AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0565450

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0565450 MtrunA17_Chr8g0380241 69.725 109 18 2 1 109 1 94 2.90e-44 140
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0565450 AT5G14285.1 43.885 139 75 2 3 140 1 137 1.34e-30 110
Msa0565450 AT3G27270.1 44.361 133 66 4 15 142 10 139 4.07e-28 104
Msa0565450 AT3G27270.2 44.361 133 66 4 15 142 10 139 4.93e-28 104
Msa0565450 AT3G25950.1 35.593 118 74 2 17 133 18 134 7.05e-17 74.7

Find 38 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGTCTCCGTCTTCGTTT+TGG 0.312642 4_1:-66304772 Msa0565450:CDS
CGAAGAAAAGCATGGCTAAT+TGG 0.313315 4_1:+66304826 None:intergenic
GAATCTGCGGGGTTCGGTCT+TGG 0.333789 4_1:+66305069 None:intergenic
GCGGCTGATAAGCCACGGTT+GGG 0.356572 4_1:+66304957 None:intergenic
TTCTTAACCGCCACCATTCT+CGG 0.383303 4_1:-66305008 Msa0565450:CDS
TTCACTTGCCGTTTCATGAT+CGG 0.402390 4_1:-66304801 Msa0565450:CDS
TGACTCGAATCTGCGGGGTT+CGG 0.408816 4_1:+66305063 None:intergenic
GGGGTTGGTGTCGGAGAAGA+AGG 0.474258 4_1:+66304977 None:intergenic
GCGAAGTAGTGAACGTAGCT+TGG 0.479988 4_1:+66304852 None:intergenic
CAGCTATCTTTAGCAGAAGA+AGG 0.482080 4_1:-66305158 Msa0565450:CDS
GGCGGCTGATAAGCCACGGT+TGG 0.485636 4_1:+66304956 None:intergenic
GATATTCTGCAAGGTAGTAT+TGG 0.489793 4_1:+66304935 None:intergenic
CGAAGTAGTGAACGTAGCTT+GGG 0.489911 4_1:+66304853 None:intergenic
GAAGGCGATTACGCCGAGAA+TGG 0.509060 4_1:+66304995 None:intergenic
AACCGAAAAGGTAAAGAGAA+AGG 0.509233 4_1:+66305105 None:intergenic
AGAAGATGAAGTAACCGAAA+AGG 0.522301 4_1:+66305093 None:intergenic
TGCCGTTTCATGATCGGTAA+CGG 0.523712 4_1:-66304795 Msa0565450:CDS
TGATAAGCCACGGTTGGGGT+TGG 0.524167 4_1:+66304962 None:intergenic
CACCGTTACCGATCATGAAA+CGG 0.536378 4_1:+66304793 None:intergenic
TATCTTTAGCAGAAGAAGGT+TGG 0.536708 4_1:-66305154 Msa0565450:CDS
GCCACGGTTGGGGTTGGTGT+CGG 0.564451 4_1:+66304968 None:intergenic
TAACAGATCGGTGATGAAGT+AGG 0.567648 4_1:+66304893 None:intergenic
GAGTATGTGACTCGAATCTG+CGG 0.574331 4_1:+66305056 None:intergenic
AACAGCAACCAAAACGAAGA+CGG 0.574348 4_1:+66304764 None:intergenic
AGTATGTGACTCGAATCTGC+GGG 0.576710 4_1:+66305057 None:intergenic
ATTCTGCAAGGTAGTATTGG+CGG 0.587733 4_1:+66304938 None:intergenic
GAAAAGGTAAAGAGAAAGGA+AGG 0.588741 4_1:+66305109 None:intergenic
CGGCTGATAAGCCACGGTTG+GGG 0.593778 4_1:+66304958 None:intergenic
GGCGATTACGCCGAGAATGG+TGG 0.608266 4_1:+66304998 None:intergenic
AGTAGTGAACGTAGCTTGGG+AGG 0.609827 4_1:+66304856 None:intergenic
TCCGACACCAACCCCAACCG+TGG 0.612983 4_1:-66304969 Msa0565450:CDS
GTCAAGAACGATATTCTGCA+AGG 0.624929 4_1:+66304926 None:intergenic
AAAGACGCAAATCAAGACGC+TGG 0.625165 4_1:+66305034 None:intergenic
GATTACGCCGAGAATGGTGG+CGG 0.626615 4_1:+66305001 None:intergenic
TATTGGCGGCTGATAAGCCA+CGG 0.657192 4_1:+66304952 None:intergenic
AGTGAAGACGAAGAAAAGCA+TGG 0.669757 4_1:+66304818 None:intergenic
AACGACGAAATGTAACAGAT+CGG 0.672930 4_1:+66304881 None:intergenic
GTATGTGACTCGAATCTGCG+GGG 0.720046 4_1:+66305058 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAAGGAAGGTGAAGAAAAAT+GGG + chr4_1:66304805-66304824 None:intergenic 30.0%
! TTCCTTTCTCTTTACCTTTT+CGG - chr4_1:66304818-66304837 Msa0565450:CDS 30.0%
TATCTTTAGCAGAAGAAGGT+TGG - chr4_1:66304771-66304790 Msa0565450:CDS 35.0%
GAAAGGAAGGTGAAGAAAAA+TGG + chr4_1:66304806-66304825 None:intergenic 35.0%
GAAAAGGTAAAGAGAAAGGA+AGG + chr4_1:66304819-66304838 None:intergenic 35.0%
AACCGAAAAGGTAAAGAGAA+AGG + chr4_1:66304823-66304842 None:intergenic 35.0%
AGAAGATGAAGTAACCGAAA+AGG + chr4_1:66304835-66304854 None:intergenic 35.0%
GATATTCTGCAAGGTAGTAT+TGG + chr4_1:66304993-66305012 None:intergenic 35.0%
AACGACGAAATGTAACAGAT+CGG + chr4_1:66305047-66305066 None:intergenic 35.0%
CAGCTATCTTTAGCAGAAGA+AGG - chr4_1:66304767-66304786 Msa0565450:CDS 40.0%
! ATTCTGCAAGGTAGTATTGG+CGG + chr4_1:66304990-66305009 None:intergenic 40.0%
GTCAAGAACGATATTCTGCA+AGG + chr4_1:66305002-66305021 None:intergenic 40.0%
TAACAGATCGGTGATGAAGT+AGG + chr4_1:66305035-66305054 None:intergenic 40.0%
! CGAAGAAAAGCATGGCTAAT+TGG + chr4_1:66305102-66305121 None:intergenic 40.0%
AGTGAAGACGAAGAAAAGCA+TGG + chr4_1:66305110-66305129 None:intergenic 40.0%
! TTCACTTGCCGTTTCATGAT+CGG - chr4_1:66305124-66305143 Msa0565450:CDS 40.0%
AACAGCAACCAAAACGAAGA+CGG + chr4_1:66305164-66305183 None:intergenic 40.0%
AGTATGTGACTCGAATCTGC+GGG + chr4_1:66304871-66304890 None:intergenic 45.0%
GAGTATGTGACTCGAATCTG+CGG + chr4_1:66304872-66304891 None:intergenic 45.0%
AAAGACGCAAATCAAGACGC+TGG + chr4_1:66304894-66304913 None:intergenic 45.0%
TTCTTAACCGCCACCATTCT+CGG - chr4_1:66304917-66304936 Msa0565450:CDS 45.0%
CGAAGTAGTGAACGTAGCTT+GGG + chr4_1:66305075-66305094 None:intergenic 45.0%
! TGCCGTTTCATGATCGGTAA+CGG - chr4_1:66305130-66305149 Msa0565450:CDS 45.0%
CACCGTTACCGATCATGAAA+CGG + chr4_1:66305135-66305154 None:intergenic 45.0%
GTATGTGACTCGAATCTGCG+GGG + chr4_1:66304870-66304889 None:intergenic 50.0%
TATTGGCGGCTGATAAGCCA+CGG + chr4_1:66304976-66304995 None:intergenic 50.0%
AGTAGTGAACGTAGCTTGGG+AGG + chr4_1:66305072-66305091 None:intergenic 50.0%
GCGAAGTAGTGAACGTAGCT+TGG + chr4_1:66305076-66305095 None:intergenic 50.0%
! TGCTGTCTCCGTCTTCGTTT+TGG - chr4_1:66305153-66305172 Msa0565450:CDS 50.0%
TGACTCGAATCTGCGGGGTT+CGG + chr4_1:66304865-66304884 None:intergenic 55.0%
GATTACGCCGAGAATGGTGG+CGG + chr4_1:66304927-66304946 None:intergenic 55.0%
GAAGGCGATTACGCCGAGAA+TGG + chr4_1:66304933-66304952 None:intergenic 55.0%
TGATAAGCCACGGTTGGGGT+TGG + chr4_1:66304966-66304985 None:intergenic 55.0%
! GAATCTGCGGGGTTCGGTCT+TGG + chr4_1:66304859-66304878 None:intergenic 60.0%
GGCGATTACGCCGAGAATGG+TGG + chr4_1:66304930-66304949 None:intergenic 60.0%
!! GGGGTTGGTGTCGGAGAAGA+AGG + chr4_1:66304951-66304970 None:intergenic 60.0%
CGGCTGATAAGCCACGGTTG+GGG + chr4_1:66304970-66304989 None:intergenic 60.0%
GCGGCTGATAAGCCACGGTT+GGG + chr4_1:66304971-66304990 None:intergenic 60.0%
TCCGACACCAACCCCAACCG+TGG - chr4_1:66304956-66304975 Msa0565450:CDS 65.0%
!! GCCACGGTTGGGGTTGGTGT+CGG + chr4_1:66304960-66304979 None:intergenic 65.0%
GGCGGCTGATAAGCCACGGT+TGG + chr4_1:66304972-66304991 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 66304758 66305189 66304758 ID=Msa0565450;Name=Msa0565450
chr4_1 mRNA 66304758 66305189 66304758 ID=Msa0565450-mRNA-1;Parent=Msa0565450;Name=Msa0565450-mRNA-1;_AED=0.38;_eAED=0.38;_QI=0|-1|0|1|-1|1|1|0|143
chr4_1 exon 66304758 66305189 66304758 ID=Msa0565450-mRNA-1:exon:21544;Parent=Msa0565450-mRNA-1
chr4_1 CDS 66304758 66305189 66304758 ID=Msa0565450-mRNA-1:cds;Parent=Msa0565450-mRNA-1
Gene Sequence

>Msa0565450

ATGGGAATGCAGCTATCTTTAGCAGAAGAAGGTTGGTTCGTTATCCCATTTTTCTTCACCTTCCTTTCTCTTTACCTTTTCGGTTACTTCATCTTCTTCCAAGACCGAACCCCGCAGATTCGAGTCACATACTCCAGCGTCTTGATTTGCGTCTTTCACTTCTTAACCGCCACCATTCTCGGCGTAATCGCCTTCTTCTCCGACACCAACCCCAACCGTGGCTTATCAGCCGCCAATACTACCTTGCAGAATATCGTTCTTGACTTCAGCATCGCCTACTTCATCACCGATCTGTTACATTTCGTCGTTTTCCTCCCAAGCTACGTTCACTACTTCGCTCACCAATTAGCCATGCTTTTCTTCGTCTTCACTTGCCGTTTCATGATCGGTAACGGTGCTGTCTCCGTCTTCGTTTTGGTTGCTGTTTTCTGA
Protein sequence

>Msa0565450

MGMQLSLAEEGWFVIPFFFTFLSLYLFGYFIFFQDRTPQIRVTYSSVLICVFHFLTATILGVIAFFSDTNPNRGLSAANTTLQNIVLDFSIAYFITDLLHFVVFLPSYVHYFAHQLAMLFFVFTCRFMIGNGAVSVFVLVAVF*