AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0488590

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0488590 MtrunA17_Chr3g0078381 100.000 147 0 0 1 147 1 147 3.49e-105 296
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0488590 AT3G22480.1 70.667 150 39 3 1 147 1 148 2.12e-67 201
Msa0488590 AT3G22480.2 70.667 150 39 3 1 147 1 148 2.12e-67 201

Find 44 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTTCAAGTTCCGTTATTT+TGG 0.192430 3_4:-8565088 None:intergenic
GCAACTGCTTGTTCATTTAC+TGG 0.248625 3_4:-8565021 None:intergenic
TACTGGCTCCTTGCGATCTT+CGG 0.331035 3_4:-8565004 None:intergenic
CAAAATAACGGAACTTGAAA+TGG 0.346568 3_4:+8565089 Msa0488590:CDS
AGCAGGCAGGACCTCTTTGA+TGG 0.408930 3_4:-8565208 None:intergenic
AGACATTGGAAAAGAAGAAA+AGG 0.418775 3_4:+8565280 Msa0488590:CDS
TTGAGACTAAATATAAAATC+AGG 0.420368 3_4:+8565316 Msa0488590:CDS
GGAGTACTTGTGGGCCCTGC+GGG 0.425415 3_4:+8565399 Msa0488590:CDS
TCTTTATTCCGCTGCACAGC+AGG 0.438536 3_4:-8565225 None:intergenic
AGACGATGCTATCGAATGAT+TGG 0.440454 3_4:+8565165 Msa0488590:CDS
TTCGATAGCATCGTCTAGAT+TGG 0.458077 3_4:-8565158 None:intergenic
GACATTGGAAAAGAAGAAAA+GGG 0.500685 3_4:+8565281 Msa0488590:CDS
GTGTAGAATCATGGCTAGTA+AGG 0.508954 3_4:+8564981 None:intergenic
GCTGAGGTGAACGATGAATC+TGG 0.515292 3_4:+8565354 Msa0488590:CDS
CCAAATTTACACCAAAATAA+CGG 0.527386 3_4:+8565077 Msa0488590:CDS
AGATTGGTCTAGCGGCTGAA+TGG 0.531922 3_4:-8565142 None:intergenic
TGTCATTCGCTACCACCCGC+AGG 0.539315 3_4:-8565414 None:intergenic
TATTCCGCTGCACAGCAGGC+AGG 0.540606 3_4:-8565221 None:intergenic
TGCAAGGCTTAACGAGACAT+TGG 0.541862 3_4:+8565266 Msa0488590:CDS
GTACTTGTGGGCCCTGCGGG+TGG 0.543152 3_4:+8565402 Msa0488590:CDS
GAACGATGAATCTGGTAAGA+AGG 0.544140 3_4:+8565362 Msa0488590:CDS
TCAGCTCAAGGAGTACTTGT+GGG 0.554339 3_4:+8565390 Msa0488590:CDS
AAGAAGGAAGGTTCAGCTCA+AGG 0.558366 3_4:+8565378 Msa0488590:CDS
GCTGTGCAGCGGAATAAAGA+AGG 0.563818 3_4:+8565228 Msa0488590:CDS
CGATGCTATCGAATGATTGG+AGG 0.563926 3_4:+8565168 Msa0488590:CDS
TTCATCGTTCACCTCAGCAT+CGG 0.575473 3_4:-8565349 None:intergenic
GATGAATCTGGTAAGAAGGA+AGG 0.587326 3_4:+8565366 Msa0488590:CDS
CTAAATATAAAATCAGGATG+AGG 0.587775 3_4:+8565322 Msa0488590:CDS
GATGAGGAAGGCCGATGCTG+AGG 0.588771 3_4:+8565338 Msa0488590:CDS
AGGTCCTGCCTGCTGTGCAG+CGG 0.589956 3_4:+8565217 Msa0488590:CDS
GACTTGAAGAGGTTGTTGCA+AGG 0.593695 3_4:+8565250 Msa0488590:CDS
GTCATTCGCTACCACCCGCA+GGG 0.594608 3_4:-8565413 None:intergenic
ATATAAAATCAGGATGAGGA+AGG 0.596264 3_4:+8565326 Msa0488590:CDS
TAGTAAGGCCGAAGATCGCA+AGG 0.597879 3_4:+8564996 Msa0488590:CDS
AGGAGTACTTGTGGGCCCTG+CGG 0.600783 3_4:+8565398 Msa0488590:CDS
TTCAGCTCAAGGAGTACTTG+TGG 0.603923 3_4:+8565389 Msa0488590:CDS
AATGATTGGAGGGGTGCTTG+TGG 0.605277 3_4:+8565179 Msa0488590:CDS
GATGCTATCGAATGATTGGA+GGG 0.617244 3_4:+8565169 Msa0488590:CDS
GGAAGTCAGTGAGCACTCGT+TGG 0.621570 3_4:+8565110 Msa0488590:CDS
CAAATATGTATGCAGCTATG+AGG 0.631644 3_4:+8565043 Msa0488590:CDS
CATCGTCTAGATTGGTCTAG+CGG 0.643268 3_4:-8565150 None:intergenic
GAATAAAGAAGGACTTGAAG+AGG 0.645797 3_4:+8565239 Msa0488590:CDS
TGTGGAAAGAACCATCAAAG+AGG 0.692372 3_4:+8565197 Msa0488590:CDS
ATGCTATCGAATGATTGGAG+GGG 0.721195 3_4:+8565170 Msa0488590:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGAGACTAAATATAAAATC+AGG + chr3_4:8565316-8565335 Msa0488590:CDS 20.0%
! CCAAATTTACACCAAAATAA+CGG + chr3_4:8565077-8565096 Msa0488590:CDS 25.0%
! CTAAATATAAAATCAGGATG+AGG + chr3_4:8565322-8565341 Msa0488590:CDS 25.0%
!! TTTTGGTGTAAATTTGGTTG+AGG - chr3_4:8565074-8565093 None:intergenic 30.0%
!!! CCGTTATTTTGGTGTAAATT+TGG - chr3_4:8565080-8565099 None:intergenic 30.0%
!!! CATTTCAAGTTCCGTTATTT+TGG - chr3_4:8565091-8565110 None:intergenic 30.0%
! CAAAATAACGGAACTTGAAA+TGG + chr3_4:8565089-8565108 Msa0488590:CDS 30.0%
AGACATTGGAAAAGAAGAAA+AGG + chr3_4:8565280-8565299 Msa0488590:CDS 30.0%
GACATTGGAAAAGAAGAAAA+GGG + chr3_4:8565281-8565300 Msa0488590:CDS 30.0%
ATATAAAATCAGGATGAGGA+AGG + chr3_4:8565326-8565345 Msa0488590:CDS 30.0%
CAAATATGTATGCAGCTATG+AGG + chr3_4:8565043-8565062 Msa0488590:CDS 35.0%
GAATAAAGAAGGACTTGAAG+AGG + chr3_4:8565239-8565258 Msa0488590:CDS 35.0%
GCAACTGCTTGTTCATTTAC+TGG - chr3_4:8565024-8565043 None:intergenic 40.0%
TTCGATAGCATCGTCTAGAT+TGG - chr3_4:8565161-8565180 None:intergenic 40.0%
AGACGATGCTATCGAATGAT+TGG + chr3_4:8565165-8565184 Msa0488590:CDS 40.0%
GATGCTATCGAATGATTGGA+GGG + chr3_4:8565169-8565188 Msa0488590:CDS 40.0%
ATGCTATCGAATGATTGGAG+GGG + chr3_4:8565170-8565189 Msa0488590:CDS 40.0%
TGTGGAAAGAACCATCAAAG+AGG + chr3_4:8565197-8565216 Msa0488590:CDS 40.0%
GAACGATGAATCTGGTAAGA+AGG + chr3_4:8565362-8565381 Msa0488590:CDS 40.0%
GATGAATCTGGTAAGAAGGA+AGG + chr3_4:8565366-8565385 Msa0488590:CDS 40.0%
!! CATCGTCTAGATTGGTCTAG+CGG - chr3_4:8565153-8565172 None:intergenic 45.0%
CGATGCTATCGAATGATTGG+AGG + chr3_4:8565168-8565187 Msa0488590:CDS 45.0%
GACTTGAAGAGGTTGTTGCA+AGG + chr3_4:8565250-8565269 Msa0488590:CDS 45.0%
TGCAAGGCTTAACGAGACAT+TGG + chr3_4:8565266-8565285 Msa0488590:CDS 45.0%
TTCATCGTTCACCTCAGCAT+CGG - chr3_4:8565352-8565371 None:intergenic 45.0%
AAGAAGGAAGGTTCAGCTCA+AGG + chr3_4:8565378-8565397 Msa0488590:CDS 45.0%
!! TTCAGCTCAAGGAGTACTTG+TGG + chr3_4:8565389-8565408 Msa0488590:CDS 45.0%
!! TCAGCTCAAGGAGTACTTGT+GGG + chr3_4:8565390-8565409 Msa0488590:CDS 45.0%
TAGTAAGGCCGAAGATCGCA+AGG + chr3_4:8564996-8565015 Msa0488590:CDS 50.0%
!! TACTGGCTCCTTGCGATCTT+CGG - chr3_4:8565007-8565026 None:intergenic 50.0%
!! AGATTGGTCTAGCGGCTGAA+TGG - chr3_4:8565145-8565164 None:intergenic 50.0%
!! AATGATTGGAGGGGTGCTTG+TGG + chr3_4:8565179-8565198 Msa0488590:CDS 50.0%
TCTTTATTCCGCTGCACAGC+AGG - chr3_4:8565228-8565247 None:intergenic 50.0%
GCTGTGCAGCGGAATAAAGA+AGG + chr3_4:8565228-8565247 Msa0488590:CDS 50.0%
GCTGAGGTGAACGATGAATC+TGG + chr3_4:8565354-8565373 Msa0488590:CDS 50.0%
GGAAGTCAGTGAGCACTCGT+TGG + chr3_4:8565110-8565129 Msa0488590:CDS 55.0%
AGCAGGCAGGACCTCTTTGA+TGG - chr3_4:8565211-8565230 None:intergenic 55.0%
TATTCCGCTGCACAGCAGGC+AGG - chr3_4:8565224-8565243 None:intergenic 60.0%
GATGAGGAAGGCCGATGCTG+AGG + chr3_4:8565338-8565357 Msa0488590:CDS 60.0%
!! AGGAGTACTTGTGGGCCCTG+CGG + chr3_4:8565398-8565417 Msa0488590:CDS 60.0%
AGGTCCTGCCTGCTGTGCAG+CGG + chr3_4:8565217-8565236 Msa0488590:CDS 65.0%
! GGAGTACTTGTGGGCCCTGC+GGG + chr3_4:8565399-8565418 Msa0488590:CDS 65.0%
GTACTTGTGGGCCCTGCGGG+TGG + chr3_4:8565402-8565421 Msa0488590:CDS 70.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 8564991 8565434 8564991 ID=Msa0488590;Name=Msa0488590
chr3_4 mRNA 8564991 8565434 8564991 ID=Msa0488590-mRNA-1;Parent=Msa0488590;Name=Msa0488590-mRNA-1;_AED=0.28;_eAED=0.29;_QI=0|-1|0|1|-1|1|1|0|147
chr3_4 exon 8564991 8565434 8564991 ID=Msa0488590-mRNA-1:exon:2794;Parent=Msa0488590-mRNA-1
chr3_4 CDS 8564991 8565434 8564991 ID=Msa0488590-mRNA-1:cds;Parent=Msa0488590-mRNA-1
Gene Sequence

>Msa0488590

ATGGCTAGTAAGGCCGAAGATCGCAAGGAGCCAGTAAATGAACAAGCAGTTGCAAATATGTATGCAGCTATGAGGTCAGACCTCAACCAAATTTACACCAAAATAACGGAACTTGAAATGGAAGTCAGTGAGCACTCGTTGGTTCTTAATGCCATTCAGCCGCTAGACCAATCTAGACGATGCTATCGAATGATTGGAGGGGTGCTTGTGGAAAGAACCATCAAAGAGGTCCTGCCTGCTGTGCAGCGGAATAAAGAAGGACTTGAAGAGGTTGTTGCAAGGCTTAACGAGACATTGGAAAAGAAGAAAAGGGAAATTGCTGAGTTTGAGACTAAATATAAAATCAGGATGAGGAAGGCCGATGCTGAGGTGAACGATGAATCTGGTAAGAAGGAAGGTTCAGCTCAAGGAGTACTTGTGGGCCCTGCGGGTGGTAGCGAATGA
Protein sequence

>Msa0488590

MASKAEDRKEPVNEQAVANMYAAMRSDLNQIYTKITELEMEVSEHSLVLNAIQPLDQSRRCYRMIGGVLVERTIKEVLPAVQRNKEGLEEVVARLNETLEKKKREIAEFETKYKIRMRKADAEVNDESGKKEGSAQGVLVGPAGGSE*