AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0288460

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0288460 MtrunA17_Chr4g0062691 47.973 148 60 5 1 137 145 286 1.99e-25 99.4
Msa0288460 MtrunA17_Chr6g0456881 40.299 134 65 3 1 119 139 272 8.30e-19 81.6
Msa0288460 MtrunA17_Chr7g0220931 57.692 52 22 0 1 52 133 184 4.44e-16 73.6
Msa0288460 MtrunA17_Chr1g0205131 50.000 50 25 0 1 50 122 171 2.09e-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
Msa0288460 AT3G18550.2 39.583 144 50 4 2 116 162 297 7.32e-18 79.3
Msa0288460 AT1G67260.2 36.842 133 69 1 1 118 100 232 2.58e-17 77.4
Msa0288460 AT1G67260.3 36.842 133 69 1 1 118 100 232 2.58e-17 77.4
Msa0288460 AT3G18550.1 38.514 148 50 4 2 116 162 301 2.69e-17 77.8
Msa0288460 AT3G18550.4 38.514 148 50 4 2 116 162 301 2.69e-17 77.8
Msa0288460 AT1G67260.1 36.842 133 69 1 1 118 100 232 2.76e-17 77.4
Msa0288460 AT3G18550.3 38.514 148 50 4 2 116 162 301 3.42e-17 77.4
Msa0288460 AT1G68800.2 58.929 56 19 1 2 53 126 181 6.13e-16 73.6
Msa0288460 AT1G68800.1 58.929 56 19 1 2 53 126 181 6.20e-16 73.6
Msa0288460 AT4G18390.1 36.975 119 62 4 2 116 56 165 1.91e-13 66.6
Msa0288460 AT4G18390.2 36.975 119 62 4 2 116 56 165 1.91e-13 66.6
Msa0288460 AT1G30210.2 33.813 139 71 3 1 138 63 181 2.62e-13 65.9
Msa0288460 AT1G30210.1 33.813 139 71 3 1 138 63 181 2.62e-13 65.9

Find 40 sgRNAs with CRISPR-Local

Find 100 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATAAGCTTATTTGTTTATT+GGG 0.218118 2_3:+33661876 Msa0288460:three_prime_UTR
TTATAAGCTTATTTGTTTAT+TGG 0.219253 2_3:+33661875 Msa0288460:three_prime_UTR
TGCAAGAGGATTATGTATTC+TGG 0.269182 2_3:-33661257 None:intergenic
TTTCAGTTCAAGTTGCTAAA+AGG 0.272883 2_3:+33660993 Msa0288460:CDS
TTGATAAAATCATAATAAAT+AGG 0.299310 2_3:-33661807 None:intergenic
ACATCTTGTACGGCCTTTGC+AGG 0.339389 2_3:-33661591 None:intergenic
TCGTTGACTGCAATCTCTTC+AGG 0.355340 2_3:-33661163 None:intergenic
TCACAAAATTTAATGGAGTA+AGG 0.374776 2_3:+33661667 Msa0288460:three_prime_UTR
CAGCTAGAGGAATGAGAGAT+AGG 0.396710 2_3:+33660960 None:intergenic
TGGGTGTGAAGAGAATTATT+AGG 0.425176 2_3:+33661224 Msa0288460:CDS
TTCCGTTTGCAAGACATGTT+AGG 0.439649 2_3:+33661019 Msa0288460:CDS
AGCTTATTTGTTTATTGGGA+GGG 0.440796 2_3:+33661880 Msa0288460:three_prime_UTR
AGAGTTTCAATCATTGAAGA+AGG 0.450602 2_3:+33661527 Msa0288460:CDS
CTTTGAAACCACATCTTGTA+CGG 0.457874 2_3:-33661601 None:intergenic
AAAATAATTTCTCAGATTCG+TGG 0.480399 2_3:-33661702 None:intergenic
ATTTCTCAGATTCGTGGATG+TGG 0.488045 2_3:-33661696 None:intergenic
GAGGATTATGTATTCTGGAA+TGG 0.490957 2_3:-33661252 None:intergenic
CATCTTGTACGGCCTTTGCA+GGG 0.499196 2_3:-33661590 None:intergenic
TGCAAGGGAGTTGAGAGAAA+AGG 0.502844 2_3:+33661276 Msa0288460:CDS
ACAAATCATATCTAATTGTA+CGG 0.507959 2_3:+33661560 Msa0288460:exon
TTACATTCATAAGTATAACT+TGG 0.515465 2_3:+33661912 Msa0288460:three_prime_UTR
AGCCTAACATGTCTTGCAAA+CGG 0.523751 2_3:-33661021 None:intergenic
GAGAGAAAAGGCAAGGGAAA+GGG 0.530804 2_3:+33661288 Msa0288460:CDS
TGAGAGAAAAGGCAAGGGAA+AGG 0.535173 2_3:+33661287 Msa0288460:CDS
TCTCTCAACTCCCTTGCAAG+AGG 0.544135 2_3:-33661271 None:intergenic
TGGTTACTAAATCAAGCAAA+AGG 0.545110 2_3:+33661070 Msa0288460:CDS
ATAATTCTCTTCACACCCAA+AGG 0.549718 2_3:-33661220 None:intergenic
AAGCTTATTTGTTTATTGGG+AGG 0.553506 2_3:+33661879 Msa0288460:three_prime_UTR
TGCAAAGGCCGTACAAGATG+TGG 0.583040 2_3:+33661593 Msa0288460:three_prime_UTR
GGGAGTTGAGAGAAAAGGCA+AGG 0.592316 2_3:+33661281 Msa0288460:CDS
ATCTTGTACGGCCTTTGCAG+GGG 0.594028 2_3:-33661589 None:intergenic
CAAGGGAAAGGGCAAGAGAG+AGG 0.597351 2_3:+33661299 Msa0288460:CDS
TACGGACATATCCCCTGCAA+AGG 0.613514 2_3:+33661578 Msa0288460:three_prime_UTR
GAATACATAATCCTCTTGCA+AGG 0.618391 2_3:+33661260 Msa0288460:CDS
AATACTATTAAACAAGCTTG+CGG 0.620564 2_3:-33661632 None:intergenic
AATACATAATCCTCTTGCAA+GGG 0.622939 2_3:+33661261 Msa0288460:CDS
TAGGTATAAGAGCAGAAACA+AGG 0.625010 2_3:-33661788 None:intergenic
GGAGTTGAGAGAAAAGGCAA+GGG 0.625355 2_3:+33661282 Msa0288460:CDS
CTGTAGAGAACTGAAAACCA+TGG 0.627809 2_3:-33661347 None:intergenic
AAGCTAGCAAAACAGTGGAG+TGG 0.654481 2_3:+33661050 Msa0288460:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGATAAAATCATAATAAAT+AGG - chr2_3:33661810-33661829 None:intergenic 10.0%
!! TTGATAAAATCATAATAAAT+AGG - chr2_3:33661810-33661829 None:intergenic 10.0%
!!! AATTATTTTTCTTAAACGTA+CGG + chr2_3:33661716-33661735 Msa0288460:three_prime_UTR 15.0%
!! TTATAAGCTTATTTGTTTAT+TGG + chr2_3:33661875-33661894 Msa0288460:three_prime_UTR 15.0%
!! TATAAGCTTATTTGTTTATT+GGG + chr2_3:33661876-33661895 Msa0288460:three_prime_UTR 15.0%
!!! AATTATTTTTCTTAAACGTA+CGG + chr2_3:33661716-33661735 Msa0288460:three_prime_UTR 15.0%
!! TTATAAGCTTATTTGTTTAT+TGG + chr2_3:33661875-33661894 Msa0288460:three_prime_UTR 15.0%
!! TATAAGCTTATTTGTTTATT+GGG + chr2_3:33661876-33661895 Msa0288460:three_prime_UTR 15.0%
!! ACAAATCATATCTAATTGTA+CGG + chr2_3:33661560-33661579 Msa0288460:exon 20.0%
!!! ACTTTTCTCACAAAATTTAA+TGG + chr2_3:33661660-33661679 Msa0288460:three_prime_UTR 20.0%
!!! TATGATTTTATCAAATGACA+TGG + chr2_3:33661816-33661835 Msa0288460:three_prime_UTR 20.0%
!! TTACATTCATAAGTATAACT+TGG + chr2_3:33661912-33661931 Msa0288460:three_prime_UTR 20.0%
!! ACAAATCATATCTAATTGTA+CGG + chr2_3:33661560-33661579 Msa0288460:exon 20.0%
!!! ACTTTTCTCACAAAATTTAA+TGG + chr2_3:33661660-33661679 Msa0288460:three_prime_UTR 20.0%
!!! TATGATTTTATCAAATGACA+TGG + chr2_3:33661816-33661835 Msa0288460:three_prime_UTR 20.0%
!! TTACATTCATAAGTATAACT+TGG + chr2_3:33661912-33661931 Msa0288460:three_prime_UTR 20.0%
! AGTAAGTCTCAATTAATTTC+TGG + chr2_3:33661372-33661391 Msa0288460:intron 25.0%
! AATACTATTAAACAAGCTTG+CGG - chr2_3:33661635-33661654 None:intergenic 25.0%
! TCACAAAATTTAATGGAGTA+AGG + chr2_3:33661667-33661686 Msa0288460:three_prime_UTR 25.0%
! AAAATAATTTCTCAGATTCG+TGG - chr2_3:33661705-33661724 None:intergenic 25.0%
! AGTAAGTCTCAATTAATTTC+TGG + chr2_3:33661372-33661391 Msa0288460:intron 25.0%
! AATACTATTAAACAAGCTTG+CGG - chr2_3:33661635-33661654 None:intergenic 25.0%
! TCACAAAATTTAATGGAGTA+AGG + chr2_3:33661667-33661686 Msa0288460:three_prime_UTR 25.0%
! AAAATAATTTCTCAGATTCG+TGG - chr2_3:33661705-33661724 None:intergenic 25.0%
!! TTTCAGTTCAAGTTGCTAAA+AGG + chr2_3:33660993-33661012 Msa0288460:CDS 30.0%
TGGTTACTAAATCAAGCAAA+AGG + chr2_3:33661070-33661089 Msa0288460:CDS 30.0%
AAGAAAAAGAAGAAGCCTTT+GGG + chr2_3:33661205-33661224 Msa0288460:CDS 30.0%
AATACATAATCCTCTTGCAA+GGG + chr2_3:33661261-33661280 Msa0288460:CDS 30.0%
CAAAAATATGAGAAGATCCA+TGG + chr2_3:33661330-33661349 Msa0288460:CDS 30.0%
CTGTACATACTAGAATTGAA+TGG - chr2_3:33661467-33661486 None:intergenic 30.0%
AGAGTTTCAATCATTGAAGA+AGG + chr2_3:33661527-33661546 Msa0288460:CDS 30.0%
! TTTTTCTTAAACGTACGGTA+CGG + chr2_3:33661721-33661740 Msa0288460:three_prime_UTR 30.0%
AAGCTTATTTGTTTATTGGG+AGG + chr2_3:33661879-33661898 Msa0288460:three_prime_UTR 30.0%
AGCTTATTTGTTTATTGGGA+GGG + chr2_3:33661880-33661899 Msa0288460:three_prime_UTR 30.0%
!! TTTCAGTTCAAGTTGCTAAA+AGG + chr2_3:33660993-33661012 Msa0288460:CDS 30.0%
TGGTTACTAAATCAAGCAAA+AGG + chr2_3:33661070-33661089 Msa0288460:CDS 30.0%
AAGAAAAAGAAGAAGCCTTT+GGG + chr2_3:33661205-33661224 Msa0288460:CDS 30.0%
AATACATAATCCTCTTGCAA+GGG + chr2_3:33661261-33661280 Msa0288460:CDS 30.0%
CAAAAATATGAGAAGATCCA+TGG + chr2_3:33661330-33661349 Msa0288460:CDS 30.0%
CTGTACATACTAGAATTGAA+TGG - chr2_3:33661467-33661486 None:intergenic 30.0%
AGAGTTTCAATCATTGAAGA+AGG + chr2_3:33661527-33661546 Msa0288460:CDS 30.0%
! TTTTTCTTAAACGTACGGTA+CGG + chr2_3:33661721-33661740 Msa0288460:three_prime_UTR 30.0%
AAGCTTATTTGTTTATTGGG+AGG + chr2_3:33661879-33661898 Msa0288460:three_prime_UTR 30.0%
AGCTTATTTGTTTATTGGGA+GGG + chr2_3:33661880-33661899 Msa0288460:three_prime_UTR 30.0%
TGAAAAAGCTAGCAAAACAG+TGG + chr2_3:33661045-33661064 Msa0288460:CDS 35.0%
GAAGAAAAAGAAGAAGCCTT+TGG + chr2_3:33661204-33661223 Msa0288460:CDS 35.0%
ATAATTCTCTTCACACCCAA+AGG - chr2_3:33661223-33661242 None:intergenic 35.0%
TGGGTGTGAAGAGAATTATT+AGG + chr2_3:33661224-33661243 Msa0288460:CDS 35.0%
! GAGGATTATGTATTCTGGAA+TGG - chr2_3:33661255-33661274 None:intergenic 35.0%
TGCAAGAGGATTATGTATTC+TGG - chr2_3:33661260-33661279 None:intergenic 35.0%
GAATACATAATCCTCTTGCA+AGG + chr2_3:33661260-33661279 Msa0288460:CDS 35.0%
!! CTTTGAAACCACATCTTGTA+CGG - chr2_3:33661604-33661623 None:intergenic 35.0%
TAGGTATAAGAGCAGAAACA+AGG - chr2_3:33661791-33661810 None:intergenic 35.0%
TGAAAAAGCTAGCAAAACAG+TGG + chr2_3:33661045-33661064 Msa0288460:CDS 35.0%
GAAGAAAAAGAAGAAGCCTT+TGG + chr2_3:33661204-33661223 Msa0288460:CDS 35.0%
ATAATTCTCTTCACACCCAA+AGG - chr2_3:33661223-33661242 None:intergenic 35.0%
TGGGTGTGAAGAGAATTATT+AGG + chr2_3:33661224-33661243 Msa0288460:CDS 35.0%
! GAGGATTATGTATTCTGGAA+TGG - chr2_3:33661255-33661274 None:intergenic 35.0%
TGCAAGAGGATTATGTATTC+TGG - chr2_3:33661260-33661279 None:intergenic 35.0%
GAATACATAATCCTCTTGCA+AGG + chr2_3:33661260-33661279 Msa0288460:CDS 35.0%
!! CTTTGAAACCACATCTTGTA+CGG - chr2_3:33661604-33661623 None:intergenic 35.0%
TAGGTATAAGAGCAGAAACA+AGG - chr2_3:33661791-33661810 None:intergenic 35.0%
TTCCGTTTGCAAGACATGTT+AGG + chr2_3:33661019-33661038 Msa0288460:CDS 40.0%
AGCCTAACATGTCTTGCAAA+CGG - chr2_3:33661024-33661043 None:intergenic 40.0%
CTGTAGAGAACTGAAAACCA+TGG - chr2_3:33661350-33661369 None:intergenic 40.0%
! CATGGTTTTCAGTTCTCTAC+AGG + chr2_3:33661348-33661367 Msa0288460:CDS 40.0%
ATTTCTCAGATTCGTGGATG+TGG - chr2_3:33661699-33661718 None:intergenic 40.0%
TTCCGTTTGCAAGACATGTT+AGG + chr2_3:33661019-33661038 Msa0288460:CDS 40.0%
AGCCTAACATGTCTTGCAAA+CGG - chr2_3:33661024-33661043 None:intergenic 40.0%
CTGTAGAGAACTGAAAACCA+TGG - chr2_3:33661350-33661369 None:intergenic 40.0%
! CATGGTTTTCAGTTCTCTAC+AGG + chr2_3:33661348-33661367 Msa0288460:CDS 40.0%
ATTTCTCAGATTCGTGGATG+TGG - chr2_3:33661699-33661718 None:intergenic 40.0%
AAGCTAGCAAAACAGTGGAG+TGG + chr2_3:33661050-33661069 Msa0288460:CDS 45.0%
! TCGTTGACTGCAATCTCTTC+AGG - chr2_3:33661166-33661185 None:intergenic 45.0%
TGCAAGGGAGTTGAGAGAAA+AGG + chr2_3:33661276-33661295 Msa0288460:CDS 45.0%
GGAGTTGAGAGAAAAGGCAA+GGG + chr2_3:33661282-33661301 Msa0288460:CDS 45.0%
TGAGAGAAAAGGCAAGGGAA+AGG + chr2_3:33661287-33661306 Msa0288460:CDS 45.0%
GAGAGAAAAGGCAAGGGAAA+GGG + chr2_3:33661288-33661307 Msa0288460:CDS 45.0%
AAGCTAGCAAAACAGTGGAG+TGG + chr2_3:33661050-33661069 Msa0288460:CDS 45.0%
! TCGTTGACTGCAATCTCTTC+AGG - chr2_3:33661166-33661185 None:intergenic 45.0%
TGCAAGGGAGTTGAGAGAAA+AGG + chr2_3:33661276-33661295 Msa0288460:CDS 45.0%
GGAGTTGAGAGAAAAGGCAA+GGG + chr2_3:33661282-33661301 Msa0288460:CDS 45.0%
TGAGAGAAAAGGCAAGGGAA+AGG + chr2_3:33661287-33661306 Msa0288460:CDS 45.0%
GAGAGAAAAGGCAAGGGAAA+GGG + chr2_3:33661288-33661307 Msa0288460:CDS 45.0%
TCTCTCAACTCCCTTGCAAG+AGG - chr2_3:33661274-33661293 None:intergenic 50.0%
GGGAGTTGAGAGAAAAGGCA+AGG + chr2_3:33661281-33661300 Msa0288460:CDS 50.0%
TACGGACATATCCCCTGCAA+AGG + chr2_3:33661578-33661597 Msa0288460:three_prime_UTR 50.0%
ATCTTGTACGGCCTTTGCAG+GGG - chr2_3:33661592-33661611 None:intergenic 50.0%
CATCTTGTACGGCCTTTGCA+GGG - chr2_3:33661593-33661612 None:intergenic 50.0%
ACATCTTGTACGGCCTTTGC+AGG - chr2_3:33661594-33661613 None:intergenic 50.0%
TGCAAAGGCCGTACAAGATG+TGG + chr2_3:33661593-33661612 Msa0288460:three_prime_UTR 50.0%
TCTCTCAACTCCCTTGCAAG+AGG - chr2_3:33661274-33661293 None:intergenic 50.0%
GGGAGTTGAGAGAAAAGGCA+AGG + chr2_3:33661281-33661300 Msa0288460:CDS 50.0%
TACGGACATATCCCCTGCAA+AGG + chr2_3:33661578-33661597 Msa0288460:three_prime_UTR 50.0%
ATCTTGTACGGCCTTTGCAG+GGG - chr2_3:33661592-33661611 None:intergenic 50.0%
CATCTTGTACGGCCTTTGCA+GGG - chr2_3:33661593-33661612 None:intergenic 50.0%
ACATCTTGTACGGCCTTTGC+AGG - chr2_3:33661594-33661613 None:intergenic 50.0%
TGCAAAGGCCGTACAAGATG+TGG + chr2_3:33661593-33661612 Msa0288460:three_prime_UTR 50.0%
CAAGGGAAAGGGCAAGAGAG+AGG + chr2_3:33661299-33661318 Msa0288460:CDS 55.0%
CAAGGGAAAGGGCAAGAGAG+AGG + chr2_3:33661299-33661318 Msa0288460:CDS 55.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 33660971 33661962 33660971 ID=Msa0288460;Name=Msa0288460
chr2_3 mRNA 33660971 33661962 33660971 ID=Msa0288460-mRNA-1;Parent=Msa0288460;Name=Msa0288460-mRNA-1;_AED=0.09;_eAED=0.09;_QI=0|0.5|0.33|1|0|0|3|402|146
chr2_3 exon 33660971 33661155 33660971 ID=Msa0288460-mRNA-1:exon:11060;Parent=Msa0288460-mRNA-1
chr2_3 exon 33661162 33661372 33661162 ID=Msa0288460-mRNA-1:exon:11061;Parent=Msa0288460-mRNA-1
chr2_3 exon 33661516 33661962 33661516 ID=Msa0288460-mRNA-1:exon:11062;Parent=Msa0288460-mRNA-1
chr2_3 CDS 33660971 33661155 33660971 ID=Msa0288460-mRNA-1:cds;Parent=Msa0288460-mRNA-1
chr2_3 CDS 33661162 33661372 33661162 ID=Msa0288460-mRNA-1:cds;Parent=Msa0288460-mRNA-1
chr2_3 CDS 33661516 33661560 33661516 ID=Msa0288460-mRNA-1:cds;Parent=Msa0288460-mRNA-1
chr2_3 three_prime_UTR 33661561 33661962 33661561 ID=Msa0288460-mRNA-1:three_prime_utr;Parent=Msa0288460-mRNA-1
Gene Sequence

>Msa0288460

ATGAGAGATAGGAGAATGAGACTTTCAGTTCAAGTTGCTAAAAGGTTTTTCCGTTTGCAAGACATGTTAGGCTTTGAAAAAGCTAGCAAAACAGTGGAGTGGTTACTAAATCAAGCAAAAGGTCAAATCAATCAAATAGCTGCATCAAAGAGTAATAATGTTTCTTCTTCAACTTTTGAATATATTCCTGAAGAGATTGCAGTCAACGAGATTAAGCAAGAACAAAAGAAGAAAAAGAAGAAGCCTTTGGGTGTGAAGAGAATTATTAGGAAAAACCATTCCAGAATACATAATCCTCTTGCAAGGGAGTTGAGAGAAAAGGCAAGGGAAAGGGCAAGAGAGAGGACTAAAGACAAAAATATGAGAAGATCCATGGTTTTCAGTTCTCTACAGGAACATCTAGTTGAAGAGTTTCAATCATTGAAGAAGGATTACATATAA
Protein sequence

>Msa0288460

MRDRRMRLSVQVAKRFFRLQDMLGFEKASKTVEWLLNQAKGQINQIAASKSNNVSSSTFEYIPEEIAVNEIKQEQKKKKKKPLGVKRIIRKNHSRIHNPLARELREKARERARERTKDKNMRRSMVFSSLQEHLVEEFQSLKKDYI*