AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0596500


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0596500 MtrunA17_Chr1g0200561 27.869 183 101 6 4 163 19 193 1.00e-12 65.9
Msa0596500 MtrunA17_Chr5g0398971 29.936 157 79 6 4 136 7 156 1.39e-12 65.1
Msa0596500 MtrunA17_Chr4g0056541 30.769 156 77 6 4 136 7 154 5.28e-12 63.5
Msa0596500 MtrunA17_Chr5g0405211 29.936 157 77 7 4 136 8 155 5.90e-12 63.5
Msa0596500 MtrunA17_Chr4g0017921 30.508 177 89 10 4 156 8 174 1.05e-11 62.8
Msa0596500 MtrunA17_Chr1g0147421 31.126 151 87 5 2 136 25 174 1.17e-11 62.8
Msa0596500 MtrunA17_Chr4g0018391 31.410 156 76 7 4 136 7 154 1.40e-11 62.4
Msa0596500 MtrunA17_Chr1g0183741 33.113 151 77 9 4 136 10 154 3.60e-11 60.8
Msa0596500 MtrunA17_Chr3g0109821 30.323 155 81 7 4 136 6 155 4.10e-11 61.2
Msa0596500 MtrunA17_Chr7g0261411 33.557 149 79 8 4 136 10 154 4.46e-11 60.5
Msa0596500 MtrunA17_Chr3g0128151 28.729 181 100 10 1 160 19 191 6.62e-11 60.8
Msa0596500 MtrunA17_Chr8g0384351 28.571 168 96 6 4 162 10 162 6.98e-11 58.9
Msa0596500 MtrunA17_Chr8g0345671 32.468 154 75 8 4 136 11 156 7.69e-11 60.5
Msa0596500 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
Msa0596500 AT2G27300.1 31.293 147 79 5 4 135 14 153 1.43e-13 68.6
Msa0596500 AT3G17730.1 31.613 155 78 8 4 136 6 154 2.31e-13 67.0
Msa0596500 AT1G71930.2 30.189 159 80 6 4 139 9 159 2.34e-12 65.1
Msa0596500 AT1G71930.1 30.189 159 80 6 4 139 9 159 2.34e-12 65.1
Msa0596500 AT3G49530.2 28.571 154 91 6 1 136 10 162 2.37e-12 65.1
Msa0596500 AT3G49530.1 28.571 154 91 6 1 136 10 162 2.98e-12 65.1
Msa0596500 AT1G62700.1 30.769 156 77 7 4 136 7 154 3.02e-12 64.7
Msa0596500 AT1G62700.2 30.769 156 77 7 4 136 7 154 3.02e-12 64.7
Msa0596500 AT4G36160.2 30.573 157 76 7 4 136 14 161 4.23e-12 64.3
Msa0596500 AT4G36160.1 30.573 157 76 7 4 136 10 157 4.23e-12 64.3
Msa0596500 AT4G36160.3 30.573 157 76 7 4 136 10 157 4.23e-12 64.3
Msa0596500 AT2G18060.3 29.936 157 77 7 4 136 9 156 5.80e-12 63.9
Msa0596500 AT2G18060.1 29.936 157 77 7 4 136 9 156 5.80e-12 63.9
Msa0596500 AT5G62380.2 32.298 161 74 8 1 136 4 154 1.01e-11 63.2
Msa0596500 AT5G62380.1 32.298 161 74 8 1 136 4 154 1.01e-11 63.2
Msa0596500 AT5G17260.1 31.447 159 74 9 4 136 6 155 1.66e-11 62.8
Msa0596500 AT5G22290.1 31.507 146 77 6 6 135 23 161 1.66e-11 62.4
Msa0596500 AT3G03200.1 30.128 156 80 7 4 136 6 155 3.83e-11 61.6
Msa0596500 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:+26863888 Msa0596500:CDS
CAATGGTTCTGACCTGATTA+AGG 0.258535 4_2:+26863430 Msa0596500:CDS
CAGAGGAGGCATTGTAAGAT+TGG 0.351545 4_2:+26863557 Msa0596500:CDS
GGCATTGTAAGATTGGGTTT+TGG 0.353732 4_2:+26863564 Msa0596500:CDS
TGAAGGAACTCAGCAACTTA+AGG 0.387687 4_2:+26863971 Msa0596500:CDS
ATAAGTTCAGCTCCTTAATC+AGG 0.404146 4_2:-26863442 None:intergenic
GAAGAGGTTCAGAATTTCAA+TGG 0.424440 4_2:+26863413 Msa0596500:CDS
GAAGGAACTCAGCAACTTAA+GGG 0.437746 4_2:+26863972 Msa0596500:CDS
CCTCCTCTGCTCATCAACTT+TGG 0.439795 4_2:-26863543 None:intergenic
AAAACGCGGCAAACAACAAA+AGG 0.449123 4_2:-26863849 None:intergenic
AGAGGAGGCATTGTAAGATT+GGG 0.450614 4_2:+26863558 Msa0596500:CDS
TGGAGTTGATAACGTGGTTG+TGG 0.453423 4_2:+26863616 Msa0596500:CDS
GAATTCCTTCCACCTGGTGT+TGG 0.454396 4_2:+26863335 Msa0596500:CDS
CTGCCCTAGAGGGATGGATC+TGG 0.463977 4_2:+26863875 Msa0596500:CDS
TTCGATGACAAGGCGAATGA+AGG 0.469350 4_2:+26863954 Msa0596500:CDS
GAGTCCAGATCCATCCCTCT+AGG 0.508074 4_2:-26863879 None:intergenic
GTGAAGCAGTAAAATTCCCT+TGG 0.508645 4_2:-26863518 None:intergenic
ACCTTCATCGACATCAGAAA+AGG 0.512248 4_2:-26863913 None:intergenic
GGAGTTGATAACGTGGTTGT+GGG 0.517524 4_2:+26863617 Msa0596500:CDS
GGAGTTGTTCGAGACATTTG+TGG 0.527780 4_2:+26863596 Msa0596500:CDS
GGCTACTCAAGCCACTCCTT+AGG 0.532323 4_2:+26864043 Msa0596500:CDS
AGTAAAATTCCCTTGGGTGA+CGG 0.539767 4_2:-26863511 None:intergenic
CCAAAGTTGATGAGCAGAGG+AGG 0.542469 4_2:+26863543 Msa0596500:CDS
TGAAGCAGTAAAATTCCCTT+GGG 0.544541 4_2:-26863517 None:intergenic
TAACAAGGAGCTCATCTGAA+GGG 0.545729 4_2:-26863364 None:intergenic
AGAACGCGATCAAAACTAGC+TGG 0.546737 4_2:+26863681 Msa0596500:CDS
AGGAGTGGCTTGAGTAGCCA+TGG 0.558328 4_2:-26864039 None:intergenic
GAAGGGGCGAAGCCAACACC+AGG 0.562826 4_2:-26863347 None:intergenic
CGAAGCCAACACCAGGTGGA+AGG 0.569669 4_2:-26863340 None:intergenic
AGGCTATGCATCGCATTCCA+TGG 0.571087 4_2:+26864022 Msa0596500:CDS
AGTCCAGATCCATCCCTCTA+GGG 0.585447 4_2:-26863878 None:intergenic
CACTCAGGTTAACAACCCTC+AGG 0.585811 4_2:+26863718 Msa0596500:CDS
CAGCCAAAGTTGATGAGCAG+AGG 0.590799 4_2:+26863540 Msa0596500:CDS
CTAACAAGGAGCTCATCTGA+AGG 0.597005 4_2:-26863365 None:intergenic
GGAATGGAATTCCTTCCACC+TGG 0.603855 4_2:+26863329 None:intergenic
AAGGAACTCAGCAACTTAAG+GGG 0.605135 4_2:+26863973 Msa0596500:CDS
TGGCAAGGTAGTAGCTAACA+AGG 0.615826 4_2:-26863379 None:intergenic
AACAAGGAGCTCATCTGAAG+GGG 0.618835 4_2:-26863363 None:intergenic
GGGGCGAAGCCAACACCAGG+TGG 0.632420 4_2:-26863344 None:intergenic
GACTATGTACGAGTACACTC+AGG 0.643748 4_2:+26863703 Msa0596500:CDS
TGATGACGACTTCGATGACA+AGG 0.644951 4_2:+26863944 Msa0596500:CDS
GCTAGTTCTAGTGCTGAGCA+AGG 0.673401 4_2:+26864002 Msa0596500:CDS
AGGAACTCAGCAACTTAAGG+GGG 0.676579 4_2:+26863974 Msa0596500:CDS
CATTTGTGGAGTTGATAACG+TGG 0.688917 4_2:+26863610 Msa0596500:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAATATAAATAATTATGC+AGG + chr4_2:26863824-26863843 Msa0596500:intron 10.0%
!!! TCTCTTTTTATGTTCTATAT+AGG + chr4_2:26863647-26863666 Msa0596500:CDS 20.0%
!! TCGATGATTAATTTATGTAT+TGG + chr4_2:26863785-26863804 Msa0596500:intron 20.0%
! TCGATGAAATAATGAACATA+TGG - chr4_2:26863769-26863788 None:intergenic 25.0%
!!! AACCTCTTCATTGTTTTTGT+TGG - chr4_2:26863402-26863421 None:intergenic 30.0%
!! AAGAAAAATGATGGACTAAG+AGG - chr4_2:26863491-26863510 None:intergenic 30.0%
!!! CTTCATTGTTTTTGTTGGCA+AGG - chr4_2:26863397-26863416 None:intergenic 35.0%
TGCCAACAAAAACAATGAAG+AGG + chr4_2:26863397-26863416 Msa0596500:CDS 35.0%
GAAGAGGTTCAGAATTTCAA+TGG + chr4_2:26863413-26863432 Msa0596500:CDS 35.0%
ATAAGTTCAGCTCCTTAATC+AGG - chr4_2:26863445-26863464 None:intergenic 35.0%
! GCAATTCTAATGGATCATAC+TGG - chr4_2:26863469-26863488 None:intergenic 35.0%
TGAAGCAGTAAAATTCCCTT+GGG - chr4_2:26863520-26863539 None:intergenic 35.0%
TAACAAGGAGCTCATCTGAA+GGG - chr4_2:26863367-26863386 None:intergenic 40.0%
!! CAATGGTTCTGACCTGATTA+AGG + chr4_2:26863430-26863449 Msa0596500:CDS 40.0%
GGACTAAGAGGCAATTCTAA+TGG - chr4_2:26863479-26863498 None:intergenic 40.0%
! ATTTTTCTTCCGTCACCCAA+GGG + chr4_2:26863502-26863521 Msa0596500:CDS 40.0%
AGTAAAATTCCCTTGGGTGA+CGG - chr4_2:26863514-26863533 None:intergenic 40.0%
GTGAAGCAGTAAAATTCCCT+TGG - chr4_2:26863521-26863540 None:intergenic 40.0%
!! AGAGGAGGCATTGTAAGATT+GGG + chr4_2:26863558-26863577 Msa0596500:CDS 40.0%
! GGCATTGTAAGATTGGGTTT+TGG + chr4_2:26863564-26863583 Msa0596500:CDS 40.0%
!!! ATTGGGTTTTGGATGCGTAA+GGG + chr4_2:26863575-26863594 Msa0596500:CDS 40.0%
!! CATTTGTGGAGTTGATAACG+TGG + chr4_2:26863610-26863629 Msa0596500:CDS 40.0%
!!! TAGTTTTGATCGCGTTCTGA+GGG - chr4_2:26863679-26863698 None:intergenic 40.0%
! AACCCTCAGGTATGTCATTT+GGG + chr4_2:26863731-26863750 Msa0596500:intron 40.0%
TTCCCAAATGACATACCTGA+GGG - chr4_2:26863736-26863755 None:intergenic 40.0%
TTTCCCAAATGACATACCTG+AGG - chr4_2:26863737-26863756 None:intergenic 40.0%
AAAACGCGGCAAACAACAAA+AGG - chr4_2:26863852-26863871 None:intergenic 40.0%
ATGGATCTGGACTCTGAATT+TGG + chr4_2:26863888-26863907 Msa0596500:CDS 40.0%
ACCTTCATCGACATCAGAAA+AGG - chr4_2:26863916-26863935 None:intergenic 40.0%
TGAAGGAACTCAGCAACTTA+AGG + chr4_2:26863971-26863990 Msa0596500:CDS 40.0%
GAAGGAACTCAGCAACTTAA+GGG + chr4_2:26863972-26863991 Msa0596500:CDS 40.0%
AAGGAACTCAGCAACTTAAG+GGG + chr4_2:26863973-26863992 Msa0596500:CDS 40.0%
AACAAGGAGCTCATCTGAAG+GGG - chr4_2:26863366-26863385 None:intergenic 45.0%
CTAACAAGGAGCTCATCTGA+AGG - chr4_2:26863368-26863387 None:intergenic 45.0%
TGGCAAGGTAGTAGCTAACA+AGG - chr4_2:26863382-26863401 None:intergenic 45.0%
!! GGGTGACGGAAGAAAAATGA+TGG - chr4_2:26863500-26863519 None:intergenic 45.0%
! CATTTTTCTTCCGTCACCCA+AGG + chr4_2:26863501-26863520 Msa0596500:CDS 45.0%
!! CAGAGGAGGCATTGTAAGAT+TGG + chr4_2:26863557-26863576 Msa0596500:CDS 45.0%
!!! GATTGGGTTTTGGATGCGTA+AGG + chr4_2:26863574-26863593 Msa0596500:CDS 45.0%
GGAGTTGTTCGAGACATTTG+TGG + chr4_2:26863596-26863615 Msa0596500:CDS 45.0%
!! TGGAGTTGATAACGTGGTTG+TGG + chr4_2:26863616-26863635 Msa0596500:CDS 45.0%
!! GGAGTTGATAACGTGGTTGT+GGG + chr4_2:26863617-26863636 Msa0596500:CDS 45.0%
!! AGTTTTGATCGCGTTCTGAG+GGG - chr4_2:26863678-26863697 None:intergenic 45.0%
!!! CTAGTTTTGATCGCGTTCTG+AGG - chr4_2:26863680-26863699 None:intergenic 45.0%
AGAACGCGATCAAAACTAGC+TGG + chr4_2:26863681-26863700 Msa0596500:CDS 45.0%
GACTATGTACGAGTACACTC+AGG + chr4_2:26863703-26863722 Msa0596500:CDS 45.0%
CAACCCTCAGGTATGTCATT+TGG + chr4_2:26863730-26863749 Msa0596500:intron 45.0%
! GCCTTTTCTGATGTCGATGA+AGG + chr4_2:26863912-26863931 Msa0596500:CDS 45.0%
! TGATGACGACTTCGATGACA+AGG + chr4_2:26863944-26863963 Msa0596500:CDS 45.0%
TTCGATGACAAGGCGAATGA+AGG + chr4_2:26863954-26863973 Msa0596500:CDS 45.0%
AGGAACTCAGCAACTTAAGG+GGG + chr4_2:26863974-26863993 Msa0596500:CDS 45.0%
GAATTCCTTCCACCTGGTGT+TGG + chr4_2:26863335-26863354 Msa0596500:CDS 50.0%
!! CAGCCAAAGTTGATGAGCAG+AGG + chr4_2:26863540-26863559 Msa0596500:CDS 50.0%
CCTCCTCTGCTCATCAACTT+TGG - chr4_2:26863546-26863565 None:intergenic 50.0%
!! CCAAAGTTGATGAGCAGAGG+AGG + chr4_2:26863543-26863562 Msa0596500:CDS 50.0%
CACTCAGGTTAACAACCCTC+AGG + chr4_2:26863718-26863737 Msa0596500:CDS 50.0%
!! CTCTAGGGCAGTCAAAAACG+CGG - chr4_2:26863866-26863885 None:intergenic 50.0%
!! GCGTTTTTGACTGCCCTAGA+GGG + chr4_2:26863865-26863884 Msa0596500:CDS 50.0%
!! TTTTGACTGCCCTAGAGGGA+TGG + chr4_2:26863869-26863888 Msa0596500:CDS 50.0%
AGTCCAGATCCATCCCTCTA+GGG - chr4_2:26863881-26863900 None:intergenic 50.0%
!! GCTAGTTCTAGTGCTGAGCA+AGG + chr4_2:26864002-26864021 Msa0596500:CDS 50.0%
AGGCTATGCATCGCATTCCA+TGG + chr4_2:26864022-26864041 Msa0596500:CDS 50.0%
!! CGCGTTTTTGACTGCCCTAG+AGG + chr4_2:26863864-26863883 Msa0596500:CDS 55.0%
GAGTCCAGATCCATCCCTCT+AGG - chr4_2:26863882-26863901 None:intergenic 55.0%
ACTCAGCAACTTAAGGGGGC+TGG + chr4_2:26863978-26863997 Msa0596500:CDS 55.0%
CTCAGCAACTTAAGGGGGCT+GGG + chr4_2:26863979-26863998 Msa0596500:CDS 55.0%
TCAGCAACTTAAGGGGGCTG+GGG + chr4_2:26863980-26863999 Msa0596500:CDS 55.0%
AGGAGTGGCTTGAGTAGCCA+TGG - chr4_2:26864042-26864061 None:intergenic 55.0%
CGAAGCCAACACCAGGTGGA+AGG - chr4_2:26863343-26863362 None:intergenic 60.0%
CTGCCCTAGAGGGATGGATC+TGG + chr4_2:26863875-26863894 Msa0596500:CDS 60.0%
GAAGGGGCGAAGCCAACACC+AGG - chr4_2:26863350-26863369 None:intergenic 65.0%
GGGGCGAAGCCAACACCAGG+TGG - chr4_2:26863347-26863366 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 26863332 26864064 26863332 ID=Msa0596500;Name=Msa0596500
chr4_2 mRNA 26863332 26864064 26863332 ID=Msa0596500-mRNA-1;Parent=Msa0596500;Name=Msa0596500-mRNA-1;_AED=0.27;_eAED=0.31;_QI=0|0|0|0.66|0.5|0.33|3|0|199
chr4_2 exon 26863332 26863468 26863332 ID=Msa0596500-mRNA-1:exon:7136;Parent=Msa0596500-mRNA-1
chr4_2 exon 26863496 26863739 26863496 ID=Msa0596500-mRNA-1:exon:7137;Parent=Msa0596500-mRNA-1
chr4_2 exon 26863846 26864064 26863846 ID=Msa0596500-mRNA-1:exon:7138;Parent=Msa0596500-mRNA-1
chr4_2 CDS 26863332 26863468 26863332 ID=Msa0596500-mRNA-1:cds;Parent=Msa0596500-mRNA-1
chr4_2 CDS 26863496 26863739 26863496 ID=Msa0596500-mRNA-1:cds;Parent=Msa0596500-mRNA-1
chr4_2 CDS 26863846 26864064 26863846 ID=Msa0596500-mRNA-1:cds;Parent=Msa0596500-mRNA-1
Gene Sequence

>Msa0596500

ATGGAATTCCTTCCACCTGGTGTTGGCTTCGCCCCTTCAGATGAGCTCCTTGTTAGCTACTACCTTGCCAACAAAAACAATGAAGAGGTTCAGAATTTCAATGGTTCTGACCTGATTAAGGAGCTGAACTTATACCATCCATCATTTTTCTTCCGTCACCCAAGGGAATTTTACTGCTTCACAGCCAAAGTTGATGAGCAGAGGAGGCATTGTAAGATTGGGTTTTGGATGCGTAAGGGAGTTGTTCGAGACATTTGTGGAGTTGATAACGTGGTTGTGGGAAAGAAGTCTCTTTTTATGTTCTATATAGGAAATTCCCCTCAGAACGCGATCAAAACTAGCTGGACTATGTACGAGTACACTCAGGTTAACAACCCTCAGGCTCCTTTTGTTGTTTGCCGCGTTTTTGACTGCCCTAGAGGGATGGATCTGGACTCTGAATTTGGAGCCTTTTCTGATGTCGATGAAGGTGATTATGCTGATGACGACTTCGATGACAAGGCGAATGAAGGAACTCAGCAACTTAAGGGGGCTGGGGCTAGTTCTAGTGCTGAGCAAGGCTATGCATCGCATTCCATGGCTACTCAAGCCACTCCTTAG

Protein sequence

>Msa0596500

MEFLPPGVGFAPSDELLVSYYLANKNNEEVQNFNGSDLIKELNLYHPSFFFRHPREFYCFTAKVDEQRRHCKIGFWMRKGVVRDICGVDNVVVGKKSLFMFYIGNSPQNAIKTSWTMYEYTQVNNPQAPFVVCRVFDCPRGMDLDSEFGAFSDVDEGDYADDDFDDKANEGTQQLKGAGASSSAEQGYASHSMATQATP*