AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0400880


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0400880 MtrunA17_Chr3g0089161 85.437 103 14 1 1 102 1 103 3.85e-49 154
Msa0400880 MtrunA17_Chr3g0089161 92.771 83 4 2 24 104 105 187 2.47e-44 142
Msa0400880 MtrunA17_Chr4g0019291 71.963 107 26 4 1 103 1 107 5.64e-42 133
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0400880 AT1G51400.1 57.407 108 40 3 1 104 1 106 1.49e-30 104
Msa0400880 AT3G21055.1 57.547 106 38 4 1 103 1 102 7.98e-25 90.5
Msa0400880 AT3G21055.2 57.547 106 38 4 1 103 41 142 1.69e-24 90.5

Find 24 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCCTCAATCCTTGGCTTCC+CGG 0.339335 3_2:-25654560 Msa0400880:CDS
GCTTCCCGGCTGTAACCAAC+CGG 0.484721 3_2:-25654546 Msa0400880:CDS
GTTGGCATAGTGACACAAAC+AGG 0.491066 3_2:+25654310 None:intergenic
AATGCTGTCCGAGCAGTTGA+AGG 0.499596 3_2:-25654490 Msa0400880:CDS
GACAACAAGGAGGGAAGTAA+TGG 0.504238 3_2:-25654448 Msa0400880:CDS
ACCATGACATCCTCAATCCT+TGG 0.515033 3_2:-25654568 Msa0400880:CDS
AGCCGGGAAGCCAAGGATTG+AGG 0.543329 3_2:+25654558 None:intergenic
TCTGCGATGCTACGGATGAC+CGG 0.544879 3_2:+25654527 None:intergenic
GAGTTTCCTCTGCGATGCTA+CGG 0.551751 3_2:+25654519 None:intergenic
TGGTTACAGCCGGGAAGCCA+AGG 0.559386 3_2:+25654551 None:intergenic
GATGACCGGTTGGTTACAGC+CGG 0.561463 3_2:+25654541 None:intergenic
ATGCTGTCCGAGCAGTTGAA+GGG 0.565277 3_2:-25654489 Msa0400880:CDS
GCCAAGGATTGAGGATGTCA+TGG 0.568229 3_2:+25654567 None:intergenic
GTGTCACTATGCCAACAGCT+AGG 0.576409 3_2:-25654303 Msa0400880:CDS
TTGCGACAAATCCTAGCTGT+TGG 0.581063 3_2:+25654292 None:intergenic
TGCTGTCCGAGCAGTTGAAG+GGG 0.590682 3_2:-25654488 Msa0400880:CDS
CGATGCTACGGATGACCGGT+TGG 0.597909 3_2:+25654531 None:intergenic
ATCAAATATGACAACAAGGA+GGG 0.605176 3_2:-25654457 Msa0400880:CDS
GCAGATGATGAACCTAAAAG+AGG 0.606913 3_2:-25654361 Msa0400880:CDS
ATGACCGGTTGGTTACAGCC+GGG 0.647755 3_2:+25654542 None:intergenic
ACAAGGAGGGAAGTAATGGA+AGG 0.655922 3_2:-25654444 Msa0400880:CDS
GATCAAATATGACAACAAGG+AGG 0.661670 3_2:-25654458 Msa0400880:CDS
GATGATCAAATATGACAACA+AGG 0.678242 3_2:-25654461 Msa0400880:CDS
GGTCATCCGTAGCATCGCAG+AGG 0.728401 3_2:-25654525 Msa0400880:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GATGATCAAATATGACAACA+AGG - chr3_2:25654407-25654426 Msa0400880:CDS 30.0%
ATCAAATATGACAACAAGGA+GGG - chr3_2:25654411-25654430 Msa0400880:CDS 30.0%
GATCAAATATGACAACAAGG+AGG - chr3_2:25654410-25654429 Msa0400880:CDS 35.0%
!!! ATACTTTTTCTTGGCTTCTG+GGG + chr3_2:25654535-25654554 None:intergenic 35.0%
!!! CATACTTTTTCTTGGCTTCT+GGG + chr3_2:25654536-25654555 None:intergenic 35.0%
!!! AACAGGAGCATACTTTTTCT+TGG + chr3_2:25654544-25654563 None:intergenic 35.0%
GCAGATGATGAACCTAAAAG+AGG - chr3_2:25654507-25654526 Msa0400880:CDS 40.0%
!!! GCATACTTTTTCTTGGCTTC+TGG + chr3_2:25654537-25654556 None:intergenic 40.0%
ACCATGACATCCTCAATCCT+TGG - chr3_2:25654300-25654319 Msa0400880:CDS 45.0%
! TCTTTTCCCCTTCAACTGCT+CGG + chr3_2:25654389-25654408 None:intergenic 45.0%
GACAACAAGGAGGGAAGTAA+TGG - chr3_2:25654420-25654439 Msa0400880:CDS 45.0%
! ACAAGGAGGGAAGTAATGGA+AGG - chr3_2:25654424-25654443 Msa0400880:CDS 45.0%
!!! CACTTTTGCTGGTGTTGCAA+TGG - chr3_2:25654485-25654504 Msa0400880:CDS 45.0%
GTTGGCATAGTGACACAAAC+AGG + chr3_2:25654561-25654580 None:intergenic 45.0%
TTGCGACAAATCCTAGCTGT+TGG + chr3_2:25654579-25654598 None:intergenic 45.0%
GCCAAGGATTGAGGATGTCA+TGG + chr3_2:25654304-25654323 None:intergenic 50.0%
ATCCTCAATCCTTGGCTTCC+CGG - chr3_2:25654308-25654327 Msa0400880:CDS 50.0%
GAGTTTCCTCTGCGATGCTA+CGG + chr3_2:25654352-25654371 None:intergenic 50.0%
AATGCTGTCCGAGCAGTTGA+AGG - chr3_2:25654378-25654397 Msa0400880:CDS 50.0%
ATGCTGTCCGAGCAGTTGAA+GGG - chr3_2:25654379-25654398 Msa0400880:CDS 50.0%
!! GCTGCTGTTTGCACTTTTGC+TGG - chr3_2:25654474-25654493 Msa0400880:CDS 50.0%
!!! GCTTCTGGGGTACCTCTTTT+AGG + chr3_2:25654522-25654541 None:intergenic 50.0%
! GTGTCACTATGCCAACAGCT+AGG - chr3_2:25654565-25654584 Msa0400880:CDS 50.0%
! ATGACCGGTTGGTTACAGCC+GGG + chr3_2:25654329-25654348 None:intergenic 55.0%
! GATGACCGGTTGGTTACAGC+CGG + chr3_2:25654330-25654349 None:intergenic 55.0%
TCTGCGATGCTACGGATGAC+CGG + chr3_2:25654344-25654363 None:intergenic 55.0%
TGCTGTCCGAGCAGTTGAAG+GGG - chr3_2:25654380-25654399 Msa0400880:CDS 55.0%
AGCCGGGAAGCCAAGGATTG+AGG + chr3_2:25654313-25654332 None:intergenic 60.0%
TGGTTACAGCCGGGAAGCCA+AGG + chr3_2:25654320-25654339 None:intergenic 60.0%
GCTTCCCGGCTGTAACCAAC+CGG - chr3_2:25654322-25654341 Msa0400880:CDS 60.0%
CGATGCTACGGATGACCGGT+TGG + chr3_2:25654340-25654359 None:intergenic 60.0%
GGTCATCCGTAGCATCGCAG+AGG - chr3_2:25654343-25654362 Msa0400880:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 25654288 25654602 25654288 ID=Msa0400880;Name=Msa0400880
chr3_2 mRNA 25654288 25654602 25654288 ID=Msa0400880-mRNA-1;Parent=Msa0400880;Name=Msa0400880-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|104
chr3_2 exon 25654288 25654602 25654288 ID=Msa0400880-mRNA-1:exon:5350;Parent=Msa0400880-mRNA-1
chr3_2 CDS 25654288 25654602 25654288 ID=Msa0400880-mRNA-1:cds;Parent=Msa0400880-mRNA-1
Gene Sequence

>Msa0400880

ATGGCATCAATCACCATGACATCCTCAATCCTTGGCTTCCCGGCTGTAACCAACCGGTCATCCGTAGCATCGCAGAGGAAACTCGTCGTCAATGCTGTCCGAGCAGTTGAAGGGGAAAAGATGATCAAATATGACAACAAGGAGGGAAGTAATGGAAGGAGAGACTTGATGTTTGCTGCAGCAGCTGCTGCTGTTTGCACTTTTGCTGGTGTTGCAATGGCAGATGATGAACCTAAAAGAGGTACCCCAGAAGCCAAGAAAAAGTATGCTCCTGTTTGTGTCACTATGCCAACAGCTAGGATTTGTCGCAATTGA

Protein sequence

>Msa0400880

MASITMTSSILGFPAVTNRSSVASQRKLVVNAVRAVEGEKMIKYDNKEGSNGRRDLMFAAAAAAVCTFAGVAMADDEPKRGTPEAKKKYAPVCVTMPTARICRN*