AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0761940


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0761940 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
Msa0761940 AT2G22640.1 90.588 85 8 0 1 85 1 85 7.13e-53 159

Find 28 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTCTTGATTGCCAATTTAT+TGG 0.221769 5_2:+19669748 Msa0761940:three_prime_UTR
AAAATCTTTAAAAGCACTTA+TGG 0.245901 5_2:+19669883 Msa0761940:three_prime_UTR
CATTGGTTTATTTGCAAATT+CGG 0.278022 5_2:+19669790 Msa0761940:three_prime_UTR
CAATTTATTGGGTTATTAGA+TGG 0.289266 5_2:+19669760 Msa0761940:three_prime_UTR
TTCTTGATTGCCAATTTATT+GGG 0.290000 5_2:+19669749 Msa0761940:three_prime_UTR
CATCTAATAACCCAATAAAT+TGG 0.317606 5_2:-19669759 None:intergenic
TGATGTATTGGAACGTCGTT+TGG 0.348132 5_2:+19669506 Msa0761940:CDS
CCACCAGCACGTGCCATTGA+TGG 0.365965 5_2:-19669218 None:intergenic
TATATAATGTATAATCTAGA+TGG 0.379960 5_2:+19669640 Msa0761940:three_prime_UTR
GAAGGATTTGAGTACCGAAT+TGG 0.381697 5_2:-19669349 None:intergenic
GAATCGCTGTTCAAGCTGAT+TGG 0.386107 5_2:+19669264 Msa0761940:CDS
TTCGATTTCCTTGTCCAATT+CGG 0.396293 5_2:+19669335 Msa0761940:CDS
CTAACTCTCGTTTACTTCTC+AGG 0.398070 5_2:-19669121 None:intergenic
GAATGAGAAGCTTGATGTAT+TGG 0.424872 5_2:+19669494 Msa0761940:CDS
TATTAGATGGTTTAATGCAT+TGG 0.431631 5_2:+19669773 Msa0761940:three_prime_UTR
AATCGCTGTTCAAGCTGATT+GGG 0.456401 5_2:+19669265 Msa0761940:CDS
ATCTAGATTATACATTATAT+AGG 0.457778 5_2:-19669638 None:intergenic
AGTTCAAGTTGGCAATGCTT+CGG 0.492873 5_2:+19669539 Msa0761940:CDS
AATAAAATCAAAATCTACAT+TGG 0.509747 5_2:+19669177 Msa0761940:five_prime_UTR
AAATCAAAGAATTCCATCAA+TGG 0.510384 5_2:+19669205 Msa0761940:exon
AGAAGTAAACGAGAGTTAGT+TGG 0.515439 5_2:+19669125 Msa0761940:five_prime_UTR
GAATTACTTGAAGTTCAAGT+TGG 0.523303 5_2:+19669528 Msa0761940:CDS
ATTATACATTATATAGGTGG+TGG 0.532369 5_2:-19669632 None:intergenic
ATTCCATCAATGGCACGTGC+TGG 0.544732 5_2:+19669215 Msa0761940:exon
CCATCAATGGCACGTGCTGG+TGG 0.566134 5_2:+19669218 Msa0761940:exon
TTTGAGTACCGAATTGGACA+AGG 0.596328 5_2:-19669343 None:intergenic
TAGATTATACATTATATAGG+TGG 0.616253 5_2:-19669635 None:intergenic
ATCACAAACGCAGTTAACGT+TGG 0.620945 5_2:+19669242 Msa0761940:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAAATCAAAATCTACAT+TGG + chr5_2:19669177-19669196 Msa0761940:five_prime_UTR 15.0%
!!! AATCTTATATCTTTTTTTGA+TGG + chr5_2:19669415-19669434 Msa0761940:intron 15.0%
!!! ATCTTATATCTTTTTTTGAT+GGG + chr5_2:19669416-19669435 Msa0761940:intron 15.0%
!! ATCTAGATTATACATTATAT+AGG - chr5_2:19669641-19669660 None:intergenic 15.0%
!! TATATAATGTATAATCTAGA+TGG + chr5_2:19669640-19669659 Msa0761940:three_prime_UTR 15.0%
!!! TTAAAGATTTTTACTCAAAT+TGG - chr5_2:19669874-19669893 None:intergenic 15.0%
!! AATAAAATCAAAATCTACAT+TGG + chr5_2:19669177-19669196 Msa0761940:five_prime_UTR 15.0%
!!! AATCTTATATCTTTTTTTGA+TGG + chr5_2:19669415-19669434 Msa0761940:intron 15.0%
!!! ATCTTATATCTTTTTTTGAT+GGG + chr5_2:19669416-19669435 Msa0761940:intron 15.0%
!! ATCTAGATTATACATTATAT+AGG - chr5_2:19669641-19669660 None:intergenic 15.0%
!! TATATAATGTATAATCTAGA+TGG + chr5_2:19669640-19669659 Msa0761940:three_prime_UTR 15.0%
!!! TTAAAGATTTTTACTCAAAT+TGG - chr5_2:19669874-19669893 None:intergenic 15.0%
!!! TGTTATTTTTGTTATTTCAG+AGG + chr5_2:19669443-19669462 Msa0761940:intron 20.0%
!! TAGATTATACATTATATAGG+TGG - chr5_2:19669638-19669657 None:intergenic 20.0%
!!! AAAATCTTTAAAAGCACTTA+TGG + chr5_2:19669883-19669902 Msa0761940:three_prime_UTR 20.0%
!!! TGTTATTTTTGTTATTTCAG+AGG + chr5_2:19669443-19669462 Msa0761940:intron 20.0%
!! TAGATTATACATTATATAGG+TGG - chr5_2:19669638-19669657 None:intergenic 20.0%
!!! AAAATCTTTAAAAGCACTTA+TGG + chr5_2:19669883-19669902 Msa0761940:three_prime_UTR 20.0%
! AAATCAAAGAATTCCATCAA+TGG + chr5_2:19669205-19669224 Msa0761940:exon 25.0%
! ATTATACATTATATAGGTGG+TGG - chr5_2:19669635-19669654 None:intergenic 25.0%
! TTCTTGATTGCCAATTTATT+GGG + chr5_2:19669749-19669768 Msa0761940:three_prime_UTR 25.0%
! CATCTAATAACCCAATAAAT+TGG - chr5_2:19669762-19669781 None:intergenic 25.0%
! CAATTTATTGGGTTATTAGA+TGG + chr5_2:19669760-19669779 Msa0761940:three_prime_UTR 25.0%
! TATTAGATGGTTTAATGCAT+TGG + chr5_2:19669773-19669792 Msa0761940:three_prime_UTR 25.0%
!!! CATTGGTTTATTTGCAAATT+CGG + chr5_2:19669790-19669809 Msa0761940:three_prime_UTR 25.0%
! AAAGAATCTTGAAATAGTTG+AGG + chr5_2:19669906-19669925 Msa0761940:three_prime_UTR 25.0%
! AAATCAAAGAATTCCATCAA+TGG + chr5_2:19669205-19669224 Msa0761940:exon 25.0%
! ATTATACATTATATAGGTGG+TGG - chr5_2:19669635-19669654 None:intergenic 25.0%
! TTCTTGATTGCCAATTTATT+GGG + chr5_2:19669749-19669768 Msa0761940:three_prime_UTR 25.0%
! CATCTAATAACCCAATAAAT+TGG - chr5_2:19669762-19669781 None:intergenic 25.0%
! CAATTTATTGGGTTATTAGA+TGG + chr5_2:19669760-19669779 Msa0761940:three_prime_UTR 25.0%
! TATTAGATGGTTTAATGCAT+TGG + chr5_2:19669773-19669792 Msa0761940:three_prime_UTR 25.0%
!!! CATTGGTTTATTTGCAAATT+CGG + chr5_2:19669790-19669809 Msa0761940:three_prime_UTR 25.0%
! AGGACTTTTTGTTCTACTTT+TGG - chr5_2:19669104-19669123 None:intergenic 30.0%
AGAAAAGGAGAAAATTGAGA+AGG - chr5_2:19669370-19669389 None:intergenic 30.0%
TTTCAACTAACAACGCAAAA+GGG - chr5_2:19669397-19669416 None:intergenic 30.0%
ATTTCAACTAACAACGCAAA+AGG - chr5_2:19669398-19669417 None:intergenic 30.0%
GAATTACTTGAAGTTCAAGT+TGG + chr5_2:19669528-19669547 Msa0761940:CDS 30.0%
GTTCTTGATTGCCAATTTAT+TGG + chr5_2:19669748-19669767 Msa0761940:three_prime_UTR 30.0%
! AGGACTTTTTGTTCTACTTT+TGG - chr5_2:19669104-19669123 None:intergenic 30.0%
AGAAAAGGAGAAAATTGAGA+AGG - chr5_2:19669370-19669389 None:intergenic 30.0%
TTTCAACTAACAACGCAAAA+GGG - chr5_2:19669397-19669416 None:intergenic 30.0%
ATTTCAACTAACAACGCAAA+AGG - chr5_2:19669398-19669417 None:intergenic 30.0%
GAATTACTTGAAGTTCAAGT+TGG + chr5_2:19669528-19669547 Msa0761940:CDS 30.0%
GTTCTTGATTGCCAATTTAT+TGG + chr5_2:19669748-19669767 Msa0761940:three_prime_UTR 30.0%
AGAAGTAAACGAGAGTTAGT+TGG + chr5_2:19669125-19669144 Msa0761940:five_prime_UTR 35.0%
TTCGATTTCCTTGTCCAATT+CGG + chr5_2:19669335-19669354 Msa0761940:CDS 35.0%
GAATGAGAAGCTTGATGTAT+TGG + chr5_2:19669494-19669513 Msa0761940:CDS 35.0%
! CATCAAGTTGCAAAAAGAGA+AGG - chr5_2:19669570-19669589 None:intergenic 35.0%
AGAAGTAAACGAGAGTTAGT+TGG + chr5_2:19669125-19669144 Msa0761940:five_prime_UTR 35.0%
TTCGATTTCCTTGTCCAATT+CGG + chr5_2:19669335-19669354 Msa0761940:CDS 35.0%
GAATGAGAAGCTTGATGTAT+TGG + chr5_2:19669494-19669513 Msa0761940:CDS 35.0%
! CATCAAGTTGCAAAAAGAGA+AGG - chr5_2:19669570-19669589 None:intergenic 35.0%
CTAACTCTCGTTTACTTCTC+AGG - chr5_2:19669124-19669143 None:intergenic 40.0%
ATCACAAACGCAGTTAACGT+TGG + chr5_2:19669242-19669261 Msa0761940:CDS 40.0%
AATCGCTGTTCAAGCTGATT+GGG + chr5_2:19669265-19669284 Msa0761940:CDS 40.0%
!! TTTGAGTACCGAATTGGACA+AGG - chr5_2:19669346-19669365 None:intergenic 40.0%
!! GAAGGATTTGAGTACCGAAT+TGG - chr5_2:19669352-19669371 None:intergenic 40.0%
ACGCAAAAGGGTCAAAGAAA+AGG - chr5_2:19669385-19669404 None:intergenic 40.0%
TGATGTATTGGAACGTCGTT+TGG + chr5_2:19669506-19669525 Msa0761940:CDS 40.0%
!! AGTTCAAGTTGGCAATGCTT+CGG + chr5_2:19669539-19669558 Msa0761940:CDS 40.0%
CTAACTCTCGTTTACTTCTC+AGG - chr5_2:19669124-19669143 None:intergenic 40.0%
ATCACAAACGCAGTTAACGT+TGG + chr5_2:19669242-19669261 Msa0761940:CDS 40.0%
AATCGCTGTTCAAGCTGATT+GGG + chr5_2:19669265-19669284 Msa0761940:CDS 40.0%
!! TTTGAGTACCGAATTGGACA+AGG - chr5_2:19669346-19669365 None:intergenic 40.0%
!! GAAGGATTTGAGTACCGAAT+TGG - chr5_2:19669352-19669371 None:intergenic 40.0%
ACGCAAAAGGGTCAAAGAAA+AGG - chr5_2:19669385-19669404 None:intergenic 40.0%
TGATGTATTGGAACGTCGTT+TGG + chr5_2:19669506-19669525 Msa0761940:CDS 40.0%
!! AGTTCAAGTTGGCAATGCTT+CGG + chr5_2:19669539-19669558 Msa0761940:CDS 40.0%
GAATCGCTGTTCAAGCTGAT+TGG + chr5_2:19669264-19669283 Msa0761940:CDS 45.0%
GAATCGCTGTTCAAGCTGAT+TGG + chr5_2:19669264-19669283 Msa0761940:CDS 45.0%
ATTCCATCAATGGCACGTGC+TGG + chr5_2:19669215-19669234 Msa0761940:exon 50.0%
ATTCCATCAATGGCACGTGC+TGG + chr5_2:19669215-19669234 Msa0761940:exon 50.0%
! CCACCAGCACGTGCCATTGA+TGG - chr5_2:19669221-19669240 None:intergenic 60.0%
CCATCAATGGCACGTGCTGG+TGG + chr5_2:19669218-19669237 Msa0761940:exon 60.0%
! CCACCAGCACGTGCCATTGA+TGG - chr5_2:19669221-19669240 None:intergenic 60.0%
CCATCAATGGCACGTGCTGG+TGG + chr5_2:19669218-19669237 Msa0761940:exon 60.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 19669091 19669927 19669091 ID=Msa0761940;Name=Msa0761940
chr5_2 mRNA 19669091 19669927 19669091 ID=Msa0761940-mRNA-1;Parent=Msa0761940;Name=Msa0761940-mRNA-1;_AED=0.35;_eAED=0.35;_QI=133|1|1|1|1|1|2|340|85
chr5_2 exon 19669091 19669356 19669091 ID=Msa0761940-mRNA-1:exon:8390;Parent=Msa0761940-mRNA-1
chr5_2 exon 19669463 19669927 19669463 ID=Msa0761940-mRNA-1:exon:8391;Parent=Msa0761940-mRNA-1
chr5_2 five_prime_UTR 19669091 19669223 19669091 ID=Msa0761940-mRNA-1:five_prime_utr;Parent=Msa0761940-mRNA-1
chr5_2 CDS 19669224 19669356 19669224 ID=Msa0761940-mRNA-1:cds;Parent=Msa0761940-mRNA-1
chr5_2 CDS 19669463 19669587 19669463 ID=Msa0761940-mRNA-1:cds;Parent=Msa0761940-mRNA-1
chr5_2 three_prime_UTR 19669588 19669927 19669588 ID=Msa0761940-mRNA-1:three_prime_utr;Parent=Msa0761940-mRNA-1
Gene Sequence

>Msa0761940

ATGGCACGTGCTGGTGGAATCACAAACGCAGTTAACGTTGGAATCGCTGTTCAAGCTGATTGGGAAAATCGTGAATTCATCTCTCACATTTCTCTCAATGTTCGTCGTCTCTTCGATTTCCTTGTCCAATTCGAGGCTACAACAAAGAGTAAATTAGCTTCATTGAATGAGAAGCTTGATGTATTGGAACGTCGTTTGGAATTACTTGAAGTTCAAGTTGGCAATGCTTCGGCAAATCCTTCTCTTTTTGCAACTTGA

Protein sequence

>Msa0761940

MARAGGITNAVNVGIAVQADWENREFISHISLNVRRLFDFLVQFEATTKSKLASLNEKLDVLERRLELLEVQVGNASANPSLFAT*