AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0145430


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0145430 MtrunA17_Chr1g0152341 91.667 156 5 2 1 153 10 160 1.10e-90 260
Msa0145430 MtrunA17_Chr3g0134971 57.325 157 52 5 2 154 13 158 5.95e-49 155
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0145430 AT1G10140.1 46.753 154 73 5 2 147 8 160 3.04e-23 90.1
Msa0145430 AT1G58420.1 43.976 166 75 4 2 150 11 175 1.49e-20 83.6

Find 20 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTGCTTCTGCTAGAACTTT+AGG 0.258479 1_4:+5099318 Msa0145430:CDS
CAACAACAGAAATTGAATAA+AGG 0.334932 1_4:+5099378 Msa0145430:CDS
AACAACAGAAATTGAATAAA+GGG 0.384474 1_4:+5099379 Msa0145430:CDS
TCTAGTGTTGAAGGAAAAGT+TGG 0.393697 1_4:+5099459 Msa0145430:CDS
ACAGCATAACTCTTTGATCT+AGG 0.434486 1_4:-5099501 None:intergenic
AAGATCATCAGCATCATTAG+AGG 0.441233 1_4:+5099266 Msa0145430:CDS
TGTGGTCAAAATATGAGTTA+TGG 0.456641 1_4:+5099162 Msa0145430:CDS
CCTTCAACACTAGAATCAAA+AGG 0.478362 1_4:-5099450 None:intergenic
TTTAGGTAATAGAATTGATG+TGG 0.523602 1_4:+5099335 Msa0145430:CDS
AATTTACTAGCAGCATCCAT+TGG 0.526181 1_4:-5099192 None:intergenic
TTACCTAAGTCTAGTAGTGT+TGG 0.528478 1_4:+5099402 Msa0145430:CDS
ATTCCAACACTACTAGACTT+AGG 0.543949 1_4:-5099405 None:intergenic
TAAGTCTAGTAGTGTTGGAA+TGG 0.550381 1_4:+5099407 Msa0145430:CDS
AGATCAAAGAGTTATGCTGT+TGG 0.581741 1_4:+5099504 Msa0145430:CDS
TGTTCACCAATAAGAGCACT+AGG 0.583455 1_4:+5099102 Msa0145430:CDS
GAGTTATGGAAGTTATCCAA+TGG 0.620886 1_4:+5099176 Msa0145430:CDS
AGATCATCAGCATCATTAGA+GGG 0.626119 1_4:+5099267 Msa0145430:CDS
AGAACCAAAACATGTTTGTG+AGG 0.637515 1_4:+5099073 None:intergenic
TGGAATGGCTAAGATTGATG+AGG 0.704946 1_4:+5099422 Msa0145430:CDS
GTAAGAAGCATAACAAACTG+TGG 0.710541 1_4:+5099144 Msa0145430:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAACAGAAATTGAATAAA+GGG + chr1_4:5099379-5099398 Msa0145430:CDS 20.0%
! TTTAGGTAATAGAATTGATG+TGG + chr1_4:5099335-5099354 Msa0145430:CDS 25.0%
! CAACAACAGAAATTGAATAA+AGG + chr1_4:5099378-5099397 Msa0145430:CDS 25.0%
TGTGGTCAAAATATGAGTTA+TGG + chr1_4:5099162-5099181 Msa0145430:CDS 30.0%
! GTAAGAAGCATAACAAACTG+TGG + chr1_4:5099144-5099163 Msa0145430:CDS 35.0%
GAGTTATGGAAGTTATCCAA+TGG + chr1_4:5099176-5099195 Msa0145430:CDS 35.0%
AATTTACTAGCAGCATCCAT+TGG - chr1_4:5099195-5099214 None:intergenic 35.0%
AAGATCATCAGCATCATTAG+AGG + chr1_4:5099266-5099285 Msa0145430:CDS 35.0%
AGATCATCAGCATCATTAGA+GGG + chr1_4:5099267-5099286 Msa0145430:CDS 35.0%
TTACCTAAGTCTAGTAGTGT+TGG + chr1_4:5099402-5099421 Msa0145430:CDS 35.0%
ATTCCAACACTACTAGACTT+AGG - chr1_4:5099408-5099427 None:intergenic 35.0%
! TAAGTCTAGTAGTGTTGGAA+TGG + chr1_4:5099407-5099426 Msa0145430:CDS 35.0%
CCTTCAACACTAGAATCAAA+AGG - chr1_4:5099453-5099472 None:intergenic 35.0%
!! CCTTTTGATTCTAGTGTTGA+AGG + chr1_4:5099450-5099469 Msa0145430:CDS 35.0%
! TCTAGTGTTGAAGGAAAAGT+TGG + chr1_4:5099459-5099478 Msa0145430:CDS 35.0%
ACAGCATAACTCTTTGATCT+AGG - chr1_4:5099504-5099523 None:intergenic 35.0%
AGATCAAAGAGTTATGCTGT+TGG + chr1_4:5099504-5099523 Msa0145430:CDS 35.0%
!! TGTTCACCAATAAGAGCACT+AGG + chr1_4:5099102-5099121 Msa0145430:CDS 40.0%
! GCTTTTCCTAGTGCTCTTAT+TGG - chr1_4:5099111-5099130 None:intergenic 40.0%
TGGAATGGCTAAGATTGATG+AGG + chr1_4:5099422-5099441 Msa0145430:CDS 40.0%
GCTGCTTCTGCTAGAACTTT+AGG + chr1_4:5099318-5099337 Msa0145430:CDS 45.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 5099084 5099554 5099084 ID=Msa0145430;Name=Msa0145430
chr1_4 mRNA 5099084 5099554 5099084 ID=Msa0145430-mRNA-1;Parent=Msa0145430;Name=Msa0145430-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|-1|0|1|-1|1|1|0|156
chr1_4 exon 5099084 5099554 5099084 ID=Msa0145430-mRNA-1:exon:2113;Parent=Msa0145430-mRNA-1
chr1_4 CDS 5099084 5099554 5099084 ID=Msa0145430-mRNA-1:cds;Parent=Msa0145430-mRNA-1
Gene Sequence

>Msa0145430

ATGTTTGTGAGGATCATGTGTTCACCAATAAGAGCACTAGGAAAAGCAAGAGATGCATACGTAAGAAGCATAACAAACTGTGGTCAAAATATGAGTTATGGAAGTTATCCAATGGATGCTGCTAGTAAATTTTCTTTATCAAGAAGTCAAAGTGCAGCAACATCAAGAAGATCATCATCAAGAAGATCATCAGCATCATTAGAGGGTAATGAAGATTTTGCTGAGCTTGTTAGAGCTGCTTCTGCTAGAACTTTAGGTAATAGAATTGATGTGGATTTAGTTCTCAAACAACAACAACAACAGAAATTGAATAAAGGGTTACCTAAGTCTAGTAGTGTTGGAATGGCTAAGATTGATGAGGATATGCCTTTTGATTCTAGTGTTGAAGGAAAAGTTGGTTTTGTTGCTGATTCTTATCCTAGATCAAAGAGTTATGCTGTTGGACATAGAAGAAATGTTGTTGCTTTCTGA

Protein sequence

>Msa0145430

MFVRIMCSPIRALGKARDAYVRSITNCGQNMSYGSYPMDAASKFSLSRSQSAATSRRSSSRRSSASLEGNEDFAELVRAASARTLGNRIDVDLVLKQQQQQKLNKGLPKSSSVGMAKIDEDMPFDSSVEGKVGFVADSYPRSKSYAVGHRRNVVAF*