AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41259

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41259.t1 MTR_1g048880 81.046 153 14 1 1 138 1 153 1.09e-86 249
MS.gene41259.t1 MTR_1g041455 53.293 167 49 4 1 138 1 167 1.35e-46 149
MS.gene41259.t1 MTR_5g056450 44.706 170 50 7 1 138 1 158 1.34e-28 102
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 35 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAAACATGTGACGGAATT+TGG 0.152253 1.4:+34920123 None:intergenic
ACCCTCAAGGACAATTTCTT+TGG 0.288680 1.4:-34920256 MS.gene41259:CDS
CGAGAAACCTATCAAGAAAA+AGG 0.292133 1.4:-34920066 MS.gene41259:CDS
TTCTCGAGTTGCATGATATA+TGG 0.301047 1.4:+34920083 None:intergenic
TTCATGTTTCGAGTATCATT+TGG 0.349932 1.4:+34920206 None:intergenic
CATGATTACTTCTGAAAACT+TGG 0.381949 1.4:+34920345 None:intergenic
TATGGCTTGGTGCCATCATT+TGG 0.403211 1.4:+34920101 None:intergenic
ACCAAAGAAATTGTCCTTGA+GGG 0.436733 1.4:+34920255 None:intergenic
GACGGAATTTGGTTTCTTGT+TGG 0.441716 1.4:+34920134 None:intergenic
AATTGTCCTTGAGGGTTGAC+AGG 0.443467 1.4:+34920263 None:intergenic
GTTGGCTGAAACATCGTCAT+AGG 0.450574 1.4:+34920152 None:intergenic
TGCAATACTCGGTCGCATGC+AGG 0.453126 1.4:-34920376 MS.gene41259:CDS
TGAATAGAATCTTCTAATTG+AGG 0.475140 1.4:+34920289 None:intergenic
CAACTCAGCTGTTCCTACAT+TGG 0.498861 1.4:-34920036 MS.gene41259:CDS
GTTACTAAAGTCGTTGGCCA+TGG 0.504250 1.4:+34920412 None:intergenic
CTTTGGTATAGTTCCCCGCC+AGG 0.516654 1.4:-34920239 MS.gene41259:CDS
TTGAGTGTTAAATCCAATGT+AGG 0.524429 1.4:+34920023 None:intergenic
GATACTCGAAACATGAATGA+TGG 0.528985 1.4:-34920200 MS.gene41259:CDS
TTGGAACATGAAAACCTGGC+GGG 0.536160 1.4:+34920225 None:intergenic
CCTCTTGTTACTAAAGTCGT+TGG 0.543235 1.4:+34920406 None:intergenic
TACCAAAGAAATTGTCCTTG+AGG 0.579677 1.4:+34920254 None:intergenic
GCAATACTCGGTCGCATGCA+GGG 0.585277 1.4:-34920375 MS.gene41259:CDS
TCAGAACCTGTCAACCCTCA+AGG 0.588149 1.4:-34920269 MS.gene41259:CDS
GAGGCATGATGTGCAATACT+CGG 0.590219 1.4:-34920387 MS.gene41259:CDS
TCATTTGGCAAAACATGTGA+CGG 0.602209 1.4:+34920116 None:intergenic
TCATTTGGAACATGAAAACC+TGG 0.609833 1.4:+34920221 None:intergenic
ATCGTCATAGGATGTGGTTG+AGG 0.614070 1.4:+34920164 None:intergenic
CTCGAAACATGAATGATGGT+AGG 0.629894 1.4:-34920196 MS.gene41259:CDS
TGAAACATCGTCATAGGATG+TGG 0.632597 1.4:+34920158 None:intergenic
TGGAACATGAAAACCTGGCG+GGG 0.647972 1.4:+34920226 None:intergenic
TCACATGGAGTCTCACGAAG+AGG 0.652004 1.4:-34920312 MS.gene41259:CDS
TCATGCATTAGTAACTCACA+TGG 0.657144 1.4:-34920327 MS.gene41259:CDS
CCAACGACTTTAGTAACAAG+AGG 0.660073 1.4:-34920406 MS.gene41259:CDS
GAGTTGCATGATATATGGCT+TGG 0.666515 1.4:+34920088 None:intergenic
TTTGGAACATGAAAACCTGG+CGG 0.719469 1.4:+34920224 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGAATAGAATCTTCTAATTG+AGG + chr1.4:34920140-34920159 None:intergenic 25.0%
TTGAGTGTTAAATCCAATGT+AGG + chr1.4:34920406-34920425 None:intergenic 30.0%
! CATGATTACTTCTGAAAACT+TGG + chr1.4:34920084-34920103 None:intergenic 30.0%
! TCATCATCCTTTTTCTTGAT+AGG + chr1.4:34920370-34920389 None:intergenic 30.0%
! TTCATGTTTCGAGTATCATT+TGG + chr1.4:34920223-34920242 None:intergenic 30.0%
ACCAAAGAAATTGTCCTTGA+GGG + chr1.4:34920174-34920193 None:intergenic 35.0%
CGAGAAACCTATCAAGAAAA+AGG - chr1.4:34920360-34920379 MS.gene41259:CDS 35.0%
GATACTCGAAACATGAATGA+TGG - chr1.4:34920226-34920245 MS.gene41259:CDS 35.0%
TACCAAAGAAATTGTCCTTG+AGG + chr1.4:34920175-34920194 None:intergenic 35.0%
TCATGCATTAGTAACTCACA+TGG - chr1.4:34920099-34920118 MS.gene41259:CDS 35.0%
TCATTTGGCAAAACATGTGA+CGG + chr1.4:34920313-34920332 None:intergenic 35.0%
! TCACATGTTTTGCCAAATGA+TGG - chr1.4:34920313-34920332 MS.gene41259:CDS 35.0%
! TCATTTGGAACATGAAAACC+TGG + chr1.4:34920208-34920227 None:intergenic 35.0%
! TTCTCGAGTTGCATGATATA+TGG + chr1.4:34920346-34920365 None:intergenic 35.0%
ACCCTCAAGGACAATTTCTT+TGG - chr1.4:34920170-34920189 MS.gene41259:CDS 40.0%
CCAACGACTTTAGTAACAAG+AGG - chr1.4:34920020-34920039 MS.gene41259:CDS 40.0%
CCTCTTGTTACTAAAGTCGT+TGG + chr1.4:34920023-34920042 None:intergenic 40.0%
CTCGAAACATGAATGATGGT+AGG - chr1.4:34920230-34920249 MS.gene41259:CDS 40.0%
GAGTTGCATGATATATGGCT+TGG + chr1.4:34920341-34920360 None:intergenic 40.0%
TGAAACATCGTCATAGGATG+TGG + chr1.4:34920271-34920290 None:intergenic 40.0%
! GACGGAATTTGGTTTCTTGT+TGG + chr1.4:34920295-34920314 None:intergenic 40.0%
! GCAAAACATGTGACGGAATT+TGG + chr1.4:34920306-34920325 None:intergenic 40.0%
! TTTGGAACATGAAAACCTGG+CGG + chr1.4:34920205-34920224 None:intergenic 40.0%
AATTGTCCTTGAGGGTTGAC+AGG + chr1.4:34920166-34920185 None:intergenic 45.0%
ATCGTCATAGGATGTGGTTG+AGG + chr1.4:34920265-34920284 None:intergenic 45.0%
CAACTCAGCTGTTCCTACAT+TGG - chr1.4:34920390-34920409 MS.gene41259:CDS 45.0%
GAGGCATGATGTGCAATACT+CGG - chr1.4:34920039-34920058 MS.gene41259:CDS 45.0%
GTTGGCTGAAACATCGTCAT+AGG + chr1.4:34920277-34920296 None:intergenic 45.0%
TTGGAACATGAAAACCTGGC+GGG + chr1.4:34920204-34920223 None:intergenic 45.0%
!! TATGGCTTGGTGCCATCATT+TGG + chr1.4:34920328-34920347 None:intergenic 45.0%
TCACATGGAGTCTCACGAAG+AGG - chr1.4:34920114-34920133 MS.gene41259:CDS 50.0%
TCAGAACCTGTCAACCCTCA+AGG - chr1.4:34920157-34920176 MS.gene41259:CDS 50.0%
TGGAACATGAAAACCTGGCG+GGG + chr1.4:34920203-34920222 None:intergenic 50.0%
CTTTGGTATAGTTCCCCGCC+AGG - chr1.4:34920187-34920206 MS.gene41259:CDS 55.0%
GCAATACTCGGTCGCATGCA+GGG - chr1.4:34920051-34920070 MS.gene41259:CDS 55.0%
TGCAATACTCGGTCGCATGC+AGG - chr1.4:34920050-34920069 MS.gene41259:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.4 gene 34920016 34920432 34920016 ID=MS.gene41259
chr1.4 mRNA 34920016 34920432 34920016 ID=MS.gene41259.t1;Parent=MS.gene41259
chr1.4 exon 34920016 34920432 34920016 ID=MS.gene41259.t1.exon1;Parent=MS.gene41259.t1
chr1.4 CDS 34920016 34920432 34920016 ID=cds.MS.gene41259.t1;Parent=MS.gene41259.t1
Gene Sequence

>MS.gene41259

ATGGCCAACGACTTTAGTAACAAGAGGCATGATGTGCAATACTCGGTCGCATGCAGGGTTTGCAACCAAGTTTTCAGAAGTAATCATGCATTAGTAACTCACATGGAGTCTCACGAAGAGGCCTCAATTAGAAGATTCTATTCAGAACCTGTCAACCCTCAAGGACAATTTCTTTGGTATAGTTCCCCGCCAGGTTTTCATGTTCCAAATGATACTCGAAACATGAATGATGGTAGGATTTTTCAACCTCAACCACATCCTATGACGATGTTTCAGCCAACAAGAAACCAAATTCCGTCACATGTTTTGCCAAATGATGGCACCAAGCCATATATCATGCAACTCGAGAAACCTATCAAGAAAAAGGATGATGACAACTCAGCTGTTCCTACATTGGATTTAACACTCAAGCTTTAG
Protein sequence

>MS.gene41259.t1

MANDFSNKRHDVQYSVACRVCNQVFRSNHALVTHMESHEEASIRRFYSEPVNPQGQFLWYSSPPGFHVPNDTRNMNDGRIFQPQPHPMTMFQPTRNQIPSHVLPNDGTKPYIMQLEKPIKKKDDDNSAVPTLDLTLKL