AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene00503

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00503.t1 MTR_1g018030 94.330 194 9 2 2 195 1 192 1.61e-134 374
MS.gene00503.t1 MTR_7g073990 42.282 149 75 2 47 187 97 242 4.56e-31 113
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene00503.t1 AT1G26220 60.591 203 65 4 2 195 1 197 9.18e-81 239
MS.gene00503.t1 AT1G32070 41.985 131 60 1 76 190 127 257 9.06e-29 108
MS.gene00503.t1 AT1G32070 41.667 132 60 1 76 190 126 257 2.82e-28 106
MS.gene00503.t1 AT1G32070 41.667 132 60 1 76 190 127 258 2.88e-28 106

Find 50 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATACTTTGTTAAGTGCTTCT+AGG 0.216082 1.2:+5103781 None:intergenic
TACTCTGAGCCAAGAGTTCT+TGG 0.233326 1.2:-5103495 MS.gene00503:CDS
GATCCTTCGTTTCAAGGGCT+TGG 0.286511 1.2:-5103588 MS.gene00503:CDS
AACAACAACATCCCATATTA+TGG 0.310068 1.2:+5103611 None:intergenic
GTTGTTGATCCTTCGTTTCA+AGG 0.353170 1.2:-5103594 MS.gene00503:CDS
CTCAGAGTAAAGAGCAATAT+TGG 0.361910 1.2:+5103509 None:intergenic
ATCCTTCGTTTCAAGGGCTT+GGG 0.363113 1.2:-5103587 MS.gene00503:CDS
TCGTTTCAAGGGCTTGGGCT+AGG 0.372956 1.2:-5103582 MS.gene00503:CDS
CTGTTGTGGAGAGGCTTATG+AGG 0.408843 1.2:-5103554 MS.gene00503:CDS
AAGTTAAGTCGTAGGGAGGA+TGG 0.419412 1.2:+5103939 None:intergenic
CGATAAAAGCCAAGAACTCT+TGG 0.431331 1.2:+5103486 None:intergenic
TAGGCTTGCTTGACAAGAAA+TGG 0.442809 1.2:+5103881 None:intergenic
CGTTTCAAGGGCTTGGGCTA+GGG 0.454257 1.2:-5103581 MS.gene00503:CDS
TTGTTGATCCTTCGTTTCAA+GGG 0.483590 1.2:-5103593 MS.gene00503:CDS
GTTGCATTTGCAAGAGCTAC+TGG 0.489343 1.2:-5103651 MS.gene00503:CDS
TTAACCCCTCTGAGGTTCTC+CGG 0.494474 1.2:+5103805 None:intergenic
TTTGAAGAAGTTAAGTCGTA+GGG 0.496530 1.2:+5103932 None:intergenic
CAAGAAATGGTGAGGTTTCG+TGG 0.507526 1.2:+5103894 None:intergenic
TGAGGGATCTTGTAGGAAGA+GGG 0.520334 1.2:-5103536 MS.gene00503:CDS
ACTCGAGCACACTGACTCAA+TGG 0.522170 1.2:-5103709 MS.gene00503:CDS
ATTTGAAGAAGTTAAGTCGT+AGG 0.522993 1.2:+5103931 None:intergenic
TGGGCTAGGGAAAGCTGTTG+TGG 0.530219 1.2:-5103568 MS.gene00503:CDS
ATGAGGGATCTTGTAGGAAG+AGG 0.534453 1.2:-5103537 MS.gene00503:CDS
AGTCGTAGGGAGGATGGAAG+AGG 0.540218 1.2:+5103945 None:intergenic
ATATTGAGAGTGGGTAGTCT+AGG 0.541441 1.2:+5103862 None:intergenic
ACCATTCCACGAATACCATC+AGG 0.547694 1.2:+5103441 None:intergenic
AGGCTTATGAGGGATCTTGT+AGG 0.549706 1.2:-5103543 MS.gene00503:CDS
AGCACACTGACTCAATGGTA+TGG 0.558828 1.2:-5103704 MS.gene00503:CDS
ACAAAGTATTCGTAGCAGTA+GGG 0.561588 1.2:-5103767 MS.gene00503:CDS
TCCTGATGGTATTCGTGGAA+TGG 0.563938 1.2:-5103442 MS.gene00503:CDS
AACAAAGTATTCGTAGCAGT+AGG 0.566118 1.2:-5103768 MS.gene00503:CDS
GAAGAAGTTAAGTCGTAGGG+AGG 0.570827 1.2:+5103935 None:intergenic
GCTGATCCTGATGGTATTCG+TGG 0.578470 1.2:-5103447 MS.gene00503:CDS
AGCCCAAGCCCTTGAAACGA+AGG 0.590595 1.2:+5103585 None:intergenic
GTTTCGTCGGATATTGAGAG+TGG 0.590666 1.2:+5103852 None:intergenic
ATTCTCCGGAGAACCTCAGA+GGG 0.594468 1.2:-5103810 MS.gene00503:CDS
TTGCTTGACAAGAAATGGTG+AGG 0.596575 1.2:+5103886 None:intergenic
TTCTAGGTTTAACCCCTCTG+AGG 0.598354 1.2:+5103797 None:intergenic
GATAATATGCTGCTCTTACG+TGG 0.618724 1.2:-5103981 None:intergenic
TGTTGTGGAGAGGCTTATGA+GGG 0.625783 1.2:-5103553 MS.gene00503:CDS
TAGGGAAAGCTGTTGTGGAG+AGG 0.629346 1.2:-5103563 MS.gene00503:CDS
AAATGGTGAGGTTTCGTGGT+GGG 0.635153 1.2:+5103898 None:intergenic
TTTGCAAGAGCTACTGGTGA+TGG 0.636078 1.2:-5103645 MS.gene00503:CDS
TTTCGTCGGATATTGAGAGT+GGG 0.646235 1.2:+5103853 None:intergenic
CATTCTCCGGAGAACCTCAG+AGG 0.650384 1.2:-5103811 MS.gene00503:CDS
TCGTAGCAGTAGGGTTTCCG+CGG 0.663293 1.2:-5103758 MS.gene00503:CDS
GGATCAGCAACAAAACCCAA+AGG 0.674227 1.2:+5103462 None:intergenic
GAAGAAGTCGCAGAATAATG+CGG 0.693298 1.2:-5103673 MS.gene00503:CDS
GAAATGGTGAGGTTTCGTGG+TGG 0.768689 1.2:+5103897 None:intergenic
TTCTCCGGAGAACCTCAGAG+GGG 0.790280 1.2:-5103809 MS.gene00503:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTTTTCAATGCCATAATAT+GGG - chr1.2:5103763-5103782 MS.gene00503:CDS 25.0%
AACAACAACATCCCATATTA+TGG + chr1.2:5103777-5103796 None:intergenic 30.0%
ATACTTTGTTAAGTGCTTCT+AGG + chr1.2:5103607-5103626 None:intergenic 30.0%
ATTTGAAGAAGTTAAGTCGT+AGG + chr1.2:5103457-5103476 None:intergenic 30.0%
TTTGAAGAAGTTAAGTCGTA+GGG + chr1.2:5103456-5103475 None:intergenic 30.0%
! GTGTTTTCAATGCCATAATA+TGG - chr1.2:5103762-5103781 MS.gene00503:CDS 30.0%
AAAAACGAGGTTTCATTCTC+CGG - chr1.2:5103561-5103580 MS.gene00503:CDS 35.0%
CTCAGAGTAAAGAGCAATAT+TGG + chr1.2:5103879-5103898 None:intergenic 35.0%
TTGTTGATCCTTCGTTTCAA+GGG - chr1.2:5103792-5103811 MS.gene00503:CDS 35.0%
! AACAAAGTATTCGTAGCAGT+AGG - chr1.2:5103617-5103636 MS.gene00503:CDS 35.0%
! ACAAAGTATTCGTAGCAGTA+GGG - chr1.2:5103618-5103637 MS.gene00503:CDS 35.0%
!! TCGTTTTTCTAGTGTTTCGT+CGG + chr1.2:5103549-5103568 None:intergenic 35.0%
ATATTGAGAGTGGGTAGTCT+AGG + chr1.2:5103526-5103545 None:intergenic 40.0%
CGATAAAAGCCAAGAACTCT+TGG + chr1.2:5103902-5103921 None:intergenic 40.0%
GAAGAAGTCGCAGAATAATG+CGG - chr1.2:5103712-5103731 MS.gene00503:CDS 40.0%
GACGAAACACTAGAAAAACG+AGG - chr1.2:5103548-5103567 MS.gene00503:CDS 40.0%
GTTGTTGATCCTTCGTTTCA+AGG - chr1.2:5103791-5103810 MS.gene00503:CDS 40.0%
TTGCTTGACAAGAAATGGTG+AGG + chr1.2:5103502-5103521 None:intergenic 40.0%
TTTCGTCGGATATTGAGAGT+GGG + chr1.2:5103535-5103554 None:intergenic 40.0%
! AGTGCAATGCGTATTTTCTC+AGG + chr1.2:5103659-5103678 None:intergenic 40.0%
! GTGCAATGCGTATTTTCTCA+GGG + chr1.2:5103658-5103677 None:intergenic 40.0%
! TAGGCTTGCTTGACAAGAAA+TGG + chr1.2:5103507-5103526 None:intergenic 40.0%
!! CTTGGCTTTTATCGACCTTT+GGG - chr1.2:5103908-5103927 MS.gene00503:CDS 40.0%
!! TCTTGGCTTTTATCGACCTT+TGG - chr1.2:5103907-5103926 MS.gene00503:CDS 40.0%
AAATGGTGAGGTTTCGTGGT+GGG + chr1.2:5103490-5103509 None:intergenic 45.0%
AAGTTAAGTCGTAGGGAGGA+TGG + chr1.2:5103449-5103468 None:intergenic 45.0%
ACCATTCCACGAATACCATC+AGG + chr1.2:5103947-5103966 None:intergenic 45.0%
AGGCTTATGAGGGATCTTGT+AGG - chr1.2:5103842-5103861 MS.gene00503:CDS 45.0%
ATCCTTCGTTTCAAGGGCTT+GGG - chr1.2:5103798-5103817 MS.gene00503:CDS 45.0%
ATGAGGGATCTTGTAGGAAG+AGG - chr1.2:5103848-5103867 MS.gene00503:CDS 45.0%
CAAGAAATGGTGAGGTTTCG+TGG + chr1.2:5103494-5103513 None:intergenic 45.0%
GAAGAAGTTAAGTCGTAGGG+AGG + chr1.2:5103453-5103472 None:intergenic 45.0%
GGATCAGCAACAAAACCCAA+AGG + chr1.2:5103926-5103945 None:intergenic 45.0%
GTTGCATTTGCAAGAGCTAC+TGG - chr1.2:5103734-5103753 MS.gene00503:CDS 45.0%
GTTTCGTCGGATATTGAGAG+TGG + chr1.2:5103536-5103555 None:intergenic 45.0%
TACTCTGAGCCAAGAGTTCT+TGG - chr1.2:5103890-5103909 MS.gene00503:CDS 45.0%
TCCTGATGGTATTCGTGGAA+TGG - chr1.2:5103943-5103962 MS.gene00503:CDS 45.0%
TGAGGGATCTTGTAGGAAGA+GGG - chr1.2:5103849-5103868 MS.gene00503:CDS 45.0%
TGTTGTGGAGAGGCTTATGA+GGG - chr1.2:5103832-5103851 MS.gene00503:CDS 45.0%
TTCTAGGTTTAACCCCTCTG+AGG + chr1.2:5103591-5103610 None:intergenic 45.0%
TTTGCAAGAGCTACTGGTGA+TGG - chr1.2:5103740-5103759 MS.gene00503:CDS 45.0%
!! AGCACACTGACTCAATGGTA+TGG - chr1.2:5103681-5103700 MS.gene00503:CDS 45.0%
!!! GGTTTTGTTGCTGATCCTGA+TGG - chr1.2:5103929-5103948 MS.gene00503:CDS 45.0%
ATTCTCCGGAGAACCTCAGA+GGG - chr1.2:5103575-5103594 MS.gene00503:CDS 50.0%
CTGTTGTGGAGAGGCTTATG+AGG - chr1.2:5103831-5103850 MS.gene00503:CDS 50.0%
GAAATGGTGAGGTTTCGTGG+TGG + chr1.2:5103491-5103510 None:intergenic 50.0%
GATCCTTCGTTTCAAGGGCT+TGG - chr1.2:5103797-5103816 MS.gene00503:CDS 50.0%
GCTGATCCTGATGGTATTCG+TGG - chr1.2:5103938-5103957 MS.gene00503:CDS 50.0%
TAGGGAAAGCTGTTGTGGAG+AGG - chr1.2:5103822-5103841 MS.gene00503:CDS 50.0%
!! ACTCGAGCACACTGACTCAA+TGG - chr1.2:5103676-5103695 MS.gene00503:CDS 50.0%
!! TTAACCCCTCTGAGGTTCTC+CGG + chr1.2:5103583-5103602 None:intergenic 50.0%
AGCCCAAGCCCTTGAAACGA+AGG + chr1.2:5103803-5103822 None:intergenic 55.0%
AGTCGTAGGGAGGATGGAAG+AGG + chr1.2:5103443-5103462 None:intergenic 55.0%
CATTCTCCGGAGAACCTCAG+AGG - chr1.2:5103574-5103593 MS.gene00503:CDS 55.0%
CGTTTCAAGGGCTTGGGCTA+GGG - chr1.2:5103804-5103823 MS.gene00503:CDS 55.0%
TCGTAGCAGTAGGGTTTCCG+CGG - chr1.2:5103627-5103646 MS.gene00503:CDS 55.0%
TCGTTTCAAGGGCTTGGGCT+AGG - chr1.2:5103803-5103822 MS.gene00503:CDS 55.0%
TTCTCCGGAGAACCTCAGAG+GGG - chr1.2:5103576-5103595 MS.gene00503:CDS 55.0%
! TGGGCTAGGGAAAGCTGTTG+TGG - chr1.2:5103817-5103836 MS.gene00503:CDS 55.0%
! ATTTTCTCAGGGTCGCGCCG+CGG + chr1.2:5103647-5103666 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 5103410 5103997 5103410 ID=MS.gene00503
chr1.2 mRNA 5103410 5103997 5103410 ID=MS.gene00503.t1;Parent=MS.gene00503
chr1.2 exon 5103410 5103997 5103410 ID=MS.gene00503.t1.exon1;Parent=MS.gene00503.t1
chr1.2 CDS 5103410 5103997 5103410 ID=cds.MS.gene00503.t1;Parent=MS.gene00503.t1
Gene Sequence

>MS.gene00503

ATGCTGCTCTTACGTGGCAACATCTATGCTCCTCTTCCATCCTCCCTACGACTTAACTTCTTCAAATCACAAACTCACCCACCACGAAACCTCACCATTTCTTGTCAAGCAAGCCTAGACTACCCACTCTCAATATCCGACGAAACACTAGAAAAACGAGGTTTCATTCTCCGGAGAACCTCAGAGGGGTTAAACCTAGAAGCACTTAACAAAGTATTCGTAGCAGTAGGGTTTCCGCGGCGCGACCCTGAGAAAATACGCATTGCACTCGAGCACACTGACTCAATGGTATGGATACAACAGAAGAAGTCGCAGAATAATGCGGTTGCATTTGCAAGAGCTACTGGTGATGGTGTTTTCAATGCCATAATATGGGATGTTGTTGTTGATCCTTCGTTTCAAGGGCTTGGGCTAGGGAAAGCTGTTGTGGAGAGGCTTATGAGGGATCTTGTAGGAAGAGGGATTACCAATATTGCTCTTTACTCTGAGCCAAGAGTTCTTGGCTTTTATCGACCTTTGGGTTTTGTTGCTGATCCTGATGGTATTCGTGGAATGGTTTACTCGACAAAAAACAAAAGAAAAAAATAG
Protein sequence

>MS.gene00503.t1

MLLLRGNIYAPLPSSLRLNFFKSQTHPPRNLTISCQASLDYPLSISDETLEKRGFILRRTSEGLNLEALNKVFVAVGFPRRDPEKIRIALEHTDSMVWIQQKKSQNNAVAFARATGDGVFNAIIWDVVVDPSFQGLGLGKAVVERLMRDLVGRGITNIALYSEPRVLGFYRPLGFVADPDGIRGMVYSTKNKRKK