AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0924840


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0924840 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0924840 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0924840 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0924840 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0924840 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0924840 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0924840 MtrunA17_Chr6g0451331 90.323 31 3 0 24 54 41 71 5.28e-14 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0924840 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0924840 ATCG00560.1 97.297 37 1 0 68 104 2 38 3.75e-19 73.9

Find 27 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTTAGCTTACGATGTATT+TGG 0.244623 6_2:+67449912 Msa0924840:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 6_2:-67450174 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 6_2:-67449878 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 6_2:+67449829 Msa0924840:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 6_2:+67449777 Msa0924840:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 6_2:+67449870 Msa0924840:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 6_2:-67449877 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 6_2:+67450232 Msa0924840:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 6_2:-67449945 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 6_2:-67450180 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 6_2:-67449835 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 6_2:+67449786 Msa0924840:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 6_2:-67450163 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 6_2:+67450233 Msa0924840:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 6_2:+67449761 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 6_2:+67449891 Msa0924840:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 6_2:-67449940 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 6_2:-67449939 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 6_2:+67449890 Msa0924840:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 6_2:+67449874 Msa0924840:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 6_2:-67449941 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 6_2:-67450241 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 6_2:+67449768 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 6_2:+67449869 Msa0924840:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 6_2:-67449873 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 6_2:-67449874 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 6_2:+67450234 Msa0924840:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr6_2:67450022-67450041 Msa0924840:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr6_2:67450212-67450231 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr6_2:67450213-67450232 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr6_2:67449971-67449990 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr6_2:67450025-67450044 Msa0924840:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr6_2:67450126-67450145 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr6_2:67449829-67449848 Msa0924840:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr6_2:67449838-67449857 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr6_2:67449948-67449967 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr6_2:67449972-67449991 Msa0924840:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr6_2:67449998-67450017 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr6_2:67450077-67450096 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr6_2:67449912-67449931 Msa0924840:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr6_2:67449943-67449962 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr6_2:67449944-67449963 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr6_2:67449954-67449973 Msa0924840:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr6_2:67449984-67450003 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr6_2:67450072-67450091 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr6_2:67450072-67450091 Msa0924840:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr6_2:67450078-67450097 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr6_2:67450076-67450095 Msa0924840:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr6_2:67450166-67450185 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr6_2:67450177-67450196 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr6_2:67450183-67450202 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr6_2:67449869-67449888 Msa0924840:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr6_2:67449880-67449899 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr6_2:67449881-67449900 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr6_2:67449942-67449961 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr6_2:67449989-67450008 Msa0924840:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr6_2:67450053-67450072 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr6_2:67450060-67450079 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr6_2:67450116-67450135 Msa0924840:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr6_2:67450122-67450141 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr6_2:67450123-67450142 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr6_2:67450244-67450263 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr6_2:67449870-67449889 Msa0924840:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr6_2:67449890-67449909 Msa0924840:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr6_2:67449891-67449910 Msa0924840:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr6_2:67450045-67450064 Msa0924840:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr6_2:67450115-67450134 Msa0924840:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr6_2:67450232-67450251 Msa0924840:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr6_2:67450233-67450252 Msa0924840:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr6_2:67450234-67450253 Msa0924840:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr6_2:67449876-67449895 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr6_2:67450086-67450105 Msa0924840:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr6_2:67449777-67449796 Msa0924840:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr6_2:67449877-67449896 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr6_2:67449874-67449893 Msa0924840:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr6_2:67450094-67450113 Msa0924840:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr6_2:67449786-67449805 Msa0924840:exon 60.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 67449775 67450308 67449775 ID=Msa0924840;Name=Msa0924840
chr6_2 mRNA 67449775 67450308 67449775 ID=Msa0924840-mRNA-1;Parent=Msa0924840;Name=Msa0924840-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr6_2 exon 67449775 67449952 67449775 ID=Msa0924840-mRNA-1:exon:10681;Parent=Msa0924840-mRNA-1
chr6_2 exon 67450158 67450308 67450158 ID=Msa0924840-mRNA-1:exon:10682;Parent=Msa0924840-mRNA-1
chr6_2 five_prime_UTR 67449775 67449791 67449775 ID=Msa0924840-mRNA-1:five_prime_utr;Parent=Msa0924840-mRNA-1
chr6_2 CDS 67449792 67449952 67449792 ID=Msa0924840-mRNA-1:cds;Parent=Msa0924840-mRNA-1
chr6_2 CDS 67450158 67450308 67450158 ID=Msa0924840-mRNA-1:cds;Parent=Msa0924840-mRNA-1
Gene Sequence

>Msa0924840

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0924840

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN