AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0026430


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0026430 MtrunA17_Chr1g0153761 100.000 108 0 0 1 108 1 108 1.54e-74 223
Msa0026430 MtrunA17_Chr2g0284651 99.048 105 0 1 4 108 1 104 7.30e-70 211
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0026430 AT5G23540.1 93.333 105 5 2 4 108 1 103 2.61e-63 194
Msa0026430 AT5G23540.2 100.000 54 0 0 55 108 1 54 4.04e-32 113

Find 35 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATCAAAACGCAAACTTTA+CGG 0.279197 1_1:+50287945 None:intergenic
GAAGTTATGGGTTTAATGTT+GGG 0.324843 1_1:+50288374 Msa0026430:CDS
TGGTGTACCTATGGAAGTTA+TGG 0.339817 1_1:+50288361 Msa0026430:CDS
GGAAGTTATGGGTTTAATGT+TGG 0.366620 1_1:+50288373 Msa0026430:CDS
AAACTTGCTCAGATGAATCT+AGG 0.385066 1_1:-50288181 None:intergenic
CTTGATATGTTGAAACAAAC+TGG 0.388419 1_1:+50288506 Msa0026430:CDS
GGTGTACCTATGGAAGTTAT+GGG 0.391133 1_1:+50288362 Msa0026430:CDS
TCGTTGATGAGTATACTGTT+AGG 0.407413 1_1:+50288402 Msa0026430:CDS
CAAAGAATGTTTGCGGGTGC+AGG 0.429014 1_1:+50288119 Msa0026430:CDS
CGTTGATGAGTATACTGTTA+GGG 0.432147 1_1:+50288403 Msa0026430:CDS
TTGGTGAATTTAGGTAGGGC+TGG 0.447981 1_1:+50288341 Msa0026430:intron
CTTTGTTAACAAGTTAAGAA+TGG 0.451674 1_1:-50288035 None:intergenic
GCTATGCCTCAGAGTGGTAC+TGG 0.454847 1_1:+50288440 Msa0026430:CDS
AGACTTCAAAGAATGTTTGC+GGG 0.454988 1_1:+50288113 Msa0026430:CDS
TTAACTTGTTAACAAAGAAA+AGG 0.458570 1_1:+50288041 Msa0026430:five_prime_UTR
AACAACAACCATGTCAGGTA+TGG 0.489135 1_1:+50288088 Msa0026430:exon
TGCTCAGATGAATCTAGGGT+GGG 0.502945 1_1:-50288176 None:intergenic
AGGTAGGGCTGGTGTACCTA+TGG 0.507375 1_1:+50288352 Msa0026430:intron
GCGGGTGCAGGTGGAGCACT+CGG 0.510885 1_1:+50288131 Msa0026430:CDS
TCGATAACAACAACCATGTC+AGG 0.518171 1_1:+50288083 Msa0026430:exon
AGAATGTTTGCGGGTGCAGG+TGG 0.533259 1_1:+50288122 Msa0026430:CDS
GCTCAGATGAATCTAGGGTG+GGG 0.536007 1_1:-50288175 None:intergenic
AACTTGCTCAGATGAATCTA+GGG 0.538949 1_1:-50288180 None:intergenic
AAGTTATGGGTTTAATGTTG+GGG 0.546173 1_1:+50288375 Msa0026430:CDS
AAGACTTCAAAGAATGTTTG+CGG 0.555255 1_1:+50288112 Msa0026430:CDS
CTCAGATGAATCTAGGGTGG+GGG 0.560533 1_1:-50288174 None:intergenic
ATTAAACCCATAACTTCCAT+AGG 0.562193 1_1:-50288368 None:intergenic
AAGTCTTTCCATACCTGACA+TGG 0.565400 1_1:-50288096 None:intergenic
ATATGTTGAAACAAACTGGA+AGG 0.596652 1_1:+50288510 Msa0026430:CDS
CTTCTCAAAATGCTCAAACA+TGG 0.601308 1_1:+50288221 Msa0026430:CDS
TTGCTCAGATGAATCTAGGG+TGG 0.606378 1_1:-50288177 None:intergenic
ACTCGGCGGTCATCCACCAC+CGG 0.646687 1_1:+50288148 Msa0026430:CDS
AGTTATGGGTTTAATGTTGG+GGG 0.647215 1_1:+50288376 Msa0026430:CDS
GGTGCAGGTGGAGCACTCGG+CGG 0.713068 1_1:+50288134 Msa0026430:CDS
CTAACACCAGTACCACTCTG+AGG 0.717528 1_1:-50288446 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAGGGTTTAAAAAATTT+GGG - chr1_1:50288305-50288324 None:intergenic 15.0%
!! AAATTAGGGTTTAAAAAATT+TGG - chr1_1:50288306-50288325 None:intergenic 15.0%
!!! TTTAAACCCTAATTTTTTAT+TGG + chr1_1:50288311-50288330 Msa0026430:intron 15.0%
!!! TTAAACCCTAATTTTTTATT+GGG + chr1_1:50288312-50288331 Msa0026430:intron 15.0%
!! AAAATCCCAATAAAAAATTA+GGG - chr1_1:50288320-50288339 None:intergenic 15.0%
!! AAAAATCCCAATAAAAAATT+AGG - chr1_1:50288321-50288340 None:intergenic 15.0%
!!! ATTTTTTATTGGGATTTTTT+TGG + chr1_1:50288322-50288341 Msa0026430:intron 15.0%
!!! TTAACTTGTTAACAAAGAAA+AGG + chr1_1:50288041-50288060 Msa0026430:five_prime_UTR 20.0%
!! ATTAGGGTTTAAAAAATTTG+GGG - chr1_1:50288304-50288323 None:intergenic 20.0%
! CTTTGTTAACAAGTTAAGAA+TGG - chr1_1:50288038-50288057 None:intergenic 25.0%
! TATCGACAATTGATGAAAAA+TGG - chr1_1:50288069-50288088 None:intergenic 25.0%
! TTAGGGTTTAAAAAATTTGG+GGG - chr1_1:50288303-50288322 None:intergenic 25.0%
!!! TTTTTTTGGTGAATTTAGGT+AGG + chr1_1:50288336-50288355 Msa0026430:intron 25.0%
!!! TTTTTTGGTGAATTTAGGTA+GGG + chr1_1:50288337-50288356 Msa0026430:intron 25.0%
AAGACTTCAAAGAATGTTTG+CGG + chr1_1:50288112-50288131 Msa0026430:CDS 30.0%
GGTATGAGAAATTGAATGAA+GGG - chr1_1:50288282-50288301 None:intergenic 30.0%
!!! GGGATTTTTTTGGTGAATTT+AGG + chr1_1:50288332-50288351 Msa0026430:intron 30.0%
ATTAAACCCATAACTTCCAT+AGG - chr1_1:50288371-50288390 None:intergenic 30.0%
GAAGTTATGGGTTTAATGTT+GGG + chr1_1:50288374-50288393 Msa0026430:CDS 30.0%
AAGTTATGGGTTTAATGTTG+GGG + chr1_1:50288375-50288394 Msa0026430:CDS 30.0%
CTTGATATGTTGAAACAAAC+TGG + chr1_1:50288506-50288525 Msa0026430:CDS 30.0%
AGACTTCAAAGAATGTTTGC+GGG + chr1_1:50288113-50288132 Msa0026430:CDS 35.0%
! AACTTGCTCAGATGAATCTA+GGG - chr1_1:50288183-50288202 None:intergenic 35.0%
! AAACTTGCTCAGATGAATCT+AGG - chr1_1:50288184-50288203 None:intergenic 35.0%
CTTCTCAAAATGCTCAAACA+TGG + chr1_1:50288221-50288240 Msa0026430:CDS 35.0%
GGGTATGAGAAATTGAATGA+AGG - chr1_1:50288283-50288302 None:intergenic 35.0%
GGAAGTTATGGGTTTAATGT+TGG + chr1_1:50288373-50288392 Msa0026430:CDS 35.0%
AGTTATGGGTTTAATGTTGG+GGG + chr1_1:50288376-50288395 Msa0026430:CDS 35.0%
! TCGTTGATGAGTATACTGTT+AGG + chr1_1:50288402-50288421 Msa0026430:CDS 35.0%
! CGTTGATGAGTATACTGTTA+GGG + chr1_1:50288403-50288422 Msa0026430:CDS 35.0%
TCGATAACAACAACCATGTC+AGG + chr1_1:50288083-50288102 Msa0026430:exon 40.0%
AACAACAACCATGTCAGGTA+TGG + chr1_1:50288088-50288107 Msa0026430:exon 40.0%
AAGTCTTTCCATACCTGACA+TGG - chr1_1:50288099-50288118 None:intergenic 40.0%
!! GAGCATTTTGAGAAGAGCAA+GGG - chr1_1:50288216-50288235 None:intergenic 40.0%
!! TGAGCATTTTGAGAAGAGCA+AGG - chr1_1:50288217-50288236 None:intergenic 40.0%
TGGTGTACCTATGGAAGTTA+TGG + chr1_1:50288361-50288380 Msa0026430:CDS 40.0%
GGTGTACCTATGGAAGTTAT+GGG + chr1_1:50288362-50288381 Msa0026430:CDS 40.0%
GAGAAGACAAAAACGCAGGA+TGG - chr1_1:50287983-50288002 None:intergenic 45.0%
CTGAGAGAAGACAAAAACGC+AGG - chr1_1:50287987-50288006 None:intergenic 45.0%
! TGCTCAGATGAATCTAGGGT+GGG - chr1_1:50288179-50288198 None:intergenic 45.0%
TTGCTCAGATGAATCTAGGG+TGG - chr1_1:50288180-50288199 None:intergenic 45.0%
TTGGTGAATTTAGGTAGGGC+TGG + chr1_1:50288341-50288360 Msa0026430:intron 45.0%
!! GTTTTTGCTATGCCTCAGAG+TGG + chr1_1:50288434-50288453 Msa0026430:CDS 45.0%
CAAAGAATGTTTGCGGGTGC+AGG + chr1_1:50288119-50288138 Msa0026430:CDS 50.0%
! CTCAGATGAATCTAGGGTGG+GGG - chr1_1:50288177-50288196 None:intergenic 50.0%
! GCTCAGATGAATCTAGGGTG+GGG - chr1_1:50288178-50288197 None:intergenic 50.0%
CTAACACCAGTACCACTCTG+AGG - chr1_1:50288449-50288468 None:intergenic 50.0%
AGAATGTTTGCGGGTGCAGG+TGG + chr1_1:50288122-50288141 Msa0026430:CDS 55.0%
! GAATCTAGGGTGGGGGAATC+CGG - chr1_1:50288170-50288189 None:intergenic 55.0%
! AGGTAGGGCTGGTGTACCTA+TGG + chr1_1:50288352-50288371 Msa0026430:intron 55.0%
GCTATGCCTCAGAGTGGTAC+TGG + chr1_1:50288440-50288459 Msa0026430:CDS 55.0%
ACTCGGCGGTCATCCACCAC+CGG + chr1_1:50288148-50288167 Msa0026430:CDS 65.0%
! TCTAGGGTGGGGGAATCCGG+TGG - chr1_1:50288167-50288186 None:intergenic 65.0%
! GCGGGTGCAGGTGGAGCACT+CGG + chr1_1:50288131-50288150 Msa0026430:CDS 70.0%
! GGTGCAGGTGGAGCACTCGG+CGG + chr1_1:50288134-50288153 Msa0026430:CDS 70.0%
AGGGTGGGGGAATCCGGTGG+TGG - chr1_1:50288164-50288183 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 50287949 50288532 50287949 ID=Msa0026430;Name=Msa0026430
chr1_1 mRNA 50287949 50288532 50287949 ID=Msa0026430-mRNA-1;Parent=Msa0026430;Name=Msa0026430-mRNA-1;_AED=0.00;_eAED=0.00;_QI=149|1|0.5|1|1|1|2|0|108
chr1_1 exon 50287949 50288242 50287949 ID=Msa0026430-mRNA-1:exon:14600;Parent=Msa0026430-mRNA-1
chr1_1 exon 50288354 50288532 50288354 ID=Msa0026430-mRNA-1:exon:14601;Parent=Msa0026430-mRNA-1
chr1_1 five_prime_UTR 50287949 50288097 50287949 ID=Msa0026430-mRNA-1:five_prime_utr;Parent=Msa0026430-mRNA-1
chr1_1 CDS 50288098 50288242 50288098 ID=Msa0026430-mRNA-1:cds;Parent=Msa0026430-mRNA-1
chr1_1 CDS 50288354 50288532 50288354 ID=Msa0026430-mRNA-1:cds;Parent=Msa0026430-mRNA-1
Gene Sequence

>Msa0026430

ATGTCAGGTATGGAAAGACTTCAAAGAATGTTTGCGGGTGCAGGTGGAGCACTCGGCGGTCATCCACCACCGGATTCCCCCACCCTAGATTCATCTGAGCAAGTTTACATCTCTTCCCTTGCTCTTCTCAAAATGCTCAAACATGGTAGGGCTGGTGTACCTATGGAAGTTATGGGTTTAATGTTGGGGGAGTTCGTTGATGAGTATACTGTTAGGGTTGTTGATGTTTTTGCTATGCCTCAGAGTGGTACTGGTGTTAGTGTTGAAGCTGTTGATCATGTTTTTCAAACTAACATGCTTGATATGTTGAAACAAACTGGAAGG

Protein sequence

>Msa0026430

MSGMERLQRMFAGAGGALGGHPPPDSPTLDSSEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVRVVDVFAMPQSGTGVSVEAVDHVFQTNMLDMLKQTGR