AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0596490


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0596490 MtrunA17_Chr1g0200561 27.869 183 101 6 4 163 19 193 1.00e-12 65.9
Msa0596490 MtrunA17_Chr5g0398971 29.936 157 79 6 4 136 7 156 1.39e-12 65.1
Msa0596490 MtrunA17_Chr4g0056541 30.769 156 77 6 4 136 7 154 5.28e-12 63.5
Msa0596490 MtrunA17_Chr5g0405211 29.936 157 77 7 4 136 8 155 5.90e-12 63.5
Msa0596490 MtrunA17_Chr4g0017921 30.508 177 89 10 4 156 8 174 1.05e-11 62.8
Msa0596490 MtrunA17_Chr1g0147421 31.126 151 87 5 2 136 25 174 1.17e-11 62.8
Msa0596490 MtrunA17_Chr4g0018391 31.410 156 76 7 4 136 7 154 1.40e-11 62.4
Msa0596490 MtrunA17_Chr1g0183741 33.113 151 77 9 4 136 10 154 3.60e-11 60.8
Msa0596490 MtrunA17_Chr3g0109821 30.323 155 81 7 4 136 6 155 4.10e-11 61.2
Msa0596490 MtrunA17_Chr7g0261411 33.557 149 79 8 4 136 10 154 4.46e-11 60.5
Msa0596490 MtrunA17_Chr3g0128151 28.729 181 100 10 1 160 19 191 6.62e-11 60.8
Msa0596490 MtrunA17_Chr8g0384351 28.571 168 96 6 4 162 10 162 6.98e-11 58.9
Msa0596490 MtrunA17_Chr8g0345671 32.468 154 75 8 4 136 11 156 7.69e-11 60.5
Msa0596490 MtrunA17_Chr7g0263931 31.013 158 77 8 4 135 11 162 8.84e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0596490 AT2G27300.1 31.293 147 79 5 4 135 14 153 1.43e-13 68.6
Msa0596490 AT3G17730.1 31.613 155 78 8 4 136 6 154 2.31e-13 67.0
Msa0596490 AT1G71930.2 30.189 159 80 6 4 139 9 159 2.34e-12 65.1
Msa0596490 AT1G71930.1 30.189 159 80 6 4 139 9 159 2.34e-12 65.1
Msa0596490 AT3G49530.2 28.571 154 91 6 1 136 10 162 2.37e-12 65.1
Msa0596490 AT3G49530.1 28.571 154 91 6 1 136 10 162 2.98e-12 65.1
Msa0596490 AT1G62700.1 30.769 156 77 7 4 136 7 154 3.02e-12 64.7
Msa0596490 AT1G62700.2 30.769 156 77 7 4 136 7 154 3.02e-12 64.7
Msa0596490 AT4G36160.2 30.573 157 76 7 4 136 14 161 4.23e-12 64.3
Msa0596490 AT4G36160.1 30.573 157 76 7 4 136 10 157 4.23e-12 64.3
Msa0596490 AT4G36160.3 30.573 157 76 7 4 136 10 157 4.23e-12 64.3
Msa0596490 AT2G18060.3 29.936 157 77 7 4 136 9 156 5.80e-12 63.9
Msa0596490 AT2G18060.1 29.936 157 77 7 4 136 9 156 5.80e-12 63.9
Msa0596490 AT5G62380.2 32.298 161 74 8 1 136 4 154 1.01e-11 63.2
Msa0596490 AT5G62380.1 32.298 161 74 8 1 136 4 154 1.01e-11 63.2
Msa0596490 AT5G17260.1 31.447 159 74 9 4 136 6 155 1.66e-11 62.8
Msa0596490 AT5G22290.1 31.507 146 77 6 6 135 23 161 1.66e-11 62.4
Msa0596490 AT3G03200.1 30.128 156 80 7 4 136 6 155 3.83e-11 61.6
Msa0596490 AT3G10490.1 32.051 156 77 8 4 136 27 176 5.05e-11 60.5

Find 44 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGGATCTGGACTCTGAATT+TGG 0.253239 4_2:-26826984 Msa0596490:CDS
CAATGGTTCTGACCTGATTA+AGG 0.258535 4_2:-26827442 Msa0596490:CDS
CAGAGGAGGCATTGTAAGAT+TGG 0.351545 4_2:-26827315 Msa0596490:CDS
GGCATTGTAAGATTGGGTTT+TGG 0.353732 4_2:-26827308 Msa0596490:CDS
TGAAGGAACTCAGCAACTTA+AGG 0.387687 4_2:-26826901 Msa0596490:CDS
ATAAGTTCAGCTCCTTAATC+AGG 0.404146 4_2:+26827430 None:intergenic
GAAGAGGTTCAGAATTTCAA+TGG 0.424440 4_2:-26827459 Msa0596490:CDS
GAAGGAACTCAGCAACTTAA+GGG 0.437746 4_2:-26826900 Msa0596490:CDS
CCTCCTCTGCTCATCAACTT+TGG 0.439795 4_2:+26827329 None:intergenic
AAAACGCGGCAAACAACAAA+AGG 0.449123 4_2:+26827023 None:intergenic
AGAGGAGGCATTGTAAGATT+GGG 0.450614 4_2:-26827314 Msa0596490:CDS
TGGAGTTGATAACGTGGTTG+TGG 0.453423 4_2:-26827256 Msa0596490:CDS
GAATTCCTTCCACCTGGTGT+TGG 0.454396 4_2:-26827537 Msa0596490:CDS
CTGCCCTAGAGGGATGGATC+TGG 0.463977 4_2:-26826997 Msa0596490:CDS
TTCGATGACAAGGCGAATGA+AGG 0.469350 4_2:-26826918 Msa0596490:CDS
GAGTCCAGATCCATCCCTCT+AGG 0.508074 4_2:+26826993 None:intergenic
GTGAAGCAGTAAAATTCCCT+TGG 0.508645 4_2:+26827354 None:intergenic
ACCTTCATCGACATCAGAAA+AGG 0.512248 4_2:+26826959 None:intergenic
GGAGTTGATAACGTGGTTGT+GGG 0.517524 4_2:-26827255 Msa0596490:CDS
GGAGTTGTTCGAGACATTTG+TGG 0.527780 4_2:-26827276 Msa0596490:CDS
GGCTACTCAAGCCACTCCTT+AGG 0.532323 4_2:-26826829 None:intergenic
AGTAAAATTCCCTTGGGTGA+CGG 0.539767 4_2:+26827361 None:intergenic
CCAAAGTTGATGAGCAGAGG+AGG 0.542469 4_2:-26827329 Msa0596490:CDS
TGAAGCAGTAAAATTCCCTT+GGG 0.544541 4_2:+26827355 None:intergenic
TAACAAGGAGCTCATCTGAA+GGG 0.545729 4_2:+26827508 None:intergenic
AGAACGCGATCAAAACTAGC+TGG 0.546737 4_2:-26827191 Msa0596490:CDS
AGGAGTGGCTTGAGTAGCCA+TGG 0.558328 4_2:+26826833 None:intergenic
GAAGGGGCGAAGCCAACACC+AGG 0.562826 4_2:+26827525 None:intergenic
CGAAGCCAACACCAGGTGGA+AGG 0.569669 4_2:+26827532 None:intergenic
AGGCTATGCATCGCATTCCA+TGG 0.571087 4_2:-26826850 Msa0596490:CDS
AGTCCAGATCCATCCCTCTA+GGG 0.585447 4_2:+26826994 None:intergenic
CACTCAGGTTAACAACCCTC+AGG 0.585811 4_2:-26827154 Msa0596490:intron
CAGCCAAAGTTGATGAGCAG+AGG 0.590799 4_2:-26827332 Msa0596490:CDS
CTAACAAGGAGCTCATCTGA+AGG 0.597005 4_2:+26827507 None:intergenic
GGAATGGAATTCCTTCCACC+TGG 0.603855 4_2:-26827543 Msa0596490:CDS
AAGGAACTCAGCAACTTAAG+GGG 0.605135 4_2:-26826899 Msa0596490:CDS
TGGCAAGGTAGTAGCTAACA+AGG 0.615826 4_2:+26827493 None:intergenic
AACAAGGAGCTCATCTGAAG+GGG 0.618835 4_2:+26827509 None:intergenic
GGGGCGAAGCCAACACCAGG+TGG 0.632420 4_2:+26827528 None:intergenic
GACTATGTACGAGTACACTC+AGG 0.643748 4_2:-26827169 Msa0596490:CDS
TGATGACGACTTCGATGACA+AGG 0.644951 4_2:-26826928 Msa0596490:CDS
GCTAGTTCTAGTGCTGAGCA+AGG 0.673401 4_2:-26826870 Msa0596490:CDS
AGGAACTCAGCAACTTAAGG+GGG 0.676579 4_2:-26826898 Msa0596490:CDS
CATTTGTGGAGTTGATAACG+TGG 0.688917 4_2:-26827262 Msa0596490:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAATATAAATAATTATGC+AGG - chr4_2:26827322-26827341 Msa0596490:CDS 10.0%
!!! TCTCTTTTTATGTTCTATAT+AGG - chr4_2:26827145-26827164 Msa0596490:intron 20.0%
!! TCGATGATTAATTTATGTAT+TGG - chr4_2:26827283-26827302 Msa0596490:CDS 20.0%
! TCGATGAAATAATGAACATA+TGG + chr4_2:26827267-26827286 None:intergenic 25.0%
!!! AACCTCTTCATTGTTTTTGT+TGG + chr4_2:26826900-26826919 None:intergenic 30.0%
!! AAGAAAAATGATGGACTAAG+AGG + chr4_2:26826989-26827008 None:intergenic 30.0%
!!! CTTCATTGTTTTTGTTGGCA+AGG + chr4_2:26826895-26826914 None:intergenic 35.0%
TGCCAACAAAAACAATGAAG+AGG - chr4_2:26826895-26826914 Msa0596490:CDS 35.0%
GAAGAGGTTCAGAATTTCAA+TGG - chr4_2:26826911-26826930 Msa0596490:CDS 35.0%
ATAAGTTCAGCTCCTTAATC+AGG + chr4_2:26826943-26826962 None:intergenic 35.0%
! GCAATTCTAATGGATCATAC+TGG + chr4_2:26826967-26826986 None:intergenic 35.0%
TGAAGCAGTAAAATTCCCTT+GGG + chr4_2:26827018-26827037 None:intergenic 35.0%
TAACAAGGAGCTCATCTGAA+GGG + chr4_2:26826865-26826884 None:intergenic 40.0%
!! CAATGGTTCTGACCTGATTA+AGG - chr4_2:26826928-26826947 Msa0596490:CDS 40.0%
GGACTAAGAGGCAATTCTAA+TGG + chr4_2:26826977-26826996 None:intergenic 40.0%
! ATTTTTCTTCCGTCACCCAA+GGG - chr4_2:26827000-26827019 Msa0596490:CDS 40.0%
AGTAAAATTCCCTTGGGTGA+CGG + chr4_2:26827012-26827031 None:intergenic 40.0%
GTGAAGCAGTAAAATTCCCT+TGG + chr4_2:26827019-26827038 None:intergenic 40.0%
!! AGAGGAGGCATTGTAAGATT+GGG - chr4_2:26827056-26827075 Msa0596490:intron 40.0%
! GGCATTGTAAGATTGGGTTT+TGG - chr4_2:26827062-26827081 Msa0596490:intron 40.0%
!!! ATTGGGTTTTGGATGCGTAA+GGG - chr4_2:26827073-26827092 Msa0596490:intron 40.0%
!! CATTTGTGGAGTTGATAACG+TGG - chr4_2:26827108-26827127 Msa0596490:intron 40.0%
!!! TAGTTTTGATCGCGTTCTGA+GGG + chr4_2:26827177-26827196 None:intergenic 40.0%
! AACCCTCAGGTATGTCATTT+GGG - chr4_2:26827229-26827248 Msa0596490:CDS 40.0%
TTCCCAAATGACATACCTGA+GGG + chr4_2:26827234-26827253 None:intergenic 40.0%
TTTCCCAAATGACATACCTG+AGG + chr4_2:26827235-26827254 None:intergenic 40.0%
AAAACGCGGCAAACAACAAA+AGG + chr4_2:26827350-26827369 None:intergenic 40.0%
ATGGATCTGGACTCTGAATT+TGG - chr4_2:26827386-26827405 Msa0596490:intron 40.0%
ACCTTCATCGACATCAGAAA+AGG + chr4_2:26827414-26827433 None:intergenic 40.0%
TGAAGGAACTCAGCAACTTA+AGG - chr4_2:26827469-26827488 Msa0596490:CDS 40.0%
GAAGGAACTCAGCAACTTAA+GGG - chr4_2:26827470-26827489 Msa0596490:CDS 40.0%
AAGGAACTCAGCAACTTAAG+GGG - chr4_2:26827471-26827490 Msa0596490:CDS 40.0%
AACAAGGAGCTCATCTGAAG+GGG + chr4_2:26826864-26826883 None:intergenic 45.0%
CTAACAAGGAGCTCATCTGA+AGG + chr4_2:26826866-26826885 None:intergenic 45.0%
TGGCAAGGTAGTAGCTAACA+AGG + chr4_2:26826880-26826899 None:intergenic 45.0%
!! GGGTGACGGAAGAAAAATGA+TGG + chr4_2:26826998-26827017 None:intergenic 45.0%
! CATTTTTCTTCCGTCACCCA+AGG - chr4_2:26826999-26827018 Msa0596490:CDS 45.0%
!! CAGAGGAGGCATTGTAAGAT+TGG - chr4_2:26827055-26827074 Msa0596490:intron 45.0%
!!! GATTGGGTTTTGGATGCGTA+AGG - chr4_2:26827072-26827091 Msa0596490:intron 45.0%
GGAGTTGTTCGAGACATTTG+TGG - chr4_2:26827094-26827113 Msa0596490:intron 45.0%
!! TGGAGTTGATAACGTGGTTG+TGG - chr4_2:26827114-26827133 Msa0596490:intron 45.0%
!! GGAGTTGATAACGTGGTTGT+GGG - chr4_2:26827115-26827134 Msa0596490:intron 45.0%
!! AGTTTTGATCGCGTTCTGAG+GGG + chr4_2:26827176-26827195 None:intergenic 45.0%
!!! CTAGTTTTGATCGCGTTCTG+AGG + chr4_2:26827178-26827197 None:intergenic 45.0%
AGAACGCGATCAAAACTAGC+TGG - chr4_2:26827179-26827198 Msa0596490:CDS 45.0%
GACTATGTACGAGTACACTC+AGG - chr4_2:26827201-26827220 Msa0596490:CDS 45.0%
CAACCCTCAGGTATGTCATT+TGG - chr4_2:26827228-26827247 Msa0596490:CDS 45.0%
! GCCTTTTCTGATGTCGATGA+AGG - chr4_2:26827410-26827429 Msa0596490:intron 45.0%
! TGATGACGACTTCGATGACA+AGG - chr4_2:26827442-26827461 Msa0596490:CDS 45.0%
TTCGATGACAAGGCGAATGA+AGG - chr4_2:26827452-26827471 Msa0596490:CDS 45.0%
AGGAACTCAGCAACTTAAGG+GGG - chr4_2:26827472-26827491 Msa0596490:CDS 45.0%
GAATTCCTTCCACCTGGTGT+TGG - chr4_2:26826833-26826852 Msa0596490:CDS 50.0%
!! CAGCCAAAGTTGATGAGCAG+AGG - chr4_2:26827038-26827057 Msa0596490:intron 50.0%
CCTCCTCTGCTCATCAACTT+TGG + chr4_2:26827044-26827063 None:intergenic 50.0%
!! CCAAAGTTGATGAGCAGAGG+AGG - chr4_2:26827041-26827060 Msa0596490:intron 50.0%
CACTCAGGTTAACAACCCTC+AGG - chr4_2:26827216-26827235 Msa0596490:CDS 50.0%
!! CTCTAGGGCAGTCAAAAACG+CGG + chr4_2:26827364-26827383 None:intergenic 50.0%
!! GCGTTTTTGACTGCCCTAGA+GGG - chr4_2:26827363-26827382 Msa0596490:CDS 50.0%
!! TTTTGACTGCCCTAGAGGGA+TGG - chr4_2:26827367-26827386 Msa0596490:CDS 50.0%
AGTCCAGATCCATCCCTCTA+GGG + chr4_2:26827379-26827398 None:intergenic 50.0%
!! GCTAGTTCTAGTGCTGAGCA+AGG - chr4_2:26827500-26827519 Msa0596490:CDS 50.0%
AGGCTATGCATCGCATTCCA+TGG - chr4_2:26827520-26827539 Msa0596490:CDS 50.0%
!! CGCGTTTTTGACTGCCCTAG+AGG - chr4_2:26827362-26827381 Msa0596490:CDS 55.0%
GAGTCCAGATCCATCCCTCT+AGG + chr4_2:26827380-26827399 None:intergenic 55.0%
ACTCAGCAACTTAAGGGGGC+TGG - chr4_2:26827476-26827495 Msa0596490:CDS 55.0%
CTCAGCAACTTAAGGGGGCT+GGG - chr4_2:26827477-26827496 Msa0596490:CDS 55.0%
TCAGCAACTTAAGGGGGCTG+GGG - chr4_2:26827478-26827497 Msa0596490:CDS 55.0%
AGGAGTGGCTTGAGTAGCCA+TGG + chr4_2:26827540-26827559 None:intergenic 55.0%
CGAAGCCAACACCAGGTGGA+AGG + chr4_2:26826841-26826860 None:intergenic 60.0%
CTGCCCTAGAGGGATGGATC+TGG - chr4_2:26827373-26827392 Msa0596490:CDS 60.0%
GAAGGGGCGAAGCCAACACC+AGG + chr4_2:26826848-26826867 None:intergenic 65.0%
GGGGCGAAGCCAACACCAGG+TGG + chr4_2:26826845-26826864 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 26826830 26827562 26826830 ID=Msa0596490;Name=Msa0596490
chr4_2 mRNA 26826830 26827562 26826830 ID=Msa0596490-mRNA-1;Parent=Msa0596490;Name=Msa0596490-mRNA-1;_AED=0.27;_eAED=0.31;_QI=0|0|0|0.66|1|0.66|3|0|199
chr4_2 exon 26827426 26827562 26827426 ID=Msa0596490-mRNA-1:exon:7141;Parent=Msa0596490-mRNA-1
chr4_2 exon 26827155 26827398 26827155 ID=Msa0596490-mRNA-1:exon:7140;Parent=Msa0596490-mRNA-1
chr4_2 exon 26826830 26827048 26826830 ID=Msa0596490-mRNA-1:exon:7139;Parent=Msa0596490-mRNA-1
chr4_2 CDS 26827426 26827562 26827426 ID=Msa0596490-mRNA-1:cds;Parent=Msa0596490-mRNA-1
chr4_2 CDS 26827155 26827398 26827155 ID=Msa0596490-mRNA-1:cds;Parent=Msa0596490-mRNA-1
chr4_2 CDS 26826830 26827048 26826830 ID=Msa0596490-mRNA-1:cds;Parent=Msa0596490-mRNA-1
Gene Sequence

>Msa0596490

ATGGAATTCCTTCCACCTGGTGTTGGCTTCGCCCCTTCAGATGAGCTCCTTGTTAGCTACTACCTTGCCAACAAAAACAATGAAGAGGTTCAGAATTTCAATGGTTCTGACCTGATTAAGGAGCTGAACTTATACCATCCATCATTTTTCTTCCGTCACCCAAGGGAATTTTACTGCTTCACAGCCAAAGTTGATGAGCAGAGGAGGCATTGTAAGATTGGGTTTTGGATGCGTAAGGGAGTTGTTCGAGACATTTGTGGAGTTGATAACGTGGTTGTGGGAAAGAAGTCTCTTTTTATGTTCTATATAGGAAATTCCCCTCAGAACGCGATCAAAACTAGCTGGACTATGTACGAGTACACTCAGGTTAACAACCCTCAGGCTCCTTTTGTTGTTTGCCGCGTTTTTGACTGCCCTAGAGGGATGGATCTGGACTCTGAATTTGGAGCCTTTTCTGATGTCGATGAAGGTGATTATGCTGATGACGACTTCGATGACAAGGCGAATGAAGGAACTCAGCAACTTAAGGGGGCTGGGGCTAGTTCTAGTGCTGAGCAAGGCTATGCATCGCATTCCATGGCTACTCAAGCCACTCCTTAG

Protein sequence

>Msa0596490

MEFLPPGVGFAPSDELLVSYYLANKNNEEVQNFNGSDLIKELNLYHPSFFFRHPREFYCFTAKVDEQRRHCKIGFWMRKGVVRDICGVDNVVVGKKSLFMFYIGNSPQNAIKTSWTMYEYTQVNNPQAPFVVCRVFDCPRGMDLDSEFGAFSDVDEGDYADDDFDDKANEGTQQLKGAGASSSAEQGYASHSMATQATP*