AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1354800


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 77 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCCTCCCGTAGGAGTC+TGG 0.214220 tig0014543:+536368 Msa1354800:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 tig0014543:-536255 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 tig0014543:+536170 Msa1354800:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 tig0014543:-536307 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 tig0014543:+536512 Msa1354800:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 tig0014543:+536480 Msa1354800:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 tig0014543:+536207 Msa1354800:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 tig0014543:+536513 Msa1354800:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 tig0014543:-536180 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 tig0014543:+536553 Msa1354800:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 tig0014543:-536189 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 tig0014543:+536123 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 tig0014543:-536552 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 tig0014543:-536469 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 tig0014543:+536558 Msa1354800:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 tig0014543:+536481 Msa1354800:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 tig0014543:+536369 Msa1354800:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 tig0014543:-536131 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 tig0014543:-536564 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 tig0014543:-536363 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 tig0014543:-536546 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 tig0014543:-536624 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 tig0014543:+536317 Msa1354800:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 tig0014543:-536364 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 tig0014543:-536254 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 tig0014543:-536570 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 tig0014543:-536493 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 tig0014543:-536598 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 tig0014543:-536179 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 tig0014543:-536618 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 tig0014543:+536590 Msa1354800:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 tig0014543:-536599 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 tig0014543:-536569 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 tig0014543:+536554 Msa1354800:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 tig0014543:-536332 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 tig0014543:-536431 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 tig0014543:-536217 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 tig0014543:-536566 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 tig0014543:-536513 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 tig0014543:-536405 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 tig0014543:-536565 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 tig0014543:-536300 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 tig0014543:-536492 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 tig0014543:-536130 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 tig0014543:-536299 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 tig0014543:+536484 Msa1354800:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 tig0014543:+536514 Msa1354800:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 tig0014543:+536431 Msa1354800:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 tig0014543:+536333 Msa1354800:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 tig0014543:-536159 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 tig0014543:+536407 Msa1354800:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 tig0014543:-536497 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 tig0014543:-536625 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 tig0014543:-536655 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 tig0014543:-536404 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 tig0014543:-536522 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 tig0014543:-536241 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 tig0014543:-536606 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 tig0014543:-536494 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 tig0014543:-536603 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 tig0014543:-536262 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 tig0014543:-536392 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 tig0014543:-536162 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 tig0014543:-536314 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 tig0014543:-536464 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 tig0014543:-536206 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 tig0014543:-536652 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 tig0014543:+536284 Msa1354800:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 tig0014543:-536510 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 tig0014543:+536391 Msa1354800:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 tig0014543:-536253 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 tig0014543:-536422 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 tig0014543:-536317 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 tig0014543:-536448 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 tig0014543:-536445 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 tig0014543:+536200 Msa1354800:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 tig0014543:-536362 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - tig0014543:536257-536276 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG - tig0014543:536182-536201 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG - tig0014543:536256-536275 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG - tig0014543:536258-536277 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - tig0014543:536265-536284 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG + tig0014543:536284-536303 Msa1354800:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG - tig0014543:536627-536646 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG - tig0014543:536628-536647 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG - tig0014543:536183-536202 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - tig0014543:536244-536263 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + tig0014543:536261-536280 Msa1354800:intron 45.0%
! GGGTCATGAACTTCTTTTCC+TGG - tig0014543:536282-536301 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG - tig0014543:536349-536368 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG - tig0014543:536448-536467 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG - tig0014543:536451-536470 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG - tig0014543:536467-536486 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - tig0014543:536165-536184 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG + tig0014543:536170-536189 Msa1354800:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG - tig0014543:536192-536211 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG + tig0014543:536200-536219 Msa1354800:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG - tig0014543:536350-536369 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG - tig0014543:536407-536426 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG + tig0014543:536407-536426 Msa1354800:CDS 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG - tig0014543:536472-536491 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG + tig0014543:536512-536531 Msa1354800:CDS 50.0%
TGCTAATACCCCGTAAGCTG+AGG - tig0014543:536525-536544 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG - tig0014543:536549-536568 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG - tig0014543:536302-536321 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - tig0014543:536303-536322 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + tig0014543:536302-536321 Msa1354800:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG - tig0014543:536310-536329 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG - tig0014543:536380-536399 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG - tig0014543:536408-536427 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG - tig0014543:536425-536444 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG - tig0014543:536513-536532 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG + tig0014543:536513-536532 Msa1354800:CDS 55.0%
CTTTCGCTCCTCAGCTTACG+GGG + tig0014543:536514-536533 Msa1354800:CDS 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG + tig0014543:536554-536573 Msa1354800:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG - tig0014543:536567-536586 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG - tig0014543:536568-536587 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG - tig0014543:536572-536591 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG - tig0014543:536573-536592 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG - tig0014543:536606-536625 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG - tig0014543:536609-536628 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG - tig0014543:536621-536640 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - tig0014543:536162-536181 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG - tig0014543:536220-536239 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG - tig0014543:536335-536354 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG + tig0014543:536333-536352 Msa1354800:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG - tig0014543:536379-536398 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG + tig0014543:536391-536410 Msa1354800:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG - tig0014543:536395-536414 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG - tig0014543:536434-536453 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG + tig0014543:536431-536450 Msa1354800:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG - tig0014543:536496-536515 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG - tig0014543:536497-536516 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG - tig0014543:536500-536519 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG - tig0014543:536516-536535 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG - tig0014543:536555-536574 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG + tig0014543:536553-536572 Msa1354800:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG - tig0014543:536569-536588 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG - tig0014543:536601-536620 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG - tig0014543:536602-536621 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG - tig0014543:536209-536228 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG + tig0014543:536207-536226 Msa1354800:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG - tig0014543:536365-536384 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG - tig0014543:536366-536385 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG - tig0014543:536367-536386 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG + tig0014543:536368-536387 Msa1354800:intron 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG + tig0014543:536369-536388 Msa1354800:intron 65.0%
AAGGCCCAGACTCCTACGGG+AGG - tig0014543:536376-536395 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG + tig0014543:536480-536499 Msa1354800:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG + tig0014543:536481-536500 Msa1354800:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG - tig0014543:536495-536514 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG + tig0014543:536558-536577 Msa1354800:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG + tig0014543:536590-536609 Msa1354800:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG - tig0014543:536317-536336 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - tig0014543:536320-536339 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG + tig0014543:536317-536336 Msa1354800:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG + tig0014543:536361-536380 Msa1354800:intron 70.0%
GACGCGAGCCCCTCCTTGGG+CGG + tig0014543:536484-536503 Msa1354800:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0014543 gene 536132 536667 536132 ID=Msa1354800;Name=Msa1354800
tig0014543 mRNA 536132 536667 536132 ID=Msa1354800-mRNA-1;Parent=Msa1354800;Name=Msa1354800-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
tig0014543 exon 536132 536269 536132 ID=Msa1354800-mRNA-1:exon:9246;Parent=Msa1354800-mRNA-1
tig0014543 exon 536283 536378 536283 ID=Msa1354800-mRNA-1:exon:9247;Parent=Msa1354800-mRNA-1
tig0014543 exon 536383 536667 536383 ID=Msa1354800-mRNA-1:exon:9248;Parent=Msa1354800-mRNA-1
tig0014543 CDS 536132 536269 536132 ID=Msa1354800-mRNA-1:cds;Parent=Msa1354800-mRNA-1
tig0014543 CDS 536283 536378 536283 ID=Msa1354800-mRNA-1:cds;Parent=Msa1354800-mRNA-1
tig0014543 CDS 536383 536667 536383 ID=Msa1354800-mRNA-1:cds;Parent=Msa1354800-mRNA-1
Gene Sequence

>Msa1354800

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1354800

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS