AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0711000

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 128 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAGCAATGCCAAGGAAAT+TGG 0.216340 5_1:+2883927 Msa0711000:CDS
CCATCACTAGAATTATAAAT+TGG 0.248930 5_1:+2884227 Msa0711000:three_prime_UTR
CAAGGAAATTGGCTTCATTA+AGG 0.318093 5_1:+2883938 Msa0711000:CDS
TCATGGGTCACTCCAACGTT+TGG 0.416385 5_1:+2883204 None:intergenic
GAACCAGGACCATAGGTCTT+GGG 0.430692 5_1:-2883236 None:intergenic
CTTAATGAAGCCAATTTCCT+TGG 0.435363 5_1:-2883937 None:intergenic
AAACATATTTACTTCCTACT+TGG 0.442515 5_1:+2884178 Msa0711000:three_prime_UTR
AGAACCAGGACCATAGGTCT+TGG 0.460388 5_1:-2883237 None:intergenic
ATTTACTTCCTACTTGGTTG+TGG 0.464265 5_1:+2884184 Msa0711000:three_prime_UTR
TAGAATTATAAATTGGATGT+TGG 0.488440 5_1:+2884234 Msa0711000:three_prime_UTR
TTCTAGTTAAAAGCTTAGAA+AGG 0.488648 5_1:-2884305 None:intergenic
CACCCCAAGACCTATGGTCC+TGG 0.491604 5_1:+2883233 Msa0711000:CDS
TTCAATAACTAAAATCATCC+TGG 0.492527 5_1:-2884088 None:intergenic
CCAATTTATAATTCTAGTGA+TGG 0.495729 5_1:-2884227 None:intergenic
AACTCTCACCCCAAGACCTA+TGG 0.505813 5_1:+2883227 Msa0711000:CDS
CCGAGCTGCAAAACGATGCC+AGG 0.511058 5_1:+2884070 Msa0711000:CDS
GATGTTGGCATCTTTGTGCA+TGG 0.537643 5_1:+2884249 Msa0711000:three_prime_UTR
CATGGATTGATCAGGAAGTA+CGG 0.572937 5_1:+2883879 Msa0711000:intron
TGTGCGAGAACCAGGACCAT+AGG 0.585453 5_1:-2883243 None:intergenic
CAATTTCCTTGGCATTGCTG+TGG 0.593734 5_1:-2883926 None:intergenic
CAACAACTCCACAACCAAGT+AGG 0.594310 5_1:-2884192 None:intergenic
AACCAGGACCATAGGTCTTG+GGG 0.607026 5_1:-2883235 None:intergenic
GTGCTTCCACAGCAATGCCA+AGG 0.623139 5_1:+2883920 Msa0711000:CDS
GGGGTGAGAGTTCCAAACGT+TGG 0.647246 5_1:-2883216 None:intergenic
TCTCCAGTCGATCAAAACCG+TGG 0.689532 5_1:-2884397 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTTTAATCTTTACAAA+TGG - chr5_1:2884366-2884385 None:intergenic 10.0%
!! TTTGTAAAGATTAAAAAAAT+AGG + chr5_1:2884366-2884385 Msa0711000:three_prime_UTR 10.0%
!! TTGTAAAGATTAAAAAAATA+GGG + chr5_1:2884367-2884386 Msa0711000:three_prime_UTR 10.0%
!!! ATTTTTTTAATCTTTACAAA+TGG - chr5_1:2884366-2884385 None:intergenic 10.0%
!! TTTGTAAAGATTAAAAAAAT+AGG + chr5_1:2884366-2884385 Msa0711000:three_prime_UTR 10.0%
!! TTGTAAAGATTAAAAAAATA+GGG + chr5_1:2884367-2884386 Msa0711000:three_prime_UTR 10.0%
!! TGATTTACTGAAACAAATTT+CGG + chr5_1:2883424-2883443 Msa0711000:intron 20.0%
!!! TCCTACTTTGAAAATAAAAT+GGG + chr5_1:2883584-2883603 Msa0711000:intron 20.0%
!! GTAAAATGATGTGAAAATTA+AGG - chr5_1:2883619-2883638 None:intergenic 20.0%
!! AAACGTTAAAAACAAAGAAT+GGG - chr5_1:2883657-2883676 None:intergenic 20.0%
!! TAGAATTATAAATTGGATGT+TGG + chr5_1:2884234-2884253 Msa0711000:three_prime_UTR 20.0%
!!! ATGATATGTAACTATTTTGT+TGG + chr5_1:2884419-2884438 Msa0711000:three_prime_UTR 20.0%
!! TGATTTACTGAAACAAATTT+CGG + chr5_1:2883424-2883443 Msa0711000:intron 20.0%
!!! TCCTACTTTGAAAATAAAAT+GGG + chr5_1:2883584-2883603 Msa0711000:intron 20.0%
!! GTAAAATGATGTGAAAATTA+AGG - chr5_1:2883619-2883638 None:intergenic 20.0%
!! AAACGTTAAAAACAAAGAAT+GGG - chr5_1:2883657-2883676 None:intergenic 20.0%
!! TAGAATTATAAATTGGATGT+TGG + chr5_1:2884234-2884253 Msa0711000:three_prime_UTR 20.0%
!!! ATGATATGTAACTATTTTGT+TGG + chr5_1:2884419-2884438 Msa0711000:three_prime_UTR 20.0%
! TCATCCAATTAACAATAAGT+TGG - chr5_1:2883407-2883426 None:intergenic 25.0%
!! GTCCTACTTTGAAAATAAAA+TGG + chr5_1:2883583-2883602 Msa0711000:intron 25.0%
!!! TCCCATTTTATTTTCAAAGT+AGG - chr5_1:2883588-2883607 None:intergenic 25.0%
! CAAACGTTAAAAACAAAGAA+TGG - chr5_1:2883658-2883677 None:intergenic 25.0%
!!! TTGTTTTTAACGTTTGTACT+TGG + chr5_1:2883662-2883681 Msa0711000:intron 25.0%
! TTCAATAACTAAAATCATCC+TGG - chr5_1:2884091-2884110 None:intergenic 25.0%
! AAACATATTTACTTCCTACT+TGG + chr5_1:2884178-2884197 Msa0711000:three_prime_UTR 25.0%
! CCAATTTATAATTCTAGTGA+TGG - chr5_1:2884230-2884249 None:intergenic 25.0%
! CCATCACTAGAATTATAAAT+TGG + chr5_1:2884227-2884246 Msa0711000:three_prime_UTR 25.0%
!! TTCTAGTTAAAAGCTTAGAA+AGG - chr5_1:2884308-2884327 None:intergenic 25.0%
! TCATCCAATTAACAATAAGT+TGG - chr5_1:2883407-2883426 None:intergenic 25.0%
!! GTCCTACTTTGAAAATAAAA+TGG + chr5_1:2883583-2883602 Msa0711000:intron 25.0%
!!! TCCCATTTTATTTTCAAAGT+AGG - chr5_1:2883588-2883607 None:intergenic 25.0%
! CAAACGTTAAAAACAAAGAA+TGG - chr5_1:2883658-2883677 None:intergenic 25.0%
!!! TTGTTTTTAACGTTTGTACT+TGG + chr5_1:2883662-2883681 Msa0711000:intron 25.0%
! TTCAATAACTAAAATCATCC+TGG - chr5_1:2884091-2884110 None:intergenic 25.0%
! AAACATATTTACTTCCTACT+TGG + chr5_1:2884178-2884197 Msa0711000:three_prime_UTR 25.0%
! CCAATTTATAATTCTAGTGA+TGG - chr5_1:2884230-2884249 None:intergenic 25.0%
! CCATCACTAGAATTATAAAT+TGG + chr5_1:2884227-2884246 Msa0711000:three_prime_UTR 25.0%
!! TTCTAGTTAAAAGCTTAGAA+AGG - chr5_1:2884308-2884327 None:intergenic 25.0%
GAACACAGTAATCAGAAATA+CGG - chr5_1:2883342-2883361 None:intergenic 30.0%
TGATGAATGACAGTAATCTA+TGG - chr5_1:2883382-2883401 None:intergenic 30.0%
CACACCAACTTATTGTTAAT+TGG + chr5_1:2883400-2883419 Msa0711000:intron 30.0%
! CATTAAGGTGAATATTTTGC+TGG + chr5_1:2883953-2883972 Msa0711000:intron 30.0%
! TGTCTGTTTTATGATGTGAA+TGG + chr5_1:2884272-2884291 Msa0711000:three_prime_UTR 30.0%
GAACACAGTAATCAGAAATA+CGG - chr5_1:2883342-2883361 None:intergenic 30.0%
TGATGAATGACAGTAATCTA+TGG - chr5_1:2883382-2883401 None:intergenic 30.0%
CACACCAACTTATTGTTAAT+TGG + chr5_1:2883400-2883419 Msa0711000:intron 30.0%
! CATTAAGGTGAATATTTTGC+TGG + chr5_1:2883953-2883972 Msa0711000:intron 30.0%
! TGTCTGTTTTATGATGTGAA+TGG + chr5_1:2884272-2884291 Msa0711000:three_prime_UTR 30.0%
GGATCTGAATGAATTAGGAT+CGG - chr5_1:2883464-2883483 None:intergenic 35.0%
GAGTTGGATCTGAATGAATT+AGG - chr5_1:2883469-2883488 None:intergenic 35.0%
! ATTGGTTTCAAGAGTTGAGT+TGG - chr5_1:2883485-2883504 None:intergenic 35.0%
AAGCACATCGAAAAATGCAT+TGG - chr5_1:2883503-2883522 None:intergenic 35.0%
CTTAATGAAGCCAATTTCCT+TGG - chr5_1:2883940-2883959 None:intergenic 35.0%
! CAAGGAAATTGGCTTCATTA+AGG + chr5_1:2883938-2883957 Msa0711000:CDS 35.0%
ATTTACTTCCTACTTGGTTG+TGG + chr5_1:2884184-2884203 Msa0711000:three_prime_UTR 35.0%
AAAAATAGGGAGTTCTTCCA+CGG + chr5_1:2884380-2884399 Msa0711000:three_prime_UTR 35.0%
GGATCTGAATGAATTAGGAT+CGG - chr5_1:2883464-2883483 None:intergenic 35.0%
GAGTTGGATCTGAATGAATT+AGG - chr5_1:2883469-2883488 None:intergenic 35.0%
! ATTGGTTTCAAGAGTTGAGT+TGG - chr5_1:2883485-2883504 None:intergenic 35.0%
AAGCACATCGAAAAATGCAT+TGG - chr5_1:2883503-2883522 None:intergenic 35.0%
CTTAATGAAGCCAATTTCCT+TGG - chr5_1:2883940-2883959 None:intergenic 35.0%
! CAAGGAAATTGGCTTCATTA+AGG + chr5_1:2883938-2883957 Msa0711000:CDS 35.0%
ATTTACTTCCTACTTGGTTG+TGG + chr5_1:2884184-2884203 Msa0711000:three_prime_UTR 35.0%
AAAAATAGGGAGTTCTTCCA+CGG + chr5_1:2884380-2884399 Msa0711000:three_prime_UTR 35.0%
TCGAAGAATCTTACAAGGGT+TGG - chr5_1:2883318-2883337 None:intergenic 40.0%
CGGATCGAAGAATCTTACAA+GGG - chr5_1:2883322-2883341 None:intergenic 40.0%
ACGGATCGAAGAATCTTACA+AGG - chr5_1:2883323-2883342 None:intergenic 40.0%
! TCGATGTGCTTGTACTTTTC+TGG + chr5_1:2883512-2883531 Msa0711000:intron 40.0%
! GAAACTCTCATGGATTGATC+AGG + chr5_1:2883871-2883890 Msa0711000:intron 40.0%
! CATGGATTGATCAGGAAGTA+CGG + chr5_1:2883879-2883898 Msa0711000:intron 40.0%
CATCACTTTCCACTTCTTTC+CGG + chr5_1:2884016-2884035 Msa0711000:intron 40.0%
TCGAAGAATCTTACAAGGGT+TGG - chr5_1:2883318-2883337 None:intergenic 40.0%
CGGATCGAAGAATCTTACAA+GGG - chr5_1:2883322-2883341 None:intergenic 40.0%
ACGGATCGAAGAATCTTACA+AGG - chr5_1:2883323-2883342 None:intergenic 40.0%
! TCGATGTGCTTGTACTTTTC+TGG + chr5_1:2883512-2883531 Msa0711000:intron 40.0%
! GAAACTCTCATGGATTGATC+AGG + chr5_1:2883871-2883890 Msa0711000:intron 40.0%
! CATGGATTGATCAGGAAGTA+CGG + chr5_1:2883879-2883898 Msa0711000:intron 40.0%
CATCACTTTCCACTTCTTTC+CGG + chr5_1:2884016-2884035 Msa0711000:intron 40.0%
ACAGACACGGCTACAAAACA+AGG - chr5_1:2883850-2883869 None:intergenic 45.0%
!! TTGTTTTGTAGCCGTGTCTG+TGG + chr5_1:2883849-2883868 Msa0711000:intron 45.0%
CATGAGAGTTTCCACAGACA+CGG - chr5_1:2883863-2883882 None:intergenic 45.0%
CAATTTCCTTGGCATTGCTG+TGG - chr5_1:2883929-2883948 None:intergenic 45.0%
CACAGCAATGCCAAGGAAAT+TGG + chr5_1:2883927-2883946 Msa0711000:CDS 45.0%
TTTCAGCGATACTGCAACAC+CGG - chr5_1:2884038-2884057 None:intergenic 45.0%
CAACAACTCCACAACCAAGT+AGG - chr5_1:2884195-2884214 None:intergenic 45.0%
GATGTTGGCATCTTTGTGCA+TGG + chr5_1:2884249-2884268 Msa0711000:three_prime_UTR 45.0%
ACAGACACGGCTACAAAACA+AGG - chr5_1:2883850-2883869 None:intergenic 45.0%
!! TTGTTTTGTAGCCGTGTCTG+TGG + chr5_1:2883849-2883868 Msa0711000:intron 45.0%
CATGAGAGTTTCCACAGACA+CGG - chr5_1:2883863-2883882 None:intergenic 45.0%
CAATTTCCTTGGCATTGCTG+TGG - chr5_1:2883929-2883948 None:intergenic 45.0%
CACAGCAATGCCAAGGAAAT+TGG + chr5_1:2883927-2883946 Msa0711000:CDS 45.0%
TTTCAGCGATACTGCAACAC+CGG - chr5_1:2884038-2884057 None:intergenic 45.0%
CAACAACTCCACAACCAAGT+AGG - chr5_1:2884195-2884214 None:intergenic 45.0%
GATGTTGGCATCTTTGTGCA+TGG + chr5_1:2884249-2884268 Msa0711000:three_prime_UTR 45.0%
AACTCTCACCCCAAGACCTA+TGG + chr5_1:2883227-2883246 Msa0711000:CDS 50.0%
AACCAGGACCATAGGTCTTG+GGG - chr5_1:2883238-2883257 None:intergenic 50.0%
GAACCAGGACCATAGGTCTT+GGG - chr5_1:2883239-2883258 None:intergenic 50.0%
AGAACCAGGACCATAGGTCT+TGG - chr5_1:2883240-2883259 None:intergenic 50.0%
CGTGTCTGTGGAAACTCTCA+TGG + chr5_1:2883861-2883880 Msa0711000:intron 50.0%
ACTGCAACACCGGAAAGAAG+TGG - chr5_1:2884028-2884047 None:intergenic 50.0%
!! CTTCCACGGTTTTGATCGAC+TGG + chr5_1:2884394-2884413 Msa0711000:three_prime_UTR 50.0%
TCTCCAGTCGATCAAAACCG+TGG - chr5_1:2884400-2884419 None:intergenic 50.0%
AACTCTCACCCCAAGACCTA+TGG + chr5_1:2883227-2883246 Msa0711000:CDS 50.0%
AACCAGGACCATAGGTCTTG+GGG - chr5_1:2883238-2883257 None:intergenic 50.0%
GAACCAGGACCATAGGTCTT+GGG - chr5_1:2883239-2883258 None:intergenic 50.0%
AGAACCAGGACCATAGGTCT+TGG - chr5_1:2883240-2883259 None:intergenic 50.0%
CGTGTCTGTGGAAACTCTCA+TGG + chr5_1:2883861-2883880 Msa0711000:intron 50.0%
ACTGCAACACCGGAAAGAAG+TGG - chr5_1:2884028-2884047 None:intergenic 50.0%
!! CTTCCACGGTTTTGATCGAC+TGG + chr5_1:2884394-2884413 Msa0711000:three_prime_UTR 50.0%
TCTCCAGTCGATCAAAACCG+TGG - chr5_1:2884400-2884419 None:intergenic 50.0%
GGGGTGAGAGTTCCAAACGT+TGG - chr5_1:2883219-2883238 None:intergenic 55.0%
TGTGCGAGAACCAGGACCAT+AGG - chr5_1:2883246-2883265 None:intergenic 55.0%
! ATGGTCCTGGTTCTCGCACA+TGG + chr5_1:2883246-2883265 Msa0711000:intron 55.0%
GCATACCATGTGCGAGAACC+AGG - chr5_1:2883254-2883273 None:intergenic 55.0%
GTGCTTCCACAGCAATGCCA+AGG + chr5_1:2883920-2883939 Msa0711000:CDS 55.0%
! GCATCGTTTTGCAGCTCGGA+AGG - chr5_1:2884069-2884088 None:intergenic 55.0%
! CCTGGCATCGTTTTGCAGCT+CGG - chr5_1:2884073-2884092 None:intergenic 55.0%
GGGGTGAGAGTTCCAAACGT+TGG - chr5_1:2883219-2883238 None:intergenic 55.0%
TGTGCGAGAACCAGGACCAT+AGG - chr5_1:2883246-2883265 None:intergenic 55.0%
! ATGGTCCTGGTTCTCGCACA+TGG + chr5_1:2883246-2883265 Msa0711000:intron 55.0%
GCATACCATGTGCGAGAACC+AGG - chr5_1:2883254-2883273 None:intergenic 55.0%
GTGCTTCCACAGCAATGCCA+AGG + chr5_1:2883920-2883939 Msa0711000:CDS 55.0%
! GCATCGTTTTGCAGCTCGGA+AGG - chr5_1:2884069-2884088 None:intergenic 55.0%
! CCTGGCATCGTTTTGCAGCT+CGG - chr5_1:2884073-2884092 None:intergenic 55.0%
CACCCCAAGACCTATGGTCC+TGG + chr5_1:2883233-2883252 Msa0711000:CDS 60.0%
CCGAGCTGCAAAACGATGCC+AGG + chr5_1:2884070-2884089 Msa0711000:CDS 60.0%
CACCCCAAGACCTATGGTCC+TGG + chr5_1:2883233-2883252 Msa0711000:CDS 60.0%
CCGAGCTGCAAAACGATGCC+AGG + chr5_1:2884070-2884089 Msa0711000:CDS 60.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 2883206 2884460 2883206 ID=Msa0711000;Name=Msa0711000
chr5_1 mRNA 2883206 2884460 2883206 ID=Msa0711000-mRNA-1;Parent=Msa0711000;Name=Msa0711000-mRNA-1;_AED=0.13;_eAED=0.21;_QI=0|0.5|0.33|1|1|1|3|332|65
chr5_1 exon 2883206 2883254 2883206 ID=Msa0711000-mRNA-1:exon:917;Parent=Msa0711000-mRNA-1
chr5_1 exon 2883893 2883959 2883893 ID=Msa0711000-mRNA-1:exon:918;Parent=Msa0711000-mRNA-1
chr5_1 exon 2884047 2884460 2884047 ID=Msa0711000-mRNA-1:exon:919;Parent=Msa0711000-mRNA-1
chr5_1 CDS 2883206 2883254 2883206 ID=Msa0711000-mRNA-1:cds;Parent=Msa0711000-mRNA-1
chr5_1 CDS 2883893 2883959 2883893 ID=Msa0711000-mRNA-1:cds;Parent=Msa0711000-mRNA-1
chr5_1 CDS 2884047 2884128 2884047 ID=Msa0711000-mRNA-1:cds;Parent=Msa0711000-mRNA-1
chr5_1 three_prime_UTR 2884129 2884460 2884129 ID=Msa0711000-mRNA-1:three_prime_utr;Parent=Msa0711000-mRNA-1
Gene Sequence

>Msa0711000

ATGGGTCACTCCAACGTTTGGAACTCTCACCCCAAGACCTATGGTCCTGGAAGTACGGACTCATGTGTTGCAGACAGTGCTTCCACAGCAATGCCAAGGAAATTGGCTTCATTAAGTATCGCTGAAAAGTTGAGTCCTTCCGAGCTGCAAAACGATGCCAGGATGATTTTAGTTATTGAAGAACTTATAATTTTGTAG
Protein sequence

>Msa0711000

MGHSNVWNSHPKTYGPGSTDSCVADSASTAMPRKLASLSIAEKLSPSELQNDARMILVIEELIIL*