AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1195190


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 5 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATCTACAGCTTCAATCTT+TGG 0.233065 8_1:-43003781 None:intergenic
CGTCTTAGCAGAGCTAGGTT+TGG 0.434111 8_1:-43003755 None:intergenic
ATCACACGCTTATTTGTTGA+AGG 0.441603 8_1:-43002202 None:intergenic
GGATTCGTCTTAGCAGAGCT+AGG 0.559567 8_1:-43003760 None:intergenic
ACGACACTTTGAAAAGAATG+TGG 0.692687 8_1:+43003804 Msa1195190:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATAAGTTTATAAATTAAAA+AGG - chr8_1:43002805-43002824 None:intergenic 10.0%
!!! TTATTTAAACTTATTTTTGT+TGG - chr8_1:43003572-43003591 None:intergenic 10.0%
!! GTATAGAAATAAATTTATTA+AGG - chr8_1:43003605-43003624 None:intergenic 10.0%
!! CATAAGTTTATAAATTAAAA+AGG - chr8_1:43002805-43002824 None:intergenic 10.0%
!!! TTATTTAAACTTATTTTTGT+TGG - chr8_1:43003572-43003591 None:intergenic 10.0%
!! GTATAGAAATAAATTTATTA+AGG - chr8_1:43003605-43003624 None:intergenic 10.0%
!! GATATTAATTAACAAATATC+AGG + chr8_1:43003292-43003311 Msa1195190:intron 15.0%
!! TTGTTTAGATTGAATAATAT+AGG + chr8_1:43003341-43003360 Msa1195190:intron 15.0%
!! AATTTAGGCAAAAAAAAAAT+TGG - chr8_1:43003549-43003568 None:intergenic 15.0%
!! ATTGATAAAAGAATAAGAAA+GGG - chr8_1:43003634-43003653 None:intergenic 15.0%
!! GATATTAATTAACAAATATC+AGG + chr8_1:43003292-43003311 Msa1195190:intron 15.0%
!! TTGTTTAGATTGAATAATAT+AGG + chr8_1:43003341-43003360 Msa1195190:intron 15.0%
!! AATTTAGGCAAAAAAAAAAT+TGG - chr8_1:43003549-43003568 None:intergenic 15.0%
!! ATTGATAAAAGAATAAGAAA+GGG - chr8_1:43003634-43003653 None:intergenic 15.0%
!! TTAAATACAATTCAACAATG+TGG - chr8_1:43003009-43003028 None:intergenic 20.0%
!! AGAATCTAATATGATAAACT+TGG + chr8_1:43003037-43003056 Msa1195190:intron 20.0%
!! AAGCAATTTATGAGTTATAT+TGG + chr8_1:43003206-43003225 Msa1195190:intron 20.0%
!!! ACCTTATTTTGATTCAAAAT+AGG + chr8_1:43003436-43003455 Msa1195190:intron 20.0%
!!! ACCTATTTTGAATCAAAATA+AGG - chr8_1:43003440-43003459 None:intergenic 20.0%
!!! ACTTATTTTTGTTGGAATTT+AGG - chr8_1:43003564-43003583 None:intergenic 20.0%
!! GATTGATAAAAGAATAAGAA+AGG - chr8_1:43003635-43003654 None:intergenic 20.0%
!!! ACTCTTTTTAAAATTTGCTT+GGG - chr8_1:43003697-43003716 None:intergenic 20.0%
!!! AACTCTTTTTAAAATTTGCT+TGG - chr8_1:43003698-43003717 None:intergenic 20.0%
!!! AGCAAATTTTAAAAAGAGTT+CGG + chr8_1:43003698-43003717 Msa1195190:CDS 20.0%
!! TTAAATACAATTCAACAATG+TGG - chr8_1:43003009-43003028 None:intergenic 20.0%
!! AGAATCTAATATGATAAACT+TGG + chr8_1:43003037-43003056 Msa1195190:intron 20.0%
!! AAGCAATTTATGAGTTATAT+TGG + chr8_1:43003206-43003225 Msa1195190:intron 20.0%
!!! ACCTTATTTTGATTCAAAAT+AGG + chr8_1:43003436-43003455 Msa1195190:intron 20.0%
!!! ACCTATTTTGAATCAAAATA+AGG - chr8_1:43003440-43003459 None:intergenic 20.0%
!!! ACTTATTTTTGTTGGAATTT+AGG - chr8_1:43003564-43003583 None:intergenic 20.0%
!! GATTGATAAAAGAATAAGAA+AGG - chr8_1:43003635-43003654 None:intergenic 20.0%
!!! ACTCTTTTTAAAATTTGCTT+GGG - chr8_1:43003697-43003716 None:intergenic 20.0%
!!! AACTCTTTTTAAAATTTGCT+TGG - chr8_1:43003698-43003717 None:intergenic 20.0%
!!! AGCAAATTTTAAAAAGAGTT+CGG + chr8_1:43003698-43003717 Msa1195190:CDS 20.0%
! GGAAATATTTGAAAAATGGA+TGG - chr8_1:43002565-43002584 None:intergenic 25.0%
! GCAAGGAAATATTTGAAAAA+TGG - chr8_1:43002569-43002588 None:intergenic 25.0%
! AAAAGGAGAGAATAAATAGA+TGG - chr8_1:43002788-43002807 None:intergenic 25.0%
! TTGAATGACAAAAAGTTAGA+TGG - chr8_1:43003109-43003128 None:intergenic 25.0%
!! TCTAACTTTTTGTCATTCAA+TGG + chr8_1:43003109-43003128 Msa1195190:intron 25.0%
!! TAGGTTACTAAATCCTTTTA+TGG + chr8_1:43003360-43003379 Msa1195190:intron 25.0%
! AAAGAATAAGAAAGGGTAAA+GGG - chr8_1:43003627-43003646 None:intergenic 25.0%
! AAAAGAATAAGAAAGGGTAA+AGG - chr8_1:43003628-43003647 None:intergenic 25.0%
!!! CTCTTTTTAAAATTTGCTTG+GGG - chr8_1:43003696-43003715 None:intergenic 25.0%
! GGAAATATTTGAAAAATGGA+TGG - chr8_1:43002565-43002584 None:intergenic 25.0%
! GCAAGGAAATATTTGAAAAA+TGG - chr8_1:43002569-43002588 None:intergenic 25.0%
! AAAAGGAGAGAATAAATAGA+TGG - chr8_1:43002788-43002807 None:intergenic 25.0%
! TTGAATGACAAAAAGTTAGA+TGG - chr8_1:43003109-43003128 None:intergenic 25.0%
!! TCTAACTTTTTGTCATTCAA+TGG + chr8_1:43003109-43003128 Msa1195190:intron 25.0%
!! TAGGTTACTAAATCCTTTTA+TGG + chr8_1:43003360-43003379 Msa1195190:intron 25.0%
! AAAGAATAAGAAAGGGTAAA+GGG - chr8_1:43003627-43003646 None:intergenic 25.0%
! AAAAGAATAAGAAAGGGTAA+AGG - chr8_1:43003628-43003647 None:intergenic 25.0%
!!! CTCTTTTTAAAATTTGCTTG+GGG - chr8_1:43003696-43003715 None:intergenic 25.0%
TTCTTTCTTTCAATGTGTTC+AGG - chr8_1:43002363-43002382 None:intergenic 30.0%
TTATAGAACAGAGTTCTCTT+TGG - chr8_1:43002464-43002483 None:intergenic 30.0%
! TGAAGTCACATTTTTGTTCT+TGG - chr8_1:43002494-43002513 None:intergenic 30.0%
GTCTTACATAATGAGTTGTT+TGG + chr8_1:43003162-43003181 Msa1195190:intron 30.0%
TTAATTCTGGTGAAGAGTAA+AGG + chr8_1:43003241-43003260 Msa1195190:intron 30.0%
GTTTCTTGCAATTCCATAAA+AGG - chr8_1:43003376-43003395 None:intergenic 30.0%
GCTGATAACAATTTGTATGA+AGG - chr8_1:43003398-43003417 None:intergenic 30.0%
TTCTTTCTTTCAATGTGTTC+AGG - chr8_1:43002363-43002382 None:intergenic 30.0%
TTATAGAACAGAGTTCTCTT+TGG - chr8_1:43002464-43002483 None:intergenic 30.0%
! TGAAGTCACATTTTTGTTCT+TGG - chr8_1:43002494-43002513 None:intergenic 30.0%
GTCTTACATAATGAGTTGTT+TGG + chr8_1:43003162-43003181 Msa1195190:intron 30.0%
TTAATTCTGGTGAAGAGTAA+AGG + chr8_1:43003241-43003260 Msa1195190:intron 30.0%
GTTTCTTGCAATTCCATAAA+AGG - chr8_1:43003376-43003395 None:intergenic 30.0%
GCTGATAACAATTTGTATGA+AGG - chr8_1:43003398-43003417 None:intergenic 30.0%
! ATCACACGCTTATTTGTTGA+AGG - chr8_1:43002205-43002224 None:intergenic 35.0%
AGCAATTCCTTGCATCAAAA+CGG + chr8_1:43002612-43002631 Msa1195190:intron 35.0%
AAGTGCAGAAGAAGATTTGT+GGG - chr8_1:43002671-43002690 None:intergenic 35.0%
GGAAGTTTAAAAGCGGAAAT+AGG - chr8_1:43002717-43002736 None:intergenic 35.0%
AGGATTCGGAAGTTTAAAAG+CGG - chr8_1:43002724-43002743 None:intergenic 35.0%
TTTAAACTTCCGAATCCTTG+CGG + chr8_1:43002726-43002745 Msa1195190:intron 35.0%
ACTTCGAATCCATCTATATC+AGG + chr8_1:43002751-43002770 Msa1195190:intron 35.0%
AGAAGAATGCCTGATATAGA+TGG - chr8_1:43002763-43002782 None:intergenic 35.0%
TCACCAGAATTAACATTCAC+AGG - chr8_1:43003234-43003253 None:intergenic 35.0%
TCATCTACAGCTTCAATCTT+TGG - chr8_1:43003784-43003803 None:intergenic 35.0%
! ACGACACTTTGAAAAGAATG+TGG + chr8_1:43003804-43003823 Msa1195190:CDS 35.0%
! ATCACACGCTTATTTGTTGA+AGG - chr8_1:43002205-43002224 None:intergenic 35.0%
AGCAATTCCTTGCATCAAAA+CGG + chr8_1:43002612-43002631 Msa1195190:intron 35.0%
AAGTGCAGAAGAAGATTTGT+GGG - chr8_1:43002671-43002690 None:intergenic 35.0%
GGAAGTTTAAAAGCGGAAAT+AGG - chr8_1:43002717-43002736 None:intergenic 35.0%
AGGATTCGGAAGTTTAAAAG+CGG - chr8_1:43002724-43002743 None:intergenic 35.0%
TTTAAACTTCCGAATCCTTG+CGG + chr8_1:43002726-43002745 Msa1195190:intron 35.0%
ACTTCGAATCCATCTATATC+AGG + chr8_1:43002751-43002770 Msa1195190:intron 35.0%
AGAAGAATGCCTGATATAGA+TGG - chr8_1:43002763-43002782 None:intergenic 35.0%
TCACCAGAATTAACATTCAC+AGG - chr8_1:43003234-43003253 None:intergenic 35.0%
TCATCTACAGCTTCAATCTT+TGG - chr8_1:43003784-43003803 None:intergenic 35.0%
! ACGACACTTTGAAAAGAATG+TGG + chr8_1:43003804-43003823 Msa1195190:CDS 35.0%
TTATGTATGACGTCTCTACG+TGG + chr8_1:43002417-43002436 Msa1195190:intron 40.0%
! TACGTGGAAAATTGGTAGCA+AGG + chr8_1:43002433-43002452 Msa1195190:intron 40.0%
CAAGGAATTGCTAGTGAACT+CGG - chr8_1:43002604-43002623 None:intergenic 40.0%
GCAATTCCTTGCATCAAAAC+GGG + chr8_1:43002613-43002632 Msa1195190:intron 40.0%
!! CTTGCATCAAAACGGGTTTT+CGG + chr8_1:43002620-43002639 Msa1195190:intron 40.0%
! TGGGAAAGGTGTATGTAGAA+TGG - chr8_1:43002652-43002671 None:intergenic 40.0%
CAGAAGAAGATTTGTGGGAA+AGG - chr8_1:43002666-43002685 None:intergenic 40.0%
CAAGTGCAGAAGAAGATTTG+TGG - chr8_1:43002672-43002691 None:intergenic 40.0%
GCAGTCAAGGCAACAATTAT+AGG + chr8_1:43002691-43002710 Msa1195190:intron 40.0%
GAGCCTGTGAATGTTAATTC+TGG + chr8_1:43003228-43003247 Msa1195190:intron 40.0%
TTATGTATGACGTCTCTACG+TGG + chr8_1:43002417-43002436 Msa1195190:intron 40.0%
! TACGTGGAAAATTGGTAGCA+AGG + chr8_1:43002433-43002452 Msa1195190:intron 40.0%
CAAGGAATTGCTAGTGAACT+CGG - chr8_1:43002604-43002623 None:intergenic 40.0%
GCAATTCCTTGCATCAAAAC+GGG + chr8_1:43002613-43002632 Msa1195190:intron 40.0%
!! CTTGCATCAAAACGGGTTTT+CGG + chr8_1:43002620-43002639 Msa1195190:intron 40.0%
! TGGGAAAGGTGTATGTAGAA+TGG - chr8_1:43002652-43002671 None:intergenic 40.0%
CAGAAGAAGATTTGTGGGAA+AGG - chr8_1:43002666-43002685 None:intergenic 40.0%
CAAGTGCAGAAGAAGATTTG+TGG - chr8_1:43002672-43002691 None:intergenic 40.0%
GCAGTCAAGGCAACAATTAT+AGG + chr8_1:43002691-43002710 Msa1195190:intron 40.0%
GAGCCTGTGAATGTTAATTC+TGG + chr8_1:43003228-43003247 Msa1195190:intron 40.0%
AAGCGTGTGATTGCATGCAT+TGG + chr8_1:43002214-43002233 Msa1195190:intron 45.0%
GACGTCTCTACGTGGAAAAT+TGG + chr8_1:43002425-43002444 Msa1195190:intron 45.0%
CTCGGAAGAATTCTGATGCA+AGG - chr8_1:43002586-43002605 None:intergenic 45.0%
!! CGAAAACCCGTTTTGATGCA+AGG - chr8_1:43002622-43002641 None:intergenic 45.0%
TTCTTCTGCACTTGCAGTCA+AGG + chr8_1:43002678-43002697 Msa1195190:intron 45.0%
AAGCGTGTGATTGCATGCAT+TGG + chr8_1:43002214-43002233 Msa1195190:intron 45.0%
GACGTCTCTACGTGGAAAAT+TGG + chr8_1:43002425-43002444 Msa1195190:intron 45.0%
CTCGGAAGAATTCTGATGCA+AGG - chr8_1:43002586-43002605 None:intergenic 45.0%
!! CGAAAACCCGTTTTGATGCA+AGG - chr8_1:43002622-43002641 None:intergenic 45.0%
TTCTTCTGCACTTGCAGTCA+AGG + chr8_1:43002678-43002697 Msa1195190:intron 45.0%
TCGAAGTCACCGCAAGGATT+CGG - chr8_1:43002738-43002757 None:intergenic 50.0%
ATGGATTCGAAGTCACCGCA+AGG - chr8_1:43002744-43002763 None:intergenic 50.0%
CGTCTTAGCAGAGCTAGGTT+TGG - chr8_1:43003758-43003777 None:intergenic 50.0%
GGATTCGTCTTAGCAGAGCT+AGG - chr8_1:43003763-43003782 None:intergenic 50.0%
TCGAAGTCACCGCAAGGATT+CGG - chr8_1:43002738-43002757 None:intergenic 50.0%
ATGGATTCGAAGTCACCGCA+AGG - chr8_1:43002744-43002763 None:intergenic 50.0%
CGTCTTAGCAGAGCTAGGTT+TGG - chr8_1:43003758-43003777 None:intergenic 50.0%
GGATTCGTCTTAGCAGAGCT+AGG - chr8_1:43003763-43003782 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 43002160 43003834 43002160 ID=Msa1195190;Name=Msa1195190
chr8_1 mRNA 43002160 43003834 43002160 ID=Msa1195190-mRNA-1;Parent=Msa1195190;Name=Msa1195190-mRNA-1;_AED=0.83;_eAED=1.00;_QI=0|0|0|0.66|0|0.66|3|0|70
chr8_1 exon 43002160 43002219 43002160 ID=Msa1195190-mRNA-1:exon:13892;Parent=Msa1195190-mRNA-1
chr8_1 exon 43002267 43002272 43002267 ID=Msa1195190-mRNA-1:exon:13893;Parent=Msa1195190-mRNA-1
chr8_1 exon 43003688 43003834 43003688 ID=Msa1195190-mRNA-1:exon:13894;Parent=Msa1195190-mRNA-1
chr8_1 CDS 43002160 43002219 43002160 ID=Msa1195190-mRNA-1:cds;Parent=Msa1195190-mRNA-1
chr8_1 CDS 43002267 43002272 43002267 ID=Msa1195190-mRNA-1:cds;Parent=Msa1195190-mRNA-1
chr8_1 CDS 43003688 43003834 43003688 ID=Msa1195190-mRNA-1:cds;Parent=Msa1195190-mRNA-1
Gene Sequence

>Msa1195190

ATGATAATCAAAGTACAAGCAGCAACAGCTTTAGTAAGATTACCTTCAACAAATAAGCGTATTTTTTATATCCCCAAGCAAATTTTAAAAAGAGTTCGGAAAGAAAAGTGCAAGAGAGATACACTCAAAAAGACCAAACCTAGCTCTGCTAAGACGAATCCAAAGATTGAAGCTGTAGATGAACGACACTTTGAAAAGAATGTGGTTGAATGA

Protein sequence

>Msa1195190

MIIKVQAATALVRLPSTNKRIFYIPKQILKRVRKEKCKRDTLKKTKPSSAKTNPKIEAVDERHFEKNVVE*