AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0841940


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0841940 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
Msa0841940 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_4:-18799259 Msa0841940:three_prime_UTR
AAAATCTTTAAAAGCACTTA+TGG 0.245901 5_4:-18799124 Msa0841940:three_prime_UTR
CATTGGTTTATTTGCAAATT+CGG 0.278022 5_4:-18799217 Msa0841940:three_prime_UTR
CAATTTATTGGGTTATTAGA+TGG 0.289266 5_4:-18799247 Msa0841940:three_prime_UTR
TTCTTGATTGCCAATTTATT+GGG 0.290000 5_4:-18799258 Msa0841940:three_prime_UTR
GTTGGAAGTGAAAGAGAAAA+AGG 0.309858 5_4:-18799864 Msa0841940:five_prime_UTR
CATCTAATAACCCAATAAAT+TGG 0.317606 5_4:+18799248 None:intergenic
TGATGTATTGGAACGTCGTT+TGG 0.348132 5_4:-18799501 Msa0841940:CDS
CCACCAGCACGTGCCATTGA+TGG 0.365965 5_4:+18799789 None:intergenic
GAAGAAATTGAGTACCGAAT+TGG 0.367198 5_4:+18799658 None:intergenic
TATATAATGTATAATCTAGA+TGG 0.379960 5_4:-18799367 Msa0841940:three_prime_UTR
GAATCGCTGTTCAAGCTGAT+TGG 0.386107 5_4:-18799743 Msa0841940:CDS
TTCGATTTCCTTGTCCAATT+CGG 0.396293 5_4:-18799672 Msa0841940:intron
CTAACTCTCGTTTACTTCTC+AGG 0.398070 5_4:+18799886 None:intergenic
GAATGAGAAGCTTGATGTAT+TGG 0.424872 5_4:-18799513 Msa0841940:CDS
TATTAGATGGTTTAATGCAT+TGG 0.431631 5_4:-18799234 Msa0841940:three_prime_UTR
AATCGCTGTTCAAGCTGATT+GGG 0.456401 5_4:-18799742 Msa0841940:CDS
ATCTAGATTATACATTATAT+AGG 0.457778 5_4:+18799369 None:intergenic
AGTTCAAGTTGGCAATGCTT+CGG 0.492873 5_4:-18799468 Msa0841940:CDS
AATAAAATCAAAATCTACAT+TGG 0.509747 5_4:-18799830 Msa0841940:five_prime_UTR
AAATCAAAGAATTCCATCAA+TGG 0.510384 5_4:-18799802 Msa0841940:exon
AGAAGTAAACGAGAGTTAGT+TGG 0.515439 5_4:-18799882 Msa0841940:five_prime_UTR
GAATTACTTGAAGTTCAAGT+TGG 0.523303 5_4:-18799479 Msa0841940:CDS
ATTATACATTATATAGGTGG+TGG 0.532369 5_4:+18799375 None:intergenic
ATTCCATCAATGGCACGTGC+TGG 0.544732 5_4:-18799792 Msa0841940:exon
CCATCAATGGCACGTGCTGG+TGG 0.566134 5_4:-18799789 Msa0841940:exon
TAGATTATACATTATATAGG+TGG 0.616253 5_4:+18799372 None:intergenic
ATCACAAACGCAGTTAACGT+TGG 0.620945 5_4:-18799765 Msa0841940:CDS
ATTGAGTACCGAATTGGACA+AGG 0.623936 5_4:+18799664 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAAAATCAAAATCTACAT+TGG - chr5_4:18799219-18799238 Msa0841940:three_prime_UTR 15.0%
!!! AATCTTATATCTTTTTTTGA+TGG - chr5_4:18799457-18799476 Msa0841940:CDS 15.0%
!!! ATCTTATATCTTTTTTTGAT+GGG - chr5_4:18799458-18799477 Msa0841940:CDS 15.0%
!! ATCTAGATTATACATTATAT+AGG + chr5_4:18799683-18799702 None:intergenic 15.0%
!! TATATAATGTATAATCTAGA+TGG - chr5_4:18799682-18799701 Msa0841940:CDS 15.0%
!!! TTAAAGATTTTTACTCAAAT+TGG + chr5_4:18799916-18799935 None:intergenic 15.0%
!! AATAAAATCAAAATCTACAT+TGG - chr5_4:18799219-18799238 Msa0841940:three_prime_UTR 15.0%
!!! AATCTTATATCTTTTTTTGA+TGG - chr5_4:18799457-18799476 Msa0841940:CDS 15.0%
!!! ATCTTATATCTTTTTTTGAT+GGG - chr5_4:18799458-18799477 Msa0841940:CDS 15.0%
!! ATCTAGATTATACATTATAT+AGG + chr5_4:18799683-18799702 None:intergenic 15.0%
!! TATATAATGTATAATCTAGA+TGG - chr5_4:18799682-18799701 Msa0841940:CDS 15.0%
!!! TTAAAGATTTTTACTCAAAT+TGG + chr5_4:18799916-18799935 None:intergenic 15.0%
!! ATATAAGATTTCAACTAACA+AGG + chr5_4:18799447-18799466 None:intergenic 20.0%
!!! TGTTATTTTTGTTATTTCAG+AGG - chr5_4:18799485-18799504 Msa0841940:CDS 20.0%
!! TAGATTATACATTATATAGG+TGG + chr5_4:18799680-18799699 None:intergenic 20.0%
!!! AAAATCTTTAAAAGCACTTA+TGG - chr5_4:18799925-18799944 Msa0841940:five_prime_UTR 20.0%
!! ATATAAGATTTCAACTAACA+AGG + chr5_4:18799447-18799466 None:intergenic 20.0%
!!! TGTTATTTTTGTTATTTCAG+AGG - chr5_4:18799485-18799504 Msa0841940:CDS 20.0%
!! TAGATTATACATTATATAGG+TGG + chr5_4:18799680-18799699 None:intergenic 20.0%
!!! AAAATCTTTAAAAGCACTTA+TGG - chr5_4:18799925-18799944 Msa0841940:five_prime_UTR 20.0%
! AAATCAAAGAATTCCATCAA+TGG - chr5_4:18799247-18799266 Msa0841940:three_prime_UTR 25.0%
! ATTATACATTATATAGGTGG+TGG + chr5_4:18799677-18799696 None:intergenic 25.0%
! TTCTTGATTGCCAATTTATT+GGG - chr5_4:18799791-18799810 Msa0841940:exon 25.0%
! CATCTAATAACCCAATAAAT+TGG + chr5_4:18799804-18799823 None:intergenic 25.0%
! CAATTTATTGGGTTATTAGA+TGG - chr5_4:18799802-18799821 Msa0841940:exon 25.0%
! TATTAGATGGTTTAATGCAT+TGG - chr5_4:18799815-18799834 Msa0841940:five_prime_UTR 25.0%
!!! CATTGGTTTATTTGCAAATT+CGG - chr5_4:18799832-18799851 Msa0841940:five_prime_UTR 25.0%
! AAATCAAAGAATTCCATCAA+TGG - chr5_4:18799247-18799266 Msa0841940:three_prime_UTR 25.0%
! ATTATACATTATATAGGTGG+TGG + chr5_4:18799677-18799696 None:intergenic 25.0%
! TTCTTGATTGCCAATTTATT+GGG - chr5_4:18799791-18799810 Msa0841940:exon 25.0%
! CATCTAATAACCCAATAAAT+TGG + chr5_4:18799804-18799823 None:intergenic 25.0%
! CAATTTATTGGGTTATTAGA+TGG - chr5_4:18799802-18799821 Msa0841940:exon 25.0%
! TATTAGATGGTTTAATGCAT+TGG - chr5_4:18799815-18799834 Msa0841940:five_prime_UTR 25.0%
!!! CATTGGTTTATTTGCAAATT+CGG - chr5_4:18799832-18799851 Msa0841940:five_prime_UTR 25.0%
! AGGACTTTTTGTTCTACTTT+TGG + chr5_4:18799146-18799165 None:intergenic 30.0%
TTTCAACTAACAAGGCAAAA+GGG + chr5_4:18799439-18799458 None:intergenic 30.0%
ATTTCAACTAACAAGGCAAA+AGG + chr5_4:18799440-18799459 None:intergenic 30.0%
GAATTACTTGAAGTTCAAGT+TGG - chr5_4:18799570-18799589 Msa0841940:intron 30.0%
GTTCTTGATTGCCAATTTAT+TGG - chr5_4:18799790-18799809 Msa0841940:exon 30.0%
! AGGACTTTTTGTTCTACTTT+TGG + chr5_4:18799146-18799165 None:intergenic 30.0%
TTTCAACTAACAAGGCAAAA+GGG + chr5_4:18799439-18799458 None:intergenic 30.0%
ATTTCAACTAACAAGGCAAA+AGG + chr5_4:18799440-18799459 None:intergenic 30.0%
GAATTACTTGAAGTTCAAGT+TGG - chr5_4:18799570-18799589 Msa0841940:intron 30.0%
GTTCTTGATTGCCAATTTAT+TGG - chr5_4:18799790-18799809 Msa0841940:exon 30.0%
AGAAGTAAACGAGAGTTAGT+TGG - chr5_4:18799167-18799186 Msa0841940:three_prime_UTR 35.0%
GTTGGAAGTGAAAGAGAAAA+AGG - chr5_4:18799185-18799204 Msa0841940:three_prime_UTR 35.0%
TTCGATTTCCTTGTCCAATT+CGG - chr5_4:18799377-18799396 Msa0841940:three_prime_UTR 35.0%
!! GAAGAAATTGAGTACCGAAT+TGG + chr5_4:18799394-18799413 None:intergenic 35.0%
GAATGAGAAGCTTGATGTAT+TGG - chr5_4:18799536-18799555 Msa0841940:CDS 35.0%
! CATCAAGTTGCAAAAAGAGA+AGG + chr5_4:18799612-18799631 None:intergenic 35.0%
AGAAGTAAACGAGAGTTAGT+TGG - chr5_4:18799167-18799186 Msa0841940:three_prime_UTR 35.0%
GTTGGAAGTGAAAGAGAAAA+AGG - chr5_4:18799185-18799204 Msa0841940:three_prime_UTR 35.0%
TTCGATTTCCTTGTCCAATT+CGG - chr5_4:18799377-18799396 Msa0841940:three_prime_UTR 35.0%
!! GAAGAAATTGAGTACCGAAT+TGG + chr5_4:18799394-18799413 None:intergenic 35.0%
GAATGAGAAGCTTGATGTAT+TGG - chr5_4:18799536-18799555 Msa0841940:CDS 35.0%
! CATCAAGTTGCAAAAAGAGA+AGG + chr5_4:18799612-18799631 None:intergenic 35.0%
CTAACTCTCGTTTACTTCTC+AGG + chr5_4:18799166-18799185 None:intergenic 40.0%
ATCACAAACGCAGTTAACGT+TGG - chr5_4:18799284-18799303 Msa0841940:three_prime_UTR 40.0%
AATCGCTGTTCAAGCTGATT+GGG - chr5_4:18799307-18799326 Msa0841940:three_prime_UTR 40.0%
!! ATTGAGTACCGAATTGGACA+AGG + chr5_4:18799388-18799407 None:intergenic 40.0%
TGATGTATTGGAACGTCGTT+TGG - chr5_4:18799548-18799567 Msa0841940:intron 40.0%
!! AGTTCAAGTTGGCAATGCTT+CGG - chr5_4:18799581-18799600 Msa0841940:intron 40.0%
CTAACTCTCGTTTACTTCTC+AGG + chr5_4:18799166-18799185 None:intergenic 40.0%
ATCACAAACGCAGTTAACGT+TGG - chr5_4:18799284-18799303 Msa0841940:three_prime_UTR 40.0%
AATCGCTGTTCAAGCTGATT+GGG - chr5_4:18799307-18799326 Msa0841940:three_prime_UTR 40.0%
!! ATTGAGTACCGAATTGGACA+AGG + chr5_4:18799388-18799407 None:intergenic 40.0%
TGATGTATTGGAACGTCGTT+TGG - chr5_4:18799548-18799567 Msa0841940:intron 40.0%
!! AGTTCAAGTTGGCAATGCTT+CGG - chr5_4:18799581-18799600 Msa0841940:intron 40.0%
GAATCGCTGTTCAAGCTGAT+TGG - chr5_4:18799306-18799325 Msa0841940:three_prime_UTR 45.0%
GAATCGCTGTTCAAGCTGAT+TGG - chr5_4:18799306-18799325 Msa0841940:three_prime_UTR 45.0%
ATTCCATCAATGGCACGTGC+TGG - chr5_4:18799257-18799276 Msa0841940:three_prime_UTR 50.0%
ATTCCATCAATGGCACGTGC+TGG - chr5_4:18799257-18799276 Msa0841940:three_prime_UTR 50.0%
! CCACCAGCACGTGCCATTGA+TGG + chr5_4:18799263-18799282 None:intergenic 60.0%
CCATCAATGGCACGTGCTGG+TGG - chr5_4:18799260-18799279 Msa0841940:three_prime_UTR 60.0%
! CCACCAGCACGTGCCATTGA+TGG + chr5_4:18799263-18799282 None:intergenic 60.0%
CCATCAATGGCACGTGCTGG+TGG - chr5_4:18799260-18799279 Msa0841940:three_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 18799105 18799966 18799105 ID=Msa0841940;Name=Msa0841940
chr5_4 mRNA 18799105 18799966 18799105 ID=Msa0841940-mRNA-1;Parent=Msa0841940;Name=Msa0841940-mRNA-1;_AED=0.00;_eAED=0.00;_QI=161|1|1|1|1|1|2|337|85
chr5_4 exon 18799105 18799566 18799105 ID=Msa0841940-mRNA-1:exon:7824;Parent=Msa0841940-mRNA-1
chr5_4 exon 18799673 18799966 18799673 ID=Msa0841940-mRNA-1:exon:7823;Parent=Msa0841940-mRNA-1
chr5_4 five_prime_UTR 18799806 18799966 18799806 ID=Msa0841940-mRNA-1:five_prime_utr;Parent=Msa0841940-mRNA-1
chr5_4 CDS 18799673 18799805 18799673 ID=Msa0841940-mRNA-1:cds;Parent=Msa0841940-mRNA-1
chr5_4 CDS 18799442 18799566 18799442 ID=Msa0841940-mRNA-1:cds;Parent=Msa0841940-mRNA-1
chr5_4 three_prime_UTR 18799105 18799441 18799105 ID=Msa0841940-mRNA-1:three_prime_utr;Parent=Msa0841940-mRNA-1
Gene Sequence

>Msa0841940

ATGGCACGTGCTGGTGGAATCACAAACGCAGTTAACGTTGGAATCGCTGTTCAAGCTGATTGGGAAAATCGTGAATTCATCTCTCACATTTCTCTCAATGTTCGTCGTCTCTTCGATTTCCTTGTCCAATTCGAGGCTACAACAAAGAGTAAATTAGCTTCATTGAATGAGAAGCTTGATGTATTGGAACGTCGTTTGGAATTACTTGAAGTTCAAGTTGGCAATGCTTCGGCAAATCCTTCTCTTTTTGCAACTTGA

Protein sequence

>Msa0841940

MARAGGITNAVNVGIAVQADWENREFISHISLNVRRLFDFLVQFEATTKSKLASLNEKLDVLERRLELLEVQVGNASANPSLFAT*