AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049285


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049285.t1 MTR_3g096290 89.091 165 12 1 1 165 1 159 5.27e-100 285
MS.gene049285.t1 MTR_3g096290 85.366 123 12 1 1 123 9 125 2.74e-65 196
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049285.t1 AT1G74880 58.788 165 61 1 1 165 1 158 1.60e-62 190

Find 45 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTTCTTAGGAAGAGTCTT+AGG 0.205905 3.3:+79789860 None:intergenic
GTAGTCTAATCCTTTGTAAT+AGG 0.224129 3.3:+79789556 None:intergenic
CTGGAATAAACAGGTTTCTT+AGG 0.242562 3.3:+79789848 None:intergenic
CTTGACTCACTGGAATAAAC+AGG 0.396415 3.3:+79789839 None:intergenic
GATATGCGTATATTTGAAAC+AGG 0.408664 3.3:-79789416 MS.gene049285:CDS
TCTTGAACTGCACGAATCAA+TGG 0.413571 3.3:+79789974 None:intergenic
GTTTCTTAGGAAGAGTCTTA+GGG 0.440236 3.3:+79789861 None:intergenic
TGCTTAATTCTCAGGTTGCA+TGG 0.442545 3.3:-79789203 MS.gene049285:intron
GCAGTTCAAGACGGTGAACC+AGG 0.447486 3.3:-79789962 MS.gene049285:CDS
TAGTCTAATCCTTTGTAATA+GGG 0.459657 3.3:+79789557 None:intergenic
GCATCAGAGCTCTTAGTTTG+TGG 0.477417 3.3:+79789926 None:intergenic
TTTGAGAAATGGGAAAGAGA+AGG 0.496635 3.3:+79790031 None:intergenic
CTTGAACTGCACGAATCAAT+GGG 0.503362 3.3:+79789975 None:intergenic
GGAAGCCAAGCTGGAGCAGT+GGG 0.508111 3.3:+79789171 None:intergenic
AGGAAGAGTCTTAGGGGCAG+TGG 0.518025 3.3:+79789868 None:intergenic
ATGGGAAAGAGAAGGAAAGG+AGG 0.524817 3.3:+79790039 None:intergenic
GAAATGGGAAAGAGAAGGAA+AGG 0.530112 3.3:+79790036 None:intergenic
GCTTAATTCTCAGGTTGCAT+GGG 0.543172 3.3:-79789202 MS.gene049285:intron
TCCTACATACATGCTTATCA+AGG 0.544432 3.3:-79789151 MS.gene049285:intron
AGGAAGCCAAGCTGGAGCAG+TGG 0.544685 3.3:+79789170 None:intergenic
GAGTCCCCACTGCTCCAGCT+TGG 0.545534 3.3:-79789176 MS.gene049285:CDS
AATTTGTGGACAGTGAAGAA+AGG 0.549691 3.3:-79789739 MS.gene049285:intron
AATTCTCAGGTTGCATGGGT+AGG 0.550094 3.3:-79789198 MS.gene049285:intron
TCTAATCCTTTGTAATAGGG+TGG 0.556199 3.3:+79789560 None:intergenic
TGAAGAAAGGTCAGATTGTG+AGG 0.558487 3.3:-79789726 MS.gene049285:CDS
ATGTATGTAGGAAGCCAAGC+TGG 0.563654 3.3:+79789162 None:intergenic
GGGCACCCACCCTATTACAA+AGG 0.572065 3.3:-79789566 MS.gene049285:CDS
TCAGATTGTGAGGGTGGACA+AGG 0.576125 3.3:-79789716 MS.gene049285:CDS
GAAAGGTCAGATTGTGAGGG+TGG 0.585375 3.3:-79789722 MS.gene049285:CDS
CTAATCCTTTGTAATAGGGT+GGG 0.595783 3.3:+79789561 None:intergenic
CAGTTCAAGACGGTGAACCA+GGG 0.597426 3.3:-79789961 MS.gene049285:CDS
AGCACTACTAGAGGAGGCTG+AGG 0.602396 3.3:+79789901 None:intergenic
TTGATTCGTGCAGTTCAAGA+CGG 0.616062 3.3:-79789971 MS.gene049285:CDS
TTTGTTTGTTTACCTCACCA+CGG 0.617430 3.3:+79789522 None:intergenic
AGTTCAAGACGGTGAACCAG+GGG 0.628235 3.3:-79789960 MS.gene049285:CDS
ACCTTGATAAGCATGTATGT+AGG 0.632174 3.3:+79789150 None:intergenic
GAATCAATGGGAAAGAAGAA+CGG 0.633893 3.3:+79789987 None:intergenic
TTTCTTAGGAAGAGTCTTAG+GGG 0.641863 3.3:+79789862 None:intergenic
GAAGAAAGGTCAGATTGTGA+GGG 0.659835 3.3:-79789725 MS.gene049285:CDS
AGACTGAGCACTACTAGAGG+AGG 0.683341 3.3:+79789895 None:intergenic
GACTACATTTACGAAGACCG+TGG 0.695548 3.3:-79789539 MS.gene049285:CDS
TGAAGACTGAGCACTACTAG+AGG 0.698555 3.3:+79789892 None:intergenic
CATTTACGAAGACCGTGGTG+AGG 0.713150 3.3:-79789534 MS.gene049285:intron
GTTCAAGACGGTGAACCAGG+GGG 0.724086 3.3:-79789959 MS.gene049285:CDS
GAAGCCAAGCTGGAGCAGTG+GGG 0.758823 3.3:+79789172 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTTTGTGTAAAAAAATTAT+TGG + chr3.3:79789731-79789750 None:intergenic 15.0%
!!! ATTTTGTTTTCATAATCTTT+TGG + chr3.3:79789553-79789572 None:intergenic 15.0%
!!! TATTCATTTTTGTTAATTTG+TGG - chr3.3:79789294-79789313 MS.gene049285:intron 15.0%
! AAATGTCAAACTGTATTTGT+AGG - chr3.3:79789603-79789622 MS.gene049285:intron 25.0%
! AGATACTGAAAAATTAACCT+TGG + chr3.3:79789454-79789473 None:intergenic 25.0%
! ATTTCTCAAAAACTTTGACA+AGG - chr3.3:79789029-79789048 MS.gene049285:intron 25.0%
! TAGTCTAATCCTTTGTAATA+GGG + chr3.3:79789493-79789512 None:intergenic 25.0%
!! GTTTTCTATGATTCCAATTA+TGG - chr3.3:79789763-79789782 MS.gene049285:intron 25.0%
!!! ATTTTTCAGTATCTTTCTGT+TGG - chr3.3:79789460-79789479 MS.gene049285:intron 25.0%
!!! TGTCAAAGTTTTTGAGAAAT+GGG + chr3.3:79789029-79789048 None:intergenic 25.0%
!!! TTGTCAAAGTTTTTGAGAAA+TGG + chr3.3:79789030-79789049 None:intergenic 25.0%
!!! TTTTTCAGTATCTTTCTGTT+GGG - chr3.3:79789461-79789480 MS.gene049285:intron 25.0%
CAACAAAAAAAGTAAGAGTG+AGG + chr3.3:79790040-79790059 None:intergenic 30.0%
CTTCACAATGTTACCATAAT+TGG + chr3.3:79789779-79789798 None:intergenic 30.0%
GTAGTCTAATCCTTTGTAAT+AGG + chr3.3:79789494-79789513 None:intergenic 30.0%
TAATGCTTTACTTGTTCCAA+TGG - chr3.3:79789919-79789938 MS.gene049285:CDS 30.0%
! GATATGCGTATATTTGAAAC+AGG - chr3.3:79789631-79789650 MS.gene049285:intron 30.0%
AATTTGTGGACAGTGAAGAA+AGG - chr3.3:79789308-79789327 MS.gene049285:intron 35.0%
ACCTTGATAAGCATGTATGT+AGG + chr3.3:79789900-79789919 None:intergenic 35.0%
CAAACTGTATTTGTAGGTCT+TGG - chr3.3:79789609-79789628 MS.gene049285:intron 35.0%
CTAATCCTTTGTAATAGGGT+GGG + chr3.3:79789489-79789508 None:intergenic 35.0%
CTGGAATAAACAGGTTTCTT+AGG + chr3.3:79789202-79789221 None:intergenic 35.0%
GAATCAATGGGAAAGAAGAA+CGG + chr3.3:79789063-79789082 None:intergenic 35.0%
GTTTCTTAGGAAGAGTCTTA+GGG + chr3.3:79789189-79789208 None:intergenic 35.0%
TATTAGATTGTAGCAGCCAT+TGG + chr3.3:79789938-79789957 None:intergenic 35.0%
TCCTACATACATGCTTATCA+AGG - chr3.3:79789896-79789915 MS.gene049285:CDS 35.0%
TCTAATCCTTTGTAATAGGG+TGG + chr3.3:79789490-79789509 None:intergenic 35.0%
TGTACCATTGCTTAATTCTC+AGG - chr3.3:79789836-79789855 MS.gene049285:intron 35.0%
TTTCTTAGGAAGAGTCTTAG+GGG + chr3.3:79789188-79789207 None:intergenic 35.0%
TTTGAGAAATGGGAAAGAGA+AGG + chr3.3:79789019-79789038 None:intergenic 35.0%
TTTGTTTGTTTACCTCACCA+CGG + chr3.3:79789528-79789547 None:intergenic 35.0%
CTTGAACTGCACGAATCAAT+GGG + chr3.3:79789075-79789094 None:intergenic 40.0%
CTTGACTCACTGGAATAAAC+AGG + chr3.3:79789211-79789230 None:intergenic 40.0%
GAAATGGGAAAGAGAAGGAA+AGG + chr3.3:79789014-79789033 None:intergenic 40.0%
GAAGAAAGGTCAGATTGTGA+GGG - chr3.3:79789322-79789341 MS.gene049285:intron 40.0%
GCAACCTGAGAATTAAGCAA+TGG + chr3.3:79789843-79789862 None:intergenic 40.0%
GGACTCAAATAACATGTCCA+AGG - chr3.3:79789434-79789453 MS.gene049285:intron 40.0%
GGTTTCTTAGGAAGAGTCTT+AGG + chr3.3:79789190-79789209 None:intergenic 40.0%
TAGTTATGTCAGCTGTGAGT+AGG - chr3.3:79789410-79789429 MS.gene049285:CDS 40.0%
TATTTGGTTGCTTGACTCAC+TGG + chr3.3:79789221-79789240 None:intergenic 40.0%
TCTTGAACTGCACGAATCAA+TGG + chr3.3:79789076-79789095 None:intergenic 40.0%
TGAAGAAAGGTCAGATTGTG+AGG - chr3.3:79789321-79789340 MS.gene049285:intron 40.0%
! GCTTAATTCTCAGGTTGCAT+GGG - chr3.3:79789845-79789864 MS.gene049285:intron 40.0%
! TGCTTAATTCTCAGGTTGCA+TGG - chr3.3:79789844-79789863 MS.gene049285:intron 40.0%
! TTGATTCGTGCAGTTCAAGA+CGG - chr3.3:79789076-79789095 MS.gene049285:intron 40.0%
ATGGGAAAGAGAAGGAAAGG+AGG + chr3.3:79789011-79789030 None:intergenic 45.0%
ATGTATGTAGGAAGCCAAGC+TGG + chr3.3:79789888-79789907 None:intergenic 45.0%
GACTACATTTACGAAGACCG+TGG - chr3.3:79789508-79789527 MS.gene049285:intron 45.0%
TGAAGACTGAGCACTACTAG+AGG + chr3.3:79789158-79789177 None:intergenic 45.0%
TTATGTCAGCTGTGAGTAGG+AGG - chr3.3:79789413-79789432 MS.gene049285:CDS 45.0%
! AATTCTCAGGTTGCATGGGT+AGG - chr3.3:79789849-79789868 MS.gene049285:CDS 45.0%
! GCATCAGAGCTCTTAGTTTG+TGG + chr3.3:79789124-79789143 None:intergenic 45.0%
!! AATTCAAATAAATATTTATT+TGG + chr3.3:79789237-79789256 None:intergenic 5.0%
AGACTGAGCACTACTAGAGG+AGG + chr3.3:79789155-79789174 None:intergenic 50.0%
AGTTCAAGACGGTGAACCAG+GGG - chr3.3:79789087-79789106 MS.gene049285:intron 50.0%
CAGTTCAAGACGGTGAACCA+GGG - chr3.3:79789086-79789105 MS.gene049285:intron 50.0%
CATTTACGAAGACCGTGGTG+AGG - chr3.3:79789513-79789532 MS.gene049285:intron 50.0%
GAAAGGTCAGATTGTGAGGG+TGG - chr3.3:79789325-79789344 MS.gene049285:intron 50.0%
GTCAGTAGTGTGTGTGCTGT+AGG - chr3.3:79789678-79789697 MS.gene049285:intron 50.0%
GTGCTGTAGGTGTGAACCAA+AGG - chr3.3:79789691-79789710 MS.gene049285:intron 50.0%
TCAGATTGTGAGGGTGGACA+AGG - chr3.3:79789331-79789350 MS.gene049285:intron 50.0%
AGCACTACTAGAGGAGGCTG+AGG + chr3.3:79789149-79789168 None:intergenic 55.0%
AGGAAGAGTCTTAGGGGCAG+TGG + chr3.3:79789182-79789201 None:intergenic 55.0%
GCAGTTCAAGACGGTGAACC+AGG - chr3.3:79789085-79789104 MS.gene049285:intron 55.0%
GGGCACCCACCCTATTACAA+AGG - chr3.3:79789481-79789500 MS.gene049285:intron 55.0%
GTTCAAGACGGTGAACCAGG+GGG - chr3.3:79789088-79789107 MS.gene049285:intron 55.0%
AGGAAGCCAAGCTGGAGCAG+TGG + chr3.3:79789880-79789899 None:intergenic 60.0%
GAAGCCAAGCTGGAGCAGTG+GGG + chr3.3:79789878-79789897 None:intergenic 60.0%
GGAAGCCAAGCTGGAGCAGT+GGG + chr3.3:79789879-79789898 None:intergenic 60.0%
GGCATGCTGTCAGCTGCCTT+TGG + chr3.3:79789710-79789729 None:intergenic 60.0%
GAGTCCCCACTGCTCCAGCT+TGG - chr3.3:79789871-79789890 MS.gene049285:CDS 65.0%
TGTGGCTGTGTACTGCCCCC+TGG + chr3.3:79789106-79789125 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 79788977 79790092 79788977 ID=MS.gene049285
chr3.3 mRNA 79788977 79790092 79788977 ID=MS.gene049285.t1;Parent=MS.gene049285
chr3.3 exon 79789849 79790092 79789849 ID=MS.gene049285.t1.exon1;Parent=MS.gene049285.t1
chr3.3 CDS 79789849 79790092 79789849 ID=cds.MS.gene049285.t1;Parent=MS.gene049285.t1
chr3.3 exon 79789693 79789748 79789693 ID=MS.gene049285.t1.exon2;Parent=MS.gene049285.t1
chr3.3 CDS 79789693 79789748 79789693 ID=cds.MS.gene049285.t1;Parent=MS.gene049285.t1
chr3.3 exon 79789535 79789600 79789535 ID=MS.gene049285.t1.exon3;Parent=MS.gene049285.t1
chr3.3 CDS 79789535 79789600 79789535 ID=cds.MS.gene049285.t1;Parent=MS.gene049285.t1
chr3.3 exon 79789403 79789444 79789403 ID=MS.gene049285.t1.exon4;Parent=MS.gene049285.t1
chr3.3 CDS 79789403 79789444 79789403 ID=cds.MS.gene049285.t1;Parent=MS.gene049285.t1
chr3.3 exon 79789152 79789211 79789152 ID=MS.gene049285.t1.exon5;Parent=MS.gene049285.t1
chr3.3 CDS 79789152 79789211 79789152 ID=cds.MS.gene049285.t1;Parent=MS.gene049285.t1
chr3.3 exon 79788977 79789006 79788977 ID=MS.gene049285.t1.exon6;Parent=MS.gene049285.t1
chr3.3 CDS 79788977 79789006 79788977 ID=cds.MS.gene049285.t1;Parent=MS.gene049285.t1
Gene Sequence

>MS.gene049285

ATGGCTTTCTGTGTAACTCTCTGCTACTACACCTCCTTTCCTTCTCTTTCCCATTTCTCAAAAACTTTGACAAGGAAACATGTCCGTTCTTCTTTCCCATTGATTCGTGCAGTTCAAGACGGTGAACCAGGGGGCAGTACACAGCCACAAACTAAGAGCTCTGATGCTTCCTCAGCCTCCTCTAGTAGTGCTCAGTCTTCAACCACTGCCCCTAAGACTCTTCCTAAGAAACCTGTTTATTCCAGTGAGTCAAGCAACCAAATAAATATTTATTTGAATTTTATATATATACTGAATGCTGCTGCTGTCTGTGTGAGTATTCATTTTTGTTAATTTGTGGACAGTGAAGAAAGGTCAGATTGTGAGGGTGGACAAGGAGAAATATCTCAATAGCATCAATGTAAGAAGACTATTATTGATTTAGTTTCAATTATAGTTATGTCAGCTGTGAGTAGGAGGACTCAAATAACATGTCCAAGGTTAATTTTTCAGTATCTTTCTGTTGGGCACCCACCCTATTACAAAGGATTAGACTACATTTACGAAGACCGTGGTGAGGTAAACAAACAAACACCAAAAGATTATGAAAACAAAATACTTTATATGATTAGTGTTTATCTAACTAGAAATGTCAAACTGTATTTGTAGGTCTTGGATATGCGTATATTTGAAACAGGAGAGCATGCACTTGTAAGTAACTTGTCAGTAGTGTGTGTGCTGTAGGTGTGAACCAAAGGCAGCTGACAGCATGCCAATAATTTTTTTACACAAACAACATGACTATTTGTTTTCTATGATTCCAATTATGGTAACATTGTGAAGTATGTGAAGTTTAAGTTTTATTATTGTGACACAAAACTGTACCATTGCTTAATTCTCAGGTTGCATGGGTAGGAGTCCCCACTGCTCCAGCTTGGCTTCCTACATACATGCTTATCAAGGTAATGCTTTACTTGTTCCAATGGCTGCTACAATCTAATAGTAAATGAAATCTGATGTAAATTGTTTATTTTTATCTACATTTACATGACTTCTTTACATTTTAGTTGCTTTGAAAGCACCTCACTCTTACTTTTTTTGTTGCAGTCAGAGAAGCTCAATTATGAGAGACTATAA

Protein sequence

>MS.gene049285.t1

MAFCVTLCYYTSFPSLSHFSKTLTRKHVRSSFPLIRAVQDGEPGGSTQPQTKSSDASSASSSSAQSSTTAPKTLPKKPVYSMKKGQIVRVDKEKYLNSINYLSVGHPPYYKGLDYIYEDRGEVLDMRIFETGEHALVAWVGVPTAPAWLPTYMLIKSEKLNYERL