AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0116340

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 19 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAACATTGGGAGGAGGTTT+AGG 0.229380 1_3:+35299528 None:intergenic
CAACATTGGGAGGAGGTTTA+GGG 0.343730 1_3:+35299529 None:intergenic
TGCTTCCATTTAAATGGATC+CGG 0.355242 1_3:-35300061 None:intergenic
CTCACTGCTTAGGCTGAGTT+TGG 0.365834 1_3:+35299456 None:intergenic
CGCATTGTAGCGAGCAACAT+TGG 0.405890 1_3:+35299515 None:intergenic
TGTAACAAACTTGTTACTCT+TGG 0.431039 1_3:+35299479 None:intergenic
AGCTGTAGTCTACAACAGTC+AGG 0.463158 1_3:-35300018 Msa0116340:CDS
GCATTGTAGCGAGCAACATT+GGG 0.497365 1_3:+35299516 None:intergenic
GCTTCCATTTAAATGGATCC+GGG 0.524769 1_3:-35300060 None:intergenic
TTGTTACTCTTGGCAACTAA+CGG 0.546330 1_3:+35299489 None:intergenic
TAGCGAGCAACATTGGGAGG+AGG 0.555104 1_3:+35299522 None:intergenic
AGATATGTTGAGCTATTACC+CGG 0.595717 1_3:+35300042 None:intergenic
CACACTCTTCATTGACAAGA+GGG 0.602074 1_3:+35299584 None:intergenic
TTGTATCTTTACAACTAACA+AGG 0.617293 1_3:-35299647 Msa0116340:CDS
CCACACTCTTCATTGACAAG+AGG 0.630729 1_3:+35299583 None:intergenic
TTGTAGCGAGCAACATTGGG+AGG 0.642624 1_3:+35299519 None:intergenic
AGTTGTAAAGATACAAGTGT+TGG 0.650517 1_3:+35299654 None:intergenic
GCTGTAGTCTACAACAGTCA+GGG 0.656780 1_3:-35300017 Msa0116340:intron
CCTCTTGTCAATGAAGAGTG+TGG 0.717573 1_3:-35299583 Msa0116340:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATATTTTTTTTTTCTTGAA+TGG - chr1_3:35299556-35299575 Msa0116340:CDS 10.0%
!!! TTATATATTTTTTTCTGGTT+GGG + chr1_3:35299956-35299975 None:intergenic 15.0%
!!! TTTATATATTTTTTTCTGGT+TGG + chr1_3:35299957-35299976 None:intergenic 15.0%
!!! GCTTTTTATATATTTTTTTC+TGG + chr1_3:35299961-35299980 None:intergenic 15.0%
!! TTGTATAAAAAATTTACGCA+AGG + chr1_3:35299825-35299844 None:intergenic 20.0%
! TTGTATCTTTACAACTAACA+AGG - chr1_3:35299865-35299884 Msa0116340:intron 25.0%
AGATTGATATTTACTCCTTC+CGG - chr1_3:35299601-35299620 Msa0116340:CDS 30.0%
CTGATTTCAACTAAGAGATA+AGG + chr1_3:35299650-35299669 None:intergenic 30.0%
AATCAGTTGAGCGAAATATA+TGG - chr1_3:35299664-35299683 Msa0116340:intron 30.0%
ATCAGTTGAGCGAAATATAT+GGG - chr1_3:35299665-35299684 Msa0116340:intron 30.0%
ACAACATTGATACCTACAAA+AGG - chr1_3:35299759-35299778 Msa0116340:intron 30.0%
CAACATTGATACCTACAAAA+GGG - chr1_3:35299760-35299779 Msa0116340:intron 30.0%
!!! ATTTTTTATACAAGCGTGTC+AGG - chr1_3:35299832-35299851 Msa0116340:intron 30.0%
!!! TTTTTTATACAAGCGTGTCA+GGG - chr1_3:35299833-35299852 Msa0116340:intron 30.0%
AGTTGTAAAGATACAAGTGT+TGG + chr1_3:35299861-35299880 None:intergenic 30.0%
!! TGTAACAAACTTGTTACTCT+TGG + chr1_3:35300036-35300055 None:intergenic 30.0%
AGATATGTTGAGCTATTACC+CGG + chr1_3:35299473-35299492 None:intergenic 35.0%
GATTGATATTTACTCCTTCC+GGG - chr1_3:35299602-35299621 Msa0116340:CDS 35.0%
TTGATACCTACAAAAGGGTT+AGG - chr1_3:35299765-35299784 Msa0116340:intron 35.0%
TCATCAAATTGGTACGCTTT+CGG + chr1_3:35299795-35299814 None:intergenic 35.0%
AAAGCGTACCAATTTGATGA+AGG - chr1_3:35299795-35299814 Msa0116340:intron 35.0%
AAGGCAATCCTTCATCAAAT+TGG + chr1_3:35299806-35299825 None:intergenic 35.0%
TTGTTACTCTTGGCAACTAA+CGG + chr1_3:35300026-35300045 None:intergenic 35.0%
ACAACAGTCAGGGTATAAGT+AGG - chr1_3:35299505-35299524 Msa0116340:CDS 40.0%
CAACAGTCAGGGTATAAGTA+GGG - chr1_3:35299506-35299525 Msa0116340:CDS 40.0%
GGGTATAAGTAGGGATATGT+TGG - chr1_3:35299515-35299534 Msa0116340:CDS 40.0%
AGAGTTCCTAGGTTTAAACC+CGG + chr1_3:35299623-35299642 None:intergenic 40.0%
GATAAGGAGTTAGAGTTCCT+AGG + chr1_3:35299634-35299653 None:intergenic 40.0%
CATCAAATTGGTACGCTTTC+GGG + chr1_3:35299794-35299813 None:intergenic 40.0%
CACACTCTTCATTGACAAGA+GGG + chr1_3:35299931-35299950 None:intergenic 40.0%
AGCTGTAGTCTACAACAGTC+AGG - chr1_3:35299494-35299513 Msa0116340:CDS 45.0%
GCTGTAGTCTACAACAGTCA+GGG - chr1_3:35299495-35299514 Msa0116340:CDS 45.0%
TTCCTAGGTTTAAACCCGGA+AGG + chr1_3:35299619-35299638 None:intergenic 45.0%
! GGGTTACCTAACCCTTTTGT+AGG + chr1_3:35299774-35299793 None:intergenic 45.0%
CCACACTCTTCATTGACAAG+AGG + chr1_3:35299932-35299951 None:intergenic 45.0%
CCTCTTGTCAATGAAGAGTG+TGG - chr1_3:35299929-35299948 Msa0116340:intron 45.0%
CAACATTGGGAGGAGGTTTA+GGG + chr1_3:35299986-35300005 None:intergenic 45.0%
GCATTGTAGCGAGCAACATT+GGG + chr1_3:35299999-35300018 None:intergenic 45.0%
CTCCTTCCGGGTTTAAACCT+AGG - chr1_3:35299614-35299633 Msa0116340:CDS 50.0%
GCAACATTGGGAGGAGGTTT+AGG + chr1_3:35299987-35300006 None:intergenic 50.0%
TTGTAGCGAGCAACATTGGG+AGG + chr1_3:35299996-35300015 None:intergenic 50.0%
CGCATTGTAGCGAGCAACAT+TGG + chr1_3:35300000-35300019 None:intergenic 50.0%
TAGCGAGCAACATTGGGAGG+AGG + chr1_3:35299993-35300012 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 35299464 35300070 35299464 ID=Msa0116340;Name=Msa0116340
chr1_3 mRNA 35299464 35300070 35299464 ID=Msa0116340-mRNA-1;Parent=Msa0116340;Name=Msa0116340-mRNA-1;_AED=0.89;_eAED=0.89;_QI=0|0|0|0.5|0|0.5|2|0|89
chr1_3 exon 35300018 35300070 35300018 ID=Msa0116340-mRNA-1:exon:11321;Parent=Msa0116340-mRNA-1
chr1_3 exon 35299464 35299680 35299464 ID=Msa0116340-mRNA-1:exon:11320;Parent=Msa0116340-mRNA-1
chr1_3 CDS 35300018 35300070 35300018 ID=Msa0116340-mRNA-1:cds;Parent=Msa0116340-mRNA-1
chr1_3 CDS 35299464 35299680 35299464 ID=Msa0116340-mRNA-1:cds;Parent=Msa0116340-mRNA-1
Gene Sequence

>Msa0116340

ATGGATCCGGGTAATAGCTCAACATATCTCAGCTGTAGTCTACAACAGTCAGGGGCACCAACACTTGTATCTTTACAACTAACAAGGTCTCAAAAACACTCTAAACATGCAACTTTTACTGTGAATGCCCTCTTGTCAATGAAGAGTGTGGACCCAACCAGAAAAAAATATATAAAAAGCATCCCTAAACCTCCTCCCAATGTTGCTCGCTACAATGCGACTCCGTTAGTTGCCAAGAGTAACAAGTTTGTTACACCAAACTCAGCCTAA
Protein sequence

>Msa0116340

MDPGNSSTYLSCSLQQSGAPTLVSLQLTRSQKHSKHATFTVNALLSMKSVDPTRKKYIKSIPKPPPNVARYNATPLVAKSNKFVTPNSA*