AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0349350

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0349350 MtrunA17_Chr3g0082821 80.000 60 10 2 1 59 1 59 6.86e-26 90.5
Msa0349350 MtrunA17_Chr3g0082851 61.017 59 20 3 1 58 1 57 3.26e-15 63.2
Msa0349350 MtrunA17_Chr3g0082801 53.731 67 26 3 1 63 4 69 4.35e-14 60.5
Msa0349350 MtrunA17_Chr3g0082831 55.172 58 23 2 1 58 1 55 1.21e-12 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATTCACATGCTTTAATAAT+TGG 0.142490 3_1:-12870279 Msa0349350:three_prime_UTR
TGTGATTATTATCTTGTTAT+TGG 0.230811 3_1:-12871040 Msa0349350:CDS
TGTTGTAGATTCTCTTAAAT+TGG 0.264924 3_1:-12871118 Msa0349350:five_prime_UTR
ACATGTTAAGAAATTTAAAA+TGG 0.267580 3_1:-12870231 Msa0349350:three_prime_UTR
TTAAAATGGTAAGTTTGTTT+TGG 0.275417 3_1:-12870217 Msa0349350:three_prime_UTR
TGAGGTGAATGAGGAATAAA+TGG 0.349895 3_1:+12871157 None:intergenic
GGAGGAGACGGACGAGGAGG+AGG 0.354746 3_1:+12870428 None:intergenic
TATTATCTTGTTATTGGAAG+TGG 0.403862 3_1:-12871034 Msa0349350:CDS
GGAGACGGACGAGGAGGAGG+AGG 0.438833 3_1:+12870431 None:intergenic
TAAATTGGCAGGAAGACATA+TGG 0.451623 3_1:-12871103 Msa0349350:exon
TCGTGATAATTCTGATGCTC+TGG 0.454699 3_1:+12870378 None:intergenic
GTAGATTCTCTTAAATTGGC+AGG 0.465512 3_1:-12871114 Msa0349350:five_prime_UTR
GGAGGAGGAGGAGACGGACG+AGG 0.509180 3_1:+12870422 None:intergenic
CTCTGGATTCATCAGCATCA+TGG 0.513217 3_1:+12870395 None:intergenic
CATCATCAACAATATAAAGT+AGG 0.517741 3_1:+12870477 None:intergenic
CATCATGGATGAGGAGGAGG+AGG 0.524144 3_1:+12870410 None:intergenic
TAAGGTGGTTATATTGAACC+TGG 0.537678 3_1:-12871073 Msa0349350:CDS
GGAGGAGGAGACGGACGAGG+AGG 0.539009 3_1:+12870425 None:intergenic
CAGCATCATGGATGAGGAGG+AGG 0.541887 3_1:+12870407 None:intergenic
ATTCATCAGCATCATGGATG+AGG 0.558987 3_1:+12870401 None:intergenic
TAATCACAAACAGCAAAGCC+AGG 0.561600 3_1:+12871055 None:intergenic
TGGAAGTGGCAACAACGGCA+AGG 0.587694 3_1:-12871020 Msa0349350:CDS
GGAAGTGGCAACAACGGCAA+GGG 0.590453 3_1:-12871019 Msa0349350:CDS
ACGTGTGTGTGAGGTGAATG+AGG 0.590530 3_1:+12871148 None:intergenic
GAGGAGGAGGAGAGTAGTGG+TGG 0.603187 3_1:+12870444 None:intergenic
CATCAGCATCATGGATGAGG+AGG 0.611713 3_1:+12870404 None:intergenic
GTTATTGGAAGTGGCAACAA+CGG 0.617293 3_1:-12871025 Msa0349350:CDS
GGAGAGTAGTGGTGGCCGTG+TGG 0.650454 3_1:+12870452 None:intergenic
CATATATTTACGTGTGTGTG+AGG 0.665325 3_1:+12871139 None:intergenic
ATTGTTGATGATGTTCCACA+CGG 0.674884 3_1:-12870467 Msa0349350:CDS
CAACGGCAAGGGTACCACCG+TGG 0.713272 3_1:-12871008 Msa0349350:CDS
GAGCATCAGAATTATCACGA+TGG 0.736384 3_1:-12870375 Msa0349350:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACATGTTAAGAAATTTAAAA+TGG - chr3_1:12871209-12871228 Msa0349350:five_prime_UTR 15.0%
!! ACATGTTAAGAAATTTAAAA+TGG - chr3_1:12871209-12871228 Msa0349350:five_prime_UTR 15.0%
!!! TTATTTTTCAAGTAGATTAG+TGG + chr3_1:12870220-12870239 None:intergenic 20.0%
!!! TGTGATTATTATCTTGTTAT+TGG - chr3_1:12870400-12870419 Msa0349350:exon 20.0%
!! ACTAACTAAAACAATTATGA+AGG + chr3_1:12870568-12870587 None:intergenic 20.0%
!! TATTCACATGCTTTAATAAT+TGG - chr3_1:12871161-12871180 Msa0349350:five_prime_UTR 20.0%
!!! TTAAAATGGTAAGTTTGTTT+TGG - chr3_1:12871223-12871242 Msa0349350:five_prime_UTR 20.0%
!!! TTATTTTTCAAGTAGATTAG+TGG + chr3_1:12870220-12870239 None:intergenic 20.0%
!!! TGTGATTATTATCTTGTTAT+TGG - chr3_1:12870400-12870419 Msa0349350:exon 20.0%
!! ACTAACTAAAACAATTATGA+AGG + chr3_1:12870568-12870587 None:intergenic 20.0%
!! TATTCACATGCTTTAATAAT+TGG - chr3_1:12871161-12871180 Msa0349350:five_prime_UTR 20.0%
!!! TTAAAATGGTAAGTTTGTTT+TGG - chr3_1:12871223-12871242 Msa0349350:five_prime_UTR 20.0%
! TGTTGTAGATTCTCTTAAAT+TGG - chr3_1:12870322-12870341 Msa0349350:three_prime_UTR 25.0%
!!! AAGACATATGGCTTATTTTA+AGG - chr3_1:12870349-12870368 Msa0349350:three_prime_UTR 25.0%
!!! TATTATCTTGTTATTGGAAG+TGG - chr3_1:12870406-12870425 Msa0349350:exon 25.0%
!! CAAGTAAGTAATACTCTTTT+TGG - chr3_1:12870477-12870496 Msa0349350:CDS 25.0%
!!! CTCTTTTTGGTCTTATAATA+AGG - chr3_1:12870490-12870509 Msa0349350:intron 25.0%
!! ATAATAAGGAGAAGAAGTTT+TGG - chr3_1:12870504-12870523 Msa0349350:intron 25.0%
!!! TTATACCATCTTTTGAAAGA+TGG - chr3_1:12870610-12870629 Msa0349350:intron 25.0%
! TTCCACTTGAAATTTATGTA+TGG - chr3_1:12870879-12870898 Msa0349350:intron 25.0%
! AACCATACATAAATTTCAAG+TGG + chr3_1:12870884-12870903 None:intergenic 25.0%
! CATCATCAACAATATAAAGT+AGG + chr3_1:12870966-12870985 None:intergenic 25.0%
! AGTTGACAACGAATAAAAAA+AGG - chr3_1:12871099-12871118 Msa0349350:exon 25.0%
! GTTGACAACGAATAAAAAAA+GGG - chr3_1:12871100-12871119 Msa0349350:exon 25.0%
! TGTTGTAGATTCTCTTAAAT+TGG - chr3_1:12870322-12870341 Msa0349350:three_prime_UTR 25.0%
!!! AAGACATATGGCTTATTTTA+AGG - chr3_1:12870349-12870368 Msa0349350:three_prime_UTR 25.0%
!!! TATTATCTTGTTATTGGAAG+TGG - chr3_1:12870406-12870425 Msa0349350:exon 25.0%
!! CAAGTAAGTAATACTCTTTT+TGG - chr3_1:12870477-12870496 Msa0349350:CDS 25.0%
!!! CTCTTTTTGGTCTTATAATA+AGG - chr3_1:12870490-12870509 Msa0349350:intron 25.0%
!! ATAATAAGGAGAAGAAGTTT+TGG - chr3_1:12870504-12870523 Msa0349350:intron 25.0%
!!! TTATACCATCTTTTGAAAGA+TGG - chr3_1:12870610-12870629 Msa0349350:intron 25.0%
! TTCCACTTGAAATTTATGTA+TGG - chr3_1:12870879-12870898 Msa0349350:intron 25.0%
! AACCATACATAAATTTCAAG+TGG + chr3_1:12870884-12870903 None:intergenic 25.0%
! CATCATCAACAATATAAAGT+AGG + chr3_1:12870966-12870985 None:intergenic 25.0%
! AGTTGACAACGAATAAAAAA+AGG - chr3_1:12871099-12871118 Msa0349350:exon 25.0%
! GTTGACAACGAATAAAAAAA+GGG - chr3_1:12871100-12871119 Msa0349350:exon 25.0%
!!! ACATATGGCTTATTTTAAGG+TGG - chr3_1:12870352-12870371 Msa0349350:three_prime_UTR 30.0%
!!! TACTTACTTGTTTTGTGATG+AGG + chr3_1:12870467-12870486 None:intergenic 30.0%
GTTAACCATCTTTCAAAAGA+TGG + chr3_1:12870618-12870637 None:intergenic 30.0%
! GTTATTCAAGTTTCGATTTG+TGG - chr3_1:12870813-12870832 Msa0349350:intron 30.0%
!!! ACATATGGCTTATTTTAAGG+TGG - chr3_1:12870352-12870371 Msa0349350:three_prime_UTR 30.0%
!!! TACTTACTTGTTTTGTGATG+AGG + chr3_1:12870467-12870486 None:intergenic 30.0%
GTTAACCATCTTTCAAAAGA+TGG + chr3_1:12870618-12870637 None:intergenic 30.0%
! GTTATTCAAGTTTCGATTTG+TGG - chr3_1:12870813-12870832 Msa0349350:intron 30.0%
TGAGGTGAATGAGGAATAAA+TGG + chr3_1:12870286-12870305 None:intergenic 35.0%
CATATATTTACGTGTGTGTG+AGG + chr3_1:12870304-12870323 None:intergenic 35.0%
GTAGATTCTCTTAAATTGGC+AGG - chr3_1:12870326-12870345 Msa0349350:three_prime_UTR 35.0%
TAAATTGGCAGGAAGACATA+TGG - chr3_1:12870337-12870356 Msa0349350:three_prime_UTR 35.0%
TAAGGTGGTTATATTGAACC+TGG - chr3_1:12870367-12870386 Msa0349350:three_prime_UTR 35.0%
TTGAGATTCCAAAACAGACA+TGG + chr3_1:12870934-12870953 None:intergenic 35.0%
!!! CTGTTTTGGAATCTCAAAGA+TGG - chr3_1:12870937-12870956 Msa0349350:intron 35.0%
!! ATTGTTGATGATGTTCCACA+CGG - chr3_1:12870973-12870992 Msa0349350:intron 35.0%
TGAGGTGAATGAGGAATAAA+TGG + chr3_1:12870286-12870305 None:intergenic 35.0%
CATATATTTACGTGTGTGTG+AGG + chr3_1:12870304-12870323 None:intergenic 35.0%
GTAGATTCTCTTAAATTGGC+AGG - chr3_1:12870326-12870345 Msa0349350:three_prime_UTR 35.0%
TAAATTGGCAGGAAGACATA+TGG - chr3_1:12870337-12870356 Msa0349350:three_prime_UTR 35.0%
TAAGGTGGTTATATTGAACC+TGG - chr3_1:12870367-12870386 Msa0349350:three_prime_UTR 35.0%
TTGAGATTCCAAAACAGACA+TGG + chr3_1:12870934-12870953 None:intergenic 35.0%
!!! CTGTTTTGGAATCTCAAAGA+TGG - chr3_1:12870937-12870956 Msa0349350:intron 35.0%
!! ATTGTTGATGATGTTCCACA+CGG - chr3_1:12870973-12870992 Msa0349350:intron 35.0%
TAATCACAAACAGCAAAGCC+AGG + chr3_1:12870388-12870407 None:intergenic 40.0%
GTTATTGGAAGTGGCAACAA+CGG - chr3_1:12870415-12870434 Msa0349350:CDS 40.0%
! TGATGAGGCTCAATTTTCCA+CGG + chr3_1:12870452-12870471 None:intergenic 40.0%
AGCTAGCAAGAATCAAGAAC+TGG - chr3_1:12870791-12870810 Msa0349350:intron 40.0%
AAACAGACATGGCAACAACA+TGG + chr3_1:12870923-12870942 None:intergenic 40.0%
! TGTTGTTGCCATGTCTGTTT+TGG - chr3_1:12870923-12870942 Msa0349350:intron 40.0%
ATTCATCAGCATCATGGATG+AGG + chr3_1:12871042-12871061 None:intergenic 40.0%
TCGTGATAATTCTGATGCTC+TGG + chr3_1:12871065-12871084 None:intergenic 40.0%
GAGCATCAGAATTATCACGA+TGG - chr3_1:12871065-12871084 Msa0349350:CDS 40.0%
TAATCACAAACAGCAAAGCC+AGG + chr3_1:12870388-12870407 None:intergenic 40.0%
GTTATTGGAAGTGGCAACAA+CGG - chr3_1:12870415-12870434 Msa0349350:CDS 40.0%
! TGATGAGGCTCAATTTTCCA+CGG + chr3_1:12870452-12870471 None:intergenic 40.0%
AGCTAGCAAGAATCAAGAAC+TGG - chr3_1:12870791-12870810 Msa0349350:intron 40.0%
AAACAGACATGGCAACAACA+TGG + chr3_1:12870923-12870942 None:intergenic 40.0%
! TGTTGTTGCCATGTCTGTTT+TGG - chr3_1:12870923-12870942 Msa0349350:intron 40.0%
ATTCATCAGCATCATGGATG+AGG + chr3_1:12871042-12871061 None:intergenic 40.0%
TCGTGATAATTCTGATGCTC+TGG + chr3_1:12871065-12871084 None:intergenic 40.0%
GAGCATCAGAATTATCACGA+TGG - chr3_1:12871065-12871084 Msa0349350:CDS 40.0%
CTCTGGATTCATCAGCATCA+TGG + chr3_1:12871048-12871067 None:intergenic 45.0%
CTCTGGATTCATCAGCATCA+TGG + chr3_1:12871048-12871067 None:intergenic 45.0%
ACGTGTGTGTGAGGTGAATG+AGG + chr3_1:12870295-12870314 None:intergenic 50.0%
! TGAGGCTCAATTTTCCACGG+TGG + chr3_1:12870449-12870468 None:intergenic 50.0%
CATCAGCATCATGGATGAGG+AGG + chr3_1:12871039-12871058 None:intergenic 50.0%
ACGTGTGTGTGAGGTGAATG+AGG + chr3_1:12870295-12870314 None:intergenic 50.0%
! TGAGGCTCAATTTTCCACGG+TGG + chr3_1:12870449-12870468 None:intergenic 50.0%
CATCAGCATCATGGATGAGG+AGG + chr3_1:12871039-12871058 None:intergenic 50.0%
TGGAAGTGGCAACAACGGCA+AGG - chr3_1:12870420-12870439 Msa0349350:CDS 55.0%
GGAAGTGGCAACAACGGCAA+GGG - chr3_1:12870421-12870440 Msa0349350:CDS 55.0%
CATCATGGATGAGGAGGAGG+AGG + chr3_1:12871033-12871052 None:intergenic 55.0%
CAGCATCATGGATGAGGAGG+AGG + chr3_1:12871036-12871055 None:intergenic 55.0%
TGGAAGTGGCAACAACGGCA+AGG - chr3_1:12870420-12870439 Msa0349350:CDS 55.0%
GGAAGTGGCAACAACGGCAA+GGG - chr3_1:12870421-12870440 Msa0349350:CDS 55.0%
CATCATGGATGAGGAGGAGG+AGG + chr3_1:12871033-12871052 None:intergenic 55.0%
CAGCATCATGGATGAGGAGG+AGG + chr3_1:12871036-12871055 None:intergenic 55.0%
GAGGAGGAGGAGAGTAGTGG+TGG + chr3_1:12870999-12871018 None:intergenic 60.0%
GAGGAGGAGGAGGAGAGTAG+TGG + chr3_1:12871002-12871021 None:intergenic 60.0%
GGATGAGGAGGAGGAGGAGA+CGG + chr3_1:12871027-12871046 None:intergenic 60.0%
GAGGAGGAGGAGAGTAGTGG+TGG + chr3_1:12870999-12871018 None:intergenic 60.0%
GAGGAGGAGGAGGAGAGTAG+TGG + chr3_1:12871002-12871021 None:intergenic 60.0%
GGATGAGGAGGAGGAGGAGA+CGG + chr3_1:12871027-12871046 None:intergenic 60.0%
!! CAACGGCAAGGGTACCACCG+TGG - chr3_1:12870432-12870451 Msa0349350:CDS 65.0%
GGAGAGTAGTGGTGGCCGTG+TGG + chr3_1:12870991-12871010 None:intergenic 65.0%
!! CAACGGCAAGGGTACCACCG+TGG - chr3_1:12870432-12870451 Msa0349350:CDS 65.0%
GGAGAGTAGTGGTGGCCGTG+TGG + chr3_1:12870991-12871010 None:intergenic 65.0%
GGAGACGGACGAGGAGGAGG+AGG + chr3_1:12871012-12871031 None:intergenic 70.0%
GGAGGAGACGGACGAGGAGG+AGG + chr3_1:12871015-12871034 None:intergenic 70.0%
GGAGGAGGAGACGGACGAGG+AGG + chr3_1:12871018-12871037 None:intergenic 70.0%
GGAGGAGGAGGAGACGGACG+AGG + chr3_1:12871021-12871040 None:intergenic 70.0%
GGAGACGGACGAGGAGGAGG+AGG + chr3_1:12871012-12871031 None:intergenic 70.0%
GGAGGAGACGGACGAGGAGG+AGG + chr3_1:12871015-12871034 None:intergenic 70.0%
GGAGGAGGAGACGGACGAGG+AGG + chr3_1:12871018-12871037 None:intergenic 70.0%
GGAGGAGGAGGAGACGGACG+AGG + chr3_1:12871021-12871040 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 12870176 12871286 12870176 ID=Msa0349350;Name=Msa0349350
chr3_1 mRNA 12870176 12871286 12870176 ID=Msa0349350-mRNA-1;Parent=Msa0349350;Name=Msa0349350-mRNA-1;_AED=0.32;_eAED=0.32;_QI=180|1|1|1|0|0|2|236|72
chr3_1 exon 12870176 12870506 12870176 ID=Msa0349350-mRNA-1:exon:3299;Parent=Msa0349350-mRNA-1
chr3_1 exon 12870983 12871286 12870983 ID=Msa0349350-mRNA-1:exon:3298;Parent=Msa0349350-mRNA-1
chr3_1 five_prime_UTR 12871107 12871286 12871107 ID=Msa0349350-mRNA-1:five_prime_utr;Parent=Msa0349350-mRNA-1
chr3_1 CDS 12870983 12871106 12870983 ID=Msa0349350-mRNA-1:cds;Parent=Msa0349350-mRNA-1
chr3_1 CDS 12870412 12870506 12870412 ID=Msa0349350-mRNA-1:cds;Parent=Msa0349350-mRNA-1
chr3_1 three_prime_UTR 12870176 12870411 12870176 ID=Msa0349350-mRNA-1:three_prime_utr;Parent=Msa0349350-mRNA-1
Gene Sequence

>Msa0349350

ATGGCTTATTTTAAGGTGGTTATATTGAACCTGGCTTTGCTGTTTGTGATTATTATCTTGTTATTGGAAGTGGCAACAACGGCAAGGGTACCACCGTGGAAAATTGAGCCTCATCACAAAACAAATGGACGCCTACTTTATATTGTTGATGATGTTCCACACGGCCACCACTACTCTCCTCCTCCTCCTCGTCCGTCTCCTCCTCCTCCTCATCCATGA
Protein sequence

>Msa0349350

MAYFKVVILNLALLFVIIILLLEVATTARVPPWKIEPHHKTNGRLLYIVDDVPHGHHYSPPPPRPSPPPPHP*