AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0751280

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0751280 MtrunA17_Chr5g0394631 85.083 181 22 3 1 178 208 386 7.58e-105 306
Msa0751280 MtrunA17_Chr5g0394631 65.341 176 54 3 9 178 1 175 1.89e-70 218
Msa0751280 MtrunA17_Chr5g0394621 71.023 176 44 3 9 178 1 175 1.60e-82 242
Msa0751280 MtrunA17_Chr1g0204951 61.677 167 57 4 16 178 12 175 2.12e-66 201
Msa0751280 MtrunA17_Chr1g0204971 59.627 161 60 3 20 178 18 175 1.01e-64 197
Msa0751280 MtrunA17_Chr7g0223361 45.570 158 81 3 20 176 3 156 6.72e-39 130
Msa0751280 MtrunA17_Chr7g0273661 43.312 157 83 3 21 175 4 156 1.07e-37 127
Msa0751280 MtrunA17_Chr7g0223351 43.671 158 81 4 24 179 7 158 1.51e-35 122
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0751280 AT2G32030.1 48.045 179 80 6 1 176 3 171 2.07e-47 153
Msa0751280 AT2G32020.1 50.641 156 67 5 24 176 18 166 2.74e-45 147
Msa0751280 AT3G22560.1 39.130 161 90 4 20 176 2 158 3.77e-30 108

Find 34 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGAAGTATGTATTCTTTAA+AGG 0.161729 5_2:+4794498 Msa0751280:CDS
TTGTTGATGTGGATAATTTA+AGG 0.203228 5_2:+4794427 Msa0751280:CDS
CAAATCAATGATCTCTTCTT+TGG 0.204931 5_2:-4794040 None:intergenic
GTTGATGCCTTGGTCTTTGC+TGG 0.262298 5_2:-4794163 None:intergenic
GCTTGAAGCCTTTCCAAGTA+TGG 0.276638 5_2:-4794402 None:intergenic
TGCCATAACGATCATGCTAT+TGG 0.288303 5_2:+4794231 Msa0751280:CDS
GCAGAACTTGGGTATGTTCT+AGG 0.307665 5_2:+4794306 Msa0751280:CDS
ATGTTCTAGGCTCTAAATAC+TGG 0.313478 5_2:+4794319 Msa0751280:CDS
CCTTGGTCTTTGCTGGTGTA+AGG 0.327596 5_2:-4794156 None:intergenic
GAAAAGATCGGAGTGTGATT+TGG 0.386444 5_2:-4794065 None:intergenic
ACCTCGATGATCTCATGGTT+TGG 0.401354 5_2:+4794097 Msa0751280:CDS
GGCTCTAAATACTGGGGTAA+AGG 0.409375 5_2:+4794327 Msa0751280:CDS
ATTCAGTGAATTTCCATACT+TGG 0.413337 5_2:+4794389 Msa0751280:CDS
GCCATAACGATCATGCTATT+GGG 0.423146 5_2:+4794232 Msa0751280:CDS
AGGATCACATGTGCAGAACT+TGG 0.424567 5_2:+4794294 Msa0751280:CDS
TTCTGACCTCGATGATCTCA+TGG 0.433346 5_2:+4794092 Msa0751280:CDS
GCTCTAAATACTGGGGTAAA+GGG 0.442106 5_2:+4794328 Msa0751280:CDS
TGAGTTCACTTGATGATAAG+AGG 0.442621 5_2:+4794271 Msa0751280:CDS
CAAAGAGTAGTTGAGAAAGT+TGG 0.450786 5_2:+4794453 Msa0751280:CDS
ACCCAATAGCATGATCGTTA+TGG 0.457877 5_2:-4794233 None:intergenic
GTAAGGTTCACCCCAGAACT+TGG 0.480302 5_2:-4794139 None:intergenic
GTGAATTTCCATACTTGGAA+AGG 0.490341 5_2:+4794394 Msa0751280:CDS
TGCTGTGAAACAAATGGTTA+AGG 0.500098 5_2:+4794362 Msa0751280:CDS
TGTTCTAGGCTCTAAATACT+GGG 0.526941 5_2:+4794320 Msa0751280:CDS
CTTATCATCAAGTGAACTCA+AGG 0.556721 5_2:-4794268 None:intergenic
GCTTCAAGCTCTTGTTGATG+TGG 0.560091 5_2:+4794416 Msa0751280:CDS
GGATCACATGTGCAGAACTT+GGG 0.577727 5_2:+4794295 Msa0751280:CDS
GGTCAGAAAGATGAAAAGAT+CGG 0.592412 5_2:-4794077 None:intergenic
CATTTGTTTCACAGCACATG+TGG 0.625218 5_2:-4794355 None:intergenic
CACATGTGCTGTGAAACAAA+TGG 0.647600 5_2:+4794356 Msa0751280:CDS
GTTCACTTGATGATAAGAGG+AGG 0.664638 5_2:+4794274 Msa0751280:CDS
CCTTACACCAGCAAAGACCA+AGG 0.673207 5_2:+4794156 Msa0751280:CDS
GTTCTAGGCTCTAAATACTG+GGG 0.712321 5_2:+4794321 Msa0751280:CDS
GCCAAACCATGAGATCATCG+AGG 0.781144 5_2:-4794098 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATCAACTTCATTAAAAATA+TGG + chr5_2:4794179-4794198 Msa0751280:CDS 20.0%
! TTGTTGATGTGGATAATTTA+AGG + chr5_2:4794427-4794446 Msa0751280:CDS 25.0%
!!! AAAGTTGGTTTTCAAAAAGA+GGG + chr5_2:4794468-4794487 Msa0751280:CDS 25.0%
!! AGGAAGTATGTATTCTTTAA+AGG + chr5_2:4794498-4794517 Msa0751280:CDS 25.0%
CAAATCAATGATCTCTTCTT+TGG - chr5_2:4794043-4794062 None:intergenic 30.0%
!!! TTTTAATGAAGTTGATGCCT+TGG - chr5_2:4794176-4794195 None:intergenic 30.0%
TCATTAAAAATATGGCAAGC+AGG + chr5_2:4794187-4794206 Msa0751280:CDS 30.0%
ATTCAGTGAATTTCCATACT+TGG + chr5_2:4794389-4794408 Msa0751280:CDS 30.0%
!!! GAAAGTTGGTTTTCAAAAAG+AGG + chr5_2:4794467-4794486 Msa0751280:CDS 30.0%
GGTCAGAAAGATGAAAAGAT+CGG - chr5_2:4794080-4794099 None:intergenic 35.0%
TTGGCATACTGATGAAAAAG+TGG + chr5_2:4794116-4794135 Msa0751280:CDS 35.0%
CTTATCATCAAGTGAACTCA+AGG - chr5_2:4794271-4794290 None:intergenic 35.0%
! TGAGTTCACTTGATGATAAG+AGG + chr5_2:4794271-4794290 Msa0751280:CDS 35.0%
!! ATGTTCTAGGCTCTAAATAC+TGG + chr5_2:4794319-4794338 Msa0751280:CDS 35.0%
!! TGTTCTAGGCTCTAAATACT+GGG + chr5_2:4794320-4794339 Msa0751280:CDS 35.0%
TGCTGTGAAACAAATGGTTA+AGG + chr5_2:4794362-4794381 Msa0751280:CDS 35.0%
GTGAATTTCCATACTTGGAA+AGG + chr5_2:4794394-4794413 Msa0751280:CDS 35.0%
CAAAGAGTAGTTGAGAAAGT+TGG + chr5_2:4794453-4794472 Msa0751280:CDS 35.0%
TTCAAAAAGAGGGAGTTCTT+AGG + chr5_2:4794478-4794497 Msa0751280:CDS 35.0%
GAAAAGATCGGAGTGTGATT+TGG - chr5_2:4794068-4794087 None:intergenic 40.0%
ATGAAAAAGTGGCCAAGTTC+TGG + chr5_2:4794127-4794146 Msa0751280:CDS 40.0%
TGAAAAAGTGGCCAAGTTCT+GGG + chr5_2:4794128-4794147 Msa0751280:CDS 40.0%
TGCCATAACGATCATGCTAT+TGG + chr5_2:4794231-4794250 Msa0751280:CDS 40.0%
GCCATAACGATCATGCTATT+GGG + chr5_2:4794232-4794251 Msa0751280:CDS 40.0%
ACCCAATAGCATGATCGTTA+TGG - chr5_2:4794236-4794255 None:intergenic 40.0%
! GTTCACTTGATGATAAGAGG+AGG + chr5_2:4794274-4794293 Msa0751280:CDS 40.0%
!! GTTCTAGGCTCTAAATACTG+GGG + chr5_2:4794321-4794340 Msa0751280:CDS 40.0%
! GCTCTAAATACTGGGGTAAA+GGG + chr5_2:4794328-4794347 Msa0751280:CDS 40.0%
CATTTGTTTCACAGCACATG+TGG - chr5_2:4794358-4794377 None:intergenic 40.0%
CACATGTGCTGTGAAACAAA+TGG + chr5_2:4794356-4794375 Msa0751280:CDS 40.0%
TTCTGACCTCGATGATCTCA+TGG + chr5_2:4794092-4794111 Msa0751280:CDS 45.0%
ACCTCGATGATCTCATGGTT+TGG + chr5_2:4794097-4794116 Msa0751280:CDS 45.0%
GAAAAAGTGGCCAAGTTCTG+GGG + chr5_2:4794129-4794148 Msa0751280:CDS 45.0%
AGGATCACATGTGCAGAACT+TGG + chr5_2:4794294-4794313 Msa0751280:CDS 45.0%
GGATCACATGTGCAGAACTT+GGG + chr5_2:4794295-4794314 Msa0751280:CDS 45.0%
GCAGAACTTGGGTATGTTCT+AGG + chr5_2:4794306-4794325 Msa0751280:CDS 45.0%
!! GGCTCTAAATACTGGGGTAA+AGG + chr5_2:4794327-4794346 Msa0751280:CDS 45.0%
GCTTGAAGCCTTTCCAAGTA+TGG - chr5_2:4794405-4794424 None:intergenic 45.0%
GCTTCAAGCTCTTGTTGATG+TGG + chr5_2:4794416-4794435 Msa0751280:CDS 45.0%
GCCAAACCATGAGATCATCG+AGG - chr5_2:4794101-4794120 None:intergenic 50.0%
GTAAGGTTCACCCCAGAACT+TGG - chr5_2:4794142-4794161 None:intergenic 50.0%
! CCTTGGTCTTTGCTGGTGTA+AGG - chr5_2:4794159-4794178 None:intergenic 50.0%
CCTTACACCAGCAAAGACCA+AGG + chr5_2:4794156-4794175 Msa0751280:CDS 50.0%
! GTTGATGCCTTGGTCTTTGC+TGG - chr5_2:4794166-4794185 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 4793994 4794536 4793994 ID=Msa0751280;Name=Msa0751280
chr5_2 mRNA 4793994 4794536 4793994 ID=Msa0751280-mRNA-1;Parent=Msa0751280;Name=Msa0751280-mRNA-1;_AED=0.46;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|180
chr5_2 exon 4793994 4794536 4793994 ID=Msa0751280-mRNA-1:exon:1905;Parent=Msa0751280-mRNA-1
chr5_2 CDS 4793994 4794536 4793994 ID=Msa0751280-mRNA-1:cds;Parent=Msa0751280-mRNA-1
Gene Sequence

>Msa0751280

ATGGAGCAAAACACAAGTATTATGATAGAGCGACTTTCTATTTCTTCCAAAGAAGAGATCATTGATTTGAACCAAATCACACTCCGATCTTTTCATCTTTCTGACCTCGATGATCTCATGGTTTGGCATACTGATGAAAAAGTGGCCAAGTTCTGGGGTGAACCTTACACCAGCAAAGACCAAGGCATCAACTTCATTAAAAATATGGCAAGCAGGTATCTAAGTTGCAAAGCAATATGCCATAACGATCATGCTATTGGGTGTATTAAGTTGTCCTTGAGTTCACTTGATGATAAGAGGAGGATCACATGTGCAGAACTTGGGTATGTTCTAGGCTCTAAATACTGGGGTAAAGGGATTGCCACATGTGCTGTGAAACAAATGGTTAAGGTTGCATTCAGTGAATTTCCATACTTGGAAAGGCTTCAAGCTCTTGTTGATGTGGATAATTTAAGGTCGCAAAGAGTAGTTGAGAAAGTTGGTTTTCAAAAAGAGGGAGTTCTTAGGAAGTATGTATTCTTTAAAGGAAAAACAGAGATATGA
Protein sequence

>Msa0751280

MEQNTSIMIERLSISSKEEIIDLNQITLRSFHLSDLDDLMVWHTDEKVAKFWGEPYTSKDQGINFIKNMASRYLSCKAICHNDHAIGCIKLSLSSLDDKRRITCAELGYVLGSKYWGKGIATCAVKQMVKVAFSEFPYLERLQALVDVDNLRSQRVVEKVGFQKEGVLRKYVFFKGKTEI*