AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0715520


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 30 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGAAGGGAAAATTGAAAA+TGG 0.224177 5_1:-8578262 None:intergenic
GAAGTTCTCCTTCAAAGTTT+TGG 0.321181 5_1:+8578857 Msa0715520:CDS
CACAATCAGATTCAACAAAA+AGG 0.337028 5_1:-8578390 None:intergenic
CAAAACCGTAAAAGAGAGAG+AGG 0.424602 5_1:-8578296 None:intergenic
AAAAGAGAGAGAGGGAGCTT+AGG 0.449508 5_1:-8578287 None:intergenic
GTGAAGGGAAAATTGAAAAT+GGG 0.459730 5_1:-8578261 None:intergenic
GAGGGAGCTTAGGTTTGTGA+AGG 0.467345 5_1:-8578277 None:intergenic
GGAAGAAGAAGATAATAGTA+AGG 0.475273 5_1:-8578049 None:intergenic
GAGGTGGCAACTGCAACAAC+TGG 0.477158 5_1:+8578485 Msa0715520:CDS
AGAAGATAATAGTAAGGCAG+AGG 0.485632 5_1:-8578043 None:intergenic
TTTGTTGAATCTGATTGTGC+AGG 0.486427 5_1:+8578394 Msa0715520:CDS
ATTCAAGGAATGGGTCGGTT+GGG 0.489585 5_1:+8578424 Msa0715520:CDS
ACGCTGGGAGATGGTGGATC+AGG 0.490895 5_1:+8578457 Msa0715520:CDS
GATGGTGGATCAGGACTTAG+AGG 0.492687 5_1:+8578466 Msa0715520:CDS
GGGAAATGAGTGGAAGGAGG+TGG 0.497421 5_1:-8578070 None:intergenic
GAAGGAACAACGCTGGGAGA+TGG 0.499001 5_1:+8578448 Msa0715520:CDS
TGTGCAGGTTGTCAGATTCA+AGG 0.512612 5_1:+8578409 Msa0715520:CDS
AGGGAGCTTAGGTTTGTGAA+GGG 0.520034 5_1:-8578276 None:intergenic
GATTCAAGGAATGGGTCGGT+TGG 0.520448 5_1:+8578423 Msa0715520:CDS
GGTTGTCAGATTCAAGGAAT+GGG 0.533310 5_1:+8578415 Msa0715520:CDS
AGGTTGTCAGATTCAAGGAA+TGG 0.541574 5_1:+8578414 Msa0715520:CDS
GGAATGGGTCGGTTGGGAGA+AGG 0.541805 5_1:+8578430 Msa0715520:CDS
GGAACAACGCTGGGAGATGG+TGG 0.563155 5_1:+8578451 Msa0715520:CDS
TTGGGAGAAGGAACAACGCT+GGG 0.568199 5_1:+8578442 Msa0715520:CDS
GTCAGATTCAAGGAATGGGT+CGG 0.597985 5_1:+8578419 Msa0715520:CDS
TTATGACAAATTGAAATCCA+AGG 0.605167 5_1:-8578208 None:intergenic
AAAGATGAAAGAAATTGTGG+AGG 0.617363 5_1:-8578103 None:intergenic
GTTGGGAGAAGGAACAACGC+TGG 0.636641 5_1:+8578441 Msa0715520:CDS
AAAACCGTAAAAGAGAGAGA+GGG 0.637385 5_1:-8578295 None:intergenic
GGTGGATCAGGACTTAGAGG+TGG 0.682012 5_1:+8578469 Msa0715520:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGGATACGTTTTTTATTTT+GGG - chr5_1:8578530-8578549 None:intergenic 20.0%
!!! TTGGATACGTTTTTTATTTT+GGG - chr5_1:8578530-8578549 None:intergenic 20.0%
! GAAAAAGATGAAAGAAATTG+TGG - chr5_1:8578109-8578128 None:intergenic 25.0%
!!! TGTTGTTATTTTTTCTTCCT+TGG + chr5_1:8578191-8578210 Msa0715520:five_prime_UTR 25.0%
! TTATGACAAATTGAAATCCA+AGG - chr5_1:8578211-8578230 None:intergenic 25.0%
! AAAAATTGAAACCCTAAAAC+TGG - chr5_1:8578326-8578345 None:intergenic 25.0%
!!! ACGTTTTTTATTTTGGGAAA+AGG - chr5_1:8578524-8578543 None:intergenic 25.0%
!!! CTTGGATACGTTTTTTATTT+TGG - chr5_1:8578531-8578550 None:intergenic 25.0%
!!! ACATTTTGATACAGAAACAA+AGG - chr5_1:8578778-8578797 None:intergenic 25.0%
!!! AACTTTTTCCAAAACTTTGA+AGG - chr5_1:8578868-8578887 None:intergenic 25.0%
! GAAAAAGATGAAAGAAATTG+TGG - chr5_1:8578109-8578128 None:intergenic 25.0%
!!! TGTTGTTATTTTTTCTTCCT+TGG + chr5_1:8578191-8578210 Msa0715520:five_prime_UTR 25.0%
! TTATGACAAATTGAAATCCA+AGG - chr5_1:8578211-8578230 None:intergenic 25.0%
! AAAAATTGAAACCCTAAAAC+TGG - chr5_1:8578326-8578345 None:intergenic 25.0%
!!! ACGTTTTTTATTTTGGGAAA+AGG - chr5_1:8578524-8578543 None:intergenic 25.0%
!!! CTTGGATACGTTTTTTATTT+TGG - chr5_1:8578531-8578550 None:intergenic 25.0%
!!! ACATTTTGATACAGAAACAA+AGG - chr5_1:8578778-8578797 None:intergenic 25.0%
!!! AACTTTTTCCAAAACTTTGA+AGG - chr5_1:8578868-8578887 None:intergenic 25.0%
GGAAGAAGAAGATAATAGTA+AGG - chr5_1:8578052-8578071 None:intergenic 30.0%
! AAATTGTGGAGGACATTTTT+GGG - chr5_1:8578095-8578114 None:intergenic 30.0%
AAAGATGAAAGAAATTGTGG+AGG - chr5_1:8578106-8578125 None:intergenic 30.0%
GTGAAGGGAAAATTGAAAAT+GGG - chr5_1:8578264-8578283 None:intergenic 30.0%
TGTGAAGGGAAAATTGAAAA+TGG - chr5_1:8578265-8578284 None:intergenic 30.0%
!!! GGTTTTGTTTTCCAGTTTTA+GGG + chr5_1:8578312-8578331 Msa0715520:five_prime_UTR 30.0%
CACAATCAGATTCAACAAAA+AGG - chr5_1:8578393-8578412 None:intergenic 30.0%
!! AGATTTAAAACAGAAGTGCT+TGG - chr5_1:8578549-8578568 None:intergenic 30.0%
! CAAAATGTGTTTTGCAGATT+CGG + chr5_1:8578790-8578809 Msa0715520:intron 30.0%
GGAAGAAGAAGATAATAGTA+AGG - chr5_1:8578052-8578071 None:intergenic 30.0%
! AAATTGTGGAGGACATTTTT+GGG - chr5_1:8578095-8578114 None:intergenic 30.0%
AAAGATGAAAGAAATTGTGG+AGG - chr5_1:8578106-8578125 None:intergenic 30.0%
GTGAAGGGAAAATTGAAAAT+GGG - chr5_1:8578264-8578283 None:intergenic 30.0%
TGTGAAGGGAAAATTGAAAA+TGG - chr5_1:8578265-8578284 None:intergenic 30.0%
!!! GGTTTTGTTTTCCAGTTTTA+GGG + chr5_1:8578312-8578331 Msa0715520:five_prime_UTR 30.0%
CACAATCAGATTCAACAAAA+AGG - chr5_1:8578393-8578412 None:intergenic 30.0%
!! AGATTTAAAACAGAAGTGCT+TGG - chr5_1:8578549-8578568 None:intergenic 30.0%
! CAAAATGTGTTTTGCAGATT+CGG + chr5_1:8578790-8578809 Msa0715520:intron 30.0%
AGAAGATAATAGTAAGGCAG+AGG - chr5_1:8578046-8578065 None:intergenic 35.0%
! AATTGTGGAGGACATTTTTG+GGG - chr5_1:8578094-8578113 None:intergenic 35.0%
! GAAATTGTGGAGGACATTTT+TGG - chr5_1:8578096-8578115 None:intergenic 35.0%
AAAACCGTAAAAGAGAGAGA+GGG - chr5_1:8578298-8578317 None:intergenic 35.0%
!!! CGGTTTTGTTTTCCAGTTTT+AGG + chr5_1:8578311-8578330 Msa0715520:five_prime_UTR 35.0%
TTTGTTGAATCTGATTGTGC+AGG + chr5_1:8578394-8578413 Msa0715520:CDS 35.0%
CAGTGTGTTTATCAATTCTG+TGG + chr5_1:8578641-8578660 Msa0715520:intron 35.0%
AAACAAAGGACATACCTGTT+TGG - chr5_1:8578764-8578783 None:intergenic 35.0%
! GAAGTTCTCCTTCAAAGTTT+TGG + chr5_1:8578857-8578876 Msa0715520:CDS 35.0%
AGAAGATAATAGTAAGGCAG+AGG - chr5_1:8578046-8578065 None:intergenic 35.0%
! AATTGTGGAGGACATTTTTG+GGG - chr5_1:8578094-8578113 None:intergenic 35.0%
! GAAATTGTGGAGGACATTTT+TGG - chr5_1:8578096-8578115 None:intergenic 35.0%
AAAACCGTAAAAGAGAGAGA+GGG - chr5_1:8578298-8578317 None:intergenic 35.0%
!!! CGGTTTTGTTTTCCAGTTTT+AGG + chr5_1:8578311-8578330 Msa0715520:five_prime_UTR 35.0%
TTTGTTGAATCTGATTGTGC+AGG + chr5_1:8578394-8578413 Msa0715520:CDS 35.0%
CAGTGTGTTTATCAATTCTG+TGG + chr5_1:8578641-8578660 Msa0715520:intron 35.0%
AAACAAAGGACATACCTGTT+TGG - chr5_1:8578764-8578783 None:intergenic 35.0%
! GAAGTTCTCCTTCAAAGTTT+TGG + chr5_1:8578857-8578876 Msa0715520:CDS 35.0%
!! ACATTTTTGGGGGAAATGAG+TGG - chr5_1:8578083-8578102 None:intergenic 40.0%
!! ATTGTGGAGGACATTTTTGG+GGG - chr5_1:8578093-8578112 None:intergenic 40.0%
CAAAACCGTAAAAGAGAGAG+AGG - chr5_1:8578299-8578318 None:intergenic 40.0%
AGGTTGTCAGATTCAAGGAA+TGG + chr5_1:8578414-8578433 Msa0715520:CDS 40.0%
GGTTGTCAGATTCAAGGAAT+GGG + chr5_1:8578415-8578434 Msa0715520:CDS 40.0%
ATCAAACGTGTGTTTGTGGA+TGG - chr5_1:8578726-8578745 None:intergenic 40.0%
CATGATCAAACGTGTGTTTG+TGG - chr5_1:8578730-8578749 None:intergenic 40.0%
CACAAACACACGTTTGATCA+TGG + chr5_1:8578728-8578747 Msa0715520:intron 40.0%
ATGGAAATACGCTACCAAAC+AGG + chr5_1:8578747-8578766 Msa0715520:intron 40.0%
!! ACATTTTTGGGGGAAATGAG+TGG - chr5_1:8578083-8578102 None:intergenic 40.0%
!! ATTGTGGAGGACATTTTTGG+GGG - chr5_1:8578093-8578112 None:intergenic 40.0%
CAAAACCGTAAAAGAGAGAG+AGG - chr5_1:8578299-8578318 None:intergenic 40.0%
AGGTTGTCAGATTCAAGGAA+TGG + chr5_1:8578414-8578433 Msa0715520:CDS 40.0%
GGTTGTCAGATTCAAGGAAT+GGG + chr5_1:8578415-8578434 Msa0715520:CDS 40.0%
ATCAAACGTGTGTTTGTGGA+TGG - chr5_1:8578726-8578745 None:intergenic 40.0%
CATGATCAAACGTGTGTTTG+TGG - chr5_1:8578730-8578749 None:intergenic 40.0%
CACAAACACACGTTTGATCA+TGG + chr5_1:8578728-8578747 Msa0715520:intron 40.0%
ATGGAAATACGCTACCAAAC+AGG + chr5_1:8578747-8578766 Msa0715520:intron 40.0%
!! TTTTGGGGGAAATGAGTGGA+AGG - chr5_1:8578079-8578098 None:intergenic 45.0%
AGGGAGCTTAGGTTTGTGAA+GGG - chr5_1:8578279-8578298 None:intergenic 45.0%
AAAAGAGAGAGAGGGAGCTT+AGG - chr5_1:8578290-8578309 None:intergenic 45.0%
! AGCTCCCTCTCTCTCTTTTA+CGG + chr5_1:8578291-8578310 Msa0715520:five_prime_UTR 45.0%
TGTGCAGGTTGTCAGATTCA+AGG + chr5_1:8578409-8578428 Msa0715520:CDS 45.0%
GTCAGATTCAAGGAATGGGT+CGG + chr5_1:8578419-8578438 Msa0715520:CDS 45.0%
ATTCAAGGAATGGGTCGGTT+GGG + chr5_1:8578424-8578443 Msa0715520:CDS 45.0%
CCAAGCTTCTGCAGTTAACA+TGG - chr5_1:8578674-8578693 None:intergenic 45.0%
CCATGTTAACTGCAGAAGCT+TGG + chr5_1:8578671-8578690 Msa0715520:intron 45.0%
TAACTGCAGAAGCTTGGTTC+TGG + chr5_1:8578677-8578696 Msa0715520:intron 45.0%
!! TCTGGAGCTTTTGTAGATCG+CGG + chr5_1:8578695-8578714 Msa0715520:intron 45.0%
!! TTTTGGGGGAAATGAGTGGA+AGG - chr5_1:8578079-8578098 None:intergenic 45.0%
AGGGAGCTTAGGTTTGTGAA+GGG - chr5_1:8578279-8578298 None:intergenic 45.0%
AAAAGAGAGAGAGGGAGCTT+AGG - chr5_1:8578290-8578309 None:intergenic 45.0%
! AGCTCCCTCTCTCTCTTTTA+CGG + chr5_1:8578291-8578310 Msa0715520:five_prime_UTR 45.0%
TGTGCAGGTTGTCAGATTCA+AGG + chr5_1:8578409-8578428 Msa0715520:CDS 45.0%
GTCAGATTCAAGGAATGGGT+CGG + chr5_1:8578419-8578438 Msa0715520:CDS 45.0%
ATTCAAGGAATGGGTCGGTT+GGG + chr5_1:8578424-8578443 Msa0715520:CDS 45.0%
CCAAGCTTCTGCAGTTAACA+TGG - chr5_1:8578674-8578693 None:intergenic 45.0%
CCATGTTAACTGCAGAAGCT+TGG + chr5_1:8578671-8578690 Msa0715520:intron 45.0%
TAACTGCAGAAGCTTGGTTC+TGG + chr5_1:8578677-8578696 Msa0715520:intron 45.0%
!! TCTGGAGCTTTTGTAGATCG+CGG + chr5_1:8578695-8578714 Msa0715520:intron 45.0%
AGAGAGAGAGAGAGAGAGAG+AGG - chr5_1:8578010-8578029 None:intergenic 50.0%
GAGGGAGCTTAGGTTTGTGA+AGG - chr5_1:8578280-8578299 None:intergenic 50.0%
GATTCAAGGAATGGGTCGGT+TGG + chr5_1:8578423-8578442 Msa0715520:CDS 50.0%
TTGGGAGAAGGAACAACGCT+GGG + chr5_1:8578442-8578461 Msa0715520:CDS 50.0%
!! GATGGTGGATCAGGACTTAG+AGG + chr5_1:8578466-8578485 Msa0715520:CDS 50.0%
AGAGAGAGAGAGAGAGAGAG+AGG - chr5_1:8578010-8578029 None:intergenic 50.0%
GAGGGAGCTTAGGTTTGTGA+AGG - chr5_1:8578280-8578299 None:intergenic 50.0%
GATTCAAGGAATGGGTCGGT+TGG + chr5_1:8578423-8578442 Msa0715520:CDS 50.0%
TTGGGAGAAGGAACAACGCT+GGG + chr5_1:8578442-8578461 Msa0715520:CDS 50.0%
!! GATGGTGGATCAGGACTTAG+AGG + chr5_1:8578466-8578485 Msa0715520:CDS 50.0%
GAGAGAGAGAGAGAGAGAGG+AGG - chr5_1:8578009-8578028 None:intergenic 55.0%
GGGAAATGAGTGGAAGGAGG+TGG - chr5_1:8578073-8578092 None:intergenic 55.0%
TGGGGGAAATGAGTGGAAGG+AGG - chr5_1:8578076-8578095 None:intergenic 55.0%
GTTGGGAGAAGGAACAACGC+TGG + chr5_1:8578441-8578460 Msa0715520:CDS 55.0%
GAAGGAACAACGCTGGGAGA+TGG + chr5_1:8578448-8578467 Msa0715520:CDS 55.0%
GGTGGATCAGGACTTAGAGG+TGG + chr5_1:8578469-8578488 Msa0715520:CDS 55.0%
GAGGTGGCAACTGCAACAAC+TGG + chr5_1:8578485-8578504 Msa0715520:CDS 55.0%
GAGAGAGAGAGAGAGAGAGG+AGG - chr5_1:8578009-8578028 None:intergenic 55.0%
GGGAAATGAGTGGAAGGAGG+TGG - chr5_1:8578073-8578092 None:intergenic 55.0%
TGGGGGAAATGAGTGGAAGG+AGG - chr5_1:8578076-8578095 None:intergenic 55.0%
GTTGGGAGAAGGAACAACGC+TGG + chr5_1:8578441-8578460 Msa0715520:CDS 55.0%
GAAGGAACAACGCTGGGAGA+TGG + chr5_1:8578448-8578467 Msa0715520:CDS 55.0%
GGTGGATCAGGACTTAGAGG+TGG + chr5_1:8578469-8578488 Msa0715520:CDS 55.0%
GAGGTGGCAACTGCAACAAC+TGG + chr5_1:8578485-8578504 Msa0715520:CDS 55.0%
GGAATGGGTCGGTTGGGAGA+AGG + chr5_1:8578430-8578449 Msa0715520:CDS 60.0%
GGAACAACGCTGGGAGATGG+TGG + chr5_1:8578451-8578470 Msa0715520:CDS 60.0%
!! ACGCTGGGAGATGGTGGATC+AGG + chr5_1:8578457-8578476 Msa0715520:CDS 60.0%
GGAATGGGTCGGTTGGGAGA+AGG + chr5_1:8578430-8578449 Msa0715520:CDS 60.0%
GGAACAACGCTGGGAGATGG+TGG + chr5_1:8578451-8578470 Msa0715520:CDS 60.0%
!! ACGCTGGGAGATGGTGGATC+AGG + chr5_1:8578457-8578476 Msa0715520:CDS 60.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 8577979 8578892 8577979 ID=Msa0715520;Name=Msa0715520
chr5_1 mRNA 8577979 8578892 8577979 ID=Msa0715520-mRNA-1;Parent=Msa0715520;Name=Msa0715520-mRNA-1;_AED=0.44;_eAED=0.52;_QI=386|0|0.5|1|1|1|2|0|75
chr5_1 exon 8577979 8578506 8577979 ID=Msa0715520-mRNA-1:exon:3516;Parent=Msa0715520-mRNA-1
chr5_1 exon 8578807 8578892 8578807 ID=Msa0715520-mRNA-1:exon:3517;Parent=Msa0715520-mRNA-1
chr5_1 five_prime_UTR 8577979 8578364 8577979 ID=Msa0715520-mRNA-1:five_prime_utr;Parent=Msa0715520-mRNA-1
chr5_1 CDS 8578365 8578506 8578365 ID=Msa0715520-mRNA-1:cds;Parent=Msa0715520-mRNA-1
chr5_1 CDS 8578807 8578892 8578807 ID=Msa0715520-mRNA-1:cds;Parent=Msa0715520-mRNA-1
Gene Sequence

>Msa0715520

ATGTGCAAAATTGTTGAATCTTATACCTTTTTGTTGAATCTGATTGTGCAGGTTGTCAGATTCAAGGAATGGGTCGGTTGGGAGAAGGAACAACGCTGGGAGATGGTGGATCAGGACTTAGAGGTGGCAACTGCAACAACTGATTCGGTTCTGACTAACGATCAGCTGAAAACATACGCACTTGCAGATATTGAAGTTCTCCTTCAAAGTTTTGGAAAAAGTTCTTGA

Protein sequence

>Msa0715520

MCKIVESYTFLLNLIVQVVRFKEWVGWEKEQRWEMVDQDLEVATATTDSVLTNDQLKTYALADIEVLLQSFGKSS*