AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0866530


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0866530 MtrunA17_Chr5g0434691 99.048 105 1 0 1 105 1 105 4.75e-71 210
Msa0866530 MtrunA17_Chr3g0110481 66.337 101 33 1 1 100 1 101 4.05e-32 110
Msa0866530 MtrunA17_Chr8g0392851 43.119 109 42 3 13 101 28 136 2.14e-16 72.8
Msa0866530 MtrunA17_Chr6g0482691 43.000 100 45 3 13 100 43 142 2.70e-15 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0866530 AT1G14900.1 63.218 87 32 0 10 96 21 107 4.75e-36 122
Msa0866530 AT3G18035.1 35.772 123 40 1 13 96 66 188 1.38e-16 73.9
Msa0866530 AT3G18035.2 35.772 123 40 1 13 96 66 188 3.23e-16 72.8
Msa0866530 AT1G48620.1 37.008 127 42 4 15 103 78 204 5.55e-15 69.3

Find 24 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTCTCTTTGGTGGTGCATT+TGG 0.255109 5_4:-68259219 None:intergenic
GGTGGAGCCAATGGATCTTT+TGG 0.315588 5_4:-68259261 None:intergenic
GATCTGAGGATTGAATTTAA+AGG 0.320514 5_4:-68258457 None:intergenic
GGTCTTCCACGTCCTCTCTT+TGG 0.323730 5_4:-68259231 None:intergenic
CTTAACCAGATGAAGGAAAA+TGG 0.327311 5_4:+68259156 Msa0866530:CDS
TTTGGTGGTGCATTTGGATC+AGG 0.346536 5_4:-68259213 None:intergenic
AGAACAATTGAATGGCCTTC+TGG 0.359176 5_4:-68259123 None:intergenic
AACTACATAGAATCAATCTA+TGG 0.397570 5_4:+68259093 Msa0866530:CDS
GATGATTTGTTTGAACCATT+TGG 0.430370 5_4:-68259063 None:intergenic
TGTGAATTTACCTCAGGGTA+TGG 0.486285 5_4:-68258638 None:intergenic
CTTCCACGTCCTCTCTTTGG+TGG 0.517078 5_4:-68259228 None:intergenic
GATTTGCAAGAACAATTGAA+TGG 0.519543 5_4:-68259131 None:intergenic
GTAGATGATTATGAAGGCAC+TGG 0.529915 5_4:+68259026 Msa0866530:intron
ACCAAAGCCAAAAGATCCAT+TGG 0.533769 5_4:+68259254 Msa0866530:CDS
GGGTATGGAGGAAGTGAAAG+AGG 0.561822 5_4:-68258623 None:intergenic
AGCTTCAATGGCTACTCAAG+AGG 0.565718 5_4:+68258592 Msa0866530:exon
AAATCACCTTAACCAGATGA+AGG 0.568245 5_4:+68259149 Msa0866530:CDS
GAAGCACTGAATGAACCAAA+TGG 0.572522 5_4:+68259048 Msa0866530:CDS
GCACCACCAAAGAGAGGACG+TGG 0.602504 5_4:+68259225 Msa0866530:CDS
ATCTATGGTGAATTACCAGA+AGG 0.621839 5_4:+68259108 Msa0866530:CDS
GAATTTACCTCAGGGTATGG+AGG 0.638966 5_4:-68258635 None:intergenic
CCAAATGCACCACCAAAGAG+AGG 0.648545 5_4:+68259219 Msa0866530:CDS
TTCACTTCCTCCATACCCTG+AGG 0.676529 5_4:+68258628 Msa0866530:CDS
TGTGATAGTTGCAAGATCTG+AGG 0.701586 5_4:-68258471 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTTGAAAAAATAAGAAAA+GGG - chr5_4:68258684-68258703 None:intergenic 15.0%
!! TTTCTTGAAAAAATAAGAAA+AGG - chr5_4:68258685-68258704 None:intergenic 15.0%
!!! TCAAATAAGGAAATTTTTTT+AGG + chr5_4:68258823-68258842 Msa0866530:intron 15.0%
!!! CAAATAAGGAAATTTTTTTA+GGG + chr5_4:68258824-68258843 Msa0866530:intron 15.0%
!! TTCTTGAAAAAATAAGAAAA+GGG - chr5_4:68258684-68258703 None:intergenic 15.0%
!! TTTCTTGAAAAAATAAGAAA+AGG - chr5_4:68258685-68258704 None:intergenic 15.0%
!!! TCAAATAAGGAAATTTTTTT+AGG + chr5_4:68258823-68258842 Msa0866530:intron 15.0%
!!! CAAATAAGGAAATTTTTTTA+GGG + chr5_4:68258824-68258843 Msa0866530:intron 15.0%
!! TCTTGAAAAAATAAGAAAAG+GGG - chr5_4:68258683-68258702 None:intergenic 20.0%
!!! TTTAACAATTTTTACTCACT+TGG + chr5_4:68258753-68258772 Msa0866530:intron 20.0%
!!! TTAACAATTTTTACTCACTT+GGG + chr5_4:68258754-68258773 Msa0866530:intron 20.0%
!! AAATCATTCAACATGTTAAT+GGG - chr5_4:68258935-68258954 None:intergenic 20.0%
!! AAAATCATTCAACATGTTAA+TGG - chr5_4:68258936-68258955 None:intergenic 20.0%
!! TCTTGAAAAAATAAGAAAAG+GGG - chr5_4:68258683-68258702 None:intergenic 20.0%
!!! TTTAACAATTTTTACTCACT+TGG + chr5_4:68258753-68258772 Msa0866530:intron 20.0%
!!! TTAACAATTTTTACTCACTT+GGG + chr5_4:68258754-68258773 Msa0866530:intron 20.0%
!! AAATCATTCAACATGTTAAT+GGG - chr5_4:68258935-68258954 None:intergenic 20.0%
!! AAAATCATTCAACATGTTAA+TGG - chr5_4:68258936-68258955 None:intergenic 20.0%
!!! GCTGTTTTTGTAATCAAATA+AGG + chr5_4:68258810-68258829 Msa0866530:intron 25.0%
!!! TACAAAGACTTTTTTCTGTT+TGG - chr5_4:68258866-68258885 None:intergenic 25.0%
!! GATTTTGTAGATGATTATGA+AGG + chr5_4:68259020-68259039 Msa0866530:intron 25.0%
! AACTACATAGAATCAATCTA+TGG + chr5_4:68259093-68259112 Msa0866530:CDS 25.0%
!!! GCTGTTTTTGTAATCAAATA+AGG + chr5_4:68258810-68258829 Msa0866530:intron 25.0%
!!! TACAAAGACTTTTTTCTGTT+TGG - chr5_4:68258866-68258885 None:intergenic 25.0%
!! GATTTTGTAGATGATTATGA+AGG + chr5_4:68259020-68259039 Msa0866530:intron 25.0%
! AACTACATAGAATCAATCTA+TGG + chr5_4:68259093-68259112 Msa0866530:CDS 25.0%
GATCTGAGGATTGAATTTAA+AGG - chr5_4:68258460-68258479 None:intergenic 30.0%
!! TCACTATTTTCAAGCTTCAA+TGG + chr5_4:68258580-68258599 Msa0866530:exon 30.0%
! TCAAGATTACTATTTGGTGA+GGG - chr5_4:68258790-68258809 None:intergenic 30.0%
AACAGCTCAAGATTACTATT+TGG - chr5_4:68258796-68258815 None:intergenic 30.0%
! GTTGAATGATTTTCTCAACA+TGG + chr5_4:68258943-68258962 Msa0866530:intron 30.0%
!! GATGATTTGTTTGAACCATT+TGG - chr5_4:68259066-68259085 None:intergenic 30.0%
GATTTGCAAGAACAATTGAA+TGG - chr5_4:68259134-68259153 None:intergenic 30.0%
AGTTGTTCTTTGCAAAAACA+AGG - chr5_4:68259185-68259204 None:intergenic 30.0%
GATCTGAGGATTGAATTTAA+AGG - chr5_4:68258460-68258479 None:intergenic 30.0%
!! TCACTATTTTCAAGCTTCAA+TGG + chr5_4:68258580-68258599 Msa0866530:exon 30.0%
! TCAAGATTACTATTTGGTGA+GGG - chr5_4:68258790-68258809 None:intergenic 30.0%
AACAGCTCAAGATTACTATT+TGG - chr5_4:68258796-68258815 None:intergenic 30.0%
! GTTGAATGATTTTCTCAACA+TGG + chr5_4:68258943-68258962 Msa0866530:intron 30.0%
!! GATGATTTGTTTGAACCATT+TGG - chr5_4:68259066-68259085 None:intergenic 30.0%
GATTTGCAAGAACAATTGAA+TGG - chr5_4:68259134-68259153 None:intergenic 30.0%
AGTTGTTCTTTGCAAAAACA+AGG - chr5_4:68259185-68259204 None:intergenic 30.0%
! AAGGGGTGTATGTTGAATTA+GGG - chr5_4:68258666-68258685 None:intergenic 35.0%
! AAAGGGGTGTATGTTGAATT+AGG - chr5_4:68258667-68258686 None:intergenic 35.0%
! CAAGATTACTATTTGGTGAG+GGG - chr5_4:68258789-68258808 None:intergenic 35.0%
! CTCAAGATTACTATTTGGTG+AGG - chr5_4:68258791-68258810 None:intergenic 35.0%
ATCTATGGTGAATTACCAGA+AGG + chr5_4:68259108-68259127 Msa0866530:CDS 35.0%
AAATCACCTTAACCAGATGA+AGG + chr5_4:68259149-68259168 Msa0866530:CDS 35.0%
! CATTTTCCTTCATCTGGTTA+AGG - chr5_4:68259158-68259177 None:intergenic 35.0%
CTTAACCAGATGAAGGAAAA+TGG + chr5_4:68259156-68259175 Msa0866530:CDS 35.0%
! AAGGGGTGTATGTTGAATTA+GGG - chr5_4:68258666-68258685 None:intergenic 35.0%
! AAAGGGGTGTATGTTGAATT+AGG - chr5_4:68258667-68258686 None:intergenic 35.0%
! CAAGATTACTATTTGGTGAG+GGG - chr5_4:68258789-68258808 None:intergenic 35.0%
! CTCAAGATTACTATTTGGTG+AGG - chr5_4:68258791-68258810 None:intergenic 35.0%
ATCTATGGTGAATTACCAGA+AGG + chr5_4:68259108-68259127 Msa0866530:CDS 35.0%
AAATCACCTTAACCAGATGA+AGG + chr5_4:68259149-68259168 Msa0866530:CDS 35.0%
! CATTTTCCTTCATCTGGTTA+AGG - chr5_4:68259158-68259177 None:intergenic 35.0%
CTTAACCAGATGAAGGAAAA+TGG + chr5_4:68259156-68259175 Msa0866530:CDS 35.0%
TGTGATAGTTGCAAGATCTG+AGG - chr5_4:68258474-68258493 None:intergenic 40.0%
TGTGAATTTACCTCAGGGTA+TGG - chr5_4:68258641-68258660 None:intergenic 40.0%
! AGGGGTGTATGTTGAATTAG+GGG - chr5_4:68258665-68258684 None:intergenic 40.0%
! GTAGATGATTATGAAGGCAC+TGG + chr5_4:68259026-68259045 Msa0866530:intron 40.0%
!! GAAGCACTGAATGAACCAAA+TGG + chr5_4:68259048-68259067 Msa0866530:CDS 40.0%
AGAACAATTGAATGGCCTTC+TGG - chr5_4:68259126-68259145 None:intergenic 40.0%
!!! AATGGATCTTTTGGCTTTGG+TGG - chr5_4:68259255-68259274 None:intergenic 40.0%
ACCAAAGCCAAAAGATCCAT+TGG + chr5_4:68259254-68259273 Msa0866530:CDS 40.0%
TGTGATAGTTGCAAGATCTG+AGG - chr5_4:68258474-68258493 None:intergenic 40.0%
TGTGAATTTACCTCAGGGTA+TGG - chr5_4:68258641-68258660 None:intergenic 40.0%
! AGGGGTGTATGTTGAATTAG+GGG - chr5_4:68258665-68258684 None:intergenic 40.0%
! GTAGATGATTATGAAGGCAC+TGG + chr5_4:68259026-68259045 Msa0866530:intron 40.0%
!! GAAGCACTGAATGAACCAAA+TGG + chr5_4:68259048-68259067 Msa0866530:CDS 40.0%
AGAACAATTGAATGGCCTTC+TGG - chr5_4:68259126-68259145 None:intergenic 40.0%
!!! AATGGATCTTTTGGCTTTGG+TGG - chr5_4:68259255-68259274 None:intergenic 40.0%
ACCAAAGCCAAAAGATCCAT+TGG + chr5_4:68259254-68259273 Msa0866530:CDS 40.0%
AGCTTCAATGGCTACTCAAG+AGG + chr5_4:68258592-68258611 Msa0866530:exon 45.0%
GAATTTACCTCAGGGTATGG+AGG - chr5_4:68258638-68258657 None:intergenic 45.0%
GGGGTGTATGTTGAATTAGG+GGG - chr5_4:68258664-68258683 None:intergenic 45.0%
! GGTCACCATTTTCCTTCATC+TGG - chr5_4:68259164-68259183 None:intergenic 45.0%
!! TTTGGTGGTGCATTTGGATC+AGG - chr5_4:68259216-68259235 None:intergenic 45.0%
!!! GCCAATGGATCTTTTGGCTT+TGG - chr5_4:68259258-68259277 None:intergenic 45.0%
AGCTTCAATGGCTACTCAAG+AGG + chr5_4:68258592-68258611 Msa0866530:exon 45.0%
GAATTTACCTCAGGGTATGG+AGG - chr5_4:68258638-68258657 None:intergenic 45.0%
GGGGTGTATGTTGAATTAGG+GGG - chr5_4:68258664-68258683 None:intergenic 45.0%
! GGTCACCATTTTCCTTCATC+TGG - chr5_4:68259164-68259183 None:intergenic 45.0%
!! TTTGGTGGTGCATTTGGATC+AGG - chr5_4:68259216-68259235 None:intergenic 45.0%
!!! GCCAATGGATCTTTTGGCTT+TGG - chr5_4:68259258-68259277 None:intergenic 45.0%
GGGTATGGAGGAAGTGAAAG+AGG - chr5_4:68258626-68258645 None:intergenic 50.0%
TTCACTTCCTCCATACCCTG+AGG + chr5_4:68258628-68258647 Msa0866530:CDS 50.0%
! GGGGGTGTGAATTTACCTCA+GGG - chr5_4:68258646-68258665 None:intergenic 50.0%
! AGGGGGTGTGAATTTACCTC+AGG - chr5_4:68258647-68258666 None:intergenic 50.0%
!! CCTCTCTTTGGTGGTGCATT+TGG - chr5_4:68259222-68259241 None:intergenic 50.0%
CCAAATGCACCACCAAAGAG+AGG + chr5_4:68259219-68259238 Msa0866530:CDS 50.0%
! GGTGGAGCCAATGGATCTTT+TGG - chr5_4:68259264-68259283 None:intergenic 50.0%
GGGTATGGAGGAAGTGAAAG+AGG - chr5_4:68258626-68258645 None:intergenic 50.0%
TTCACTTCCTCCATACCCTG+AGG + chr5_4:68258628-68258647 Msa0866530:CDS 50.0%
! GGGGGTGTGAATTTACCTCA+GGG - chr5_4:68258646-68258665 None:intergenic 50.0%
! AGGGGGTGTGAATTTACCTC+AGG - chr5_4:68258647-68258666 None:intergenic 50.0%
!! CCTCTCTTTGGTGGTGCATT+TGG - chr5_4:68259222-68259241 None:intergenic 50.0%
CCAAATGCACCACCAAAGAG+AGG + chr5_4:68259219-68259238 Msa0866530:CDS 50.0%
! GGTGGAGCCAATGGATCTTT+TGG - chr5_4:68259264-68259283 None:intergenic 50.0%
CTTCCACGTCCTCTCTTTGG+TGG - chr5_4:68259231-68259250 None:intergenic 55.0%
GGTCTTCCACGTCCTCTCTT+TGG - chr5_4:68259234-68259253 None:intergenic 55.0%
CTTCCACGTCCTCTCTTTGG+TGG - chr5_4:68259231-68259250 None:intergenic 55.0%
GGTCTTCCACGTCCTCTCTT+TGG - chr5_4:68259234-68259253 None:intergenic 55.0%
GCACCACCAAAGAGAGGACG+TGG + chr5_4:68259225-68259244 Msa0866530:CDS 60.0%
GCACCACCAAAGAGAGGACG+TGG + chr5_4:68259225-68259244 Msa0866530:CDS 60.0%
!! GCAGCTGGTGGTGGAGCCAA+TGG - chr5_4:68259273-68259292 None:intergenic 65.0%
!! GCAGCTGGTGGTGGAGCCAA+TGG - chr5_4:68259273-68259292 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 68258456 68259293 68258456 ID=Msa0866530;Name=Msa0866530
chr5_4 mRNA 68258456 68259293 68258456 ID=Msa0866530-mRNA-1;Parent=Msa0866530;Name=Msa0866530-mRNA-1;_AED=0.00;_eAED=0.00;_QI=143|1|0.5|1|1|1|2|0|105
chr5_4 exon 68258456 68258649 68258456 ID=Msa0866530-mRNA-1:exon:21576;Parent=Msa0866530-mRNA-1
chr5_4 exon 68259030 68259293 68259030 ID=Msa0866530-mRNA-1:exon:21577;Parent=Msa0866530-mRNA-1
chr5_4 five_prime_UTR 68258456 68258598 68258456 ID=Msa0866530-mRNA-1:five_prime_utr;Parent=Msa0866530-mRNA-1
chr5_4 CDS 68258599 68258649 68258599 ID=Msa0866530-mRNA-1:cds;Parent=Msa0866530-mRNA-1
chr5_4 CDS 68259030 68259293 68259030 ID=Msa0866530-mRNA-1:cds;Parent=Msa0866530-mRNA-1
Gene Sequence

>Msa0866530

ATGGCTACTCAAGAGGTTAATAAGCCTCTTTCACTTCCTCCATACCCTGAGATGATTATGAAGGCACTGGAAGCACTGAATGAACCAAATGGTTCAAACAAATCATCAATTTCAAACTACATAGAATCAATCTATGGTGAATTACCAGAAGGCCATTCAATTGTTCTTGCAAATCACCTTAACCAGATGAAGGAAAATGGTGACCTTGTTTTTGCAAAGAACAACTACATGAAGCCTGATCCAAATGCACCACCAAAGAGAGGACGTGGAAGACCACCAAAGCCAAAAGATCCATTGGCTCCACCACCAGCTGCT

Protein sequence

>Msa0866530

MATQEVNKPLSLPPYPEMIMKALEALNEPNGSNKSSISNYIESIYGELPEGHSIVLANHLNQMKENGDLVFAKNNYMKPDPNAPPKRGRGRPPKPKDPLAPPPAA