AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0720820


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0720820 MtrunA17_Chr5g0411641 100.000 85 0 0 1 85 1 85 2.12e-57 171
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0720820 AT2G22640.1 90.588 85 8 0 1 85 1 85 7.13e-53 159

Find 29 sgRNAs with CRISPR-Local

Find 76 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTCTTGATTGCCAATTTAT+TGG 0.221769 5_1:-17080302 Msa0720820:three_prime_UTR
AAAATCTTTAAAAGCACTTA+TGG 0.245901 5_1:-17080167 Msa0720820:three_prime_UTR
CATTGGTTTATTTGCAAATT+CGG 0.278022 5_1:-17080260 Msa0720820:three_prime_UTR
CAATTTATTGGGTTATTAGA+TGG 0.289266 5_1:-17080290 Msa0720820:three_prime_UTR
TTCTTGATTGCCAATTTATT+GGG 0.290000 5_1:-17080301 Msa0720820:three_prime_UTR
GTTGGAAGTGAAAGAGAAAA+AGG 0.309858 5_1:-17080906 Msa0720820:five_prime_UTR
CATCTAATAACCCAATAAAT+TGG 0.317606 5_1:+17080291 None:intergenic
TGATGTATTGGAACGTCGTT+TGG 0.348132 5_1:-17080544 Msa0720820:CDS
CCACCAGCACGTGCCATTGA+TGG 0.365965 5_1:+17080831 None:intergenic
GAAGAAATTGAGTACCGAAT+TGG 0.367198 5_1:+17080700 None:intergenic
TATATAATGTATAATCTAGA+TGG 0.379960 5_1:-17080410 Msa0720820:three_prime_UTR
GAATCGCTGTTCAAGCTGAT+TGG 0.386107 5_1:-17080785 Msa0720820:CDS
TTCGATTTCCTTGTCCAATT+CGG 0.396293 5_1:-17080714 Msa0720820:intron
CTAACTCTCGTTTACTTCTC+AGG 0.398070 5_1:+17080928 None:intergenic
GAATGAGAAGCTTGATGTAT+TGG 0.424872 5_1:-17080556 Msa0720820:CDS
TATTAGATGGTTTAATGCAT+TGG 0.431631 5_1:-17080277 Msa0720820:three_prime_UTR
AATCGCTGTTCAAGCTGATT+GGG 0.456401 5_1:-17080784 Msa0720820:CDS
ATCTAGATTATACATTATAT+AGG 0.457778 5_1:+17080412 None:intergenic
AGTTCAAGTTGGCAATGCTT+CGG 0.492873 5_1:-17080511 Msa0720820:CDS
AATAAAATCAAAATCTACAT+TGG 0.509747 5_1:-17080872 Msa0720820:five_prime_UTR
AAATCAAAGAATTCCATCAA+TGG 0.510384 5_1:-17080844 Msa0720820:exon
AGAAGTAAACGAGAGTTAGT+TGG 0.515439 5_1:-17080924 Msa0720820:five_prime_UTR
GAATTACTTGAAGTTCAAGT+TGG 0.523303 5_1:-17080522 Msa0720820:CDS
ATTATACATTATATAGGTGG+TGG 0.532369 5_1:+17080418 None:intergenic
ATTCCATCAATGGCACGTGC+TGG 0.544732 5_1:-17080834 Msa0720820:exon
CCATCAATGGCACGTGCTGG+TGG 0.566134 5_1:-17080831 Msa0720820:exon
TAGATTATACATTATATAGG+TGG 0.616253 5_1:+17080415 None:intergenic
ATCACAAACGCAGTTAACGT+TGG 0.620945 5_1:-17080807 Msa0720820:CDS
ATTGAGTACCGAATTGGACA+AGG 0.623936 5_1:+17080706 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAAATCAAAATCTACAT+TGG - chr5_1:17080262-17080281 Msa0720820:three_prime_UTR 15.0%
!!! AAATCTTATATCTTTTTTGA+TGG - chr5_1:17080499-17080518 Msa0720820:CDS 15.0%
!!! AATCTTATATCTTTTTTGAT+GGG - chr5_1:17080500-17080519 Msa0720820:CDS 15.0%
!! ATCTAGATTATACATTATAT+AGG + chr5_1:17080725-17080744 None:intergenic 15.0%
!! TATATAATGTATAATCTAGA+TGG - chr5_1:17080724-17080743 Msa0720820:CDS 15.0%
!!! TTAAAGATTTTTACTCAAAT+TGG + chr5_1:17080958-17080977 None:intergenic 15.0%
!! AATAAAATCAAAATCTACAT+TGG - chr5_1:17080262-17080281 Msa0720820:three_prime_UTR 15.0%
!!! AAATCTTATATCTTTTTTGA+TGG - chr5_1:17080499-17080518 Msa0720820:CDS 15.0%
!!! AATCTTATATCTTTTTTGAT+GGG - chr5_1:17080500-17080519 Msa0720820:CDS 15.0%
!! ATCTAGATTATACATTATAT+AGG + chr5_1:17080725-17080744 None:intergenic 15.0%
!! TATATAATGTATAATCTAGA+TGG - chr5_1:17080724-17080743 Msa0720820:CDS 15.0%
!!! TTAAAGATTTTTACTCAAAT+TGG + chr5_1:17080958-17080977 None:intergenic 15.0%
!! ATATAAGATTTCAACTAACA+AGG + chr5_1:17080490-17080509 None:intergenic 20.0%
!!! TGTTATTTTTGTTATTTCAG+AGG - chr5_1:17080527-17080546 Msa0720820:CDS 20.0%
!! TAGATTATACATTATATAGG+TGG + chr5_1:17080722-17080741 None:intergenic 20.0%
!!! AAAATCTTTAAAAGCACTTA+TGG - chr5_1:17080967-17080986 Msa0720820:five_prime_UTR 20.0%
!! ATATAAGATTTCAACTAACA+AGG + chr5_1:17080490-17080509 None:intergenic 20.0%
!!! TGTTATTTTTGTTATTTCAG+AGG - chr5_1:17080527-17080546 Msa0720820:CDS 20.0%
!! TAGATTATACATTATATAGG+TGG + chr5_1:17080722-17080741 None:intergenic 20.0%
!!! AAAATCTTTAAAAGCACTTA+TGG - chr5_1:17080967-17080986 Msa0720820:five_prime_UTR 20.0%
! AAATCAAAGAATTCCATCAA+TGG - chr5_1:17080290-17080309 Msa0720820:three_prime_UTR 25.0%
! ATTATACATTATATAGGTGG+TGG + chr5_1:17080719-17080738 None:intergenic 25.0%
! TTCTTGATTGCCAATTTATT+GGG - chr5_1:17080833-17080852 Msa0720820:exon 25.0%
! CATCTAATAACCCAATAAAT+TGG + chr5_1:17080846-17080865 None:intergenic 25.0%
! CAATTTATTGGGTTATTAGA+TGG - chr5_1:17080844-17080863 Msa0720820:exon 25.0%
! TATTAGATGGTTTAATGCAT+TGG - chr5_1:17080857-17080876 Msa0720820:five_prime_UTR 25.0%
!!! CATTGGTTTATTTGCAAATT+CGG - chr5_1:17080874-17080893 Msa0720820:five_prime_UTR 25.0%
! AAATCAAAGAATTCCATCAA+TGG - chr5_1:17080290-17080309 Msa0720820:three_prime_UTR 25.0%
! ATTATACATTATATAGGTGG+TGG + chr5_1:17080719-17080738 None:intergenic 25.0%
! TTCTTGATTGCCAATTTATT+GGG - chr5_1:17080833-17080852 Msa0720820:exon 25.0%
! CATCTAATAACCCAATAAAT+TGG + chr5_1:17080846-17080865 None:intergenic 25.0%
! CAATTTATTGGGTTATTAGA+TGG - chr5_1:17080844-17080863 Msa0720820:exon 25.0%
! TATTAGATGGTTTAATGCAT+TGG - chr5_1:17080857-17080876 Msa0720820:five_prime_UTR 25.0%
!!! CATTGGTTTATTTGCAAATT+CGG - chr5_1:17080874-17080893 Msa0720820:five_prime_UTR 25.0%
! AGGACTTTTTGTTCTACTTT+TGG + chr5_1:17080189-17080208 None:intergenic 30.0%
TTTCAACTAACAAGGCAAAA+GGG + chr5_1:17080482-17080501 None:intergenic 30.0%
ATTTCAACTAACAAGGCAAA+AGG + chr5_1:17080483-17080502 None:intergenic 30.0%
GAATTACTTGAAGTTCAAGT+TGG - chr5_1:17080612-17080631 Msa0720820:intron 30.0%
GTTCTTGATTGCCAATTTAT+TGG - chr5_1:17080832-17080851 Msa0720820:exon 30.0%
! AGGACTTTTTGTTCTACTTT+TGG + chr5_1:17080189-17080208 None:intergenic 30.0%
TTTCAACTAACAAGGCAAAA+GGG + chr5_1:17080482-17080501 None:intergenic 30.0%
ATTTCAACTAACAAGGCAAA+AGG + chr5_1:17080483-17080502 None:intergenic 30.0%
GAATTACTTGAAGTTCAAGT+TGG - chr5_1:17080612-17080631 Msa0720820:intron 30.0%
GTTCTTGATTGCCAATTTAT+TGG - chr5_1:17080832-17080851 Msa0720820:exon 30.0%
AGAAGTAAACGAGAGTTAGT+TGG - chr5_1:17080210-17080229 Msa0720820:three_prime_UTR 35.0%
GTTGGAAGTGAAAGAGAAAA+AGG - chr5_1:17080228-17080247 Msa0720820:three_prime_UTR 35.0%
TTCGATTTCCTTGTCCAATT+CGG - chr5_1:17080420-17080439 Msa0720820:three_prime_UTR 35.0%
!! GAAGAAATTGAGTACCGAAT+TGG + chr5_1:17080437-17080456 None:intergenic 35.0%
GAATGAGAAGCTTGATGTAT+TGG - chr5_1:17080578-17080597 Msa0720820:CDS 35.0%
! CATCAAGTTGCAAAAAGAGA+AGG + chr5_1:17080654-17080673 None:intergenic 35.0%
AGAAGTAAACGAGAGTTAGT+TGG - chr5_1:17080210-17080229 Msa0720820:three_prime_UTR 35.0%
GTTGGAAGTGAAAGAGAAAA+AGG - chr5_1:17080228-17080247 Msa0720820:three_prime_UTR 35.0%
TTCGATTTCCTTGTCCAATT+CGG - chr5_1:17080420-17080439 Msa0720820:three_prime_UTR 35.0%
!! GAAGAAATTGAGTACCGAAT+TGG + chr5_1:17080437-17080456 None:intergenic 35.0%
GAATGAGAAGCTTGATGTAT+TGG - chr5_1:17080578-17080597 Msa0720820:CDS 35.0%
! CATCAAGTTGCAAAAAGAGA+AGG + chr5_1:17080654-17080673 None:intergenic 35.0%
CTAACTCTCGTTTACTTCTC+AGG + chr5_1:17080209-17080228 None:intergenic 40.0%
ATCACAAACGCAGTTAACGT+TGG - chr5_1:17080327-17080346 Msa0720820:three_prime_UTR 40.0%
AATCGCTGTTCAAGCTGATT+GGG - chr5_1:17080350-17080369 Msa0720820:three_prime_UTR 40.0%
!! ATTGAGTACCGAATTGGACA+AGG + chr5_1:17080431-17080450 None:intergenic 40.0%
TGATGTATTGGAACGTCGTT+TGG - chr5_1:17080590-17080609 Msa0720820:CDS 40.0%
!! AGTTCAAGTTGGCAATGCTT+CGG - chr5_1:17080623-17080642 Msa0720820:intron 40.0%
CTAACTCTCGTTTACTTCTC+AGG + chr5_1:17080209-17080228 None:intergenic 40.0%
ATCACAAACGCAGTTAACGT+TGG - chr5_1:17080327-17080346 Msa0720820:three_prime_UTR 40.0%
AATCGCTGTTCAAGCTGATT+GGG - chr5_1:17080350-17080369 Msa0720820:three_prime_UTR 40.0%
!! ATTGAGTACCGAATTGGACA+AGG + chr5_1:17080431-17080450 None:intergenic 40.0%
TGATGTATTGGAACGTCGTT+TGG - chr5_1:17080590-17080609 Msa0720820:CDS 40.0%
!! AGTTCAAGTTGGCAATGCTT+CGG - chr5_1:17080623-17080642 Msa0720820:intron 40.0%
GAATCGCTGTTCAAGCTGAT+TGG - chr5_1:17080349-17080368 Msa0720820:three_prime_UTR 45.0%
GAATCGCTGTTCAAGCTGAT+TGG - chr5_1:17080349-17080368 Msa0720820:three_prime_UTR 45.0%
ATTCCATCAATGGCACGTGC+TGG - chr5_1:17080300-17080319 Msa0720820:three_prime_UTR 50.0%
ATTCCATCAATGGCACGTGC+TGG - chr5_1:17080300-17080319 Msa0720820:three_prime_UTR 50.0%
! CCACCAGCACGTGCCATTGA+TGG + chr5_1:17080306-17080325 None:intergenic 60.0%
CCATCAATGGCACGTGCTGG+TGG - chr5_1:17080303-17080322 Msa0720820:three_prime_UTR 60.0%
! CCACCAGCACGTGCCATTGA+TGG + chr5_1:17080306-17080325 None:intergenic 60.0%
CCATCAATGGCACGTGCTGG+TGG - chr5_1:17080303-17080322 Msa0720820:three_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 17080148 17081008 17080148 ID=Msa0720820;Name=Msa0720820
chr5_1 mRNA 17080148 17081008 17080148 ID=Msa0720820-mRNA-1;Parent=Msa0720820;Name=Msa0720820-mRNA-1;_AED=0.06;_eAED=0.06;_QI=161|1|1|1|1|1|2|337|85
chr5_1 exon 17080148 17080609 17080148 ID=Msa0720820-mRNA-1:exon:6477;Parent=Msa0720820-mRNA-1
chr5_1 exon 17080715 17081008 17080715 ID=Msa0720820-mRNA-1:exon:6476;Parent=Msa0720820-mRNA-1
chr5_1 five_prime_UTR 17080848 17081008 17080848 ID=Msa0720820-mRNA-1:five_prime_utr;Parent=Msa0720820-mRNA-1
chr5_1 CDS 17080715 17080847 17080715 ID=Msa0720820-mRNA-1:cds;Parent=Msa0720820-mRNA-1
chr5_1 CDS 17080485 17080609 17080485 ID=Msa0720820-mRNA-1:cds;Parent=Msa0720820-mRNA-1
chr5_1 three_prime_UTR 17080148 17080484 17080148 ID=Msa0720820-mRNA-1:three_prime_utr;Parent=Msa0720820-mRNA-1
Gene Sequence

>Msa0720820

ATGGCACGTGCTGGTGGAATCACAAACGCAGTTAACGTTGGAATCGCTGTTCAAGCTGATTGGGAAAATCGTGAATTCATCTCTCACATTTCTCTCAATGTTCGTCGTCTCTTCGATTTCCTTGTCCAATTCGAGGCTACAACAAAGAGTAAATTAGCTTCATTGAATGAGAAGCTTGATGTATTGGAACGTCGTTTGGAATTACTTGAAGTTCAAGTTGGCAATGCTTCGGCAAATCCTTCTCTTTTTGCAACTTGA

Protein sequence

>Msa0720820

MARAGGITNAVNVGIAVQADWENREFISHISLNVRRLFDFLVQFEATTKSKLASLNEKLDVLERRLELLEVQVGNASANPSLFAT*