AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene037974

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene037974.t1 MTR_1g048880 82.353 153 12 1 1 138 1 153 2.35e-88 254
MS.gene037974.t1 MTR_1g041455 54.491 167 47 4 1 138 1 167 2.40e-48 153
MS.gene037974.t1 MTR_5g056450 44.118 170 51 7 1 138 1 158 6.72e-28 100
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 36 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 1.1:+33394229 None:intergenic
ACCCTCAAGGACAATTTCTT+TGG 0.288680 1.1:-33394362 MS.gene037974:CDS
CGAGAAACCTATCAAGAAAA+AGG 0.292133 1.1:-33394172 MS.gene037974:CDS
TTCTCGAGTTGCATGATATA+TGG 0.301047 1.1:+33394189 None:intergenic
CATGATTACTTCTGAAAACT+TGG 0.381949 1.1:+33394451 None:intergenic
TATGGCTTGGTGCCATCATT+TGG 0.403211 1.1:+33394207 None:intergenic
GTTGGCTGAAACATCATCAT+AGG 0.427829 1.1:+33394258 None:intergenic
ACCAAAGAAATTGTCCTTGA+GGG 0.436733 1.1:+33394361 None:intergenic
GACGGAATTTGGTTTCTTGT+TGG 0.441716 1.1:+33394240 None:intergenic
AATTGTCCTTGAGGGTTGAC+AGG 0.443467 1.1:+33394369 None:intergenic
TGCAATACTCGGTCGCATGC+AGG 0.453126 1.1:-33394482 MS.gene037974:CDS
TGAATAGAATCTTCTAATTG+AGG 0.475140 1.1:+33394395 None:intergenic
CTTTGGTATAGTTCCCCACC+AGG 0.476657 1.1:-33394345 MS.gene037974:CDS
CAACTCAGCTGTTCCTACAT+TGG 0.498861 1.1:-33394142 MS.gene037974:CDS
GTTACTAAAGTCGTTGGCCA+TGG 0.504250 1.1:+33394518 None:intergenic
TTGAGTGTTAAATCCAATGT+AGG 0.524429 1.1:+33394129 None:intergenic
GATACTCAAAACATGAATGA+TGG 0.528985 1.1:-33394306 MS.gene037974:CDS
ATCATCATAGGATGTGGTTG+AGG 0.539731 1.1:+33394270 None:intergenic
CCTCTTGTTACTAAAGTCGT+TGG 0.543235 1.1:+33394512 None:intergenic
TACCAAAGAAATTGTCCTTG+AGG 0.579677 1.1:+33394360 None:intergenic
GCAATACTCGGTCGCATGCA+GGG 0.585277 1.1:-33394481 MS.gene037974:CDS
TCAGAACCTGTCAACCCTCA+AGG 0.588149 1.1:-33394375 MS.gene037974:CDS
GAGGCATGATGTGCAATACT+CGG 0.590219 1.1:-33394493 MS.gene037974:CDS
TTGGAACATGAAAACCTGGT+GGG 0.591198 1.1:+33394331 None:intergenic
TCATTTGGCAAAACATGTGA+CGG 0.602209 1.1:+33394222 None:intergenic
TCATTTGGAACATGAAAACC+TGG 0.608295 1.1:+33394327 None:intergenic
CTCAAAACATGAATGATGGT+AGG 0.612081 1.1:-33394302 MS.gene037974:CDS
CTCACATGGAGTCTCACGAA+GGG 0.634625 1.1:-33394419 MS.gene037974:CDS
TGGAACATGAAAACCTGGTG+GGG 0.648382 1.1:+33394332 None:intergenic
TGAAACATCATCATAGGATG+TGG 0.653978 1.1:+33394264 None:intergenic
TCATGCATTAGTAACTCACA+TGG 0.657144 1.1:-33394433 MS.gene037974:CDS
CCAACGACTTTAGTAACAAG+AGG 0.660073 1.1:-33394512 MS.gene037974:CDS
GAGTTGCATGATATATGGCT+TGG 0.666515 1.1:+33394194 None:intergenic
TCACATGGAGTCTCACGAAG+GGG 0.674235 1.1:-33394418 MS.gene037974:CDS
ACTCACATGGAGTCTCACGA+AGG 0.681368 1.1:-33394420 MS.gene037974:CDS
TTTGGAACATGAAAACCTGG+TGG 0.685806 1.1:+33394330 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGAATAGAATCTTCTAATTG+AGG + chr1.1:33394246-33394265 None:intergenic 25.0%
!!! TTCATGTTTTGAGTATCATT+TGG + chr1.1:33394329-33394348 None:intergenic 25.0%
GATACTCAAAACATGAATGA+TGG - chr1.1:33394332-33394351 MS.gene037974:CDS 30.0%
TTGAGTGTTAAATCCAATGT+AGG + chr1.1:33394512-33394531 None:intergenic 30.0%
! CATGATTACTTCTGAAAACT+TGG + chr1.1:33394190-33394209 None:intergenic 30.0%
! TCATCATCCTTTTTCTTGAT+AGG + chr1.1:33394476-33394495 None:intergenic 30.0%
ACCAAAGAAATTGTCCTTGA+GGG + chr1.1:33394280-33394299 None:intergenic 35.0%
CGAGAAACCTATCAAGAAAA+AGG - chr1.1:33394466-33394485 MS.gene037974:CDS 35.0%
CTCAAAACATGAATGATGGT+AGG - chr1.1:33394336-33394355 MS.gene037974:CDS 35.0%
TACCAAAGAAATTGTCCTTG+AGG + chr1.1:33394281-33394300 None:intergenic 35.0%
TCATGCATTAGTAACTCACA+TGG - chr1.1:33394205-33394224 MS.gene037974:CDS 35.0%
TCATTTGGCAAAACATGTGA+CGG + chr1.1:33394419-33394438 None:intergenic 35.0%
TGAAACATCATCATAGGATG+TGG + chr1.1:33394377-33394396 None:intergenic 35.0%
! TCACATGTTTTGCCAAATGA+TGG - chr1.1:33394419-33394438 MS.gene037974:CDS 35.0%
! TCATTTGGAACATGAAAACC+TGG + chr1.1:33394314-33394333 None:intergenic 35.0%
! TTCTCGAGTTGCATGATATA+TGG + chr1.1:33394452-33394471 None:intergenic 35.0%
ACCCTCAAGGACAATTTCTT+TGG - chr1.1:33394276-33394295 MS.gene037974:CDS 40.0%
ATCATCATAGGATGTGGTTG+AGG + chr1.1:33394371-33394390 None:intergenic 40.0%
CCAACGACTTTAGTAACAAG+AGG - chr1.1:33394126-33394145 MS.gene037974:CDS 40.0%
CCTCTTGTTACTAAAGTCGT+TGG + chr1.1:33394129-33394148 None:intergenic 40.0%
GAGTTGCATGATATATGGCT+TGG + chr1.1:33394447-33394466 None:intergenic 40.0%
GTTGGCTGAAACATCATCAT+AGG + chr1.1:33394383-33394402 None:intergenic 40.0%
TTGGAACATGAAAACCTGGT+GGG + chr1.1:33394310-33394329 None:intergenic 40.0%
! GACGGAATTTGGTTTCTTGT+TGG + chr1.1:33394401-33394420 None:intergenic 40.0%
! GCAAAACATGTGACGGAATT+TGG + chr1.1:33394412-33394431 None:intergenic 40.0%
! TTTGGAACATGAAAACCTGG+TGG + chr1.1:33394311-33394330 None:intergenic 40.0%
AATTGTCCTTGAGGGTTGAC+AGG + chr1.1:33394272-33394291 None:intergenic 45.0%
CAACTCAGCTGTTCCTACAT+TGG - chr1.1:33394496-33394515 MS.gene037974:CDS 45.0%
GAGGCATGATGTGCAATACT+CGG - chr1.1:33394145-33394164 MS.gene037974:CDS 45.0%
TGGAACATGAAAACCTGGTG+GGG + chr1.1:33394309-33394328 None:intergenic 45.0%
!! TATGGCTTGGTGCCATCATT+TGG + chr1.1:33394434-33394453 None:intergenic 45.0%
ACTCACATGGAGTCTCACGA+AGG - chr1.1:33394218-33394237 MS.gene037974:CDS 50.0%
CTCACATGGAGTCTCACGAA+GGG - chr1.1:33394219-33394238 MS.gene037974:CDS 50.0%
CTTTGGTATAGTTCCCCACC+AGG - chr1.1:33394293-33394312 MS.gene037974:CDS 50.0%
TCACATGGAGTCTCACGAAG+GGG - chr1.1:33394220-33394239 MS.gene037974:CDS 50.0%
TCAGAACCTGTCAACCCTCA+AGG - chr1.1:33394263-33394282 MS.gene037974:CDS 50.0%
GCAATACTCGGTCGCATGCA+GGG - chr1.1:33394157-33394176 MS.gene037974:CDS 55.0%
TGCAATACTCGGTCGCATGC+AGG - chr1.1:33394156-33394175 MS.gene037974:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 33394122 33394538 33394122 ID=MS.gene037974
chr1.1 mRNA 33394122 33394538 33394122 ID=MS.gene037974.t1;Parent=MS.gene037974
chr1.1 exon 33394122 33394538 33394122 ID=MS.gene037974.t1.exon1;Parent=MS.gene037974.t1
chr1.1 CDS 33394122 33394538 33394122 ID=cds.MS.gene037974.t1;Parent=MS.gene037974.t1
Gene Sequence

>MS.gene037974

ATGGCCAACGACTTTAGTAACAAGAGGCATGATGTGCAATACTCGGTCGCATGCAGGGTTTGCAACCAAGTTTTCAGAAGTAATCATGCATTAGTAACTCACATGGAGTCTCACGAAGGGGCCTCAATTAGAAGATTCTATTCAGAACCTGTCAACCCTCAAGGACAATTTCTTTGGTATAGTTCCCCACCAGGTTTTCATGTTCCAAATGATACTCAAAACATGAATGATGGTAGGATTTTTCAACCTCAACCACATCCTATGATGATGTTTCAGCCAACAAGAAACCAAATTCCGTCACATGTTTTGCCAAATGATGGCACCAAGCCATATATCATGCAACTCGAGAAACCTATCAAGAAAAAGGATGATGACAACTCAGCTGTTCCTACATTGGATTTAACACTCAAGCTTTAG
Protein sequence

>MS.gene037974.t1

MANDFSNKRHDVQYSVACRVCNQVFRSNHALVTHMESHEGASIRRFYSEPVNPQGQFLWYSSPPGFHVPNDTQNMNDGRIFQPQPHPMMMFQPTRNQIPSHVLPNDGTKPYIMQLEKPIKKKDDDNSAVPTLDLTLKL