AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0406120


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0406120 MtrunA17_Chr3g0097011 93.617 188 12 0 4 191 144 331 1.57e-125 360
Msa0406120 MtrunA17_Chr3g0108171 72.821 195 46 2 4 191 1693 1887 6.69e-83 268
Msa0406120 MtrunA17_Chr3g0108171 41.463 123 54 4 4 115 1511 1626 4.19e-13 67.8
Msa0406120 MtrunA17_Chr3g0087641 66.138 189 54 2 4 191 144 323 1.93e-77 236
Msa0406120 MtrunA17_Chr3g0107261 63.366 202 60 3 4 191 118 319 3.52e-77 237
Msa0406120 MtrunA17_Chr3g0091861 55.417 240 54 2 5 191 1568 1807 3.46e-71 235
Msa0406120 MtrunA17_Chr3g0108091 72.152 158 38 2 45 196 310 467 5.90e-69 219
Msa0406120 MtrunA17_Chr3g0091851 66.492 191 59 4 4 191 1061 1249 1.90e-67 224
Msa0406120 MtrunA17_Chr3g0108071 72.152 158 38 2 45 196 773 930 5.00e-66 219
Msa0406120 MtrunA17_Chr3g0107931 63.492 189 46 4 4 191 1641 1807 6.46e-64 214
Msa0406120 MtrunA17_Chr3g0105471 63.580 162 54 1 35 191 12 173 7.50e-61 190
Msa0406120 MtrunA17_Chr3g0105591 57.789 199 64 5 4 195 175 360 3.68e-60 194
Msa0406120 MtrunA17_Chr3g0105521 59.585 193 60 3 5 191 1357 1537 3.13e-59 201
Msa0406120 MtrunA17_Chr3g0108821 58.500 200 64 4 4 191 1530 1722 5.54e-59 200
Msa0406120 MtrunA17_Chr3g0108811 57.500 200 66 4 4 191 1674 1866 2.59e-58 198
Msa0406120 MtrunA17_Chr3g0105551 57.071 198 67 3 4 195 1604 1789 6.79e-58 197
Msa0406120 MtrunA17_Chr3g0108761 85.437 103 15 0 89 191 12 114 1.53e-57 180
Msa0406120 MtrunA17_Chr2g0304131 53.723 188 74 2 17 191 48 235 1.93e-55 179
Msa0406120 MtrunA17_Chr3g0108151 59.474 190 59 5 4 191 1297 1470 2.71e-55 189
Msa0406120 MtrunA17_Chr3g0107641 71.818 110 31 0 82 191 3 112 2.35e-47 154
Msa0406120 MtrunA17_Chr7g0229711 64.516 93 24 2 99 191 2 85 4.02e-32 114
Msa0406120 MtrunA17_Chr3g0107171 74.194 62 16 0 130 191 242 303 2.22e-24 99.0
Msa0406120 MtrunA17_Chr3g0096771 41.317 167 62 4 38 191 66 209 1.47e-23 95.5
Msa0406120 MtrunA17_Chr7g0223911 75.862 58 14 0 134 191 30 87 2.05e-23 92.0
Msa0406120 MtrunA17_Chr3g0108201 46.067 89 37 2 10 87 1 89 1.43e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATCCTTCAATTCCTTTAA+AGG 0.136199 3_2:-42198212 Msa0406120:CDS
CTCAATGAAGTGTCCTTTAA+AGG 0.175932 3_2:+42198199 None:intergenic
TGAAAGTGCGCTTTGTTTAC+TGG 0.251734 3_2:-42198014 Msa0406120:CDS
GAGTAGAAGCTACGGCTATT+TGG 0.307788 3_2:+42198732 None:intergenic
AATACAATATGGTATTGATT+TGG 0.375134 3_2:+42198467 None:intergenic
TCAACATCTTGAGTGGCTAT+TGG 0.388913 3_2:+42198710 None:intergenic
TACTGAGATGCAATACAATA+TGG 0.422165 3_2:+42198456 None:intergenic
ATACCTCCAGTAGGCTTTGA+AGG 0.423715 3_2:+42198432 None:intergenic
TAGCTCAGCTAGGCAATTGT+AGG 0.442686 3_2:+42198156 None:intergenic
TTCTTCTTTGTTTGTCAAGA+GGG 0.449409 3_2:-42198308 Msa0406120:CDS
CATAGTGTGTTGGATGTGTT+AGG 0.454033 3_2:-42198115 Msa0406120:CDS
CAGTATCCTTCAAAGCCTAC+TGG 0.463825 3_2:-42198438 Msa0406120:CDS
TCCAACCATTCCTTATCAAA+AGG 0.474355 3_2:+42198043 None:intergenic
GTGTCCTTTAAAGGAATTGA+AGG 0.476534 3_2:+42198208 None:intergenic
CCAACACACTATGAGTTTGA+AGG 0.495152 3_2:+42198125 None:intergenic
AAGATGTTGATGTTGAAATC+TGG 0.495281 3_2:-42198697 Msa0406120:CDS
TTCATTGAGTAACAGATACA+AGG 0.528560 3_2:-42198185 Msa0406120:CDS
GAAAGTAAGCTCAAATATTG+AGG 0.535836 3_2:-42198523 Msa0406120:CDS
AGAAAGACTGATGATGATCA+AGG 0.563867 3_2:-42198665 Msa0406120:intron
CCTTCAAACTCATAGTGTGT+TGG 0.566941 3_2:-42198125 Msa0406120:CDS
GTTCTTCTTTGTTTGTCAAG+AGG 0.570622 3_2:-42198309 Msa0406120:CDS
GGCTATTGGAGTAGAAGCTA+CGG 0.571106 3_2:+42198724 None:intergenic
TTTGATAAGGAATGGTTGGA+TGG 0.580527 3_2:-42198040 Msa0406120:CDS
GGAATTTCAATAGCTCAGCT+AGG 0.596316 3_2:+42198146 None:intergenic
AGAAATAAAATACCTCCAGT+AGG 0.601884 3_2:+42198423 None:intergenic
TTCAACATCAACATCTTGAG+TGG 0.608521 3_2:+42198703 None:intergenic
TGTTGATGTTGAAATCTGGC+AGG 0.610558 3_2:-42198693 Msa0406120:CDS
TCATTGAGTAACAGATACAA+GGG 0.655882 3_2:-42198184 Msa0406120:CDS
TATCCTTCAAAGCCTACTGG+AGG 0.675742 3_2:-42198435 Msa0406120:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTTAAATTTTAGGAAGA+CGG - chr3_2:42197967-42197986 Msa0406120:CDS 15.0%
!!! ACTAATATTTCATCATTTTT+AGG + chr3_2:42198239-42198258 None:intergenic 15.0%
!!! TATTTTAAATTTTAGGAAGA+CGG - chr3_2:42197967-42197986 Msa0406120:CDS 15.0%
!!! ACTAATATTTCATCATTTTT+AGG + chr3_2:42198239-42198258 None:intergenic 15.0%
!!! AATACAATATGGTATTGATT+TGG + chr3_2:42198264-42198283 None:intergenic 20.0%
!!! TTAAATCTTCTTTTTGAGAA+AGG + chr3_2:42198399-42198418 None:intergenic 20.0%
!!! AATACAATATGGTATTGATT+TGG + chr3_2:42198264-42198283 None:intergenic 20.0%
!!! TTAAATCTTCTTTTTGAGAA+AGG + chr3_2:42198399-42198418 None:intergenic 20.0%
! TGATCAAGGTAAAAAATCTT+TGG - chr3_2:42198077-42198096 Msa0406120:CDS 25.0%
! AAGGTAAAAAATCTTTGGAT+CGG - chr3_2:42198082-42198101 Msa0406120:CDS 25.0%
!! TAATTTTCTTGTGCTCAAAT+AGG - chr3_2:42198342-42198361 Msa0406120:intron 25.0%
! TGATCAAGGTAAAAAATCTT+TGG - chr3_2:42198077-42198096 Msa0406120:CDS 25.0%
! AAGGTAAAAAATCTTTGGAT+CGG - chr3_2:42198082-42198101 Msa0406120:CDS 25.0%
!! TAATTTTCTTGTGCTCAAAT+AGG - chr3_2:42198342-42198361 Msa0406120:intron 25.0%
AAGATGTTGATGTTGAAATC+TGG - chr3_2:42198031-42198050 Msa0406120:CDS 30.0%
ATTTAGAGAAACTGGACAAA+GGG + chr3_2:42198171-42198190 None:intergenic 30.0%
TCATCATCATTTAGAGAAAC+TGG + chr3_2:42198179-42198198 None:intergenic 30.0%
GAAAGTAAGCTCAAATATTG+AGG - chr3_2:42198205-42198224 Msa0406120:CDS 30.0%
TACTGAGATGCAATACAATA+TGG + chr3_2:42198275-42198294 None:intergenic 30.0%
AGAAATAAAATACCTCCAGT+AGG + chr3_2:42198308-42198327 None:intergenic 30.0%
TTATTCTTGCCTATACTTTC+AGG - chr3_2:42198370-42198389 Msa0406120:intron 30.0%
TATTCTTGCCTATACTTTCA+GGG - chr3_2:42198371-42198390 Msa0406120:intron 30.0%
! TTCTTCTTTGTTTGTCAAGA+GGG - chr3_2:42198420-42198439 Msa0406120:intron 30.0%
TTCATTGAGTAACAGATACA+AGG - chr3_2:42198543-42198562 Msa0406120:CDS 30.0%
TCATTGAGTAACAGATACAA+GGG - chr3_2:42198544-42198563 Msa0406120:CDS 30.0%
! GATTTCCTTTTGATAAGGAA+TGG - chr3_2:42198680-42198699 Msa0406120:CDS 30.0%
AGATGCATTGCAAAAATTGT+TGG - chr3_2:42198755-42198774 Msa0406120:intron 30.0%
AAGATGTTGATGTTGAAATC+TGG - chr3_2:42198031-42198050 Msa0406120:CDS 30.0%
ATTTAGAGAAACTGGACAAA+GGG + chr3_2:42198171-42198190 None:intergenic 30.0%
TCATCATCATTTAGAGAAAC+TGG + chr3_2:42198179-42198198 None:intergenic 30.0%
GAAAGTAAGCTCAAATATTG+AGG - chr3_2:42198205-42198224 Msa0406120:CDS 30.0%
TACTGAGATGCAATACAATA+TGG + chr3_2:42198275-42198294 None:intergenic 30.0%
AGAAATAAAATACCTCCAGT+AGG + chr3_2:42198308-42198327 None:intergenic 30.0%
TTATTCTTGCCTATACTTTC+AGG - chr3_2:42198370-42198389 Msa0406120:intron 30.0%
TATTCTTGCCTATACTTTCA+GGG - chr3_2:42198371-42198390 Msa0406120:intron 30.0%
! TTCTTCTTTGTTTGTCAAGA+GGG - chr3_2:42198420-42198439 Msa0406120:intron 30.0%
TTCATTGAGTAACAGATACA+AGG - chr3_2:42198543-42198562 Msa0406120:CDS 30.0%
TCATTGAGTAACAGATACAA+GGG - chr3_2:42198544-42198563 Msa0406120:CDS 30.0%
! GATTTCCTTTTGATAAGGAA+TGG - chr3_2:42198680-42198699 Msa0406120:CDS 30.0%
AGATGCATTGCAAAAATTGT+TGG - chr3_2:42198755-42198774 Msa0406120:intron 30.0%
TTCAACATCAACATCTTGAG+TGG + chr3_2:42198028-42198047 None:intergenic 35.0%
! AGAAAGACTGATGATGATCA+AGG - chr3_2:42198063-42198082 Msa0406120:CDS 35.0%
TCAAAATGAAAAGAGCGATG+AGG + chr3_2:42198126-42198145 None:intergenic 35.0%
CATTTAGAGAAACTGGACAA+AGG + chr3_2:42198172-42198191 None:intergenic 35.0%
! GTTCTTCTTTGTTTGTCAAG+AGG - chr3_2:42198419-42198438 Msa0406120:intron 35.0%
GCATCCTTCAATTCCTTTAA+AGG - chr3_2:42198516-42198535 Msa0406120:CDS 35.0%
! GTGTCCTTTAAAGGAATTGA+AGG + chr3_2:42198523-42198542 None:intergenic 35.0%
! CTCAATGAAGTGTCCTTTAA+AGG + chr3_2:42198532-42198551 None:intergenic 35.0%
! GCACAGATTTCCTTTTGATA+AGG - chr3_2:42198675-42198694 Msa0406120:CDS 35.0%
! TCCTTTTGATAAGGAATGGT+TGG - chr3_2:42198684-42198703 Msa0406120:CDS 35.0%
TCCAACCATTCCTTATCAAA+AGG + chr3_2:42198688-42198707 None:intergenic 35.0%
TTTGATAAGGAATGGTTGGA+TGG - chr3_2:42198688-42198707 Msa0406120:CDS 35.0%
TTCAACATCAACATCTTGAG+TGG + chr3_2:42198028-42198047 None:intergenic 35.0%
! AGAAAGACTGATGATGATCA+AGG - chr3_2:42198063-42198082 Msa0406120:CDS 35.0%
TCAAAATGAAAAGAGCGATG+AGG + chr3_2:42198126-42198145 None:intergenic 35.0%
CATTTAGAGAAACTGGACAA+AGG + chr3_2:42198172-42198191 None:intergenic 35.0%
! GTTCTTCTTTGTTTGTCAAG+AGG - chr3_2:42198419-42198438 Msa0406120:intron 35.0%
GCATCCTTCAATTCCTTTAA+AGG - chr3_2:42198516-42198535 Msa0406120:CDS 35.0%
! GTGTCCTTTAAAGGAATTGA+AGG + chr3_2:42198523-42198542 None:intergenic 35.0%
! CTCAATGAAGTGTCCTTTAA+AGG + chr3_2:42198532-42198551 None:intergenic 35.0%
! GCACAGATTTCCTTTTGATA+AGG - chr3_2:42198675-42198694 Msa0406120:CDS 35.0%
! TCCTTTTGATAAGGAATGGT+TGG - chr3_2:42198684-42198703 Msa0406120:CDS 35.0%
TCCAACCATTCCTTATCAAA+AGG + chr3_2:42198688-42198707 None:intergenic 35.0%
TTTGATAAGGAATGGTTGGA+TGG - chr3_2:42198688-42198707 Msa0406120:CDS 35.0%
TCAACATCTTGAGTGGCTAT+TGG + chr3_2:42198021-42198040 None:intergenic 40.0%
TGTTGATGTTGAAATCTGGC+AGG - chr3_2:42198035-42198054 Msa0406120:CDS 40.0%
! GAAAGGTTCCCTGAAAGTAT+AGG + chr3_2:42198382-42198401 None:intergenic 40.0%
GGAATTTCAATAGCTCAGCT+AGG + chr3_2:42198585-42198604 None:intergenic 40.0%
CCAACACACTATGAGTTTGA+AGG + chr3_2:42198606-42198625 None:intergenic 40.0%
CCTTCAAACTCATAGTGTGT+TGG - chr3_2:42198603-42198622 Msa0406120:intron 40.0%
CATAGTGTGTTGGATGTGTT+AGG - chr3_2:42198613-42198632 Msa0406120:intron 40.0%
!! TGAAAGTGCGCTTTGTTTAC+TGG - chr3_2:42198714-42198733 Msa0406120:CDS 40.0%
TCAACATCTTGAGTGGCTAT+TGG + chr3_2:42198021-42198040 None:intergenic 40.0%
TGTTGATGTTGAAATCTGGC+AGG - chr3_2:42198035-42198054 Msa0406120:CDS 40.0%
! GAAAGGTTCCCTGAAAGTAT+AGG + chr3_2:42198382-42198401 None:intergenic 40.0%
GGAATTTCAATAGCTCAGCT+AGG + chr3_2:42198585-42198604 None:intergenic 40.0%
CCAACACACTATGAGTTTGA+AGG + chr3_2:42198606-42198625 None:intergenic 40.0%
CCTTCAAACTCATAGTGTGT+TGG - chr3_2:42198603-42198622 Msa0406120:intron 40.0%
CATAGTGTGTTGGATGTGTT+AGG - chr3_2:42198613-42198632 Msa0406120:intron 40.0%
!! TGAAAGTGCGCTTTGTTTAC+TGG - chr3_2:42198714-42198733 Msa0406120:CDS 40.0%
GAGTAGAAGCTACGGCTATT+TGG + chr3_2:42197999-42198018 None:intergenic 45.0%
GGCTATTGGAGTAGAAGCTA+CGG + chr3_2:42198007-42198026 None:intergenic 45.0%
CAGTATCCTTCAAAGCCTAC+TGG - chr3_2:42198290-42198309 Msa0406120:CDS 45.0%
TATCCTTCAAAGCCTACTGG+AGG - chr3_2:42198293-42198312 Msa0406120:CDS 45.0%
! ATACCTCCAGTAGGCTTTGA+AGG + chr3_2:42198299-42198318 None:intergenic 45.0%
TAGCTCAGCTAGGCAATTGT+AGG + chr3_2:42198575-42198594 None:intergenic 45.0%
GAGTAGAAGCTACGGCTATT+TGG + chr3_2:42197999-42198018 None:intergenic 45.0%
GGCTATTGGAGTAGAAGCTA+CGG + chr3_2:42198007-42198026 None:intergenic 45.0%
CAGTATCCTTCAAAGCCTAC+TGG - chr3_2:42198290-42198309 Msa0406120:CDS 45.0%
TATCCTTCAAAGCCTACTGG+AGG - chr3_2:42198293-42198312 Msa0406120:CDS 45.0%
! ATACCTCCAGTAGGCTTTGA+AGG + chr3_2:42198299-42198318 None:intergenic 45.0%
TAGCTCAGCTAGGCAATTGT+AGG + chr3_2:42198575-42198594 None:intergenic 45.0%
!!! TAAAATTTAAAATAAACAAA+TGG + chr3_2:42197961-42197980 None:intergenic 5.0%
!!! ATTTGTTTATTTTAAATTTT+AGG - chr3_2:42197960-42197979 Msa0406120:CDS 5.0%
!!! TAAAATTTAAAATAAACAAA+TGG + chr3_2:42197961-42197980 None:intergenic 5.0%
!!! ATTTGTTTATTTTAAATTTT+AGG - chr3_2:42197960-42197979 Msa0406120:CDS 5.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 42197955 42198795 42197955 ID=Msa0406120;Name=Msa0406120
chr3_2 mRNA 42197955 42198795 42197955 ID=Msa0406120-mRNA-1;Parent=Msa0406120;Name=Msa0406120-mRNA-1;_AED=0.34;_eAED=0.36;_QI=0|0|0|1|0.66|0.75|4|0|216
chr3_2 exon 42198787 42198795 42198787 ID=Msa0406120-mRNA-1:exon:8143;Parent=Msa0406120-mRNA-1
chr3_2 exon 42198666 42198768 42198666 ID=Msa0406120-mRNA-1:exon:8142;Parent=Msa0406120-mRNA-1
chr3_2 exon 42198436 42198570 42198436 ID=Msa0406120-mRNA-1:exon:8141;Parent=Msa0406120-mRNA-1
chr3_2 exon 42197955 42198358 42197955 ID=Msa0406120-mRNA-1:exon:8140;Parent=Msa0406120-mRNA-1
chr3_2 CDS 42198787 42198795 42198787 ID=Msa0406120-mRNA-1:cds;Parent=Msa0406120-mRNA-1
chr3_2 CDS 42198666 42198768 42198666 ID=Msa0406120-mRNA-1:cds;Parent=Msa0406120-mRNA-1
chr3_2 CDS 42198436 42198570 42198436 ID=Msa0406120-mRNA-1:cds;Parent=Msa0406120-mRNA-1
chr3_2 CDS 42197955 42198358 42197955 ID=Msa0406120-mRNA-1:cds;Parent=Msa0406120-mRNA-1
Gene Sequence

>Msa0406120

ATGCCATTTGAAGACGGTGATGTCCAAATAGCCGTAGCTTCTACTCCAATAGCCACTCAAGATGTTGATGTTGAAATCTGGCAGGAAACTAGAAAGACTGATGATGATCAAGTTTCTCTAAATGATGATGATGTTGTGAAAGTAAGCTCAAATATTGAGGATCAGTTTCCTAAAAATGATGAAATATTAGTTTCCAAATCAATACCATATTGTATTGCATCTCAGTATCCTTCAAAGCCTACTGGAGGGAACCTTTCTCAAAAAGAAGATTTAAGTTCTTCTTTGTTTGTCAAGAGGGAGCTTGATCAACTAGTCTCGAAGAAGCATTTCGATTATGAGAACTTGTCTTTTTTGACTGATTTCTTTGTTAAGCATCCTTCAATTCCTTTAAAGGACACTTCATTGAGTAACAGATACAAGGGTTATGCCTACAATTGCCTAGCTGAGCTATTGAAATTCCTTCAAACTCATAGTGTGTTGGATGTGTTAGGTTCAAGCAACTCTGAATTTGTCGAGTTATTACAAGATGTGCACAGATTTCCTTTTGATAAGGAATGGTTGGATGGTGTTGAAAGTGCGCTTTGTTTACTGGTTTACAAGTCTCACAAGAAGATGCATTGCAAAAATTGTTGGACTCAAAACACATTTTGA

Protein sequence

>Msa0406120

MPFEDGDVQIAVASTPIATQDVDVEIWQETRKTDDDQVSLNDDDVVKVSSNIEDQFPKNDEILVSKSIPYCIASQYPSKPTGGNLSQKEDLSSSLFVKRELDQLVSKKHFDYENLSFLTDFFVKHPSIPLKDTSLSNRYKGYAYNCLAELLKFLQTHSVLDVLGSSNSEFVELLQDVHRFPFDKEWLDGVESALCLLVYKSHKKMHCKNCWTQNTF*