AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1334910

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 8_4:+55733023 Msa1334910:five_prime_UTR
CTGTAAATTAAATCCTCTTT+TGG 0.220274 8_4:+55732942 None:intergenic
ATTATTGCTTTCTAGTACCT+TGG 0.297387 8_4:+55733228 Msa1334910:five_prime_UTR
TAGGAACTACCTTATACTTT+TGG 0.309505 8_4:+55733468 Msa1334910:intron
AGGAATTTGCCAAAAGTATA+AGG 0.322050 8_4:-55733477 None:intergenic
AATCGTGATGTTTCACTCTA+AGG 0.341127 8_4:-55733497 None:intergenic
GAACTACAACCATTCTTTGT+TGG 0.379466 8_4:+55733054 Msa1334910:five_prime_UTR
CGATTATTCTACGAGTTTAG+TGG 0.386306 8_4:+55733198 Msa1334910:five_prime_UTR
ACCTTTGAAGTTCCTATCGC+TGG 0.405792 8_4:+55733348 Msa1334910:CDS
TCCGAACATCACATTTGGTA+TGG 0.417548 8_4:-55733583 None:intergenic
CCGAACATCACATTTGGTAT+GGG 0.451435 8_4:-55733582 None:intergenic
TAGCAATGGCACTTGCTAGA+TGG 0.455163 8_4:+55733099 Msa1334910:five_prime_UTR
TGCCGCACTCATGGAATGAT+AGG 0.462626 8_4:-55733310 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 8_4:+55733623 Msa1334910:CDS
GTCAAGCATTTATCAACGCT+TGG 0.466111 8_4:-55733706 None:intergenic
TGATAGGGTGGATAATCAAC+TGG 0.472004 8_4:-55733294 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.475440 8_4:+55733588 Msa1334910:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 8_4:+55733582 Msa1334910:CDS
GGCCGTTGTTGACAGATGGT+TGG 0.487397 8_4:+55733166 Msa1334910:five_prime_UTR
GCACGATGCTGCCGCACTCA+TGG 0.495354 8_4:-55733319 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 8_4:+55733624 Msa1334910:CDS
GAAGTTCCTATCGCTGGATA+CGG 0.503294 8_4:+55733354 Msa1334910:CDS
AAATATTCACCAACAAAGAA+TGG 0.520659 8_4:-55733063 None:intergenic
ACAGGAATGATATTGTCATA+AGG 0.528831 8_4:-55733537 None:intergenic
AGTCGGCCGTTGTTGACAGA+TGG 0.531450 8_4:+55733162 Msa1334910:five_prime_UTR
ATATTAAATCCAACCAAAAG+AGG 0.531474 8_4:-55732955 None:intergenic
ATTGCTTTCTAGTACCTTGG+TGG 0.537055 8_4:+55733231 Msa1334910:five_prime_UTR
CGAACATCACATTTGGTATG+GGG 0.552019 8_4:-55733581 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 8_4:-55733555 None:intergenic
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 8_4:+55733662 Msa1334910:CDS
TTGTCTAACTTCTAGGATGT+CGG 0.574486 8_4:+55733030 Msa1334910:five_prime_UTR
TGTTCAACAAATCAGTTAGT+CGG 0.579019 8_4:+55733145 Msa1334910:five_prime_UTR
GTCTCCGCCCTCAATACCAT+TGG 0.581950 8_4:-55733631 None:intergenic
TGGCACTTGCTAGATGGTGA+TGG 0.587936 8_4:+55733105 Msa1334910:five_prime_UTR
TCTAGCAAGTGCCATTGCTA+CGG 0.595706 8_4:-55733096 None:intergenic
CACGATTACGTCGTGTTGTG+CGG 0.599800 8_4:+55733513 Msa1334910:CDS
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 8_4:+55733592 Msa1334910:CDS
GGCACTTGCTAGATGGTGAT+GGG 0.608333 8_4:+55733106 Msa1334910:five_prime_UTR
GCCGCACTCATGGAATGATA+GGG 0.629158 8_4:-55733309 None:intergenic
GACGATCCGTATCCAGCGAT+AGG 0.637595 8_4:-55733360 None:intergenic
ACCCTATCATTCCATGAGTG+CGG 0.640367 8_4:+55733308 Msa1334910:exon
TCTACGAGCTACCGTAGCAA+TGG 0.643591 8_4:+55733085 Msa1334910:five_prime_UTR
GCACTCATGGAATGATAGGG+TGG 0.649652 8_4:-55733306 None:intergenic
TCCAGCGATAGGAACTTCAA+AGG 0.649902 8_4:-55733349 None:intergenic
CTCCAACCATCTGTCAACAA+CGG 0.679074 8_4:-55733168 None:intergenic
TTTGAAATCTACTTCCACCA+AGG 0.681040 8_4:-55733245 None:intergenic
CGGATCGTCGAAATCACCGA+AGG 0.693947 8_4:+55733374 Msa1334910:CDS
GCTGCCAATGGTATTGAGGG+CGG 0.739556 8_4:+55733627 Msa1334910:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTATTTTTTTTTATTTTT+AGG + chr8_4:55733449-55733468 Msa1334910:intron 0.0%
!!! TTTTATTTTTTTTTATTTTT+AGG + chr8_4:55733449-55733468 Msa1334910:intron 0.0%
!! ATGGACAAAAAATATGTTAT+CGG + chr8_4:55733681-55733700 Msa1334910:CDS 20.0%
!! ATGGACAAAAAATATGTTAT+CGG + chr8_4:55733681-55733700 Msa1334910:CDS 20.0%
!! AAATTAAATCCTCTTTTGGT+TGG + chr8_4:55732946-55732965 Msa1334910:five_prime_UTR 25.0%
! ATATTAAATCCAACCAAAAG+AGG - chr8_4:55732958-55732977 None:intergenic 25.0%
! TAATACATTGTCTAACTTCT+AGG + chr8_4:55733023-55733042 Msa1334910:five_prime_UTR 25.0%
! AAATATTCACCAACAAAGAA+TGG - chr8_4:55733066-55733085 None:intergenic 25.0%
!! AAATTAAATCCTCTTTTGGT+TGG + chr8_4:55732946-55732965 Msa1334910:five_prime_UTR 25.0%
! ATATTAAATCCAACCAAAAG+AGG - chr8_4:55732958-55732977 None:intergenic 25.0%
! TAATACATTGTCTAACTTCT+AGG + chr8_4:55733023-55733042 Msa1334910:five_prime_UTR 25.0%
! AAATATTCACCAACAAAGAA+TGG - chr8_4:55733066-55733085 None:intergenic 25.0%
TGTTCAACAAATCAGTTAGT+CGG + chr8_4:55733145-55733164 Msa1334910:five_prime_UTR 30.0%
! ATTATTGCTTTCTAGTACCT+TGG + chr8_4:55733228-55733247 Msa1334910:five_prime_UTR 30.0%
GACATACAATAAACAACCTT+CGG - chr8_4:55733393-55733412 None:intergenic 30.0%
! TAGGAACTACCTTATACTTT+TGG + chr8_4:55733468-55733487 Msa1334910:intron 30.0%
! AGGAATTTGCCAAAAGTATA+AGG - chr8_4:55733480-55733499 None:intergenic 30.0%
ACAGGAATGATATTGTCATA+AGG - chr8_4:55733540-55733559 None:intergenic 30.0%
TGTTCAACAAATCAGTTAGT+CGG + chr8_4:55733145-55733164 Msa1334910:five_prime_UTR 30.0%
! ATTATTGCTTTCTAGTACCT+TGG + chr8_4:55733228-55733247 Msa1334910:five_prime_UTR 30.0%
GACATACAATAAACAACCTT+CGG - chr8_4:55733393-55733412 None:intergenic 30.0%
! TAGGAACTACCTTATACTTT+TGG + chr8_4:55733468-55733487 Msa1334910:intron 30.0%
! AGGAATTTGCCAAAAGTATA+AGG - chr8_4:55733480-55733499 None:intergenic 30.0%
ACAGGAATGATATTGTCATA+AGG - chr8_4:55733540-55733559 None:intergenic 30.0%
!! TTGTCTAACTTCTAGGATGT+CGG + chr8_4:55733030-55733049 Msa1334910:five_prime_UTR 35.0%
GAACTACAACCATTCTTTGT+TGG + chr8_4:55733054-55733073 Msa1334910:five_prime_UTR 35.0%
CGATTATTCTACGAGTTTAG+TGG + chr8_4:55733198-55733217 Msa1334910:five_prime_UTR 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr8_4:55733248-55733267 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr8_4:55733500-55733519 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr8_4:55733558-55733577 None:intergenic 35.0%
!! TTGTCTAACTTCTAGGATGT+CGG + chr8_4:55733030-55733049 Msa1334910:five_prime_UTR 35.0%
GAACTACAACCATTCTTTGT+TGG + chr8_4:55733054-55733073 Msa1334910:five_prime_UTR 35.0%
CGATTATTCTACGAGTTTAG+TGG + chr8_4:55733198-55733217 Msa1334910:five_prime_UTR 35.0%
! TTTGAAATCTACTTCCACCA+AGG - chr8_4:55733248-55733267 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG - chr8_4:55733500-55733519 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG - chr8_4:55733558-55733577 None:intergenic 35.0%
! ATTGCTTTCTAGTACCTTGG+TGG + chr8_4:55733231-55733250 Msa1334910:five_prime_UTR 40.0%
TGATAGGGTGGATAATCAAC+TGG - chr8_4:55733297-55733316 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - chr8_4:55733584-55733603 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr8_4:55733585-55733604 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr8_4:55733582-55733601 Msa1334910:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr8_4:55733586-55733605 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr8_4:55733591-55733610 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr8_4:55733588-55733607 Msa1334910:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr8_4:55733592-55733611 Msa1334910:CDS 40.0%
! ATTGCTTTCTAGTACCTTGG+TGG + chr8_4:55733231-55733250 Msa1334910:five_prime_UTR 40.0%
TGATAGGGTGGATAATCAAC+TGG - chr8_4:55733297-55733316 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - chr8_4:55733584-55733603 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG - chr8_4:55733585-55733604 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG + chr8_4:55733582-55733601 Msa1334910:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr8_4:55733586-55733605 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr8_4:55733591-55733610 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr8_4:55733588-55733607 Msa1334910:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr8_4:55733592-55733611 Msa1334910:CDS 40.0%
! TCTAGCAAGTGCCATTGCTA+CGG - chr8_4:55733099-55733118 None:intergenic 45.0%
! TAGCAATGGCACTTGCTAGA+TGG + chr8_4:55733099-55733118 Msa1334910:five_prime_UTR 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr8_4:55733171-55733190 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG + chr8_4:55733308-55733327 Msa1334910:exon 45.0%
!! ACCTTTGAAGTTCCTATCGC+TGG + chr8_4:55733348-55733367 Msa1334910:CDS 45.0%
TCCAGCGATAGGAACTTCAA+AGG - chr8_4:55733352-55733371 None:intergenic 45.0%
GAAGTTCCTATCGCTGGATA+CGG + chr8_4:55733354-55733373 Msa1334910:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr8_4:55733615-55733634 Msa1334910:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr8_4:55733623-55733642 Msa1334910:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr8_4:55733624-55733643 Msa1334910:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr8_4:55733662-55733681 Msa1334910:CDS 45.0%
! TCTAGCAAGTGCCATTGCTA+CGG - chr8_4:55733099-55733118 None:intergenic 45.0%
! TAGCAATGGCACTTGCTAGA+TGG + chr8_4:55733099-55733118 Msa1334910:five_prime_UTR 45.0%
CTCCAACCATCTGTCAACAA+CGG - chr8_4:55733171-55733190 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG + chr8_4:55733308-55733327 Msa1334910:exon 45.0%
!! ACCTTTGAAGTTCCTATCGC+TGG + chr8_4:55733348-55733367 Msa1334910:CDS 45.0%
TCCAGCGATAGGAACTTCAA+AGG - chr8_4:55733352-55733371 None:intergenic 45.0%
GAAGTTCCTATCGCTGGATA+CGG + chr8_4:55733354-55733373 Msa1334910:CDS 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG + chr8_4:55733615-55733634 Msa1334910:CDS 45.0%
TTGTGCTGCCAATGGTATTG+AGG + chr8_4:55733623-55733642 Msa1334910:CDS 45.0%
! TGTGCTGCCAATGGTATTGA+GGG + chr8_4:55733624-55733643 Msa1334910:CDS 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr8_4:55733662-55733681 Msa1334910:CDS 45.0%
TCTACGAGCTACCGTAGCAA+TGG + chr8_4:55733085-55733104 Msa1334910:five_prime_UTR 50.0%
! TGGCACTTGCTAGATGGTGA+TGG + chr8_4:55733105-55733124 Msa1334910:five_prime_UTR 50.0%
! GGCACTTGCTAGATGGTGAT+GGG + chr8_4:55733106-55733125 Msa1334910:five_prime_UTR 50.0%
GCACTCATGGAATGATAGGG+TGG - chr8_4:55733309-55733328 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - chr8_4:55733312-55733331 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG - chr8_4:55733313-55733332 None:intergenic 50.0%
CACGATTACGTCGTGTTGTG+CGG + chr8_4:55733513-55733532 Msa1334910:CDS 50.0%
TCTACGAGCTACCGTAGCAA+TGG + chr8_4:55733085-55733104 Msa1334910:five_prime_UTR 50.0%
! TGGCACTTGCTAGATGGTGA+TGG + chr8_4:55733105-55733124 Msa1334910:five_prime_UTR 50.0%
! GGCACTTGCTAGATGGTGAT+GGG + chr8_4:55733106-55733125 Msa1334910:five_prime_UTR 50.0%
GCACTCATGGAATGATAGGG+TGG - chr8_4:55733309-55733328 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG - chr8_4:55733312-55733331 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG - chr8_4:55733313-55733332 None:intergenic 50.0%
CACGATTACGTCGTGTTGTG+CGG + chr8_4:55733513-55733532 Msa1334910:CDS 50.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr8_4:55733162-55733181 Msa1334910:five_prime_UTR 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr8_4:55733166-55733185 Msa1334910:five_prime_UTR 55.0%
GACGATCCGTATCCAGCGAT+AGG - chr8_4:55733363-55733382 None:intergenic 55.0%
CGGATCGTCGAAATCACCGA+AGG + chr8_4:55733374-55733393 Msa1334910:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr8_4:55733627-55733646 Msa1334910:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr8_4:55733634-55733653 None:intergenic 55.0%
AGTCGGCCGTTGTTGACAGA+TGG + chr8_4:55733162-55733181 Msa1334910:five_prime_UTR 55.0%
GGCCGTTGTTGACAGATGGT+TGG + chr8_4:55733166-55733185 Msa1334910:five_prime_UTR 55.0%
GACGATCCGTATCCAGCGAT+AGG - chr8_4:55733363-55733382 None:intergenic 55.0%
CGGATCGTCGAAATCACCGA+AGG + chr8_4:55733374-55733393 Msa1334910:CDS 55.0%
! GCTGCCAATGGTATTGAGGG+CGG + chr8_4:55733627-55733646 Msa1334910:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG - chr8_4:55733634-55733653 None:intergenic 55.0%
GCACGATGCTGCCGCACTCA+TGG - chr8_4:55733322-55733341 None:intergenic 65.0%
GCACGATGCTGCCGCACTCA+TGG - chr8_4:55733322-55733341 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr8_4 gene 55732943 55733716 55732943 ID=Msa1334910;Name=Msa1334910
chr8_4 mRNA 55732943 55733716 55732943 ID=Msa1334910-mRNA-1;Parent=Msa1334910;Name=Msa1334910-mRNA-1;_AED=0.09;_eAED=0.09;_QI=378|1|0.5|1|1|1|2|0|106
chr8_4 exon 55732943 55733395 55732943 ID=Msa1334910-mRNA-1:exon:17347;Parent=Msa1334910-mRNA-1
chr8_4 exon 55733471 55733716 55733471 ID=Msa1334910-mRNA-1:exon:17348;Parent=Msa1334910-mRNA-1
chr8_4 five_prime_UTR 55732943 55733320 55732943 ID=Msa1334910-mRNA-1:five_prime_utr;Parent=Msa1334910-mRNA-1
chr8_4 CDS 55733321 55733395 55733321 ID=Msa1334910-mRNA-1:cds;Parent=Msa1334910-mRNA-1
chr8_4 CDS 55733471 55733716 55733471 ID=Msa1334910-mRNA-1:cds;Parent=Msa1334910-mRNA-1
Gene Sequence

>Msa1334910

ATGAGTGCGGCAGCATCGTGCTATTGTACCTTTGAAGTTCCTATCGCTGGATACGGATCGTCGAAATCACCGAAGGAACTACCTTATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCGTGTTGTGCGGACCTTATGACAATATCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGGATCCAAGCGTTGA
Protein sequence

>Msa1334910

MSAAASCYCTFEVPIAGYGSSKSPKELPYTFGKFLRVKHHDYVVLCGPYDNIIPVRLKYTDDPIPNVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIGSKR*