AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene00444

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00444.t1 MTR_1g047060 58.163 98 34 2 56 153 3 93 8.04e-32 110
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACACTGCAGGACCGGATTC+TGG 0.279523 1.3:-4276669 MS.gene00444:CDS
GACCGGATTCTGGAGGAAAA+AGG 0.317490 1.3:-4276659 MS.gene00444:CDS
ATGGATCTGGATGCTGAGTT+TGG 0.391512 1.3:-4276346 MS.gene00444:CDS
TCAGCATCCAGATCCATCTT+TGG 0.442178 1.3:+4276352 None:intergenic
GTTAGTTCTGATAGCAGTGT+TGG 0.458231 1.3:+4276555 None:intergenic
TTAGTTCTGATAGCAGTGTT+GGG 0.461166 1.3:+4276556 None:intergenic
CTGCCCACCAAAGATGGATC+TGG 0.482322 1.3:-4276359 MS.gene00444:CDS
ACACTGCTATCAGAACTAAC+TGG 0.486063 1.3:-4276552 MS.gene00444:CDS
TGGAGTTACTCAGAAACCTA+TGG 0.490884 1.3:-4276263 MS.gene00444:CDS
TGGTGCTGGTAATGTTGTGT+TGG 0.499495 1.3:-4276617 MS.gene00444:CDS
GAGAGAAGACACTGCAGGAC+CGG 0.504565 1.3:-4276676 MS.gene00444:CDS
GATAATGTATGAGCATGCTT+TGG 0.511387 1.3:-4276530 MS.gene00444:CDS
GGTGCTGGTAATGTTGTGTT+GGG 0.514976 1.3:-4276616 MS.gene00444:CDS
GACTCTGCTGACAAGATGAA+TGG 0.517567 1.3:-4276283 MS.gene00444:CDS
TGCTTTGGCTGACAAGCCTC+AGG 0.528648 1.3:-4276515 MS.gene00444:intron
GCATCCAGATCCATCTTTGG+TGG 0.546474 1.3:+4276355 None:intergenic
ACCATCACCTTCATCAACCT+TGG 0.550147 1.3:+4276315 None:intergenic
GTTCAAGACATCACTGGTGC+TGG 0.556036 1.3:-4276631 MS.gene00444:CDS
GCGTTATCCAAGGTTGATGA+AGG 0.556534 1.3:-4276322 MS.gene00444:CDS
GGAGTTACTCAGAAACCTAT+GGG 0.559803 1.3:-4276262 MS.gene00444:CDS
ACTAGTGTTGCTGCTGAGCA+AGG 0.563406 1.3:-4276220 MS.gene00444:CDS
TAGTTCTGATAGCAGTGTTG+GGG 0.568976 1.3:+4276557 None:intergenic
CATCCAGATCCATCTTTGGT+GGG 0.591585 1.3:+4276356 None:intergenic
GGAGCTGTTCAAGACATCAC+TGG 0.599122 1.3:-4276637 MS.gene00444:CDS
TGAGTTTGGAGCGTTATCCA+AGG 0.615415 1.3:-4276332 MS.gene00444:CDS
AGTTCTGATAGCAGTGTTGG+GGG 0.663335 1.3:+4276558 None:intergenic
TCCAAGGTTGATGAAGGTGA+TGG 0.681651 1.3:-4276316 MS.gene00444:CDS
ACTGCAGGACCGGATTCTGG+AGG 0.686245 1.3:-4276666 MS.gene00444:CDS
GAGTTACTCAGAAACCTATG+GGG 0.687052 1.3:-4276261 MS.gene00444:CDS
AGTGTTGCTGCTGAGCAAGG+CGG 0.699580 1.3:-4276217 MS.gene00444:CDS
ACATTGAGAGAAGACACTGC+AGG 0.700620 1.3:-4276681 MS.gene00444:CDS
AGTTACTCAGAAACCTATGG+GGG 0.734801 1.3:-4276260 MS.gene00444:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAATTTTAAAATATTAA+TGG - chr1.3:4276339-4276358 MS.gene00444:CDS 0.0%
!! AATAATAGTAATTGTAAAAT+AGG - chr1.3:4276500-4276519 MS.gene00444:intron 10.0%
!! AATTAATCATCAATGATTTA+AGG + chr1.3:4275907-4275926 None:intergenic 15.0%
!! TAATGGAAATTATTGATATA+TGG - chr1.3:4276356-4276375 MS.gene00444:CDS 15.0%
!! TTATAAACAAAATATTGTCA+AGG - chr1.3:4276381-4276400 MS.gene00444:CDS 15.0%
!!! TTTTCTTTCAATTATTTTGT+AGG - chr1.3:4275950-4275969 MS.gene00444:intron 15.0%
!! ATTTATTACTAGAGAAAAGA+CGG + chr1.3:4276483-4276502 None:intergenic 20.0%
!! TTAATAAAGAGAGATCAAAA+TGG + chr1.3:4276218-4276237 None:intergenic 20.0%
! AAAAAACGACAAATGACAAA+AGG + chr1.3:4275978-4275997 None:intergenic 25.0%
! ACTGCGGAAATAAAAAAAAA+AGG + chr1.3:4276713-4276732 None:intergenic 25.0%
! ATCAATGATTTAAGGAATCA+AGG + chr1.3:4275899-4275918 None:intergenic 25.0%
! TCAATGATTTAAGGAATCAA+GGG + chr1.3:4275898-4275917 None:intergenic 25.0%
! TGCGTGATAAAAAATAAACA+GGG + chr1.3:4275778-4275797 None:intergenic 25.0%
! TTGCGTGATAAAAAATAAAC+AGG + chr1.3:4275779-4275798 None:intergenic 25.0%
! TTTATTACTAGAGAAAAGAC+GGG + chr1.3:4276482-4276501 None:intergenic 25.0%
!! TAATTTTGCTTCTTTGTCAT+GGG - chr1.3:4276586-4276605 MS.gene00444:CDS 25.0%
!! TCAAATTTCACAGATTTTGA+AGG - chr1.3:4276170-4276189 MS.gene00444:intron 25.0%
!! TTAATTTTGCTTCTTTGTCA+TGG - chr1.3:4276585-4276604 MS.gene00444:CDS 25.0%
!! TTTTCAAATACACACTTTCA+AGG + chr1.3:4276614-4276633 None:intergenic 25.0%
AAATAAAAAGAGCGGAAAGA+CGG - chr1.3:4276445-4276464 MS.gene00444:intron 30.0%
CATAGCTGTGAAAATTTGAT+TGG - chr1.3:4276637-4276656 MS.gene00444:CDS 30.0%
CGTTAGTGAAATAAAAAGAG+CGG - chr1.3:4276437-4276456 MS.gene00444:intron 30.0%
GACGAGAAAATTATAAACTG+CGG + chr1.3:4276729-4276748 None:intergenic 30.0%
GTACGATCAACAACATTAAT+TGG + chr1.3:4276241-4276260 None:intergenic 30.0%
TTTATCACTAACCAAGTGTT+GGG - chr1.3:4276545-4276564 MS.gene00444:CDS 30.0%
! ATGGAATATATTTTACCTGC+AGG + chr1.3:4276199-4276218 None:intergenic 30.0%
! GAAAGAGATAATTTTGCGTT+TGG + chr1.3:4275656-4275675 None:intergenic 30.0%
! TGGAATATATTTTACCTGCA+GGG + chr1.3:4276198-4276217 None:intergenic 30.0%
! TTTTATCACTAACCAAGTGT+TGG - chr1.3:4276544-4276563 MS.gene00444:CDS 30.0%
AGTAGAAAGAGAGAACAAAC+GGG + chr1.3:4276263-4276282 None:intergenic 35.0%
CAGTAGAAAGAGAGAACAAA+CGG + chr1.3:4276264-4276283 None:intergenic 35.0%
GATAATGTATGAGCATGCTT+TGG - chr1.3:4275830-4275849 MS.gene00444:intron 35.0%
GATTTAAGGAATCAAGGGAA+TGG + chr1.3:4275893-4275912 None:intergenic 35.0%
TACATTAATGACCCAACACT+TGG + chr1.3:4276559-4276578 None:intergenic 35.0%
! AAAATTTGATTGGCCACGTT+TGG - chr1.3:4276647-4276666 MS.gene00444:CDS 35.0%
! AGTGTTGGGTCATTAATGTA+TGG - chr1.3:4276559-4276578 MS.gene00444:CDS 35.0%
!! TTAGTTCTGATAGCAGTGTT+GGG + chr1.3:4275807-4275826 None:intergenic 35.0%
ACACTGCTATCAGAACTAAC+TGG - chr1.3:4275808-4275827 MS.gene00444:intron 40.0%
AGTTACTCAGAAACCTATGG+GGG - chr1.3:4276100-4276119 MS.gene00444:intron 40.0%
GAGTTACTCAGAAACCTATG+GGG - chr1.3:4276099-4276118 MS.gene00444:intron 40.0%
GGAGTTACTCAGAAACCTAT+GGG - chr1.3:4276098-4276117 MS.gene00444:intron 40.0%
TAAGGAATCAAGGGAATGGT+GGG + chr1.3:4275889-4275908 None:intergenic 40.0%
TGATATCATTGAGCCAAACG+TGG + chr1.3:4276663-4276682 None:intergenic 40.0%
TGGAGTTACTCAGAAACCTA+TGG - chr1.3:4276097-4276116 MS.gene00444:intron 40.0%
TTAAGGAATCAAGGGAATGG+TGG + chr1.3:4275890-4275909 None:intergenic 40.0%
TTCAAAAAGTCCCATACCTG+AGG + chr1.3:4275864-4275883 None:intergenic 40.0%
!! GTTAGTTCTGATAGCAGTGT+TGG + chr1.3:4275808-4275827 None:intergenic 40.0%
!! TAGTTCTGATAGCAGTGTTG+GGG + chr1.3:4275806-4275825 None:intergenic 40.0%
ACATTGAGAGAAGACACTGC+AGG - chr1.3:4275679-4275698 MS.gene00444:intron 45.0%
ACCATCACCTTCATCAACCT+TGG + chr1.3:4276048-4276067 None:intergenic 45.0%
ATGGATCTGGATGCTGAGTT+TGG - chr1.3:4276014-4276033 MS.gene00444:intron 45.0%
CATCCAGATCCATCTTTGGT+GGG + chr1.3:4276007-4276026 None:intergenic 45.0%
GACTCTGCTGACAAGATGAA+TGG - chr1.3:4276077-4276096 MS.gene00444:intron 45.0%
TCAGCATCCAGATCCATCTT+TGG + chr1.3:4276011-4276030 None:intergenic 45.0%
! ACCGGATTCTGGAGGAAAAA+GGG - chr1.3:4275702-4275721 MS.gene00444:intron 45.0%
! AGTTCTGATAGCAGTGTTGG+GGG + chr1.3:4275805-4275824 None:intergenic 45.0%
! TCCCTTTTTCCTCCAGAATC+CGG + chr1.3:4275706-4275725 None:intergenic 45.0%
! TGAGTTTGGAGCGTTATCCA+AGG - chr1.3:4276028-4276047 MS.gene00444:intron 45.0%
!! GCGTTATCCAAGGTTGATGA+AGG - chr1.3:4276038-4276057 MS.gene00444:intron 45.0%
!! GGTGCTGGTAATGTTGTGTT+GGG - chr1.3:4275744-4275763 MS.gene00444:intron 45.0%
!! TCCAAGGTTGATGAAGGTGA+TGG - chr1.3:4276044-4276063 MS.gene00444:intron 45.0%
!! TGGTGCTGGTAATGTTGTGT+TGG - chr1.3:4275743-4275762 MS.gene00444:intron 45.0%
!! TTTTGACTGCCCACCAAAGA+TGG - chr1.3:4275995-4276014 MS.gene00444:intron 45.0%
GCATCCAGATCCATCTTTGG+TGG + chr1.3:4276008-4276027 None:intergenic 50.0%
GGAGCTGTTCAAGACATCAC+TGG - chr1.3:4275723-4275742 MS.gene00444:intron 50.0%
GTTCAAGACATCACTGGTGC+TGG - chr1.3:4275729-4275748 MS.gene00444:intron 50.0%
! ACTAGTGTTGCTGCTGAGCA+AGG - chr1.3:4276140-4276159 MS.gene00444:intron 50.0%
! GACCGGATTCTGGAGGAAAA+AGG - chr1.3:4275701-4275720 MS.gene00444:intron 50.0%
!!! AGATTTTGAAGGCACCCTGC+AGG - chr1.3:4276181-4276200 MS.gene00444:CDS 50.0%
ACTCAGAAACCTATGGGGGC+TGG - chr1.3:4276104-4276123 MS.gene00444:intron 55.0%
CTCAGAAACCTATGGGGGCT+GGG - chr1.3:4276105-4276124 MS.gene00444:intron 55.0%
CTGCCCACCAAAGATGGATC+TGG - chr1.3:4276001-4276020 MS.gene00444:intron 55.0%
GAGAGAAGACACTGCAGGAC+CGG - chr1.3:4275684-4275703 MS.gene00444:intron 55.0%
GGCTGACAAGCCTCAGGTAT+GGG - chr1.3:4275851-4275870 MS.gene00444:intron 55.0%
TCAGAAACCTATGGGGGCTG+GGG - chr1.3:4276106-4276125 MS.gene00444:intron 55.0%
TGCTTTGGCTGACAAGCCTC+AGG - chr1.3:4275845-4275864 MS.gene00444:intron 55.0%
TGGCTGACAAGCCTCAGGTA+TGG - chr1.3:4275850-4275869 MS.gene00444:intron 55.0%
! AGTGTTGCTGCTGAGCAAGG+CGG - chr1.3:4276143-4276162 MS.gene00444:intron 55.0%
AAACCTATGGGGGCTGGGGA+TGG - chr1.3:4276110-4276129 MS.gene00444:intron 60.0%
AACCTATGGGGGCTGGGGAT+GGG - chr1.3:4276111-4276130 MS.gene00444:intron 60.0%
ACTGCAGGACCGGATTCTGG+AGG - chr1.3:4275694-4275713 MS.gene00444:intron 60.0%
GACACTGCAGGACCGGATTC+TGG - chr1.3:4275691-4275710 MS.gene00444:intron 60.0%
ACCTATGGGGGCTGGGGATG+GGG - chr1.3:4276112-4276131 MS.gene00444:intron 65.0%
ATGGGGGCTGGGGATGGGGC+TGG - chr1.3:4276116-4276135 MS.gene00444:intron 75.0%
GCCCCATCCCCAGCCCCCAT+AGG + chr1.3:4276116-4276135 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 4275624 4276758 4275624 ID=MS.gene00444
chr1.3 mRNA 4275624 4276758 4275624 ID=MS.gene00444.t1;Parent=MS.gene00444
chr1.3 exon 4276516 4276758 4276516 ID=MS.gene00444.t1.exon1;Parent=MS.gene00444.t1
chr1.3 CDS 4276516 4276758 4276516 ID=cds.MS.gene00444.t1;Parent=MS.gene00444.t1
chr1.3 exon 4276180 4276410 4276180 ID=MS.gene00444.t1.exon2;Parent=MS.gene00444.t1
chr1.3 CDS 4276180 4276410 4276180 ID=cds.MS.gene00444.t1;Parent=MS.gene00444.t1
chr1.3 exon 4275624 4275650 4275624 ID=MS.gene00444.t1.exon3;Parent=MS.gene00444.t1
chr1.3 CDS 4275624 4275650 4275624 ID=cds.MS.gene00444.t1;Parent=MS.gene00444.t1
Gene Sequence

>MS.gene00444

ATGAAGGATGTTCATACTCAATCTCAATGCCAAACGCAAAATTATCTCTTTCAACACATTGAGAGAAGACACTGCAGGACCGGATTCTGGAGGAAAAAGGGAGCTGTTCAAGACATCACTGGTGCTGGTAATGTTGTGTTGGGCAAGAAGACCCTGTTTATTTTTTATCACGCAAGTTCCCCCAACACTGCTATCAGAACTAACTGGATAATGTATGAGCATGCTTTGGCTGACAAGCCTCAGGTATGGGACTTTTTGAAAACCCACCATTCCCTTGATTCCTTAAATCATTGATGATTAATTAATGTATTCATAACTACTAACTATTTTCTTTCAATTATTTTGTAGGCTCCTTTTGTCATTTGTCGTTTTTTTGACTGCCCACCAAAGATGGATCTGGATGCTGAGTTTGGAGCGTTATCCAAGGTTGATGAAGGTGATGGTGCTAGAGATGACTCTGCTGACAAGATGAATGGAGTTACTCAGAAACCTATGGGGGCTGGGGATGGGGCTGGTACTAGTGTTGCTGCTGAGCAAGGCGGTGCTTCAAATTTCACAGATTTTGAAGGCACCCTGCAGGTAAAATATATTCCATTTTGATCTCTCTTTATTAACCAATTAATGTTGTTGATCGTACCCGTTTGTTCTCTCTTTCTACTGCGCTAACGCATGTGATTATTTTATTATGTTTGTTTGTATAATTTTGATTAAAACTTTTAAATTTTAAAATATTAATGGAAATTATTGATATATGGATTTATAAACAAAATATTGTCAAGGCATATAACAATTATTTATGAACTCAACAATTAACGTTAGTGAAATAAAAAGAGCGGAAAGACGGACACGTGAGTGCCCGTCTTTTCTCTAGTAATAAATAATAGTAATTGTAAAATAGGTGTAAAAGTATATAATTTTGTTTTTATCACTAACCAAGTGTTGGGTCATTAATGTATGGTAGTTAATTTTGCTTCTTTGTCATGGGTTCCTTGAAAGTGTGTATTTGAAAAATTCATAGCTGTGAAAATTTGATTGGCCACGTTTGGCTCAATGATATCATTAGTGCATGATATTTCAAGTTCATTTCCTTTTTTTTTTATTTCCGCAGTTTATAATTTTCTCGTCTTTGAAGTAG
Protein sequence

>MS.gene00444.t1

MKDVHTQSQCQTQNYLFQHIERRHCRTGFWRKKGAVQDITGAGNVVLGKKTLFIFYHASSPNTAIRTNWIMYEHALADKPQAPFVICRFFDCPPKMDLDAEFGALSKVDEGDGARDDSADKMNGVTQKPMGAGDGAGTSVAAEQGGASNFTDFEGTLQFIIFSSLK