AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0357390


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 23 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTAAACTTGACCGAACTA+TGG 0.324856 3_1:-39530177 Msa0357390:three_prime_UTR
TGAATTTGAAGTGGACGATT+TGG 0.365773 3_1:-39530263 Msa0357390:three_prime_UTR
CCTCTTGAATTTCATCATCT+AGG 0.384014 3_1:+39530299 None:intergenic
CAAGATAAATTTGAATGAGT+TGG 0.400423 3_1:-39530229 Msa0357390:three_prime_UTR
GTTGGTTCGCGTAGGAATAC+TGG 0.404620 3_1:-39531164 Msa0357390:CDS
TATCAATGAAGATGTTGAAA+AGG 0.471255 3_1:-39530427 Msa0357390:CDS
GCACTTGATCTAGCTTGAAA+AGG 0.475883 3_1:+39531113 None:intergenic
AAAATAACAAAACCATAGTT+CGG 0.496331 3_1:+39530165 None:intergenic
CTATGCTTTAAAATGCAAGA+AGG 0.510840 3_1:-39531194 None:intergenic
GAAATTCTCGAGGGCAACAT+AGG 0.514832 3_1:-39530363 Msa0357390:CDS
AGGATGATATAGATGATAAG+AGG 0.519091 3_1:-39530326 Msa0357390:CDS
ATGCAAGAAGGATTAGATGT+TGG 0.539382 3_1:-39531182 Msa0357390:CDS
CATCGATGATGAATTTGAAG+TGG 0.587100 3_1:-39530272 Msa0357390:three_prime_UTR
GATAGATGAGGAATTGCAAG+AGG 0.601318 3_1:-39530400 Msa0357390:CDS
ACTGGTCAAAGTTCTGCTGA+AGG 0.601331 3_1:-39531146 Msa0357390:CDS
ATAAATTTGAATGAGTTGGA+TGG 0.622667 3_1:-39530225 Msa0357390:three_prime_UTR
GATTAGATGTTGGTTCGCGT+AGG 0.623215 3_1:-39531172 Msa0357390:CDS
CATAGGTGATGAATTTCAAG+AGG 0.627468 3_1:-39530346 Msa0357390:CDS
TGATATAGATGATAAGAGGA+CGG 0.634825 3_1:-39530322 Msa0357390:CDS
CGTAGATGATGAAATTCTCG+AGG 0.645005 3_1:-39530373 Msa0357390:CDS
CCTAGATGATGAAATTCAAG+AGG 0.646389 3_1:-39530299 Msa0357390:exon
TGAAAAGGATGAGATAGATG+AGG 0.656088 3_1:-39530412 Msa0357390:CDS
GTAGATGATGAAATTCTCGA+GGG 0.693006 3_1:-39530372 Msa0357390:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAACAAATTTCCTATTTG+CGG - chr3_1:39530678-39530697 Msa0357390:intron 20.0%
!! AAAATAACAAAACCATAGTT+CGG + chr3_1:39531101-39531120 None:intergenic 20.0%
!! TAAAACAAATTTCCTATTTG+CGG - chr3_1:39530678-39530697 Msa0357390:intron 20.0%
!! AAAATAACAAAACCATAGTT+CGG + chr3_1:39531101-39531120 None:intergenic 20.0%
!!! AATTTTGTTTCTGCATTTTG+TGG - chr3_1:39530531-39530550 Msa0357390:intron 25.0%
! AAGTTACGGAAACTTAAATA+TGG - chr3_1:39530622-39530641 Msa0357390:intron 25.0%
! AGTTACGGAAACTTAAATAT+GGG - chr3_1:39530623-39530642 Msa0357390:intron 25.0%
! ATGTAATGATAGAATAAGGA+AGG - chr3_1:39530647-39530666 Msa0357390:intron 25.0%
! TGTAATGATAGAATAAGGAA+GGG - chr3_1:39530648-39530667 Msa0357390:intron 25.0%
!!! TTTTGGTTTTTATTTGTGTG+AGG - chr3_1:39530727-39530746 Msa0357390:intron 25.0%
! TATCAATGAAGATGTTGAAA+AGG - chr3_1:39530836-39530855 Msa0357390:intron 25.0%
! CAAGATAAATTTGAATGAGT+TGG - chr3_1:39531034-39531053 Msa0357390:intron 25.0%
!! ATAAATTTGAATGAGTTGGA+TGG - chr3_1:39531038-39531057 Msa0357390:intron 25.0%
!!! TATGGTTTTGTTATTTTGCT+AGG - chr3_1:39531104-39531123 Msa0357390:CDS 25.0%
!!! AATTTTGTTTCTGCATTTTG+TGG - chr3_1:39530531-39530550 Msa0357390:intron 25.0%
! AAGTTACGGAAACTTAAATA+TGG - chr3_1:39530622-39530641 Msa0357390:intron 25.0%
! AGTTACGGAAACTTAAATAT+GGG - chr3_1:39530623-39530642 Msa0357390:intron 25.0%
! ATGTAATGATAGAATAAGGA+AGG - chr3_1:39530647-39530666 Msa0357390:intron 25.0%
! TGTAATGATAGAATAAGGAA+GGG - chr3_1:39530648-39530667 Msa0357390:intron 25.0%
!!! TTTTGGTTTTTATTTGTGTG+AGG - chr3_1:39530727-39530746 Msa0357390:intron 25.0%
! TATCAATGAAGATGTTGAAA+AGG - chr3_1:39530836-39530855 Msa0357390:intron 25.0%
! CAAGATAAATTTGAATGAGT+TGG - chr3_1:39531034-39531053 Msa0357390:intron 25.0%
!! ATAAATTTGAATGAGTTGGA+TGG - chr3_1:39531038-39531057 Msa0357390:intron 25.0%
!!! TATGGTTTTGTTATTTTGCT+AGG - chr3_1:39531104-39531123 Msa0357390:CDS 25.0%
! AAGTGCTAAGTTGAAAAAGA+TGG - chr3_1:39530167-39530186 Msa0357390:three_prime_UTR 30.0%
ACATGCAAGTTAACAATTTC+AGG + chr3_1:39530404-39530423 None:intergenic 30.0%
GTGTGAACTTATGATTATGT+TGG - chr3_1:39530444-39530463 Msa0357390:intron 30.0%
GAACTTATGATTATGTTGGT+TGG - chr3_1:39530448-39530467 Msa0357390:intron 30.0%
!!! GTGTGTTTTACTTGTTGTTT+TGG - chr3_1:39530710-39530729 Msa0357390:intron 30.0%
ACATCAACCATAGATATTGT+TGG + chr3_1:39530791-39530810 None:intergenic 30.0%
AGGATGATATAGATGATAAG+AGG - chr3_1:39530937-39530956 Msa0357390:intron 30.0%
TGATATAGATGATAAGAGGA+CGG - chr3_1:39530941-39530960 Msa0357390:intron 30.0%
AATTAAACTTGACCGAACTA+TGG - chr3_1:39531086-39531105 Msa0357390:intron 30.0%
! AAGTGCTAAGTTGAAAAAGA+TGG - chr3_1:39530167-39530186 Msa0357390:three_prime_UTR 30.0%
ACATGCAAGTTAACAATTTC+AGG + chr3_1:39530404-39530423 None:intergenic 30.0%
GTGTGAACTTATGATTATGT+TGG - chr3_1:39530444-39530463 Msa0357390:intron 30.0%
GAACTTATGATTATGTTGGT+TGG - chr3_1:39530448-39530467 Msa0357390:intron 30.0%
!!! GTGTGTTTTACTTGTTGTTT+TGG - chr3_1:39530710-39530729 Msa0357390:intron 30.0%
ACATCAACCATAGATATTGT+TGG + chr3_1:39530791-39530810 None:intergenic 30.0%
AGGATGATATAGATGATAAG+AGG - chr3_1:39530937-39530956 Msa0357390:intron 30.0%
TGATATAGATGATAAGAGGA+CGG - chr3_1:39530941-39530960 Msa0357390:intron 30.0%
AATTAAACTTGACCGAACTA+TGG - chr3_1:39531086-39531105 Msa0357390:intron 30.0%
ATGCAAGAAGGATTAGATGT+TGG - chr3_1:39530081-39530100 Msa0357390:three_prime_UTR 35.0%
ACAACTTCTACAATCTCATG+AGG + chr3_1:39530264-39530283 None:intergenic 35.0%
GAGATTGTAGAAGTTGTAGA+CGG - chr3_1:39530267-39530286 Msa0357390:three_prime_UTR 35.0%
GAATTGTTTAAGTGTGTCCA+AGG - chr3_1:39530473-39530492 Msa0357390:intron 35.0%
ACACAATCAAAATCCAACCT+TGG + chr3_1:39530493-39530512 None:intergenic 35.0%
! TGTTTCTGTGTTGCATAACA+TGG - chr3_1:39530596-39530615 Msa0357390:intron 35.0%
GGGCATGTAATGATAGAATA+AGG - chr3_1:39530643-39530662 Msa0357390:intron 35.0%
!! CATAGATATTGTTGGTTCAG+AGG + chr3_1:39530783-39530802 None:intergenic 35.0%
CTCTGAACCAACAATATCTA+TGG - chr3_1:39530781-39530800 Msa0357390:intron 35.0%
!! TTTGTTGTTCTTATGCAGCA+AGG - chr3_1:39530813-39530832 Msa0357390:intron 35.0%
TGAAAAGGATGAGATAGATG+AGG - chr3_1:39530851-39530870 Msa0357390:intron 35.0%
GTAGATGATGAAATTCTCGA+GGG - chr3_1:39530891-39530910 Msa0357390:intron 35.0%
CATAGGTGATGAATTTCAAG+AGG - chr3_1:39530917-39530936 Msa0357390:intron 35.0%
CCTCTTGAATTTCATCATCT+AGG + chr3_1:39530967-39530986 None:intergenic 35.0%
CCTAGATGATGAAATTCAAG+AGG - chr3_1:39530964-39530983 Msa0357390:intron 35.0%
CATCGATGATGAATTTGAAG+TGG - chr3_1:39530991-39531010 Msa0357390:intron 35.0%
! TGAATTTGAAGTGGACGATT+TGG - chr3_1:39531000-39531019 Msa0357390:intron 35.0%
ATGCAAGAAGGATTAGATGT+TGG - chr3_1:39530081-39530100 Msa0357390:three_prime_UTR 35.0%
ACAACTTCTACAATCTCATG+AGG + chr3_1:39530264-39530283 None:intergenic 35.0%
GAGATTGTAGAAGTTGTAGA+CGG - chr3_1:39530267-39530286 Msa0357390:three_prime_UTR 35.0%
GAATTGTTTAAGTGTGTCCA+AGG - chr3_1:39530473-39530492 Msa0357390:intron 35.0%
ACACAATCAAAATCCAACCT+TGG + chr3_1:39530493-39530512 None:intergenic 35.0%
! TGTTTCTGTGTTGCATAACA+TGG - chr3_1:39530596-39530615 Msa0357390:intron 35.0%
GGGCATGTAATGATAGAATA+AGG - chr3_1:39530643-39530662 Msa0357390:intron 35.0%
!! CATAGATATTGTTGGTTCAG+AGG + chr3_1:39530783-39530802 None:intergenic 35.0%
CTCTGAACCAACAATATCTA+TGG - chr3_1:39530781-39530800 Msa0357390:intron 35.0%
!! TTTGTTGTTCTTATGCAGCA+AGG - chr3_1:39530813-39530832 Msa0357390:intron 35.0%
TGAAAAGGATGAGATAGATG+AGG - chr3_1:39530851-39530870 Msa0357390:intron 35.0%
GTAGATGATGAAATTCTCGA+GGG - chr3_1:39530891-39530910 Msa0357390:intron 35.0%
CATAGGTGATGAATTTCAAG+AGG - chr3_1:39530917-39530936 Msa0357390:intron 35.0%
CCTCTTGAATTTCATCATCT+AGG + chr3_1:39530967-39530986 None:intergenic 35.0%
CCTAGATGATGAAATTCAAG+AGG - chr3_1:39530964-39530983 Msa0357390:intron 35.0%
CATCGATGATGAATTTGAAG+TGG - chr3_1:39530991-39531010 Msa0357390:intron 35.0%
! TGAATTTGAAGTGGACGATT+TGG - chr3_1:39531000-39531019 Msa0357390:intron 35.0%
! GCACTTGATCTAGCTTGAAA+AGG + chr3_1:39530153-39530172 None:intergenic 40.0%
TGTTTAAGTGTGTCCAAGGT+TGG - chr3_1:39530477-39530496 Msa0357390:intron 40.0%
GCATAACATGGCACAAGTTA+CGG - chr3_1:39530608-39530627 Msa0357390:intron 40.0%
CACACAACATAACCGCAAAT+AGG + chr3_1:39530693-39530712 None:intergenic 40.0%
GATAGATGAGGAATTGCAAG+AGG - chr3_1:39530863-39530882 Msa0357390:intron 40.0%
CGTAGATGATGAAATTCTCG+AGG - chr3_1:39530890-39530909 Msa0357390:intron 40.0%
! GCACTTGATCTAGCTTGAAA+AGG + chr3_1:39530153-39530172 None:intergenic 40.0%
TGTTTAAGTGTGTCCAAGGT+TGG - chr3_1:39530477-39530496 Msa0357390:intron 40.0%
GCATAACATGGCACAAGTTA+CGG - chr3_1:39530608-39530627 Msa0357390:intron 40.0%
CACACAACATAACCGCAAAT+AGG + chr3_1:39530693-39530712 None:intergenic 40.0%
GATAGATGAGGAATTGCAAG+AGG - chr3_1:39530863-39530882 Msa0357390:intron 40.0%
CGTAGATGATGAAATTCTCG+AGG - chr3_1:39530890-39530909 Msa0357390:intron 40.0%
!! GATTAGATGTTGGTTCGCGT+AGG - chr3_1:39530091-39530110 Msa0357390:three_prime_UTR 45.0%
ACTGGTCAAAGTTCTGCTGA+AGG - chr3_1:39530117-39530136 Msa0357390:three_prime_UTR 45.0%
AAAGTTGCATGAGAAGCTGC+AGG - chr3_1:39530221-39530240 Msa0357390:three_prime_UTR 45.0%
AAGTTGCATGAGAAGCTGCA+GGG - chr3_1:39530222-39530241 Msa0357390:three_prime_UTR 45.0%
!! TGTTGGTTCAGAGGACAATC+AGG + chr3_1:39530774-39530793 None:intergenic 45.0%
GAAATTCTCGAGGGCAACAT+AGG - chr3_1:39530900-39530919 Msa0357390:intron 45.0%
!! GATTAGATGTTGGTTCGCGT+AGG - chr3_1:39530091-39530110 Msa0357390:three_prime_UTR 45.0%
ACTGGTCAAAGTTCTGCTGA+AGG - chr3_1:39530117-39530136 Msa0357390:three_prime_UTR 45.0%
AAAGTTGCATGAGAAGCTGC+AGG - chr3_1:39530221-39530240 Msa0357390:three_prime_UTR 45.0%
AAGTTGCATGAGAAGCTGCA+GGG - chr3_1:39530222-39530241 Msa0357390:three_prime_UTR 45.0%
!! TGTTGGTTCAGAGGACAATC+AGG + chr3_1:39530774-39530793 None:intergenic 45.0%
GAAATTCTCGAGGGCAACAT+AGG - chr3_1:39530900-39530919 Msa0357390:intron 45.0%
!! GTTGGTTCGCGTAGGAATAC+TGG - chr3_1:39530099-39530118 Msa0357390:three_prime_UTR 50.0%
!! GTTGGTTCGCGTAGGAATAC+TGG - chr3_1:39530099-39530118 Msa0357390:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 39530081 39531204 39530081 ID=Msa0357390;Name=Msa0357390
chr3_1 mRNA 39530081 39531204 39530081 ID=Msa0357390-mRNA-1;Parent=Msa0357390;Name=Msa0357390-mRNA-1;_AED=0.33;_eAED=0.35;_QI=0|0|0.5|1|1|1|2|236|81
chr3_1 exon 39530081 39530454 39530081 ID=Msa0357390-mRNA-1:exon:7050;Parent=Msa0357390-mRNA-1
chr3_1 exon 39531097 39531204 39531097 ID=Msa0357390-mRNA-1:exon:7049;Parent=Msa0357390-mRNA-1
chr3_1 CDS 39531097 39531204 39531097 ID=Msa0357390-mRNA-1:cds;Parent=Msa0357390-mRNA-1
chr3_1 CDS 39530317 39530454 39530317 ID=Msa0357390-mRNA-1:cds;Parent=Msa0357390-mRNA-1
chr3_1 three_prime_UTR 39530081 39530316 39530081 ID=Msa0357390-mRNA-1:three_prime_utr;Parent=Msa0357390-mRNA-1
Gene Sequence

>Msa0357390

ATGCAAGAAGGATTAGATGTTGGTTCGCGTAGGAATACTGGTCAAAGTTCTGCTGAAGGATTAGATTTACCTTTTCAAGCTAGATCAAGTGCTAAGTTGAAAAAGATGCAAGGTATCAATGAAGATGTTGAAAAGGATGAGATAGATGAGGAATTGCAAGAGGAAGACGTAGATGATGAAATTCTCGAGGGCAACATAGGTGATGAATTTCAAGAGGATGATATAGATGATAAGAGGACGGCCTAG

Protein sequence

>Msa0357390

MQEGLDVGSRRNTGQSSAEGLDLPFQARSSAKLKKMQGINEDVEKDEIDEELQEEDVDDEILEGNIGDEFQEDDIDDKRTA*