AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85094

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85094.t1 MTR_4g073100 48.718 156 62 4 1 144 1 150 5.80e-41 139
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene85094.t1 AT3G51960 49.333 150 66 4 4 144 10 158 1.26e-39 134
MS.gene85094.t1 AT3G51960 49.664 149 66 4 4 144 10 157 1.52e-39 134
MS.gene85094.t1 AT3G51960 56.364 110 42 1 41 144 10 119 2.59e-39 132
MS.gene85094.t1 AT2G16770 48.993 149 59 4 1 144 1 137 3.00e-36 126
MS.gene85094.t1 AT2G16770 48.993 149 59 4 1 144 1 137 3.00e-36 126
MS.gene85094.t1 AT4G35040 45.860 157 67 5 1 144 1 152 4.07e-34 121
MS.gene85094.t1 AT4G35040 45.860 157 67 5 1 144 1 152 4.07e-34 121
MS.gene85094.t1 AT4G35040 45.860 157 67 5 1 144 1 152 4.07e-34 121
MS.gene85094.t1 AT4G35040 45.860 157 67 5 1 144 1 152 4.07e-34 121

Find 22 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGGCAGAAACAGCTTATT+TGG 0.185081 3.4:+26176224 MS.gene85094:CDS
GTCAAGGTTAAGGAACATTT+TGG 0.239454 3.4:+26176329 MS.gene85094:CDS
CTATTTCCAGAAGTCCTCTT+TGG 0.283237 3.4:-26176171 None:intergenic
AAAGTATAGGGAGAAGAAAA+AGG 0.319200 3.4:+26176206 MS.gene85094:CDS
TCAAGGCCAAAGAGGACTTC+TGG 0.352816 3.4:+26176165 MS.gene85094:CDS
AAGCTGAATTGTCAAGGTTA+AGG 0.395629 3.4:+26176319 MS.gene85094:CDS
ACATGCAGGATCATCATCTA+AGG 0.417339 3.4:+26176428 MS.gene85094:intron
TGAAAATTGCTACATGACTC+TGG 0.465225 3.4:-26175979 None:intergenic
AAGAAAGAAAATATGGATGA+TGG 0.479572 3.4:+26175907 None:intergenic
GAAGTTATTCACTGTATCCA+TGG 0.491570 3.4:-26176500 None:intergenic
CTGAAGATGACACAAATTCA+AGG 0.502147 3.4:+26176148 MS.gene85094:CDS
TGTGTGTGATAAGCATCATC+TGG 0.502148 3.4:-26176090 None:intergenic
GTCCTTTAGTACTACTCATG+TGG 0.520570 3.4:-26176474 None:intergenic
TTTGAGGAAATTACAAGGGC+AGG 0.531022 3.4:+26176287 MS.gene85094:CDS
AACCACATGAGTAGTACTAA+AGG 0.554702 3.4:+26176472 MS.gene85094:CDS
TATGGATGATGGAAATTCTG+AGG 0.560716 3.4:+26175918 None:intergenic
TACTTGAAGCTGAATTGTCA+AGG 0.575730 3.4:+26176313 MS.gene85094:CDS
TAGTACTAAAGGACAAACCA+TGG 0.638865 3.4:+26176483 MS.gene85094:CDS
ACACAAATTCAAGGCCAAAG+AGG 0.655610 3.4:+26176157 MS.gene85094:CDS
TGATAAGCATCATCTGGACC+AGG 0.660245 3.4:-26176084 None:intergenic
GCTCACACTTGTAATCCACC+TGG 0.667325 3.4:+26176066 MS.gene85094:CDS
TAAGCATCATCTGGACCAGG+TGG 0.681695 3.4:-26176081 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAGCTGTTAAAAAGTATA+GGG + chr3.4:26176194-26176213 MS.gene85094:CDS 25.0%
!! ATGGTAGATTTTTCTCAAAA+GGG - chr3.4:26176398-26176417 None:intergenic 25.0%
!!! AACATTTTGGTACAACTTAA+GGG + chr3.4:26176342-26176361 MS.gene85094:intron 25.0%
!!! AACTTTTGAGGAAATTACAA+GGG + chr3.4:26176283-26176302 MS.gene85094:CDS 25.0%
AAAGTATAGGGAGAAGAAAA+AGG + chr3.4:26176206-26176225 MS.gene85094:CDS 30.0%
! CATGGTAGATTTTTCTCAAA+AGG - chr3.4:26176399-26176418 None:intergenic 30.0%
! GAGAAGCTGTTAAAAAGTAT+AGG + chr3.4:26176193-26176212 MS.gene85094:CDS 30.0%
! TTGTGAATCAACAACTTTTG+AGG + chr3.4:26176271-26176290 MS.gene85094:CDS 30.0%
!! CAACTTTTGAGGAAATTACA+AGG + chr3.4:26176282-26176301 MS.gene85094:CDS 30.0%
!! GAACATTTTGGTACAACTTA+AGG + chr3.4:26176341-26176360 MS.gene85094:intron 30.0%
AAAGGCAGAAACAGCTTATT+TGG + chr3.4:26176224-26176243 MS.gene85094:CDS 35.0%
AACCACATGAGTAGTACTAA+AGG + chr3.4:26176472-26176491 MS.gene85094:CDS 35.0%
AAGCTGAATTGTCAAGGTTA+AGG + chr3.4:26176319-26176338 MS.gene85094:CDS 35.0%
CTGAAGATGACACAAATTCA+AGG + chr3.4:26176148-26176167 MS.gene85094:CDS 35.0%
GAAGTTATTCACTGTATCCA+TGG - chr3.4:26176503-26176522 None:intergenic 35.0%
GGAAAAGTTGACAATGAACT+AGG + chr3.4:26176363-26176382 MS.gene85094:intron 35.0%
TACTTGAAGCTGAATTGTCA+AGG + chr3.4:26176313-26176332 MS.gene85094:CDS 35.0%
TAGTACTAAAGGACAAACCA+TGG + chr3.4:26176483-26176502 MS.gene85094:CDS 35.0%
TGAAAATTGCTACATGACTC+TGG - chr3.4:26175982-26176001 None:intergenic 35.0%
! GTCAAGGTTAAGGAACATTT+TGG + chr3.4:26176329-26176348 MS.gene85094:CDS 35.0%
ACACAAATTCAAGGCCAAAG+AGG + chr3.4:26176157-26176176 MS.gene85094:CDS 40.0%
ACATGCAGGATCATCATCTA+AGG + chr3.4:26176428-26176447 MS.gene85094:intron 40.0%
CTATTTCCAGAAGTCCTCTT+TGG - chr3.4:26176174-26176193 None:intergenic 40.0%
GTCCTTTAGTACTACTCATG+TGG - chr3.4:26176477-26176496 None:intergenic 40.0%
TGTGTGTGATAAGCATCATC+TGG - chr3.4:26176093-26176112 None:intergenic 40.0%
TTAGATGATGATCCTGCATG+TGG - chr3.4:26176429-26176448 None:intergenic 40.0%
TTTGAGGAAATTACAAGGGC+AGG + chr3.4:26176287-26176306 MS.gene85094:CDS 40.0%
!! AGCGTGAATGCATGTTTTTG+TGG - chr3.4:26176049-26176068 None:intergenic 40.0%
TGATAAGCATCATCTGGACC+AGG - chr3.4:26176087-26176106 None:intergenic 45.0%
CCATGTTTGCATCCACATGC+AGG + chr3.4:26176414-26176433 MS.gene85094:intron 50.0%
CCTGCATGTGGATGCAAACA+TGG - chr3.4:26176417-26176436 None:intergenic 50.0%
GCTCACACTTGTAATCCACC+TGG + chr3.4:26176066-26176085 MS.gene85094:CDS 50.0%
TAAGCATCATCTGGACCAGG+TGG - chr3.4:26176084-26176103 None:intergenic 50.0%
TCAAGGCCAAAGAGGACTTC+TGG + chr3.4:26176165-26176184 MS.gene85094:CDS 50.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 26175919 26176552 26175919 ID=MS.gene85094
chr3.4 mRNA 26175919 26176552 26175919 ID=MS.gene85094.t1;Parent=MS.gene85094
chr3.4 exon 26175919 26176350 26175919 ID=MS.gene85094.t1.exon1;Parent=MS.gene85094.t1
chr3.4 CDS 26175919 26176350 26175919 ID=cds.MS.gene85094.t1;Parent=MS.gene85094.t1
chr3.4 exon 26176436 26176552 26176436 ID=MS.gene85094.t1.exon2;Parent=MS.gene85094.t1
chr3.4 CDS 26176436 26176552 26176436 ID=cds.MS.gene85094.t1;Parent=MS.gene85094.t1
Gene Sequence

>MS.gene85094

ATGGATGATGGAAATTCTGAGGTTTCTGATAAACTTTCAGATAATGTTCTATTTTCAAATCCAGAGTCATGTAGCAATTTTCAAACTTCAACATCTATGAACACAGTTACTGAATTGTCTAATAGCACCACAAAAACATGCATTCACGCTCACACTTGTAATCCACCTGGTCCAGATGATGCTTATCACACACACACATGTTTTCATACACATACTCAAGTTTTTGCATCTGAAGATGACACAAATTCAAGGCCAAAGAGGACTTCTGGAAATAGAGAAGCTGTTAAAAAGTATAGGGAGAAGAAAAAGGCAGAAACAGCTTATTTGGAAGAAGAAGTTAAGAAATTGAAACTTGTGAATCAACAACTTTTGAGGAAATTACAAGGGCAGGCACTACTTGAAGCTGAATTGTCAAGGTTAAGGAACATTTTGGTACAACTTAAGGGAAAAGTTGACAATGAACTAGGTTGTTCTTTCCCTTTTGAGAAAAATCTACCATGTTTGCATCCACATGCAGGATCATCATCTAAGGTTAACAATTGTGCATATTGCAAACCACATGAGTAGTACTAAAGGACAAACCATGGATACAGTGAATAACTTCATGTCATCTGCACACAAGTATGATCTCTAA
Protein sequence

>MS.gene85094.t1

MDDGNSEVSDKLSDNVLFSNPESCSNFQTSTSMNTVTELSNSTTKTCIHAHTCNPPGPDDAYHTHTCFHTHTQVFASEDDTNSRPKRTSGNREAVKKYREKKKAETAYLEEEVKKLKLVNQQLLRKLQGQALLEAELSRLRNILDHHLRLTIVHIANHMSSTKGQTMDTVNNFMSSAHKYDL