTTTGACCCAAAT+TGG - chr6.2:21629904-21629923 None:intergenic 35.0%
AGAGTTGGATGAAATGTGGA+AGG + chr6.2:21630151-21630170 MS.gene042565:CDS 40.0%
CTAAGAAGCCATTGAGAATG+AGG - chr6.2:21629872-21629891 None:intergenic 40.0%
GACGAAATCCTCATTCTCAA+TGG + chr6.2:21629861-21629880 MS.gene042565:CDS 40.0%
GATTTCGTCATCGAAAGTGA+AGG - chr6.2:21629850-21629869 None:intergenic 40.0%
GGAATTGAAAGTTCAAGAGC+CGG + chr6.2:21630172-21630191 MS.gene042565:CDS 40.0%
GGATAGAGTTGGATGAAATG+TGG + chr6.2:21630147-21630166 MS.gene042565:CDS 40.0%
TTACTGTGAAAACCACACCA+GGG + chr6.2:21629964-21629983 MS.gene042565:CDS 40.0%
! ACAAGAGTTGATTGGGGAAT+CGG + chr6.2:21630121-21630140 MS.gene042565:CDS 40.0%
! ATTTGGGGACAAGAGTTGAT+TGG + chr6.2:21630113-21630132 MS.gene042565:CDS 40.0%
! TTTGGGGACAAGAGTTGATT+GGG + chr6.2:21630114-21630133 MS.gene042565:CDS 40.0%
!! GAAGAGGGTTTCTCTTGTTT+TGG - chr6.2:21629789-21629808 None:intergenic 40.0%
AGTTGATTGGGGAATCGGAT+CGG + chr6.2:21630126-21630145 MS.gene042565:CDS 45.0%
CTTACTGTGAAAACCACACC+AGG + chr6.2:21629963-21629982 MS.gene042565:CDS 45.0%
GAAAGTTCAAGAGCCGGAAT+TGG + chr6.2:21630178-21630197 MS.gene042565:CDS 45.0%
GGCAGCTTAGAAAGAGGATA+TGG + chr6.2:21629985-21630004 MS.gene042565:CDS 45.0%
GTCCCCAAATCTTGTGAGAA+AGG - chr6.2:21630103-21630122 None:intergenic 45.0%
TCAAGAGCCGGAATTGGATT+TGG + chr6.2:21630184-21630203 MS.gene042565:CDS 45.0%
! AATTGGATTTGGAGCGTGCA+CGG + chr6.2:21630195-21630214 MS.gene042565:CDS 45.0%
! TTGGGGACAAGAGTTGATTG+GGG + chr6.2:21630115-21630134 MS.gene042565:CDS 45.0%
ATCCTCTTTCTAAGCTGCCC+TGG - chr6.2:21629984-21630003 None:intergenic 50.0%
GCACGCTCCAAATCCAATTC+CGG - chr6.2:21630194-21630213 None:intergenic 50.0%
GGAATCGGATCGGATAGAGT+TGG + chr6.2:21630136-21630155 MS.gene042565:CDS 50.0%
GGAGCGTGCACGGTTAATTA+AGG + chr6.2:21630205-21630224 MS.gene042565:CDS 50.0%
CACCAGGGCAGCTTAGAAAG+AGG + chr6.2:21629979-21629998 MS.gene042565:CDS 55.0%
CTTTCTAAGCTGCCCTGGTG+TGG - chr6.2:21629979-21629998 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr6.2 gene 21629747 21630277 21629747 ID=MS.gene042565
chr6.2 mRNA 21629747 21630277 21629747 ID=MS.gene042565.t1;Parent=MS.gene042565
chr6.2 exon 21629747 21630277 21629747 ID=MS.gene042565.t1.exon1;Parent=MS.gene042565.t1
chr6.2 CDS 21629747 21630277 21629747 ID=cds.MS.gene042565.t1;Parent=MS.gene042565.t1
Gene Sequence

>MS.gene042565

ATGGCAAAGAAATCAAGTTGTTCTTCTTCATCCCAAAATCCAAAACAAGAGAAACCCTCTTCTTCCTTAAAGAAGCAAACATCAAACTCACGTAAGAAAACCTTCACTTTCGATGACGAAATCCTCATTCTCAATGGCTTCTTAGATTTCAAATCCAATTTGGGTCAAAATGCAATGACAGATTACACACTTTTTTATAACTCTGTGAAAGATTTGCTTACTGTGAAAACCACACCAGGGCAGCTTAGAAAGAGGATATGGAAGTTAAAACAAAAATATGAGAACATGAAGAAAGAGGAAAACCAAAAATTTCCTCCTAAATTCTATAATGATCTTGAGCAGGAAATAATTTACCTTTCTCACAAGATTTGGGGACAAGAGTTGATTGGGGAATCGGATCGGATAGAGTTGGATGAAATGTGGAAGGAATTGAAAGTTCAAGAGCCGGAATTGGATTTGGAGCGTGCACGGTTAATTAAGGACTCGATTGACGTCATTTCTAAGTTATTGCAAGGATCATCTTCGTCTTAG
Protein sequence

>MS.gene042565.t1

MAKKSSCSSSSQNPKQEKPSSSLKKQTSNSRKKTFTFDDEILILNGFLDFKSNLGQNAMTDYTLFYNSVKDLLTVKTTPGQLRKRIWKLKQKYENMKKEENQKFPPKFYNDLEQEIIYLSHKIWGQELIGESDRIELDEMWKELKVQEPELDLERARLIKDSIDVISKLLQGSSSS