AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0591100

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 48 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAATACATTGTCTAACTTCT+AGG 0.159906 4_2:+15305076 Msa0591100:five_prime_UTR
CTGTAAATTAAATCCTCTTT+TGG 0.220274 4_2:+15304995 None:intergenic
ATTATTGCTTTCTAGTACCT+TGG 0.297387 4_2:+15305281 Msa0591100:five_prime_UTR
TAGGAACTACCTTATACTTT+TGG 0.309505 4_2:+15305522 Msa0591100:intron
AGGAATTTGCCAAAAGTATA+AGG 0.322050 4_2:-15305531 None:intergenic
AATCGTGATGTTTCACTCTA+AGG 0.341127 4_2:-15305551 None:intergenic
GAACTACAACCATTCTTTGT+TGG 0.379466 4_2:+15305107 Msa0591100:five_prime_UTR
CGATTATTCTACGAGTTTAG+TGG 0.386306 4_2:+15305251 Msa0591100:five_prime_UTR
ACCTTTGAAGTTCCTATCGC+TGG 0.405792 4_2:+15305401 Msa0591100:CDS
TCCGAACATCACATTTGGTA+TGG 0.417548 4_2:-15305637 None:intergenic
CCGAACATCACATTTGGTAT+GGG 0.451435 4_2:-15305636 None:intergenic
TAGCAATGGCACTTGCTAGA+TGG 0.455163 4_2:+15305152 Msa0591100:five_prime_UTR
TGCCGCACTCATGGAATGAT+AGG 0.462626 4_2:-15305363 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 4_2:+15305677 Msa0591100:CDS
GTCAAGCATTTATCAACGCT+TGG 0.466111 4_2:-15305760 None:intergenic
TGATAGGGTGGATAATCAAC+TGG 0.472004 4_2:-15305347 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.475440 4_2:+15305642 Msa0591100:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 4_2:+15305636 Msa0591100:CDS
GGCCGTTGTTGACAGATGGT+TGG 0.487397 4_2:+15305219 Msa0591100:five_prime_UTR
GCACGATGCTGCCGCACTCA+TGG 0.495354 4_2:-15305372 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 4_2:+15305678 Msa0591100:CDS
GAAGTTCCTATCGCTGGATA+CGG 0.503294 4_2:+15305407 Msa0591100:CDS
AAATATTCACCAACAAAGAA+TGG 0.520659 4_2:-15305116 None:intergenic
ACAGGAATGATATTGTCATA+AGG 0.528831 4_2:-15305591 None:intergenic
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 4_2:+15305215 Msa0591100:five_prime_UTR
ATATTAAATCCAACCAAAAG+AGG 0.531474 4_2:-15305008 None:intergenic
ATTGCTTTCTAGTACCTTGG+TGG 0.537055 4_2:+15305284 Msa0591100:five_prime_UTR
CGAACATCACATTTGGTATG+GGG 0.552019 4_2:-15305635 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 4_2:-15305609 None:intergenic
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 4_2:+15305716 Msa0591100:CDS
TTGTCTAACTTCTAGGATGT+CGG 0.574486 4_2:+15305083 Msa0591100:five_prime_UTR
TGTTCAACAAATCAGTTAGT+CGG 0.579019 4_2:+15305198 Msa0591100:five_prime_UTR
GTCTCCGCCCTCAATACCAT+TGG 0.581950 4_2:-15305685 None:intergenic
TGGCACTTGCTAGATGGTGA+TGG 0.587936 4_2:+15305158 Msa0591100:five_prime_UTR
TCTAGCAAGTGCCATTGCTA+CGG 0.595706 4_2:-15305149 None:intergenic
CACGATTACGTCGTGTTGTG+CGG 0.599800 4_2:+15305567 Msa0591100:CDS
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 4_2:+15305646 Msa0591100:CDS
GGCACTTGCTAGATGGTGAT+GGG 0.608333 4_2:+15305159 Msa0591100:five_prime_UTR
GCCGCACTCATGGAATGATA+GGG 0.629158 4_2:-15305362 None:intergenic
GACGATCCGTATCCAGCGAT+AGG 0.637595 4_2:-15305413 None:intergenic
ACCCTATCATTCCATGAGTG+CGG 0.640367 4_2:+15305361 Msa0591100:exon
TCTACGAGCTACCGTAGCAA+TGG 0.643591 4_2:+15305138 Msa0591100:five_prime_UTR
GCACTCATGGAATGATAGGG+TGG 0.649652 4_2:-15305359 None:intergenic
TCCAGCGATAGGAACTTCAA+AGG 0.649902 4_2:-15305402 None:intergenic
CTCCAACCATCTGTCAACAA+CGG 0.679074 4_2:-15305221 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 4_2:-15305298 None:intergenic
CGGATCGTCGAAATCACCGA+AGG 0.693947 4_2:+15305427 Msa0591100:CDS
GCTGCCAATGGTATTGAGGG+CGG 0.739556 4_2:+15305681 Msa0591100:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTATTTTTTTTTATTTTT+AGG + chr4_2:15305503-15305522 Msa0591100:intron 0.0%
!!! TTTTATTTTTTTTTATTTTT+AGG + chr4_2:15305503-15305522 Msa0591100:intron 0.0%
!! ATGGACAAAAAATATGTTAT+CGG + chr4_2:15305735-15305754 Msa0591100:CDS 20.0%
!! ATGGACAAAAAATATGTTAT+CGG + chr4_2:15305735-15305754 Msa0591100:CDS 20.0%
!! AAATTAAATCCTCTTTTGGT+TGG + chr4_2:15304999-15305018 Msa0591100:five_prime_UTR 25.0%
! ATATTAAATCCAACCAAAAG+AGG - chr4_2:15305011-15305030 None:intergenic 25.0%
! TAATACATTGTCTAACTTCT+AGG + chr4_2:15305076-15305095 Msa0591100:five_prime_UTR 25.0%
! AAATATTCACCAACAAAGAA+TGG - chr4_2:15305119-15305138 None:intergenic 25.0%
!! AAATTAAATCCTCTTTTGGT+TGG + chr4_2:15304999-15305018 Msa0591100:five_prime_UTR 25.0%
! ATATTAAATCCAACCAAAAG+AGG - chr4_2:15305011-15305030 None:intergenic 25.0%
! TAATACATTGTCTAACTTCT+AGG + chr4_2:15305076-15305095 Msa0591100:five_prime_UTR 25.0%
! AAATATTCACCAACAAAGAA+TGG - chr4_2:15305119-15305138 None:intergenic 25.0%
TGTTCAACAAATCAGTTAGT+CGG + chr4_2:15305198-15305217 Msa0591100:five_prime_UTR 30.0%
! ATTATTGCTTTCTAGTACCT+TGG + chr4_2:15305281-15305300 Msa0591100:five_prime_UTR 30.0%
GACATACAATAAACAACCTT+CGG - chr4_2:15305446-15305465 None:intergenic 30.0%
! TAGGAACTACCTTATACTTT+TGG + chr4_2:15305522-15305541 Msa0591100:intron 30.0%
! AGGAATTTGCCAAAAGTATA+AGG - chr4_2:15305534-15305553 None:intergenic 30.0%
ACAGGAATGATATTGTCATA+AGG - chr4_2:15305594-15305613 None:intergenic 30.0%
TGTTCAACAAATCAGTTAGT+CGG + chr4_2:15305198-15305217 Msa0591100:five_prime_UTR 30.0%
! ATTATTGCTTTCTAGTACCT+TGG + chr4_2:15305281-15305300 Msa0591100:five_prime_UTR 30.0%
GACATACAATAAACAACCTT+CGG - chr4_2:15305446-15305465 None:intergenic 30.0%
! TAGGAACTACCTTATACTTT+TGG + chr4_2:15305522-15305541 Msa0591100:intron 30.0%
! AGGAATTTGCCAAAAGTATA+AGG - chr4_2:15305534-15305553 None:intergenic 30.0%
ACAGGAATGATATTGTCATA+AGG - chr4_2:15305594-15305613 None:intergenic 30.0%
!! TTGTCTAACTTCTAGGATGT+CGG + chr4_2:15305083-15305102 Msa0591100:five_prime_UTR 35.0%
GAACTACAACCATTCTTTGT+TGG + chr4_2:15305107-15305126 Msa0591100:five_prime_UTR 35.0%
CGATTATTCTACGAGTTTAG+TGG + chr4_2:15305251-15305270 Msa0591100:five_prime_UTR 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr4_2:15305301-15305320 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr4_2:15305554-15305573 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr4_2:15305612-15305631 None:intergenic 35.0%
!! TTGTCTAACTTCTAGGATGT+CGG + chr4_2:15305083-15305102 Msa0591100:five_prime_UTR 35.0%
GAACTACAACCATTCTTTGT+TGG + chr4_2:15305107-15305126 Msa0591100:five_prime_UTR 35.0%
CGATTATTCTACGAGTTTAG+TGG + chr4_2:15305251-15305270 Msa0591100:five_prime_UTR 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr4_2:15305301-15305320 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr4_2:15305554-15305573 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr4_2:15305612-15305631 None:intergenic 35.0%
! ATTGCTTTCTAGTACCTTGG+TGG + chr4_2:15305284-15305303 Msa0591100:five_prime_UTR 40.0%
TGATAGGGTGGATAATCAAC+TGG - chr4_2:15305350-15305369 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - chr4_2:15305638-15305657 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr4_2:15305639-15305658 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr4_2:15305636-15305655 Msa0591100:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr4_2:15305640-15305659 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr4_2:15305645-15305664 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr4_2:15305642-15305661 Msa0591100:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr4_2:15305646-15305665 Msa0591100:CDS 40.0%
! ATTGCTTTCTAGTACCTTGG+TGG + chr4_2:15305284-15305303 Msa0591100:five_prime_UTR 40.0%
TGATAGGGTGGATAATCAAC+TGG - chr4_2:15305350-15305369 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - chr4_2:15305638-15305657 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr4_2:15305639-15305658 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr4_2:15305636-15305655 Msa0591100:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr4_2:15305640-15305659 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr4_2:15305645-15305664 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr4_2:15305642-15305661 Msa0591100:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr4_2:15305646-15305665 Msa0591100:CDS 40.0%
! TCTAGCAAGTGCCATTGCTA+CGG - chr4_2:15305152-15305171 None:intergenic 45.0%
! TAGCAATGGCACTTGCTAGA+TGG + chr4_2:15305152-15305171 Msa0591100:five_prime_UTR 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr4_2:15305224-15305243 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG + chr4_2:15305361-15305380 Msa0591100:exon 45.0%
!! ACCTTTGAAGTTCCTATCGC+TGG + chr4_2:15305401-15305420 Msa0591100:CDS 45.0%
TCCAGCGATAGGAACTTCAA+AGG - chr4_2:15305405-15305424 None:intergenic 45.0%
GAAGTTCCTATCGCTGGATA+CGG + chr4_2:15305407-15305426 Msa0591100:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr4_2:15305669-15305688 Msa0591100:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr4_2:15305677-15305696 Msa0591100:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr4_2:15305678-15305697 Msa0591100:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr4_2:15305716-15305735 Msa0591100:CDS 45.0%
! TCTAGCAAGTGCCATTGCTA+CGG - chr4_2:15305152-15305171 None:intergenic 45.0%
! TAGCAATGGCACTTGCTAGA+TGG + chr4_2:15305152-15305171 Msa0591100:five_prime_UTR 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr4_2:15305224-15305243 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG + chr4_2:15305361-15305380 Msa0591100:exon 45.0%
!! ACCTTTGAAGTTCCTATCGC+TGG + chr4_2:15305401-15305420 Msa0591100:CDS 45.0%
TCCAGCGATAGGAACTTCAA+AGG - chr4_2:15305405-15305424 None:intergenic 45.0%
GAAGTTCCTATCGCTGGATA+CGG + chr4_2:15305407-15305426 Msa0591100:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr4_2:15305669-15305688 Msa0591100:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr4_2:15305677-15305696 Msa0591100:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr4_2:15305678-15305697 Msa0591100:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr4_2:15305716-15305735 Msa0591100:CDS 45.0%
TCTACGAGCTACCGTAGCAA+TGG + chr4_2:15305138-15305157 Msa0591100:five_prime_UTR 50.0%
! TGGCACTTGCTAGATGGTGA+TGG + chr4_2:15305158-15305177 Msa0591100:five_prime_UTR 50.0%
! GGCACTTGCTAGATGGTGAT+GGG + chr4_2:15305159-15305178 Msa0591100:five_prime_UTR 50.0%
GCACTCATGGAATGATAGGG+TGG - chr4_2:15305362-15305381 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - chr4_2:15305365-15305384 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG - chr4_2:15305366-15305385 None:intergenic 50.0%
CACGATTACGTCGTGTTGTG+CGG + chr4_2:15305567-15305586 Msa0591100:CDS 50.0%
TCTACGAGCTACCGTAGCAA+TGG + chr4_2:15305138-15305157 Msa0591100:five_prime_UTR 50.0%
! TGGCACTTGCTAGATGGTGA+TGG + chr4_2:15305158-15305177 Msa0591100:five_prime_UTR 50.0%
! GGCACTTGCTAGATGGTGAT+GGG + chr4_2:15305159-15305178 Msa0591100:five_prime_UTR 50.0%
GCACTCATGGAATGATAGGG+TGG - chr4_2:15305362-15305381 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - chr4_2:15305365-15305384 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG - chr4_2:15305366-15305385 None:intergenic 50.0%
CACGATTACGTCGTGTTGTG+CGG + chr4_2:15305567-15305586 Msa0591100:CDS 50.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr4_2:15305215-15305234 Msa0591100:five_prime_UTR 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr4_2:15305219-15305238 Msa0591100:five_prime_UTR 55.0%
GACGATCCGTATCCAGCGAT+AGG - chr4_2:15305416-15305435 None:intergenic 55.0%
CGGATCGTCGAAATCACCGA+AGG + chr4_2:15305427-15305446 Msa0591100:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr4_2:15305681-15305700 Msa0591100:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr4_2:15305688-15305707 None:intergenic 55.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr4_2:15305215-15305234 Msa0591100:five_prime_UTR 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr4_2:15305219-15305238 Msa0591100:five_prime_UTR 55.0%
GACGATCCGTATCCAGCGAT+AGG - chr4_2:15305416-15305435 None:intergenic 55.0%
CGGATCGTCGAAATCACCGA+AGG + chr4_2:15305427-15305446 Msa0591100:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr4_2:15305681-15305700 Msa0591100:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr4_2:15305688-15305707 None:intergenic 55.0%
GCACGATGCTGCCGCACTCA+TGG - chr4_2:15305375-15305394 None:intergenic 65.0%
GCACGATGCTGCCGCACTCA+TGG - chr4_2:15305375-15305394 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 15304996 15305770 15304996 ID=Msa0591100;Name=Msa0591100
chr4_2 mRNA 15304996 15305770 15304996 ID=Msa0591100-mRNA-1;Parent=Msa0591100;Name=Msa0591100-mRNA-1;_AED=0.05;_eAED=0.05;_QI=378|1|0.5|1|1|1|2|0|106
chr4_2 exon 15304996 15305448 15304996 ID=Msa0591100-mRNA-1:exon:4362;Parent=Msa0591100-mRNA-1
chr4_2 exon 15305525 15305770 15305525 ID=Msa0591100-mRNA-1:exon:4363;Parent=Msa0591100-mRNA-1
chr4_2 five_prime_UTR 15304996 15305373 15304996 ID=Msa0591100-mRNA-1:five_prime_utr;Parent=Msa0591100-mRNA-1
chr4_2 CDS 15305374 15305448 15305374 ID=Msa0591100-mRNA-1:cds;Parent=Msa0591100-mRNA-1
chr4_2 CDS 15305525 15305770 15305525 ID=Msa0591100-mRNA-1:cds;Parent=Msa0591100-mRNA-1
Gene Sequence

>Msa0591100

ATGAGTGCGGCAGCATCGTGCTATTGTACCTTTGAAGTTCCTATCGCTGGATACGGATCGTCGAAATCACCGAAGGAACTACCTTATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCGTGTTGTGCGGACCTTATGACAATATCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGGATCCAAGCGTTGA
Protein sequence

>Msa0591100

MSAAASCYCTFEVPIAGYGSSKSPKELPYTFGKFLRVKHHDYVVLCGPYDNIIPVRLKYTDDPIPNVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIGSKR*