AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0530790

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0530790 MtrunA17_Chr4g0003741 96.454 141 4 1 1 141 25 164 3.26e-88 254
Msa0530790 MtrunA17_Chr4g0003721 95.035 141 6 1 1 141 25 164 6.02e-81 235
Msa0530790 MtrunA17_Chr4g0003751 66.423 137 18 3 1 137 25 133 9.42e-50 155
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0530790 AT1G52690.1 49.624 133 58 4 1 129 26 153 2.25e-28 102
Msa0530790 AT1G52690.2 49.624 133 58 4 1 129 26 153 2.25e-28 102
Msa0530790 AT3G15670.1 48.819 127 57 3 8 127 76 201 1.23e-23 92.0
Msa0530790 AT4G13560.1 46.392 97 48 1 22 118 15 107 3.00e-17 72.4
Msa0530790 AT4G13560.2 46.392 97 48 1 22 118 15 107 3.00e-17 72.4

Find 39 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTGCTTGGGCTGTTTGC+TGG 0.217726 4_1:-4883856 None:intergenic
TCCTGATTGGGCAGTTTCTT+TGG 0.242344 4_1:-4883942 None:intergenic
TTACTGCTTGGGCTGTTTGC+TGG 0.254500 4_1:-4883823 None:intergenic
CTGAGTTGTCCTTTCCTGAT+TGG 0.261169 4_1:-4883955 None:intergenic
GAGGCTGTTAAGAACACTTT+AGG 0.327547 4_1:+4884034 Msa0530790:CDS
AGCTTGACCAGTTGTGTCTT+GGG 0.346499 4_1:-4883888 None:intergenic
TAGCTTGACCAGTTGTGTCT+TGG 0.346890 4_1:-4883889 None:intergenic
TACTGCTTGGGCTGTTTGCT+GGG 0.347910 4_1:-4883822 None:intergenic
CTGTCTTCTCCTTAGCTGCT+TGG 0.355767 4_1:-4883769 None:intergenic
TGAGTTGTCCTTTCCTGATT+GGG 0.358541 4_1:-4883954 None:intergenic
GGGCAGTTTCTTTGGTAGCC+TGG 0.369272 4_1:-4883934 None:intergenic
TGTCTTCTCCTTAGCTGCTT+GGG 0.380418 4_1:-4883768 None:intergenic
TGTTGCTTGGGCTGTTTGCT+GGG 0.405323 4_1:-4883855 None:intergenic
ACAGACAGGTGAAAAGGTTA+AGG 0.409547 4_1:+4883991 Msa0530790:CDS
ACCAAAGAAACTGCCCAATC+AGG 0.426421 4_1:+4883941 Msa0530790:CDS
GCAAACAGCCCAAGCAGTAA+AGG 0.474093 4_1:+4883826 Msa0530790:CDS
AGCCCAAGCTGCAAAGGAAA+AGG 0.475347 4_1:+4883733 Msa0530790:CDS
TTTGCAACAGACAGGTGAAA+AGG 0.484901 4_1:+4883985 Msa0530790:CDS
TCAGGAAAGGACAACTCAGC+TGG 0.488267 4_1:+4883959 Msa0530790:CDS
CAGACAGGTGAAAAGGTTAA+GGG 0.501139 4_1:+4883992 Msa0530790:CDS
GATAAAACCCAAGACACAAC+TGG 0.501444 4_1:+4883881 Msa0530790:CDS
ACAGACAGCCCAAGCTGCAA+AGG 0.520144 4_1:+4883793 Msa0530790:CDS
ACAAACAGCCCAAGCAGCTA+AGG 0.522462 4_1:+4883760 Msa0530790:CDS
AGGTGAAAAGGTTAAGGGTA+TGG 0.530822 4_1:+4883997 Msa0530790:CDS
TAGAGACAAGGGTTATGAGA+TGG 0.536052 4_1:+4883910 Msa0530790:CDS
CAAGCAGCTAAGGAGAAGAC+AGG 0.539522 4_1:+4883770 Msa0530790:CDS
AGAGACAAGGGTTATGAGAT+GGG 0.559398 4_1:+4883911 Msa0530790:CDS
GCAAACAGCCCAAGCAACAA+AGG 0.560474 4_1:+4883859 Msa0530790:CDS
TGACAAAGCCCAAGCTGCAA+AGG 0.561029 4_1:+4883727 Msa0530790:CDS
CAAGGGTTATGAGATGGGCC+AGG 0.585538 4_1:+4883916 Msa0530790:CDS
TCAATCAACAACGTTACGAC+GGG 0.588754 4_1:-4884116 None:intergenic
AACCAGATGATGGGCAACAT+AGG 0.591141 4_1:+4883704 None:intergenic
CTCAATCAACAACGTTACGA+CGG 0.597111 4_1:-4884117 None:intergenic
AGAAACTGCCCAATCAGGAA+AGG 0.617206 4_1:+4883946 Msa0530790:CDS
AACTGGTCAAGCTAGAGACA+AGG 0.623107 4_1:+4883898 Msa0530790:CDS
AAGGTTAAGGGTATGGCACA+AGG 0.628466 4_1:+4884004 Msa0530790:CDS
TGAAAATCAAGATGAAGACA+AGG 0.635276 4_1:+4884063 Msa0530790:CDS
TATGGCACAAGGTGCTACTG+AGG 0.642781 4_1:+4884015 Msa0530790:CDS
ACTGGTCAAGCTAGAGACAA+GGG 0.688619 4_1:+4883899 Msa0530790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGTTGTTTTTGTTGTGAAA+TGG - chr4_1:4884090-4884109 None:intergenic 25.0%
TGAAAATCAAGATGAAGACA+AGG + chr4_1:4884063-4884082 Msa0530790:CDS 30.0%
!! GGTTTTATCCTTTGTTGCTT+GGG - chr4_1:4883870-4883889 None:intergenic 35.0%
!! GGTTTTGTCCTTTACTGCTT+GGG - chr4_1:4883837-4883856 None:intergenic 40.0%
!! GGGTTTTATCCTTTGTTGCT+TGG - chr4_1:4883871-4883890 None:intergenic 40.0%
GATAAAACCCAAGACACAAC+TGG + chr4_1:4883881-4883900 Msa0530790:CDS 40.0%
TAGAGACAAGGGTTATGAGA+TGG + chr4_1:4883910-4883929 Msa0530790:CDS 40.0%
AGAGACAAGGGTTATGAGAT+GGG + chr4_1:4883911-4883930 Msa0530790:CDS 40.0%
TGAGTTGTCCTTTCCTGATT+GGG - chr4_1:4883957-4883976 None:intergenic 40.0%
TTTGCAACAGACAGGTGAAA+AGG + chr4_1:4883985-4884004 Msa0530790:CDS 40.0%
ACAGACAGGTGAAAAGGTTA+AGG + chr4_1:4883991-4884010 Msa0530790:CDS 40.0%
CAGACAGGTGAAAAGGTTAA+GGG + chr4_1:4883992-4884011 Msa0530790:CDS 40.0%
AGGTGAAAAGGTTAAGGGTA+TGG + chr4_1:4883997-4884016 Msa0530790:CDS 40.0%
GAGGCTGTTAAGAACACTTT+AGG + chr4_1:4884034-4884053 Msa0530790:CDS 40.0%
TCAATCAACAACGTTACGAC+GGG - chr4_1:4884119-4884138 None:intergenic 40.0%
! AGCCTTTTCCTTTGCAGCTT+GGG - chr4_1:4883738-4883757 None:intergenic 45.0%
TGTCTTCTCCTTAGCTGCTT+GGG - chr4_1:4883771-4883790 None:intergenic 45.0%
! GGTTTTCTCCTTTGCAGCTT+GGG - chr4_1:4883804-4883823 None:intergenic 45.0%
!! GGGTTTTGTCCTTTACTGCT+TGG - chr4_1:4883838-4883857 None:intergenic 45.0%
AGCTTGACCAGTTGTGTCTT+GGG - chr4_1:4883891-4883910 None:intergenic 45.0%
TAGCTTGACCAGTTGTGTCT+TGG - chr4_1:4883892-4883911 None:intergenic 45.0%
AACTGGTCAAGCTAGAGACA+AGG + chr4_1:4883898-4883917 Msa0530790:CDS 45.0%
ACTGGTCAAGCTAGAGACAA+GGG + chr4_1:4883899-4883918 Msa0530790:CDS 45.0%
ACCAAAGAAACTGCCCAATC+AGG + chr4_1:4883941-4883960 Msa0530790:CDS 45.0%
TCCTGATTGGGCAGTTTCTT+TGG - chr4_1:4883945-4883964 None:intergenic 45.0%
AGAAACTGCCCAATCAGGAA+AGG + chr4_1:4883946-4883965 Msa0530790:CDS 45.0%
CTGAGTTGTCCTTTCCTGAT+TGG - chr4_1:4883958-4883977 None:intergenic 45.0%
! GCTGGATTTTTGCAACAGAC+AGG + chr4_1:4883977-4883996 Msa0530790:CDS 45.0%
! AAGGTTAAGGGTATGGCACA+AGG + chr4_1:4884004-4884023 Msa0530790:CDS 45.0%
TGACAAAGCCCAAGCTGCAA+AGG + chr4_1:4883727-4883746 Msa0530790:CDS 50.0%
AGCCCAAGCTGCAAAGGAAA+AGG + chr4_1:4883733-4883752 Msa0530790:CDS 50.0%
! GAGCCTTTTCCTTTGCAGCT+TGG - chr4_1:4883739-4883758 None:intergenic 50.0%
ACAAACAGCCCAAGCAGCTA+AGG + chr4_1:4883760-4883779 Msa0530790:CDS 50.0%
CTGTCTTCTCCTTAGCTGCT+TGG - chr4_1:4883772-4883791 None:intergenic 50.0%
CAAGCAGCTAAGGAGAAGAC+AGG + chr4_1:4883770-4883789 Msa0530790:CDS 50.0%
! GGGTTTTCTCCTTTGCAGCT+TGG - chr4_1:4883805-4883824 None:intergenic 50.0%
TACTGCTTGGGCTGTTTGCT+GGG - chr4_1:4883825-4883844 None:intergenic 50.0%
TTACTGCTTGGGCTGTTTGC+TGG - chr4_1:4883826-4883845 None:intergenic 50.0%
GCAAACAGCCCAAGCAGTAA+AGG + chr4_1:4883826-4883845 Msa0530790:CDS 50.0%
! TGTTGCTTGGGCTGTTTGCT+GGG - chr4_1:4883858-4883877 None:intergenic 50.0%
! TTGTTGCTTGGGCTGTTTGC+TGG - chr4_1:4883859-4883878 None:intergenic 50.0%
GCAAACAGCCCAAGCAACAA+AGG + chr4_1:4883859-4883878 Msa0530790:CDS 50.0%
TCAGGAAAGGACAACTCAGC+TGG + chr4_1:4883959-4883978 Msa0530790:CDS 50.0%
!! TATGGCACAAGGTGCTACTG+AGG + chr4_1:4884015-4884034 Msa0530790:CDS 50.0%
ACAGACAGCCCAAGCTGCAA+AGG + chr4_1:4883793-4883812 Msa0530790:CDS 55.0%
CAAGGGTTATGAGATGGGCC+AGG + chr4_1:4883916-4883935 Msa0530790:CDS 55.0%
! GGGCAGTTTCTTTGGTAGCC+TGG - chr4_1:4883937-4883956 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 4883713 4884138 4883713 ID=Msa0530790;Name=Msa0530790
chr4_1 mRNA 4883713 4884138 4883713 ID=Msa0530790-mRNA-1;Parent=Msa0530790;Name=Msa0530790-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|141
chr4_1 exon 4883713 4884138 4883713 ID=Msa0530790-mRNA-1:exon:1468;Parent=Msa0530790-mRNA-1
chr4_1 CDS 4883713 4884138 4883713 ID=Msa0530790-mRNA-1:cds;Parent=Msa0530790-mRNA-1
Gene Sequence

>Msa0530790

ATGGGCAACATAGGTGACAAAGCCCAAGCTGCAAAGGAAAAGGCTCAACAAACAGCCCAAGCAGCTAAGGAGAAGACAGGACAGACAGCCCAAGCTGCAAAGGAGAAAACCCAGCAAACAGCCCAAGCAGTAAAGGACAAAACCCAGCAAACAGCCCAAGCAACAAAGGATAAAACCCAAGACACAACTGGTCAAGCTAGAGACAAGGGTTATGAGATGGGCCAGGCTACCAAAGAAACTGCCCAATCAGGAAAGGACAACTCAGCTGGATTTTTGCAACAGACAGGTGAAAAGGTTAAGGGTATGGCACAAGGTGCTACTGAGGCTGTTAAGAACACTTTAGGAATGAATGAAAATCAAGATGAAGACAAGGACCATTTCACAACAAAAACAACAACAACAACCCGTCGTAACGTTGTTGATTGA
Protein sequence

>Msa0530790

MGNIGDKAQAAKEKAQQTAQAAKEKTGQTAQAAKEKTQQTAQAVKDKTQQTAQATKDKTQDTTGQARDKGYEMGQATKETAQSGKDNSAGFLQQTGEKVKGMAQGATEAVKNTLGMNENQDEDKDHFTTKTTTTTRRNVVD*