AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06036

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06036.t1 MTR_8g099150 100.000 106 0 0 1 106 1 106 2.78e-76 220
MS.gene06036.t1 MTR_8g016300 98.113 106 2 0 1 106 1 106 4.01e-75 217
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06036.t1 AT5G55140 63.810 105 37 1 3 106 1 105 1.15e-45 143

Find 42 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTGCGCCTATGTTGCTTTC+TGG 0.240202 4.1:-4934554 None:intergenic
AACGCTAGTGAGGGGTATTC+CGG 0.301510 4.1:+4934528 MS.gene06036:CDS
GGTTTCCTCCTTCTCTTTGC+GGG 0.349900 4.1:-4934788 None:intergenic
TCAACCTGCTTCTTCTGCTT+AGG 0.384301 4.1:+4934846 MS.gene06036:CDS
CAACCTGCTTCTTCTGCTTA+GGG 0.390606 4.1:+4934847 MS.gene06036:CDS
GATGGAACACACCTACTGTT+AGG 0.400025 4.1:+4934620 MS.gene06036:CDS
CACTAGCGTTATGTAGAGAT+TGG 0.401453 4.1:-4934515 None:intergenic
ACGCTAGTGAGGGGTATTCC+GGG 0.415196 4.1:+4934529 MS.gene06036:CDS
GGGTTTCCTCCTTCTCTTTG+CGG 0.418532 4.1:-4934789 None:intergenic
AGATTGGGGCTATAAGCAAT+TGG 0.427253 4.1:-4934499 None:intergenic
CATGAGCATGAATGCGTTCA+AGG 0.431873 4.1:+4934459 None:intergenic
AAGCAGAAGAAGCAGGTTGA+TGG 0.435151 4.1:-4934843 None:intergenic
ACTAGCGTTATGTAGAGATT+GGG 0.460548 4.1:-4934514 None:intergenic
ATGGAACACACCTACTGTTA+GGG 0.464145 4.1:+4934621 MS.gene06036:CDS
GTTAGTTGTTGTTGAGACAG+AGG 0.465463 4.1:+4934753 MS.gene06036:CDS
CTATGTTGCTTTCTGGTCCC+CGG 0.474886 4.1:-4934547 None:intergenic
CAGAGCTCTTCGTCCTCCAT+TGG 0.509479 4.1:+4934813 MS.gene06036:CDS
TGTTCCATCGCATGACAGTT+CGG 0.511917 4.1:-4934606 None:intergenic
AAAGCAACATAGGCGCACTT+TGG 0.520220 4.1:+4934558 MS.gene06036:CDS
GGTTGATGGTTTATGACCAA+TGG 0.522943 4.1:-4934829 None:intergenic
GATTGGGGCTATAAGCAATT+GGG 0.527244 4.1:-4934498 None:intergenic
TGTATTTGATATAGGTCAAG+AGG 0.544788 4.1:+4934731 MS.gene06036:intron
GTACCCTAAGCAGAAGAAGC+AGG 0.555500 4.1:-4934850 None:intergenic
GTACAAGGCCCGCAAAGAGA+AGG 0.555978 4.1:+4934780 MS.gene06036:CDS
CGGGGACCAGAAAGCAACAT+AGG 0.565331 4.1:+4934548 MS.gene06036:CDS
TGGAGGACGAAGAGCTCTGT+GGG 0.570519 4.1:-4934809 None:intergenic
TGTTAGGGGAATGATCCAGC+AGG 0.585091 4.1:+4934636 MS.gene06036:CDS
GCTATAAGCAATTGGGACAC+AGG 0.590348 4.1:-4934491 None:intergenic
GCAACCGAACTGTCATGCGA+TGG 0.602415 4.1:+4934602 MS.gene06036:CDS
CAAGGCCCGCAAAGAGAAGG+AGG 0.604236 4.1:+4934783 MS.gene06036:CDS
ATCTCTACATAACGCTAGTG+AGG 0.609634 4.1:+4934518 MS.gene06036:CDS
CTAGCGTTATGTAGAGATTG+GGG 0.616077 4.1:-4934513 None:intergenic
TGGATCATTCCCCTAACAGT+AGG 0.620579 4.1:-4934631 None:intergenic
TGATGGTTTATGACCAATGG+AGG 0.622285 4.1:-4934826 None:intergenic
CAGTTCGGTTGCATTTGCCG+AGG 0.626107 4.1:-4934591 None:intergenic
TCTCTACATAACGCTAGTGA+GGG 0.627577 4.1:+4934519 MS.gene06036:CDS
TGAGACAGAGGAGATGTACA+AGG 0.642473 4.1:+4934765 MS.gene06036:CDS
ACTTTGGAAGCACTACGCCT+CGG 0.645701 4.1:+4934574 MS.gene06036:CDS
TGGAACACACCTACTGTTAG+GGG 0.654422 4.1:+4934622 MS.gene06036:CDS
ATGGAGGACGAAGAGCTCTG+TGG 0.663844 4.1:-4934810 None:intergenic
CGCTAGTGAGGGGTATTCCG+GGG 0.667158 4.1:+4934530 MS.gene06036:CDS
CTCTACATAACGCTAGTGAG+GGG 0.670443 4.1:+4934520 MS.gene06036:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GGTAACTTTGTATTTGATAT+AGG + chr4.1:4934723-4934742 MS.gene06036:intron 25.0%
ACCAATGTTGTTAGTATACA+GGG - chr4.1:4934706-4934725 None:intergenic 30.0%
TACCAATGTTGTTAGTATAC+AGG - chr4.1:4934707-4934726 None:intergenic 30.0%
TGTATTTGATATAGGTCAAG+AGG + chr4.1:4934731-4934750 MS.gene06036:intron 30.0%
ACTAGCGTTATGTAGAGATT+GGG - chr4.1:4934517-4934536 None:intergenic 35.0%
GGAGATAGGTAGTTTCAAAA+TGG - chr4.1:4934685-4934704 None:intergenic 35.0%
TCCCTGTATACTAACAACAT+TGG + chr4.1:4934702-4934721 MS.gene06036:intron 35.0%
TTGTTAGTATACAGGGAGAT+AGG - chr4.1:4934699-4934718 None:intergenic 35.0%
AGATTGGGGCTATAAGCAAT+TGG - chr4.1:4934502-4934521 None:intergenic 40.0%
ATCTCTACATAACGCTAGTG+AGG + chr4.1:4934518-4934537 MS.gene06036:CDS 40.0%
ATGGAACACACCTACTGTTA+GGG + chr4.1:4934621-4934640 MS.gene06036:CDS 40.0%
CACTAGCGTTATGTAGAGAT+TGG - chr4.1:4934518-4934537 None:intergenic 40.0%
CTAGCGTTATGTAGAGATTG+GGG - chr4.1:4934516-4934535 None:intergenic 40.0%
GATTGGGGCTATAAGCAATT+GGG - chr4.1:4934501-4934520 None:intergenic 40.0%
TCTCTACATAACGCTAGTGA+GGG + chr4.1:4934519-4934538 MS.gene06036:CDS 40.0%
TGATGGTTTATGACCAATGG+AGG - chr4.1:4934829-4934848 None:intergenic 40.0%
! GTTAGTTGTTGTTGAGACAG+AGG + chr4.1:4934753-4934772 MS.gene06036:CDS 40.0%
!! GGTTGATGGTTTATGACCAA+TGG - chr4.1:4934832-4934851 None:intergenic 40.0%
AAAGCAACATAGGCGCACTT+TGG + chr4.1:4934558-4934577 MS.gene06036:CDS 45.0%
CTCTACATAACGCTAGTGAG+GGG + chr4.1:4934520-4934539 MS.gene06036:CDS 45.0%
GATGGAACACACCTACTGTT+AGG + chr4.1:4934620-4934639 MS.gene06036:CDS 45.0%
GCTATAAGCAATTGGGACAC+AGG - chr4.1:4934494-4934513 None:intergenic 45.0%
TGAGACAGAGGAGATGTACA+AGG + chr4.1:4934765-4934784 MS.gene06036:CDS 45.0%
TGGAACACACCTACTGTTAG+GGG + chr4.1:4934622-4934641 MS.gene06036:CDS 45.0%
TGGATCATTCCCCTAACAGT+AGG - chr4.1:4934634-4934653 None:intergenic 45.0%
TGTTCCATCGCATGACAGTT+CGG - chr4.1:4934609-4934628 None:intergenic 45.0%
! AAGCAGAAGAAGCAGGTTGA+TGG - chr4.1:4934846-4934865 None:intergenic 45.0%
GATCTTGTGCTGAAACCTGC+TGG - chr4.1:4934654-4934673 None:intergenic 50.0%
GGGTTTCCTCCTTCTCTTTG+CGG - chr4.1:4934792-4934811 None:intergenic 50.0%
GGTTTCCTCCTTCTCTTTGC+GGG - chr4.1:4934791-4934810 None:intergenic 50.0%
TGTTAGGGGAATGATCCAGC+AGG + chr4.1:4934636-4934655 MS.gene06036:CDS 50.0%
!! AACGCTAGTGAGGGGTATTC+CGG + chr4.1:4934528-4934547 MS.gene06036:CDS 50.0%
!! ACTTTGGAAGCACTACGCCT+CGG + chr4.1:4934574-4934593 MS.gene06036:CDS 50.0%
!! AGTGCGCCTATGTTGCTTTC+TGG - chr4.1:4934557-4934576 None:intergenic 50.0%
!! CTATGTTGCTTTCTGGTCCC+CGG - chr4.1:4934550-4934569 None:intergenic 50.0%
ATGGAGGACGAAGAGCTCTG+TGG - chr4.1:4934813-4934832 None:intergenic 55.0%
CAGAGCTCTTCGTCCTCCAT+TGG + chr4.1:4934813-4934832 MS.gene06036:CDS 55.0%
CAGTTCGGTTGCATTTGCCG+AGG - chr4.1:4934594-4934613 None:intergenic 55.0%
CGGGGACCAGAAAGCAACAT+AGG + chr4.1:4934548-4934567 MS.gene06036:CDS 55.0%
GCAACCGAACTGTCATGCGA+TGG + chr4.1:4934602-4934621 MS.gene06036:CDS 55.0%
GTACAAGGCCCGCAAAGAGA+AGG + chr4.1:4934780-4934799 MS.gene06036:CDS 55.0%
TGGAGGACGAAGAGCTCTGT+GGG - chr4.1:4934812-4934831 None:intergenic 55.0%
!! ACGCTAGTGAGGGGTATTCC+GGG + chr4.1:4934529-4934548 MS.gene06036:CDS 55.0%
CAAGGCCCGCAAAGAGAAGG+AGG + chr4.1:4934783-4934802 MS.gene06036:CDS 60.0%
!! CGCTAGTGAGGGGTATTCCG+GGG + chr4.1:4934530-4934549 MS.gene06036:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 4934460 4934867 4934460 ID=MS.gene06036
chr4.1 mRNA 4934460 4934867 4934460 ID=MS.gene06036.t1;Parent=MS.gene06036
chr4.1 exon 4934460 4934657 4934460 ID=MS.gene06036.t1.exon1;Parent=MS.gene06036.t1
chr4.1 CDS 4934460 4934657 4934460 ID=cds.MS.gene06036.t1;Parent=MS.gene06036.t1
chr4.1 exon 4934745 4934867 4934745 ID=MS.gene06036.t1.exon2;Parent=MS.gene06036.t1
chr4.1 CDS 4934745 4934867 4934745 ID=cds.MS.gene06036.t1;Parent=MS.gene06036.t1
Gene Sequence

>MS.gene06036

ATGAGCATGAATGCGTTCAAGGCATATAAGTCCTGTGTCCCAATTGCTTATAGCCCCAATCTCTACATAACGCTAGTGAGGGGTATTCCGGGGACCAGAAAGCAACATAGGCGCACTTTGGAAGCACTACGCCTCGGCAAATGCAACCGAACTGTCATGCGATGGAACACACCTACTGTTAGGGGAATGATCCAGCAGGTTTCAGCACAAGATCTATCAGATCCATTTTGAAACTACCTATCTCCCTGTATACTAACAACATTGGTAACTTTGTATTTGATATAGGTCAAGAGGTTAGTTGTTGTTGAGACAGAGGAGATGTACAAGGCCCGCAAAGAGAAGGAGGAAACCCACAGAGCTCTTCGTCCTCCATTGGTCATAAACCATCAACCTGCTTCTTCTGCTTAG
Protein sequence

>MS.gene06036.t1

MSMNAFKAYKSCVPIAYSPNLYITLVRGIPGTRKQHRRTLEALRLGKCNRTVMRWNTPTVRGMIQQVKRLVVVETEEMYKARKEKEETHRALRPPLVINHQPASSA