AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene49315


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49315.t1 MTR_1g070190 96.190 105 4 0 19 123 24 128 2.11e-65 196
MS.gene49315.t1 MTR_7g096640 68.868 106 33 0 18 123 23 128 1.27e-50 158
MS.gene49315.t1 MTR_7g096640 62.857 70 26 0 18 87 23 92 1.07e-28 101
MS.gene49315.t1 MTR_1g073940 41.509 106 59 1 17 119 37 142 1.27e-22 87.8
MS.gene49315.t1 MTR_1g073940 40.741 108 61 1 19 123 24 131 1.29e-21 84.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49315.t1 AT4G14420 60.396 101 40 0 19 119 24 124 6.71e-41 134
MS.gene49315.t1 AT1G04340 45.714 105 57 0 19 123 24 128 1.69e-29 104
MS.gene49315.t1 AT5G43460 43.434 99 56 0 25 123 26 124 2.49e-24 91.7
MS.gene49315.t1 AT5G43460 43.434 99 56 0 25 123 26 124 2.49e-24 91.7
MS.gene49315.t1 AT3G23180 45.312 64 35 0 57 120 66 129 1.89e-12 62.0
MS.gene49315.t1 AT3G23180 45.312 64 35 0 57 120 66 129 1.89e-12 62.0
MS.gene49315.t1 AT3G23190 38.710 93 44 1 27 119 45 124 2.83e-12 61.6

Find 27 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTATATAGATATAACGAATT+TGG 0.168785 1.1:-52533670 MS.gene49315:intron
TCCATTCAGAACACTAATTA+TGG 0.249137 1.1:-52534280 MS.gene49315:CDS
CAGATTAAACTTGTAATTAC+TGG 0.264664 1.1:-52532929 MS.gene49315:CDS
TTCATATTCGGAAGCTCTTT+CGG 0.294913 1.1:-52532872 MS.gene49315:CDS
CTCTTTCGGAGCTTTGCTGC+TGG 0.368078 1.1:-52532858 MS.gene49315:intron
GCTATTGCTCTGAAGGGCCT+TGG 0.375035 1.1:-52532905 MS.gene49315:CDS
ATTGCTCTGAAGGGCCTTGG+AGG 0.394581 1.1:-52532902 MS.gene49315:CDS
TATAACGAATTTGGAGTTGA+GGG 0.426480 1.1:-52533661 MS.gene49315:CDS
GTTGAAAGCCAACTTGAGAA+TGG 0.444032 1.1:+52533584 None:intergenic
TCCATAATTAGTGTTCTGAA+TGG 0.445382 1.1:+52534279 None:intergenic
TGTGCAAAGGAATCAAGCTT+TGG 0.445686 1.1:+52533613 None:intergenic
GGTTTCAGTGCTGTTGCAGA+AGG 0.469228 1.1:+52533634 None:intergenic
TTGCTCTGAAGGGCCTTGGA+GGG 0.470152 1.1:-52532901 MS.gene49315:CDS
TGCTCTGAAGGGCCTTGGAG+GGG 0.472119 1.1:-52532900 MS.gene49315:CDS
AGATTAAACTTGTAATTACT+GGG 0.475430 1.1:-52532928 MS.gene49315:CDS
GAGAGACTAACATCAATCTC+TGG 0.486838 1.1:+52533559 None:intergenic
TACTGGGGCTATTGCTCTGA+AGG 0.491768 1.1:-52532912 MS.gene49315:CDS
CATCGAATCCATTCTCAAGT+TGG 0.513513 1.1:-52533592 MS.gene49315:CDS
ATATAACGAATTTGGAGTTG+AGG 0.561681 1.1:-52533662 MS.gene49315:CDS
CTAATTATGGAAACAAAAGT+AGG 0.569448 1.1:-52534267 MS.gene49315:intron
TAACGAATTTGGAGTTGAGG+GGG 0.607819 1.1:-52533659 MS.gene49315:CDS
ACTGGGGCTATTGCTCTGAA+GGG 0.616718 1.1:-52532911 MS.gene49315:CDS
AGAATGGATTCGATGTGCAA+AGG 0.617931 1.1:+52533600 None:intergenic
ATAACGAATTTGGAGTTGAG+GGG 0.638240 1.1:-52533660 MS.gene49315:CDS
AACGAATTTGGAGTTGAGGG+GGG 0.640083 1.1:-52533658 MS.gene49315:CDS
ATATGAAAAGAACCCCTCCA+AGG 0.650548 1.1:+52532888 None:intergenic
GATTAAACTTGTAATTACTG+GGG 0.669590 1.1:-52532927 MS.gene49315:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGAACAATTATAATATCAAA+TGG + chr1.1:52533148-52533167 None:intergenic 15.0%
!! AATGCAAAAAAGTTAACAAA+TGG + chr1.1:52533841-52533860 None:intergenic 20.0%
!! AATGGAAAAAACTGTATATA+TGG - chr1.1:52532704-52532723 MS.gene49315:CDS 20.0%
!! AGATTAAACTTGTAATTACT+GGG - chr1.1:52534007-52534026 MS.gene49315:intron 20.0%
!! ATAGAAAATAATGAGCAAAA+GGG + chr1.1:52533953-52533972 None:intergenic 20.0%
!! ATGCTTCTTATATAAAAGAA+TGG + chr1.1:52532833-52532852 None:intergenic 20.0%
!! ATTCAGTAAGAATTAAAACA+TGG + chr1.1:52532972-52532991 None:intergenic 20.0%
!! CTATATAGATATAACGAATT+TGG - chr1.1:52533265-52533284 MS.gene49315:intron 20.0%
!! TTAAGTTAAATTGAAAAGAC+CGG - chr1.1:52533793-52533812 MS.gene49315:intron 20.0%
!! TTCACTAAAGCATAAAAATA+GGG + chr1.1:52533215-52533234 None:intergenic 20.0%
!! TTGTAAAAATCATAACGAAT+TGG + chr1.1:52534213-52534232 None:intergenic 20.0%
!!! AAGTTTTCAATCACTTAAAA+TGG + chr1.1:52532754-52532773 None:intergenic 20.0%
!!! TAATTTGTGATGAAATTGTA+TGG + chr1.1:52533690-52533709 None:intergenic 20.0%
! AACAATAGAAAAAGTTTACC+AGG + chr1.1:52532864-52532883 None:intergenic 25.0%
! CAGATTAAACTTGTAATTAC+TGG - chr1.1:52534006-52534025 MS.gene49315:intron 25.0%
! CATAGAAAATAATGAGCAAA+AGG + chr1.1:52533954-52533973 None:intergenic 25.0%
! CTAATTATGGAAACAAAAGT+AGG - chr1.1:52532668-52532687 MS.gene49315:CDS 25.0%
! CTTCACTAAAGCATAAAAAT+AGG + chr1.1:52533216-52533235 None:intergenic 25.0%
! GATTAAACTTGTAATTACTG+GGG - chr1.1:52534008-52534027 MS.gene49315:intron 25.0%
! GTAGGTAGTATTTAATGAAA+TGG - chr1.1:52532686-52532705 MS.gene49315:CDS 25.0%
! TAATAGCACATTACATAGAA+CGG + chr1.1:52532936-52532955 None:intergenic 25.0%
! TATGGCACAAATATTTATTG+TGG + chr1.1:52533672-52533691 None:intergenic 25.0%
! TCACTAAAGCATAAAAATAG+GGG + chr1.1:52533214-52533233 None:intergenic 25.0%
! TCTTATATAAAAGAATGGTC+TGG + chr1.1:52532828-52532847 None:intergenic 25.0%
! TTATTTAATAATCCTGACAG+CGG - chr1.1:52533176-52533195 MS.gene49315:intron 25.0%
!! ACTTTTCATCAAATTTACAC+AGG - chr1.1:52534263-52534282 MS.gene49315:intron 25.0%
!! TTTTTACAATTATGACAACG+AGG - chr1.1:52534224-52534243 MS.gene49315:intron 25.0%
AAAGAATAATAAGGACAAGG+TGG - chr1.1:52533770-52533789 MS.gene49315:intron 30.0%
CACATCACATCAGTTATATT+AGG + chr1.1:52533986-52534005 None:intergenic 30.0%
CTGTTATTATGCTAAATTGC+CGG - chr1.1:52533864-52533883 MS.gene49315:intron 30.0%
GCTGTCAGGATTATTAAATA+AGG + chr1.1:52533177-52533196 None:intergenic 30.0%
GGAAAAGAATAATAAGGACA+AGG - chr1.1:52533767-52533786 MS.gene49315:intron 30.0%
TAAGAATTAAAACATGGCCA+AGG + chr1.1:52532966-52532985 None:intergenic 30.0%
TCAGTTATATTAGGTAACAC+TGG + chr1.1:52533977-52533996 None:intergenic 30.0%
TCCATTCAGAACACTAATTA+TGG - chr1.1:52532655-52532674 MS.gene49315:CDS 30.0%
TCGTTCGGAAAAGAATAATA+AGG - chr1.1:52533761-52533780 MS.gene49315:intron 30.0%
! ATATAACGAATTTGGAGTTG+AGG - chr1.1:52533273-52533292 MS.gene49315:intron 30.0%
! TATAACGAATTTGGAGTTGA+GGG - chr1.1:52533274-52533293 MS.gene49315:intron 30.0%
! TCCATAATTAGTGTTCTGAA+TGG + chr1.1:52532659-52532678 None:intergenic 30.0%
! TTATTATTCTTTTCCGAACG+AGG + chr1.1:52533762-52533781 None:intergenic 30.0%
!! CTATTGTTGAATTTTTGAGC+TGG - chr1.1:52532876-52532895 MS.gene49315:CDS 30.0%
!!! TTTCATTTTTTATGCCAGAC+CGG + chr1.1:52533886-52533905 None:intergenic 30.0%
AAAAACATGATCTGTCCTTC+AGG - chr1.1:52533607-52533626 MS.gene49315:CDS 35.0%
AATGGACATGTAATATCCAC+TGG + chr1.1:52533823-52533842 None:intergenic 35.0%
CTGAGCAAATGAGATGAATA+TGG + chr1.1:52534126-52534145 None:intergenic 35.0%
GAAAATAATGAGCAAAAGGG+AGG + chr1.1:52533950-52533969 None:intergenic 35.0%
GGCTCTTGTACTTTATTGAA+GGG + chr1.1:52533736-52533755 None:intergenic 35.0%
TAATAGATGTCCAAATGCAC+TGG + chr1.1:52532804-52532823 None:intergenic 35.0%
TAGCATTGCACTTTATAAGC+TGG - chr1.1:52533094-52533113 MS.gene49315:intron 35.0%
TGTTTCTTAACCAGTGCATT+TGG - chr1.1:52532791-52532810 MS.gene49315:intron 35.0%
TTCATATTCGGAAGCTCTTT+CGG - chr1.1:52534063-52534082 MS.gene49315:intron 35.0%
! ACTTTTGCAGACACAGATAA+TGG + chr1.1:52533065-52533084 None:intergenic 35.0%
! ATAACGAATTTGGAGTTGAG+GGG - chr1.1:52533275-52533294 MS.gene49315:intron 35.0%
! TGGTTTGTCAGATTCTCTAT+TGG - chr1.1:52534097-52534116 MS.gene49315:intron 35.0%
! TGTGCTATTATACATTGCCT+TGG - chr1.1:52532946-52532965 MS.gene49315:intron 35.0%
!! TGTTGAATTTTTGAGCTGGA+AGG - chr1.1:52532880-52532899 MS.gene49315:CDS 35.0%
ACTAATCCAGTGTTACCTGA+AGG + chr1.1:52533625-52533644 None:intergenic 40.0%
ATATGAAAAGAACCCCTCCA+AGG + chr1.1:52534050-52534069 None:intergenic 40.0%
ATTATGCTAAATTGCCGGTC+TGG - chr1.1:52533869-52533888 MS.gene49315:intron 40.0%
CACATTACATAGAACGGATG+AGG + chr1.1:52532930-52532949 None:intergenic 40.0%
CATCGAATCCATTCTCAAGT+TGG - chr1.1:52533343-52533362 MS.gene49315:intron 40.0%
CGGCTCTTGTACTTTATTGA+AGG + chr1.1:52533737-52533756 None:intergenic 40.0%
GAGAGACTAACATCAATCTC+TGG + chr1.1:52533379-52533398 None:intergenic 40.0%
GGAAGGCTTATGTCATTATG+TGG - chr1.1:52532897-52532916 MS.gene49315:CDS 40.0%
GTTGAAAGCCAACTTGAGAA+TGG + chr1.1:52533354-52533373 None:intergenic 40.0%
TGTAATATCCACTGGCATAC+CGG + chr1.1:52533815-52533834 None:intergenic 40.0%
TGTGCAAAGGAATCAAGCTT+TGG + chr1.1:52533325-52533344 None:intergenic 40.0%
! AGAATGGATTCGATGTGCAA+AGG + chr1.1:52533338-52533357 None:intergenic 40.0%
! GGAGGGGTTCTTTTCATATT+CGG - chr1.1:52534051-52534070 MS.gene49315:intron 40.0%
! TAACGAATTTGGAGTTGAGG+GGG - chr1.1:52533276-52533295 MS.gene49315:intron 40.0%
! TAAGAAGCATGATGTTAGCC+TGG - chr1.1:52532843-52532862 MS.gene49315:intron 40.0%
ATCTGTCCTTCAGGTAACAC+TGG - chr1.1:52533616-52533635 MS.gene49315:CDS 45.0%
! AACGAATTTGGAGTTGAGGG+GGG - chr1.1:52533277-52533296 MS.gene49315:intron 45.0%
! ATTCTTTTCCGAACGAGGCA+CGG + chr1.1:52533757-52533776 None:intergenic 45.0%
AGAGAGAGAGAGAGAGAGAG+AGG + chr1.1:52533394-52533413 None:intergenic 50.0%
AGAGAGAGAGAGAGAGAGAG+GGG + chr1.1:52533394-52533413 None:intergenic 50.0%
ATGAAGAGAGAACCGCTGTC+AGG + chr1.1:52533191-52533210 None:intergenic 50.0%
GAGAGAGAGAGAGAGAGAGA+GGG + chr1.1:52533393-52533412 None:intergenic 50.0%
TACTGGGGCTATTGCTCTGA+AGG - chr1.1:52534023-52534042 MS.gene49315:intron 50.0%
TGAAAAGACCGGTATGCCAG+TGG - chr1.1:52533804-52533823 MS.gene49315:intron 50.0%
! ACTGGGGCTATTGCTCTGAA+GGG - chr1.1:52534024-52534043 MS.gene49315:intron 50.0%
! GGTTTCAGTGCTGTTGCAGA+AGG + chr1.1:52533304-52533323 None:intergenic 50.0%
AGAGAGAGAGAGAGAGAGGG+GGG + chr1.1:52533498-52533517 None:intergenic 55.0%
CTCTTTCGGAGCTTTGCTGC+TGG - chr1.1:52534077-52534096 MS.gene49315:intron 55.0%
GAGAGAGAGAGAGAGAGAGG+GGG + chr1.1:52533499-52533518 None:intergenic 55.0%
TACAAGAGCCGTGCCTCGTT+CGG - chr1.1:52533746-52533765 MS.gene49315:intron 55.0%
!! ATTGCTCTGAAGGGCCTTGG+AGG - chr1.1:52534033-52534052 MS.gene49315:intron 55.0%
!! GCTATTGCTCTGAAGGGCCT+TGG - chr1.1:52534030-52534049 MS.gene49315:intron 55.0%
!! TTGCTCTGAAGGGCCTTGGA+GGG - chr1.1:52534034-52534053 MS.gene49315:intron 55.0%
GAGAGAGAGAGAGAGAGGGG+GGG + chr1.1:52533497-52533516 None:intergenic 60.0%
!! TGCTCTGAAGGGCCTTGGAG+GGG - chr1.1:52534035-52534054 MS.gene49315:intron 60.0%
AGAGAGAGAGAGAGGGGGGG+AGG + chr1.1:52533494-52533513 None:intergenic 65.0%
GAGAGAGAGAGAGGGGGGGA+GGG + chr1.1:52533493-52533512 None:intergenic 65.0%
AGAGAGAGAGGGGGGGAGGG+AGG + chr1.1:52533490-52533509 None:intergenic 70.0%
GAGAGAGAGGGGGGGAGGGA+GGG + chr1.1:52533489-52533508 None:intergenic 70.0%
AGAGAGGGGGGGAGGGAGGG+AGG + chr1.1:52533486-52533505 None:intergenic 75.0%
AGGGAGGGAGGGAGGGAGGG+AGG + chr1.1:52533458-52533477 None:intergenic 75.0%
GAGAGGGGGGGAGGGAGGGA+GGG + chr1.1:52533485-52533504 None:intergenic 75.0%
GGGAGGGAGGGAGGGAGGGA+GGG + chr1.1:52533457-52533476 None:intergenic 75.0%
! AGGGGGGGAGGGAGGGAGGG+AGG + chr1.1:52533482-52533501 None:intergenic 80.0%
! GGGGAGGGAGGGAGGGAGGG+AGG + chr1.1:52533478-52533497 None:intergenic 80.0%
! GGGGGGGAGGGAGGGAGGGA+GGG + chr1.1:52533481-52533500 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 52532637 52534320 52532637 ID=MS.gene49315
chr1.1 mRNA 52532637 52534320 52532637 ID=MS.gene49315.t1;Parent=MS.gene49315
chr1.1 exon 52534268 52534320 52534268 ID=MS.gene49315.t1.exon1;Parent=MS.gene49315.t1
chr1.1 CDS 52534268 52534320 52534268 ID=cds.MS.gene49315.t1;Parent=MS.gene49315.t1
chr1.1 exon 52533570 52533684 52533570 ID=MS.gene49315.t1.exon2;Parent=MS.gene49315.t1
chr1.1 CDS 52533570 52533684 52533570 ID=cds.MS.gene49315.t1;Parent=MS.gene49315.t1
chr1.1 exon 52532859 52532948 52532859 ID=MS.gene49315.t1.exon3;Parent=MS.gene49315.t1
chr1.1 CDS 52532859 52532948 52532859 ID=cds.MS.gene49315.t1;Parent=MS.gene49315.t1
chr1.1 exon 52532637 52532771 52532637 ID=MS.gene49315.t1.exon4;Parent=MS.gene49315.t1
chr1.1 CDS 52532637 52532771 52532637 ID=cds.MS.gene49315.t1;Parent=MS.gene49315.t1
Gene Sequence

>MS.gene49315

ATGGAGAATGCTATTGAGTCCATTCAGAACACTAATTATGGAAACAAAAGTAGGTAGTATTTAATGAAATGGAAAAAACTGTATATATGGAATCACAATCATATTAAATACTTGCCATTTTAAGTGATTGAAAACTTTGATGTAGTGATTTATATGTTTCTTAACCAGTGCATTTGGACATCTATTAGCCAGACCATTCTTTTATATAAGAAGCATGATGTTAGCCTGGTAAACTTTTTCTATTGTTGAATTTTTGAGCTGGAAGGCTTATGTCATTATGTGGATTACTGCCTCATCCGTTCTATGTAATGTGCTATTATACATTGCCTTGGCCATGTTTTAATTCTTACTGAATTAGATTACTTTGAATTTTTGTGTAAACATCTTCATGATAACAATACTTTCTATTGCACTTGATTTAAGAACCATTATCTGTGTCTGCAAAAGTTGATGTTGTTAGCATTGCACTTTATAAGCTGGATTAAGAGCTATAAGCTAAAAGTTTCTTCCATTTGATATTATAATTGTTCAAACACTCCTTATTTAATAATCCTGACAGCGGTTCTCTCTTCATCCCCTATTTTTATGCTTTAGTGAAGTTTCTTGCTTATGTATCTTCTGTTCTTTGCTATATAGATATAACGAATTTGGAGTTGAGGGGGGACCTTCTGCAACAGCACTGAAACCAAAGCTTGATTCCTTTGCACATCGAATCCATTCTCAAGTTGGCTTTCAACTTCCAGAGATTGATGTTAGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCGCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCCCCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGTACGAATGTTTATGTTGTGTTAATTTTTTAAGAAAAACATGATCTGTCCTTCAGGTAACACTGGATTAGTTTTTAATTTAAAATTCATAAAACTCCACAATAAATATTTGTGCCATACAATTTCATCACAAATTAATTTTTTTTTAATGATGACTGTACCCTTCAATAAAGTACAAGAGCCGTGCCTCGTTCGGAAAAGAATAATAAGGACAAGGTGGTTAAGTTAAATTGAAAAGACCGGTATGCCAGTGGATATTACATGTCCATTTGTTAACTTTTTTGCATTTTTCTGTTATTATGCTAAATTGCCGGTCTGGCATAAAAAATGAAATTGTCTGCTGATGAAATTATGAACATTACATGTAGAGTTTTCCTCCCTTTTGCTCATTATTTTCTATGCCAGTGTTACCTAATATAACTGATGTGATGTGCAGATTAAACTTGTAATTACTGGGGCTATTGCTCTGAAGGGCCTTGGAGGGGTTCTTTTCATATTCGGAAGCTCTTTCGGAGCTTTGCTGCTGGTTTGTCAGATTCTCTATTGGATTCCATATTCATCTCATTTGCTCAGTTTTTTTAGTTACGATCTTTTTTTTTTTGTTTTGTTGTAGCTTCTGCATCAGTTGATTGCTACTCCAATTCGTTATGATTTTTACAATTATGACAACGAGGACAAAGAATTTACTCAACTTTTCATCAAATTTACACAGGTCAGAGCAGTGAATTATTTTTTATTTGAGAATTAG

Protein sequence

>MS.gene49315.t1

MENAIESIQNTNYGNKSRYNEFGVEGGPSATALKPKLDSFAHRIHSQVGFQLPEIDIKLVITGAIALKGLGGVLFIFGSSFGALLLLLHQLIATPIRYDFYNYDNEDKEFTQLFIKFTQVRAVNYFLFEN