AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0994370


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0994370 MtrunA17_Chr6g0479131 79.464 112 4 2 4 96 1 112 1.83e-54 164
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 27 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGGTCACCGTTGGGAATTTC+AGG 0.186797 6_4:-69083629 Msa0994370:CDS
GGTTAGGAACTGGTCTTATA+AGG 0.295808 6_4:-69083304 Msa0994370:CDS
CTGAGATAAGACCTGTTCTA+AGG 0.312109 6_4:-69083673 Msa0994370:CDS
TTCACAACTTGACTATGAAT+TGG 0.323676 6_4:+69083743 None:intergenic
CAAGTTCATTGGTGGAGGTT+AGG 0.381608 6_4:-69083320 Msa0994370:intron
ATATGTTTCATCAAGTTCAT+TGG 0.400281 6_4:-69083331 Msa0994370:intron
CTTAGAACAGGTCTTATCTC+AGG 0.409951 6_4:+69083674 None:intergenic
GGATGAAGGTGTTGGACAAA+AGG 0.436976 6_4:-69083771 Msa0994370:CDS
CGAATTTCGCGGTCACCGTT+GGG 0.446075 6_4:-69083638 Msa0994370:CDS
CGCGAAATCTCCCTTAGAAC+AGG 0.449387 6_4:+69083662 None:intergenic
TGTTTCATCAAGTTCATTGG+TGG 0.501550 6_4:-69083328 Msa0994370:intron
TTCATCAAGTTCATTGGTGG+AGG 0.503017 6_4:-69083325 Msa0994370:intron
CATTGGTGGAGGTTAGGAAC+TGG 0.510727 6_4:-69083314 Msa0994370:CDS
GATGAAGGTGTTGGACAAAA+GGG 0.511350 6_4:-69083770 Msa0994370:CDS
TCAGGCCAAGCTATTTCAGT+TGG 0.530276 6_4:-69083611 Msa0994370:intron
AATCACCAACTGAAATAGCT+TGG 0.541732 6_4:+69083606 None:intergenic
AAGAGTAACAAGAAGGATGA+AGG 0.544397 6_4:-69083785 Msa0994370:CDS
AATCAGAGAAAGTATTCGAT+TGG 0.545615 6_4:-69083709 Msa0994370:CDS
GGTCTTATCTCAGGTTTACC+AGG 0.545864 6_4:+69083683 None:intergenic
AAAGTATTCGATTGGTCACC+TGG 0.550724 6_4:-69083701 Msa0994370:CDS
TGAGATAAGACCTGTTCTAA+GGG 0.567147 6_4:-69083672 Msa0994370:CDS
AGATTTCGCGACGAATTTCG+CGG 0.567955 6_4:-69083649 Msa0994370:CDS
AACAAGAAGGATGAAGGTGT+TGG 0.575319 6_4:-69083779 Msa0994370:CDS
GAACATGAAGAGTAACAAGA+AGG 0.578943 6_4:-69083792 Msa0994370:CDS
GGTTTAGTGGGAAAGTTCAA+AGG 0.586118 6_4:-69083265 Msa0994370:CDS
TAGTGGGAAAGTTCAAAGGA+AGG 0.619708 6_4:-69083261 Msa0994370:CDS
GCTTGGCCTGAAATTCCCAA+CGG 0.707149 6_4:+69083623 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAATATATCATGTAAGGTTT+TGG - chr6_4:69083480-69083499 Msa0994370:intron 25.0%
! TATCTCTGATTAAAAAACAG+AGG + chr6_4:69083588-69083607 None:intergenic 25.0%
! ATATGTTTCATCAAGTTCAT+TGG - chr6_4:69083722-69083741 Msa0994370:CDS 25.0%
!! TAAGGTTTCTCAATTTTGAA+TGG - chr6_4:69083767-69083786 Msa0994370:CDS 25.0%
!! TCAATTTTGAATGGTTTAGT+GGG - chr6_4:69083776-69083795 Msa0994370:CDS 25.0%
TTCACAACTTGACTATGAAT+TGG + chr6_4:69083313-69083332 None:intergenic 30.0%
!! AATCAGAGAAAGTATTCGAT+TGG - chr6_4:69083344-69083363 Msa0994370:intron 30.0%
GAGGAAGAATATATCATGTA+AGG - chr6_4:69083474-69083493 Msa0994370:intron 30.0%
! ATGATGATGATGATGATGTA+TGG - chr6_4:69083512-69083531 Msa0994370:intron 30.0%
! CTCAATTTTGAATGGTTTAG+TGG - chr6_4:69083775-69083794 Msa0994370:CDS 30.0%
GAACATGAAGAGTAACAAGA+AGG - chr6_4:69083261-69083280 Msa0994370:CDS 35.0%
AAGAGTAACAAGAAGGATGA+AGG - chr6_4:69083268-69083287 Msa0994370:CDS 35.0%
TGAGATAAGACCTGTTCTAA+GGG - chr6_4:69083381-69083400 Msa0994370:intron 35.0%
AATCACCAACTGAAATAGCT+TGG + chr6_4:69083450-69083469 None:intergenic 35.0%
!! TTTCAGTTGGTGATTCATAG+AGG - chr6_4:69083455-69083474 Msa0994370:intron 35.0%
ATGATGTATGGAGATTGTAG+AGG - chr6_4:69083524-69083543 Msa0994370:intron 35.0%
TGATGTATGGAGATTGTAGA+GGG - chr6_4:69083525-69083544 Msa0994370:intron 35.0%
GAAAACAGAGAAAGAAACAG+GGG + chr6_4:69083566-69083585 None:intergenic 35.0%
GGAAAACAGAGAAAGAAACA+GGG + chr6_4:69083567-69083586 None:intergenic 35.0%
AGGAAAACAGAGAAAGAAAC+AGG + chr6_4:69083568-69083587 None:intergenic 35.0%
TGTTTCATCAAGTTCATTGG+TGG - chr6_4:69083725-69083744 Msa0994370:CDS 35.0%
! AACAAGAAGGATGAAGGTGT+TGG - chr6_4:69083274-69083293 Msa0994370:CDS 40.0%
!! GATGAAGGTGTTGGACAAAA+GGG - chr6_4:69083283-69083302 Msa0994370:CDS 40.0%
! AAAGTATTCGATTGGTCACC+TGG - chr6_4:69083352-69083371 Msa0994370:intron 40.0%
! CTTAGAACAGGTCTTATCTC+AGG + chr6_4:69083382-69083401 None:intergenic 40.0%
CTGAGATAAGACCTGTTCTA+AGG - chr6_4:69083380-69083399 Msa0994370:intron 40.0%
TTCATCAAGTTCATTGGTGG+AGG - chr6_4:69083728-69083747 Msa0994370:CDS 40.0%
!! GGTTAGGAACTGGTCTTATA+AGG - chr6_4:69083749-69083768 Msa0994370:CDS 40.0%
GGTTTAGTGGGAAAGTTCAA+AGG - chr6_4:69083788-69083807 Msa0994370:CDS 40.0%
TAGTGGGAAAGTTCAAAGGA+AGG - chr6_4:69083792-69083811 Msa0994370:CDS 40.0%
!! GGATGAAGGTGTTGGACAAA+AGG - chr6_4:69083282-69083301 Msa0994370:CDS 45.0%
! GGTCTTATCTCAGGTTTACC+AGG + chr6_4:69083373-69083392 None:intergenic 45.0%
AGATTTCGCGACGAATTTCG+CGG - chr6_4:69083404-69083423 Msa0994370:intron 45.0%
! TCAGGCCAAGCTATTTCAGT+TGG - chr6_4:69083442-69083461 Msa0994370:intron 45.0%
TGTATGGAGATTGTAGAGGG+AGG - chr6_4:69083528-69083547 Msa0994370:intron 45.0%
CAAGTTCATTGGTGGAGGTT+AGG - chr6_4:69083733-69083752 Msa0994370:CDS 45.0%
CGCGAAATCTCCCTTAGAAC+AGG + chr6_4:69083394-69083413 None:intergenic 50.0%
GCTTGGCCTGAAATTCCCAA+CGG + chr6_4:69083433-69083452 None:intergenic 50.0%
CATTGGTGGAGGTTAGGAAC+TGG - chr6_4:69083739-69083758 Msa0994370:CDS 50.0%
ACGAATTTCGCGGTCACCGT+TGG - chr6_4:69083414-69083433 Msa0994370:intron 55.0%
CGAATTTCGCGGTCACCGTT+GGG - chr6_4:69083415-69083434 Msa0994370:intron 55.0%
CGGTCACCGTTGGGAATTTC+AGG - chr6_4:69083424-69083443 Msa0994370:intron 55.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 69083256 69083819 69083256 ID=Msa0994370;Name=Msa0994370
chr6_4 mRNA 69083256 69083819 69083256 ID=Msa0994370-mRNA-1;Parent=Msa0994370;Name=Msa0994370-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|0|0|1|0|0.5|2|0|96
chr6_4 exon 69083612 69083819 69083612 ID=Msa0994370-mRNA-1:exon:12727;Parent=Msa0994370-mRNA-1
chr6_4 exon 69083256 69083338 69083256 ID=Msa0994370-mRNA-1:exon:12726;Parent=Msa0994370-mRNA-1
chr6_4 CDS 69083612 69083819 69083612 ID=Msa0994370-mRNA-1:cds;Parent=Msa0994370-mRNA-1
chr6_4 CDS 69083256 69083338 69083256 ID=Msa0994370-mRNA-1:cds;Parent=Msa0994370-mRNA-1
Gene Sequence

>Msa0994370

ATGAAGAACATGAAGAGTAACAAGAAGGATGAAGGTGTTGGACAAAAGGGTATTCCAATTCATAGTCAAGTTGTGAAGATCAAGCAAGAATCAGAGAAAGTATTCGATTGGTCACCTGGTAAACCTGAGATAAGACCTGTTCTAAGGGAGATTTCGCGACGAATTTCGCGGTCACCGTTGGGAATTTCAGGCCAAGCTATTTCAGTTGTTCATTGGTGGAGGTTAGGAACTGGTCTTATAAGGTTTCTCAATTTTGAATGGTTTAGTGGGAAAGTTCAAAGGAAGGACTAG

Protein sequence

>Msa0994370

MKNMKSNKKDEGVGQKGIPIHSQVVKIKQESEKVFDWSPGKPEIRPVLREISRRISRSPLGISGQAISVVHWWRLGTGLIRFLNFEWFSGKVQRKD*