AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene71415

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71415.t1 MTR_1g075720 99.248 133 1 0 1 133 1 133 2.34e-90 258
MS.gene71415.t1 MTR_4g120770 95.489 133 6 0 1 133 1 133 4.44e-89 254
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71415.t1 AT2G20450 84.962 133 20 0 1 133 1 133 7.52e-77 224
MS.gene71415.t1 AT4G27090 85.385 130 19 0 1 130 1 130 6.52e-76 221

Find 40 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAACCTATCAAAATCATTA+AGG 0.237759 1.3:-54250845 None:intergenic
TTGACGAGATCCTTCTTCTT+AGG 0.248112 1.3:-54250612 None:intergenic
GTCAACTATGGCCCAGATTA+TGG 0.258615 1.3:+54250364 MS.gene71415:CDS
GATTATGTTGGCCAAGATTA+AGG 0.263288 1.3:+54250869 MS.gene71415:CDS
ACAACGAGCTTGCCATAATC+TGG 0.305463 1.3:-54250376 None:intergenic
GAAAGTCTCTTGAAATTGAT+TGG 0.327908 1.3:-54250555 None:intergenic
GAAAATGGGTTACCCTAGTT+TGG 0.329740 1.3:-54250417 None:intergenic
AAAGTCTCTTGAAATTGATT+GGG 0.347849 1.3:-54250554 None:intergenic
CTAAAATTATACCTTAATCT+TGG 0.381940 1.3:-54250880 None:intergenic
TCTTGTTGATGCACCTGATA+TGG 0.389997 1.3:+54250524 MS.gene71415:CDS
ATTGGGGCTCTCTCCATATC+AGG 0.404038 1.3:-54250537 None:intergenic
TGCAGAGGGCTGGTGTTGTT+AGG 0.431787 1.3:+54251565 MS.gene71415:intron
TTGATGTTATCGACCAAACT+AGG 0.433748 1.3:+54250404 MS.gene71415:CDS
GAACCTATCAAAATCATTAA+GGG 0.440003 1.3:-54250844 None:intergenic
AACAATCAATTTCCTTCCCC+AGG 0.448020 1.3:-54250805 None:intergenic
GCTGAGGAAGACCGCTGCTT+AGG 0.472651 1.3:+54251602 MS.gene71415:CDS
AGAGTTGCACTTGTCAACTA+TGG 0.476767 1.3:+54250352 MS.gene71415:CDS
TTTCAATTTGTGCAGAGGGC+TGG 0.483986 1.3:+54251555 MS.gene71415:intron
GGAAATTGATTGTTAAGAAG+AGG 0.493248 1.3:+54250814 MS.gene71415:CDS
TTCAAGAGGTTTGTTGAGAT+CGG 0.494020 1.3:+54250328 MS.gene71415:CDS
AAATCTACCTGCAGCTTCCA+TGG 0.499985 1.3:-54250637 None:intergenic
CAAGAGAGTTCCTAAGAAGA+AGG 0.504705 1.3:+54250602 MS.gene71415:CDS
ACAAGTGGGAGAAGAGCTCC+TGG 0.539704 1.3:+54250787 MS.gene71415:CDS
AATTGATTGTTAAGAAGAGG+AGG 0.539799 1.3:+54250817 MS.gene71415:CDS
TGATAGGTTCAAGATTATGT+TGG 0.542816 1.3:+54250857 MS.gene71415:CDS
CAACGAGCTTGCCATAATCT+GGG 0.548769 1.3:-54250375 None:intergenic
GTCAAAGCCATGGAAGCTGC+AGG 0.563654 1.3:+54250630 MS.gene71415:CDS
AAGTCTCTTGAAATTGATTG+GGG 0.567547 1.3:-54250553 None:intergenic
ATCTCAACAAACCTCTTGAA+CGG 0.571035 1.3:-54250325 None:intergenic
GAAGGATCTCGTCAAAGCCA+TGG 0.572972 1.3:+54250620 MS.gene71415:CDS
TGATAGATGTGAAGAACAAG+TGG 0.578995 1.3:+54250772 MS.gene71415:intron
GGGAGAAGAGCTCCTGGGGA+AGG 0.586483 1.3:+54250793 MS.gene71415:CDS
TCTTTGTTCAGCCGTTCAAG+AGG 0.591089 1.3:+54250314 MS.gene71415:intron
ATTGATTGTTAAGAAGAGGA+GGG 0.602431 1.3:+54250818 MS.gene71415:CDS
TGATGTTATCGACCAAACTA+GGG 0.607546 1.3:+54250405 MS.gene71415:CDS
GGCAAGAACTTGCTAAGCTG+AGG 0.613930 1.3:+54251586 MS.gene71415:CDS
AAGTGGGAGAAGAGCTCCTG+GGG 0.619297 1.3:+54250789 MS.gene71415:CDS
CAAGTGGGAGAAGAGCTCCT+GGG 0.641380 1.3:+54250788 MS.gene71415:CDS
GATAGATGTGAAGAACAAGT+GGG 0.669553 1.3:+54250773 MS.gene71415:intron
ATGAAGTAATGCCTAAGCAG+CGG 0.686386 1.3:-54251613 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAAAAAAAATATATACAT+AGG - chr1.3:54250671-54250690 None:intergenic 10.0%
!! TATGTTCAAAAATTGTTAAA+TGG - chr1.3:54251388-54251407 None:intergenic 15.0%
!! TTTGGTTAAATAACTTAATT+AGG + chr1.3:54250951-54250970 MS.gene71415:intron 15.0%
!! AAAGATTGGAAATTTGAAAA+TGG - chr1.3:54250435-54250454 None:intergenic 20.0%
!! AAGATTGGAAATTTGAAAAT+GGG - chr1.3:54250434-54250453 None:intergenic 20.0%
!! CTAAAATTATACCTTAATCT+TGG - chr1.3:54250883-54250902 None:intergenic 20.0%
!! TTAAGTTATTTAACCAAACA+AGG - chr1.3:54250949-54250968 None:intergenic 20.0%
!! TTAAGTTATTTATCCAAACA+GGG - chr1.3:54251031-54251050 None:intergenic 20.0%
!! TTTGGATAAATAACTTAACT+TGG + chr1.3:54251033-54251052 MS.gene71415:intron 20.0%
!!! AATCTGTTTCTTAAGTTATT+TGG + chr1.3:54251345-54251364 MS.gene71415:intron 20.0%
!!! ATTGTTTTTGTATAAGCTTT+AGG + chr1.3:54251135-54251154 MS.gene71415:intron 20.0%
!!! TATGTTTTGTTTGTTGAAAT+TGG + chr1.3:54250714-54250733 MS.gene71415:intron 20.0%
!!! TGTTTTTTCAAATTGTGTTT+TGG + chr1.3:54251494-54251513 MS.gene71415:intron 20.0%
!!! TTGTTTTTGTATAAGCTTTA+GGG + chr1.3:54251136-54251155 MS.gene71415:intron 20.0%
!!! TTTTGAGAAATTAAGCAAAT+GGG - chr1.3:54250475-54250494 None:intergenic 20.0%
!!! TTTTTGAGAAATTAAGCAAA+TGG - chr1.3:54250476-54250495 None:intergenic 20.0%
! AAAGTCTCTTGAAATTGATT+GGG - chr1.3:54250557-54250576 None:intergenic 25.0%
! ATAATTTCAATTTGTGCAGA+GGG + chr1.3:54251551-54251570 MS.gene71415:intron 25.0%
! GAACCTATCAAAATCATTAA+GGG - chr1.3:54250847-54250866 None:intergenic 25.0%
! GATTGAGATTTGAAAAAGAT+TGG - chr1.3:54250449-54250468 None:intergenic 25.0%
! GTTAAGTTATTTATCCAAAC+AGG - chr1.3:54251032-54251051 None:intergenic 25.0%
! TGAACCTATCAAAATCATTA+AGG - chr1.3:54250848-54250867 None:intergenic 25.0%
!! TTTTCATAAGTCAATCCAAA+CGG - chr1.3:54251163-54251182 None:intergenic 25.0%
!!! GAAATTGGATTTGTTTTATG+TGG + chr1.3:54250729-54250748 MS.gene71415:intron 25.0%
!!! GATTTGTTTTATGTGGTAAT+TGG + chr1.3:54250736-54250755 MS.gene71415:intron 25.0%
!!! TTGTGAAATGCTTTTAAGTT+AGG + chr1.3:54251005-54251024 MS.gene71415:intron 25.0%
!!! TTGTGAAATGCTTTTTAGTT+AGG + chr1.3:54250923-54250942 MS.gene71415:intron 25.0%
!!! TTGTGATTTGTTTGTTTTTC+AGG + chr1.3:54250500-54250519 MS.gene71415:intron 25.0%
AAAGTTGTATCTTCATAAGC+TGG + chr1.3:54251238-54251257 MS.gene71415:intron 30.0%
AAGTCTCTTGAAATTGATTG+GGG - chr1.3:54250556-54250575 None:intergenic 30.0%
AATTGATTGTTAAGAAGAGG+AGG + chr1.3:54250817-54250836 MS.gene71415:CDS 30.0%
ATTGATTGTTAAGAAGAGGA+GGG + chr1.3:54250818-54250837 MS.gene71415:CDS 30.0%
CATAATTTCAATTTGTGCAG+AGG + chr1.3:54251550-54251569 MS.gene71415:intron 30.0%
GAAAGTCTCTTGAAATTGAT+TGG - chr1.3:54250558-54250577 None:intergenic 30.0%
GGAAATTGATTGTTAAGAAG+AGG + chr1.3:54250814-54250833 MS.gene71415:CDS 30.0%
TGATAGGTTCAAGATTATGT+TGG + chr1.3:54250857-54250876 MS.gene71415:CDS 30.0%
! AATTAGGCTTTTAGTGTAAG+TGG + chr1.3:54250967-54250986 MS.gene71415:intron 30.0%
AAACCCTATAAACTCAGCTA+AGG - chr1.3:54251469-54251488 None:intergenic 35.0%
AACCCTATAAACTCAGCTAA+GGG - chr1.3:54251468-54251487 None:intergenic 35.0%
ACCAACTTGAAACTTATGTG+TGG - chr1.3:54251411-54251430 None:intergenic 35.0%
ATCTCAACAAACCTCTTGAA+CGG - chr1.3:54250328-54250347 None:intergenic 35.0%
CAGATTAAGTCTGTTCAGAT+TGG - chr1.3:54251331-54251350 None:intergenic 35.0%
GATAGATGTGAAGAACAAGT+GGG + chr1.3:54250773-54250792 MS.gene71415:intron 35.0%
GATTATGTTGGCCAAGATTA+AGG + chr1.3:54250869-54250888 MS.gene71415:CDS 35.0%
GGTTATTATACGAGCTGTTA+TGG + chr1.3:54251074-54251093 MS.gene71415:intron 35.0%
TGATAGATGTGAAGAACAAG+TGG + chr1.3:54250772-54250791 MS.gene71415:intron 35.0%
TGATGTTATCGACCAAACTA+GGG + chr1.3:54250405-54250424 MS.gene71415:CDS 35.0%
TGGAGCTTATTGTGTAAATG+TGG + chr1.3:54251053-54251072 MS.gene71415:intron 35.0%
TTGATGTTATCGACCAAACT+AGG + chr1.3:54250404-54250423 MS.gene71415:CDS 35.0%
! ACCACACATAAGTTTCAAGT+TGG + chr1.3:54251407-54251426 MS.gene71415:intron 35.0%
!! CTGCCCTTAATGATTTTGAT+AGG + chr1.3:54250841-54250860 MS.gene71415:CDS 35.0%
!! TTCAAGAGGTTTGTTGAGAT+CGG + chr1.3:54250328-54250347 MS.gene71415:CDS 35.0%
!!! CTTTTTAGTTAGGCCTTGTT+TGG + chr1.3:54250933-54250952 MS.gene71415:intron 35.0%
AACAATCAATTTCCTTCCCC+AGG - chr1.3:54250808-54250827 None:intergenic 40.0%
AAGCCCTTAGCTGAGTTTAT+AGG + chr1.3:54251462-54251481 MS.gene71415:intron 40.0%
AGAGTTGCACTTGTCAACTA+TGG + chr1.3:54250352-54250371 MS.gene71415:CDS 40.0%
AGCCCTTAGCTGAGTTTATA+GGG + chr1.3:54251463-54251482 MS.gene71415:intron 40.0%
CAAGAGAGTTCCTAAGAAGA+AGG + chr1.3:54250602-54250621 MS.gene71415:CDS 40.0%
TCTTGTTGATGCACCTGATA+TGG + chr1.3:54250524-54250543 MS.gene71415:CDS 40.0%
TTGACGAGATCCTTCTTCTT+AGG - chr1.3:54250615-54250634 None:intergenic 40.0%
!! GAAAATGGGTTACCCTAGTT+TGG - chr1.3:54250420-54250439 None:intergenic 40.0%
!! TATAAGCTTTAGGGTCCGTT+TGG + chr1.3:54251145-54251164 MS.gene71415:intron 40.0%
!!! CTTTTAAGTTAGGCCCTGTT+TGG + chr1.3:54251015-54251034 MS.gene71415:intron 40.0%
AAATCTACCTGCAGCTTCCA+TGG - chr1.3:54250640-54250659 None:intergenic 45.0%
ACAACGAGCTTGCCATAATC+TGG - chr1.3:54250379-54250398 None:intergenic 45.0%
CAACGAGCTTGCCATAATCT+GGG - chr1.3:54250378-54250397 None:intergenic 45.0%
GTCAACTATGGCCCAGATTA+TGG + chr1.3:54250364-54250383 MS.gene71415:CDS 45.0%
TCTTTGTTCAGCCGTTCAAG+AGG + chr1.3:54250314-54250333 MS.gene71415:intron 45.0%
TTTCAATTTGTGCAGAGGGC+TGG + chr1.3:54251555-54251574 MS.gene71415:intron 45.0%
! AACTCAGCTAAGGGCTTGTT+TGG - chr1.3:54251459-54251478 None:intergenic 45.0%
! AGCTAAGGGCTTGTTTGGAT+TGG - chr1.3:54251454-54251473 None:intergenic 45.0%
ATTGGGGCTCTCTCCATATC+AGG - chr1.3:54250540-54250559 None:intergenic 50.0%
GAAGGATCTCGTCAAAGCCA+TGG + chr1.3:54250620-54250639 MS.gene71415:CDS 50.0%
!! GGCAAGAACTTGCTAAGCTG+AGG + chr1.3:54251586-54251605 MS.gene71415:CDS 50.0%
AAGTGGGAGAAGAGCTCCTG+GGG + chr1.3:54250789-54250808 MS.gene71415:CDS 55.0%
ACAAGTGGGAGAAGAGCTCC+TGG + chr1.3:54250787-54250806 MS.gene71415:CDS 55.0%
CAAGTGGGAGAAGAGCTCCT+GGG + chr1.3:54250788-54250807 MS.gene71415:CDS 55.0%
GTCAAAGCCATGGAAGCTGC+AGG + chr1.3:54250630-54250649 MS.gene71415:CDS 55.0%
!! TGCAGAGGGCTGGTGTTGTT+AGG + chr1.3:54251565-54251584 MS.gene71415:intron 55.0%
GGGAGAAGAGCTCCTGGGGA+AGG + chr1.3:54250793-54250812 MS.gene71415:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 54250240 54251623 54250240 ID=MS.gene71415
chr1.3 mRNA 54250240 54251623 54250240 ID=MS.gene71415.t1;Parent=MS.gene71415
chr1.3 exon 54250240 54250242 54250240 ID=MS.gene71415.t1.exon1;Parent=MS.gene71415.t1
chr1.3 CDS 54250240 54250242 54250240 ID=cds.MS.gene71415.t1;Parent=MS.gene71415.t1
chr1.3 exon 54250325 54250426 54250325 ID=MS.gene71415.t1.exon2;Parent=MS.gene71415.t1
chr1.3 CDS 54250325 54250426 54250325 ID=cds.MS.gene71415.t1;Parent=MS.gene71415.t1
chr1.3 exon 54250522 54250651 54250522 ID=MS.gene71415.t1.exon3;Parent=MS.gene71415.t1
chr1.3 CDS 54250522 54250651 54250522 ID=cds.MS.gene71415.t1;Parent=MS.gene71415.t1
chr1.3 exon 54250778 54250890 54250778 ID=MS.gene71415.t1.exon4;Parent=MS.gene71415.t1
chr1.3 CDS 54250778 54250890 54250778 ID=cds.MS.gene71415.t1;Parent=MS.gene71415.t1
chr1.3 exon 54251570 54251623 54251570 ID=MS.gene71415.t1.exon5;Parent=MS.gene71415.t1
chr1.3 CDS 54251570 54251623 54251570 ID=cds.MS.gene71415.t1;Parent=MS.gene71415.t1
Gene Sequence

>MS.gene71415

ATGGTGAATCATGCTTCTCTATTCATCTCTGTTTCATTTTCATTTCTTAATCTTTCTGTAATCTTACTATGTGTTCTTTGTTCAGCCGTTCAAGAGGTTTGTTGAGATCGGAAGAGTTGCACTTGTCAACTATGGCCCAGATTATGGCAAGCTCGTTGTAATCGTTGATGTTATCGACCAAACTAGGGTAACCCATTTTCAAATTTCCAATCTTTTTCAAATCTCAATCATACCCATTTGCTTAATTTCTCAAAAAATGTTTGTGATTTGTTTGTTTTTCAGGCTCTTGTTGATGCACCTGATATGGAGAGAGCCCCAATCAATTTCAAGAGACTTTCTCTAACTGATATCAAGATTGATATCAAGAGAGTTCCTAAGAAGAAGGATCTCGTCAAAGCCATGGAAGCTGCAGGTAGATTTTCTACTAACCTATGTATATATTTTTTTTTGTATGTTTTTTTGTAAAGTAGTTTTTATGTTTTGTTTGTTGAAATTGGATTTGTTTTATGTGGTAATTGGTTTTGTTTGAACTTGATAGATGTGAAGAACAAGTGGGAGAAGAGCTCCTGGGGAAGGAAATTGATTGTTAAGAAGAGGAGGGCTGCCCTTAATGATTTTGATAGGTTCAAGATTATGTTGGCCAAGATTAAGGTATAATTTTAGTTGCTGTTTTTTGTTTTCTGTTGTGAAATGCTTTTTAGTTAGGCCTTGTTTGGTTAAATAACTTAATTAGGCTTTTAGTGTAAGTGGCTATTATAGAAGCTGTTGTGAAATGCTTTTAAGTTAGGCCCTGTTTGGATAAATAACTTAACTTGGAGCTTATTGTGTAAATGTGGTTATTATACGAGCTGTTATGGATGAGCTGTTTCTGTCGCACAAGATAAAATGAAGTCAAATTGTTTTTGTATAAGCTTTAGGGTCCGTTTGGATTGACTTATGAAAAATAGCTTATGCAAACATATATGCTTTGAACTTAATTCACAAGTTCTCACTAACAAAAAGTTGTATCTTCATAAGCTGGTTTTTCATAGACTGACTTCATGAATATTACATAATTTTTTTTTATTTGTATAAAGCTCAAAGAGAAGCCAATCTGAACAGACTTAATCTGTTTCTTAAGTTATTTGGAGAACTTGTCAAATGAACCATTTAACAATTTTTGAACATACCACACATAAGTTTCAAGTTGGTAGTTGATAAGCTAAAAGAAGCCAATCCAAACAAGCCCTTAGCTGAGTTTATAGGGTTTGATTCTGTTTTTTCAAATTGTGTTTTGGTTGTATTCATTCTTATGTAGTGTTGACGACGATCATAATTTCAATTTGTGCAGAGGGCTGGTGTTGTTAGGCAAGAACTTGCTAAGCTGAGGAAGACCGCTGCTTAG
Protein sequence

>MS.gene71415.t1

MPFKRFVEIGRVALVNYGPDYGKLVVIVDVIDQTRALVDAPDMERAPINFKRLSLTDIKIDIKRVPKKKDLVKAMEAADVKNKWEKSSWGRKLIVKKRRAALNDFDRFKIMLAKIKRAGVVRQELAKLRKTAA