AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0808170

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0808170 MtrunA17_Chr5g0423041 74.672 229 20 1 6 196 42 270 2.14e-115 329
Msa0808170 MtrunA17_Chr5g0423061 50.467 214 74 8 6 193 39 246 3.02e-50 171
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 40 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTCTATCAACGGTGGTAAA+AGG 0.204443 5_3:+31989790 None:intergenic
TTCTGAATTGGCTCTAATTC+AGG 0.216122 5_3:+31989634 None:intergenic
GCTCTAATTCAGGGAAATTT+AGG 0.217699 5_3:+31989644 None:intergenic
AAATGACGATCATTTCTCTT+AGG 0.261854 5_3:+31989164 None:intergenic
TGCTATCAATTTCATAGGTT+TGG 0.298307 5_3:+31989701 None:intergenic
AACTGAAATTTAAAGTTTCC+TGG 0.308434 5_3:+31989329 None:intergenic
AATAATTCAGTTATCATATA+TGG 0.311793 5_3:-31989667 Msa0808170:CDS
ACTGATGCTATCAATTTCAT+AGG 0.317940 5_3:+31989696 None:intergenic
TTGAAAGTTTCAAATGGAAC+TGG 0.324695 5_3:+31989442 None:intergenic
TGTGGAGGATGTTATCTTGC+AGG 0.342062 5_3:-31989370 Msa0808170:CDS
GAAGCTTCCTGTGGATATCT+TGG 0.353447 5_3:-31989825 None:intergenic
GGGAACATGGGAGGTTTATC+AGG 0.359493 5_3:+31989487 None:intergenic
CATTTGAAGGATGCCGTAAT+AGG 0.369051 5_3:-31989146 Msa0808170:CDS
TATATTTGAACTTGTTATCA+TGG 0.377054 5_3:+31989548 None:intergenic
TTCTATCAACGGTGGTAAAA+GGG 0.389556 5_3:+31989791 None:intergenic
AAGTTTGGCGTATTCTGAAT+TGG 0.406948 5_3:+31989622 None:intergenic
ATAGTGTTAATGCTGAAGTT+TGG 0.408935 5_3:+31989607 None:intergenic
AACTTCTATGTATGCAATCA+TGG 0.414576 5_3:-31989583 Msa0808170:CDS
TTAAATTTCAGTTGTGGCCC+AGG 0.434450 5_3:-31989319 Msa0808170:intron
CGATCATTTCTCTTAGGAAT+CGG 0.452060 5_3:+31989170 None:intergenic
TCTGAATTGGCTCTAATTCA+GGG 0.452523 5_3:+31989635 None:intergenic
AAGCTTCCTGTGGATATCTT+GGG 0.454584 5_3:-31989824 None:intergenic
ACACAATTGAAAGTTTCAAA+TGG 0.468211 5_3:+31989436 None:intergenic
TTACAATAGAGTGCCTATTA+CGG 0.496542 5_3:+31989133 None:intergenic
GAGAAATGATCGTCATTTGA+AGG 0.502367 5_3:-31989159 Msa0808170:CDS
GAATGTGGCTCTTACATAAG+TGG 0.551810 5_3:-31989766 Msa0808170:CDS
AAAGTTGATTTAGAGTCTTG+TGG 0.561215 5_3:-31989388 Msa0808170:CDS
TCTATCAACGGTGGTAAAAG+GGG 0.569939 5_3:+31989792 None:intergenic
GAAACTTTAAATTTCAGTTG+TGG 0.573815 5_3:-31989325 Msa0808170:CDS
CTATCAACGGTGGTAAAAGG+GGG 0.574219 5_3:+31989793 None:intergenic
TGAAAGTTTCAAATGGAACT+GGG 0.581443 5_3:+31989443 None:intergenic
AAAGTCATGTCTACTAAACC+AGG 0.587810 5_3:-31989347 Msa0808170:CDS
AGATTTCCCAAGATATCCAC+AGG 0.588070 5_3:+31989818 None:intergenic
TCATTTCTCTTAGGAATCGG+AGG 0.602178 5_3:+31989173 None:intergenic
GCCACATTCTATTCTATCAA+CGG 0.611935 5_3:+31989780 None:intergenic
GGAACTGGGAAACATGCCAA+TGG 0.619846 5_3:+31989457 None:intergenic
GTTGATTTAGAGTCTTGTGG+AGG 0.623581 5_3:-31989385 Msa0808170:CDS
ACCGTTGATAGAATAGAATG+TGG 0.672433 5_3:-31989781 Msa0808170:CDS
ACATTCTATTCTATCAACGG+TGG 0.712385 5_3:+31989783 None:intergenic
TATCAACGGTGGTAAAAGGG+GGG 0.731832 5_3:+31989794 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATTCAGTTATCATATA+TGG - chr5_3:31989283-31989302 Msa0808170:intron 15.0%
!!! TATATTTGAACTTGTTATCA+TGG + chr5_3:31989405-31989424 None:intergenic 20.0%
! ACACAATTGAAAGTTTCAAA+TGG + chr5_3:31989517-31989536 None:intergenic 25.0%
!! AACTGAAATTTAAAGTTTCC+TGG + chr5_3:31989624-31989643 None:intergenic 25.0%
! GAAACTTTAAATTTCAGTTG+TGG - chr5_3:31989625-31989644 Msa0808170:CDS 25.0%
! TTAGACTAATGTATTTACCT+GGG + chr5_3:31989651-31989670 None:intergenic 25.0%
! ATTAGACTAATGTATTTACC+TGG + chr5_3:31989652-31989671 None:intergenic 25.0%
TGCTATCAATTTCATAGGTT+TGG + chr5_3:31989252-31989271 None:intergenic 30.0%
ACTGATGCTATCAATTTCAT+AGG + chr5_3:31989257-31989276 None:intergenic 30.0%
ATAGTGTTAATGCTGAAGTT+TGG + chr5_3:31989346-31989365 None:intergenic 30.0%
AACTTCTATGTATGCAATCA+TGG - chr5_3:31989367-31989386 Msa0808170:CDS 30.0%
AATGGAAAAATAGGGAACAT+GGG + chr5_3:31989478-31989497 None:intergenic 30.0%
AACATGCCAATGGAAAAATA+GGG + chr5_3:31989486-31989505 None:intergenic 30.0%
AAACATGCCAATGGAAAAAT+AGG + chr5_3:31989487-31989506 None:intergenic 30.0%
TGAAAGTTTCAAATGGAACT+GGG + chr5_3:31989510-31989529 None:intergenic 30.0%
TTGAAAGTTTCAAATGGAAC+TGG + chr5_3:31989511-31989530 None:intergenic 30.0%
! AAAGTTGATTTAGAGTCTTG+TGG - chr5_3:31989562-31989581 Msa0808170:CDS 30.0%
AAATGACGATCATTTCTCTT+AGG + chr5_3:31989789-31989808 None:intergenic 30.0%
! TTACAATAGAGTGCCTATTA+CGG + chr5_3:31989820-31989839 None:intergenic 30.0%
TTCTATCAACGGTGGTAAAA+GGG + chr5_3:31989162-31989181 None:intergenic 35.0%
ATTCTATCAACGGTGGTAAA+AGG + chr5_3:31989163-31989182 None:intergenic 35.0%
ACATTCTATTCTATCAACGG+TGG + chr5_3:31989170-31989189 None:intergenic 35.0%
! ACCGTTGATAGAATAGAATG+TGG - chr5_3:31989169-31989188 Msa0808170:CDS 35.0%
GCCACATTCTATTCTATCAA+CGG + chr5_3:31989173-31989192 None:intergenic 35.0%
GCTCTAATTCAGGGAAATTT+AGG + chr5_3:31989309-31989328 None:intergenic 35.0%
!! TCTGAATTGGCTCTAATTCA+GGG + chr5_3:31989318-31989337 None:intergenic 35.0%
!! TTCTGAATTGGCTCTAATTC+AGG + chr5_3:31989319-31989338 None:intergenic 35.0%
AAGTTTGGCGTATTCTGAAT+TGG + chr5_3:31989331-31989350 None:intergenic 35.0%
CAATGGAAAAATAGGGAACA+TGG + chr5_3:31989479-31989498 None:intergenic 35.0%
!! CATGTTCCCTATTTTTCCAT+TGG - chr5_3:31989477-31989496 Msa0808170:CDS 35.0%
AAAGTCATGTCTACTAAACC+AGG - chr5_3:31989603-31989622 Msa0808170:CDS 35.0%
ATGCTCTAACACTCATTCTT+TGG - chr5_3:31989670-31989689 Msa0808170:CDS 35.0%
CGATCATTTCTCTTAGGAAT+CGG + chr5_3:31989783-31989802 None:intergenic 35.0%
GAGAAATGATCGTCATTTGA+AGG - chr5_3:31989791-31989810 Msa0808170:CDS 35.0%
TCTATCAACGGTGGTAAAAG+GGG + chr5_3:31989161-31989180 None:intergenic 40.0%
GAATGTGGCTCTTACATAAG+TGG - chr5_3:31989184-31989203 Msa0808170:CDS 40.0%
! GTTGATTTAGAGTCTTGTGG+AGG - chr5_3:31989565-31989584 Msa0808170:CDS 40.0%
TTAAATTTCAGTTGTGGCCC+AGG - chr5_3:31989631-31989650 Msa0808170:CDS 40.0%
TCATTTCTCTTAGGAATCGG+AGG + chr5_3:31989780-31989799 None:intergenic 40.0%
CATTTGAAGGATGCCGTAAT+AGG - chr5_3:31989804-31989823 Msa0808170:CDS 40.0%
TATCAACGGTGGTAAAAGGG+GGG + chr5_3:31989159-31989178 None:intergenic 45.0%
CTATCAACGGTGGTAAAAGG+GGG + chr5_3:31989160-31989179 None:intergenic 45.0%
GGAAAAATAGGGAACATGGG+AGG + chr5_3:31989475-31989494 None:intergenic 45.0%
TGTGGAGGATGTTATCTTGC+AGG - chr5_3:31989580-31989599 Msa0808170:CDS 45.0%
GGGAACATGGGAGGTTTATC+AGG + chr5_3:31989466-31989485 None:intergenic 50.0%
GGAACTGGGAAACATGCCAA+TGG + chr5_3:31989496-31989515 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 31989133 31989839 31989133 ID=Msa0808170;Name=Msa0808170
chr5_3 mRNA 31989133 31989839 31989133 ID=Msa0808170-mRNA-1;Parent=Msa0808170;Name=Msa0808170-mRNA-1;_AED=0.09;_eAED=0.09;_QI=0|0|0|1|1|1|2|0|196
chr5_3 exon 31989320 31989839 31989320 ID=Msa0808170-mRNA-1:exon:10565;Parent=Msa0808170-mRNA-1
chr5_3 exon 31989133 31989203 31989133 ID=Msa0808170-mRNA-1:exon:10564;Parent=Msa0808170-mRNA-1
chr5_3 CDS 31989320 31989839 31989320 ID=Msa0808170-mRNA-1:cds;Parent=Msa0808170-mRNA-1
chr5_3 CDS 31989133 31989203 31989133 ID=Msa0808170-mRNA-1:cds;Parent=Msa0808170-mRNA-1
Gene Sequence

>Msa0808170

CTGTGGATATCTTGGGAAATCTTCCCCCCTTTTACCACCGTTGATAGAATAGAATGTGGCTCTTACATAAGTGGTTGTGACAAAAACAGTTCAGTGAAAAAGATCAAGCTGATAAACCAAACCTATGAAATTGATAGCATCAGTTATATGAATAATTCAGTTATCATATATGGCCTAAATTTCCCTGAATTAGAGCCAATTCAGAATACGCCAAACTTCAGCATTAACACTATTAACTTCTATGTATGCAATCATGGCTATGACAACAGCCATGATAACAAGTTCAAATATAAAAACTGTGCTGATTATGATATCTACTTTACTTCTACACCTGATAAACCTCCCATGTTCCCTATTTTTCCATTGGCATGTTTCCCAGTTCCATTTGAAACTTTCAATTGTGTAGATATAATTTCATTACTCGAAATTAAAGTTGATTTAGAGTCTTGTGGAGGATGTTATCTTGCAGGAAAGTCATGTCTACTAAACCAGGAAACTTTAAATTTCAGTTGTGGCCCAGTACTGAAACCTCCGATTCCTAAGAGAAATGATCGTCATTTGAAGGATGCCGTAATAGGCACTCTATTGTAA
Protein sequence

>Msa0808170

LWISWEIFPPFTTVDRIECGSYISGCDKNSSVKKIKLINQTYEIDSISYMNNSVIIYGLNFPELEPIQNTPNFSINTINFYVCNHGYDNSHDNKFKYKNCADYDIYFTSTPDKPPMFPIFPLACFPVPFETFNCVDIISLLEIKVDLESCGGCYLAGKSCLLNQETLNFSCGPVLKPPIPKRNDRHLKDAVIGTLL*