AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0271360


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0271360 MtrunA17_Chr2g0278531 92.593 54 4 0 6 59 11 64 1.91e-31 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0271360 AT1G25275.3 52.308 65 27 1 1 61 2 66 2.21e-17 68.9
Msa0271360 AT1G25275.1 52.381 63 26 1 1 59 2 64 2.32e-16 66.2
Msa0271360 AT1G25275.2 50.794 63 27 1 1 59 2 64 1.43e-15 64.3

Find 18 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGCTTCTGATTGCCTTGA+TGG 0.154913 2_3:+2727588 Msa0271360:CDS
CTCTTTGAACGCAGGCAGTT+TGG 0.316423 2_3:-2727614 None:intergenic
GTAGTTTCTCAAGATTATTA+TGG 0.419164 2_3:+2727378 Msa0271360:five_prime_UTR
GATGTACTAGTCGTAGTTAA+TGG 0.445314 2_3:+2727278 None:intergenic
TGCTCGATTAGATGCGGTCC+AGG 0.477134 2_3:+2727856 Msa0271360:CDS
TAGTTGTGCATTTATGACTT+TGG 0.516007 2_3:+2727348 Msa0271360:five_prime_UTR
TCAAGGCAATCAGAAGCATC+AGG 0.516390 2_3:-2727585 None:intergenic
GTGACATGCAGCAAGGCTTA+CGG 0.519988 2_3:+2727816 Msa0271360:intron
ATAATAATCTTGAGAAACTA+CGG 0.529331 2_3:-2727376 None:intergenic
TTTGGGTAATGTTAATTACC+TGG 0.537482 2_3:-2727874 None:intergenic
AGGCAGTTTGGCAACCATCA+AGG 0.564306 2_3:-2727602 None:intergenic
ATGCAGCAAGGCTTACGGCA+AGG 0.642528 2_3:+2727821 Msa0271360:intron
CGCAAGTGCTCGATTAGATG+CGG 0.643345 2_3:+2727850 Msa0271360:CDS
AGTATGCATGTACTTCCACA+TGG 0.664590 2_3:+2727324 Msa0271360:five_prime_UTR
CTAACAGTCTCTTTGAACGC+AGG 0.676017 2_3:-2727622 None:intergenic
TAAATGCACAACTATCCATG+TGG 0.693119 2_3:-2727339 None:intergenic
GAAGATGATGAAGAAGACGA+CGG 0.724386 2_3:+2727509 Msa0271360:exon
GATGATGAAGAAGACGACGG+TGG 0.786514 2_3:+2727512 Msa0271360:exon

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTAAGAAAAGTAATTAAC+AGG - chr2_3:2727668-2727687 None:intergenic 15.0%
!! ATAATAATCTTGAGAAACTA+CGG - chr2_3:2727379-2727398 None:intergenic 20.0%
!! GAATCATAAAAAAAACATCT+AGG - chr2_3:2727441-2727460 None:intergenic 20.0%
!!! ATTTGTGATATTTTCTCAAA+TGG + chr2_3:2727551-2727570 Msa0271360:CDS 20.0%
!!! CATTGTCTTCTTTTAATTTA+AGG + chr2_3:2727691-2727710 Msa0271360:intron 20.0%
! GTAGTTTCTCAAGATTATTA+TGG + chr2_3:2727378-2727397 Msa0271360:five_prime_UTR 25.0%
TAGTTGTGCATTTATGACTT+TGG + chr2_3:2727348-2727367 Msa0271360:five_prime_UTR 30.0%
TAAATGCACAACTATCCATG+TGG - chr2_3:2727342-2727361 None:intergenic 35.0%
! CTCTTTTCTCTTTGATCGTT+TGG - chr2_3:2727475-2727494 None:intergenic 35.0%
AGTATGCATGTACTTCCACA+TGG + chr2_3:2727324-2727343 Msa0271360:five_prime_UTR 40.0%
GAAGATGATGAAGAAGACGA+CGG + chr2_3:2727509-2727528 Msa0271360:exon 40.0%
TATGTATGTGACATGCAGCA+AGG + chr2_3:2727809-2727828 Msa0271360:intron 40.0%
!! TCAAGGCAATCAGAAGCATC+AGG - chr2_3:2727588-2727607 None:intergenic 45.0%
GATGCTTCTGATTGCCTTGA+TGG + chr2_3:2727588-2727607 Msa0271360:CDS 45.0%
CTAACAGTCTCTTTGAACGC+AGG - chr2_3:2727625-2727644 None:intergenic 45.0%
GATGATGAAGAAGACGACGG+TGG + chr2_3:2727512-2727531 Msa0271360:exon 50.0%
AGGCAGTTTGGCAACCATCA+AGG - chr2_3:2727605-2727624 None:intergenic 50.0%
CTCTTTGAACGCAGGCAGTT+TGG - chr2_3:2727617-2727636 None:intergenic 50.0%
GTGACATGCAGCAAGGCTTA+CGG + chr2_3:2727816-2727835 Msa0271360:intron 50.0%
CGCAAGTGCTCGATTAGATG+CGG + chr2_3:2727850-2727869 Msa0271360:CDS 50.0%
ATGCAGCAAGGCTTACGGCA+AGG + chr2_3:2727821-2727840 Msa0271360:intron 55.0%
TGCTCGATTAGATGCGGTCC+AGG + chr2_3:2727856-2727875 Msa0271360:CDS 55.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 2727287 2727885 2727287 ID=Msa0271360;Name=Msa0271360
chr2_3 mRNA 2727287 2727885 2727287 ID=Msa0271360-mRNA-1;Parent=Msa0271360;Name=Msa0271360-mRNA-1;_AED=0.24;_eAED=0.24;_QI=226|1|0.5|1|0|0.5|2|0|61
chr2_3 exon 2727287 2727639 2727287 ID=Msa0271360-mRNA-1:exon:1353;Parent=Msa0271360-mRNA-1
chr2_3 exon 2727827 2727885 2727827 ID=Msa0271360-mRNA-1:exon:1354;Parent=Msa0271360-mRNA-1
chr2_3 five_prime_UTR 2727287 2727512 2727287 ID=Msa0271360-mRNA-1:five_prime_utr;Parent=Msa0271360-mRNA-1
chr2_3 CDS 2727513 2727639 2727513 ID=Msa0271360-mRNA-1:cds;Parent=Msa0271360-mRNA-1
chr2_3 CDS 2727827 2727885 2727827 ID=Msa0271360-mRNA-1:cds;Parent=Msa0271360-mRNA-1
Gene Sequence

>Msa0271360

ATGATGAAGAAGACGACGGTGGTTGCTATGATGCTTTTATTTGTGATATTTTCTCAAATGGATAGCGTTGTTCCTGATGCTTCTGATTGCCTTGATGGTTGCCAAACTGCCTGCGTTCAAAGAGACTCAAGGCTTACGGCAAGGTGTGAGCGCAAGTGCTCGATTAGATGCGGTCCAGGTAATTAA

Protein sequence

>Msa0271360

MMKKTTVVAMMLLFVIFSQMDSVVPDASDCLDGCQTACVQRDSRLTARCERKCSIRCGPGN*