AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene019998

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene019998.t1 MTR_3g070120 32.911 158 92 4 29 175 146 300 7.84e-13 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTTGATGTTTGCTTCTTTA+AGG 0.138534 6.1:+12255711 None:intergenic
CTTAGATTTCAAATCCAAAT+TGG 0.175377 6.1:-12255635 MS.gene019998:CDS
TTTACCTTTCTCACAAGATT+TGG 0.226819 6.1:-12255426 MS.gene019998:CDS
GAAGAGGGTTTCTCTTGTTT+TGG 0.245975 6.1:+12255736 None:intergenic
CTAAGAAGCCATTGAGAATA+AGG 0.247836 6.1:+12255653 None:intergenic
GGAGCGTGCACGGTTAATTA+AGG 0.290096 6.1:-12255317 MS.gene019998:CDS
TTTCTAAGCTGCCCTTGTTT+AGG 0.299863 6.1:+12255547 None:intergenic
TCAAGAGCCGGAATTGGATT+TGG 0.301896 6.1:-12255338 MS.gene019998:CDS
TTACCTTTCTCACAAGATTT+GGG 0.302378 6.1:-12255425 MS.gene019998:CDS
TCCTTCACAGAGTTATAAAA+AGG 0.345114 6.1:+12255586 None:intergenic
GAAAGTTCAAGAGCCGGAAT+TGG 0.391991 6.1:-12255344 MS.gene019998:CDS
TTAGATTTCAAATCCAAATT+GGG 0.401807 6.1:-12255634 MS.gene019998:CDS
GGCAGCTTAGAAAGAGGATC+TGG 0.431103 6.1:-12255537 MS.gene019998:CDS
GCACGCTCCAAATCCAATTC+CGG 0.440433 6.1:+12255331 None:intergenic
GACGAAATCCTTATTCTCAA+TGG 0.457404 6.1:-12255661 MS.gene019998:CDS
GTCCCCAAATCTTGTGAGAA+AGG 0.458776 6.1:+12255422 None:intergenic
TCAAGATCATTATAGAATCT+AGG 0.460182 6.1:+12255460 None:intergenic
ATATGAGAACATGAAGAAAG+AGG 0.508111 6.1:-12255500 MS.gene019998:CDS
GTCATTTCTAAGTTATTGCA+AGG 0.515777 6.1:-12255283 MS.gene019998:CDS
ATTCTATAATGATCTTGAGC+AGG 0.520209 6.1:-12255455 MS.gene019998:CDS
GTTGACTGAGGAATCGAATC+GGG 0.521747 6.1:-12255395 MS.gene019998:CDS
AGTTGACTGAGGAATCGAAT+CGG 0.535931 6.1:-12255396 MS.gene019998:CDS
AATTGGATTTGGAGCGTGCA+CGG 0.556576 6.1:-12255327 MS.gene019998:CDS
GGAATCGAATCGGGTAGAGT+TGG 0.557159 6.1:-12255386 MS.gene019998:CDS
TGCTTCTTTAAGGAAGAAGA+GGG 0.572401 6.1:+12255721 None:intergenic
TACCTTTCTCACAAGATTTG+GGG 0.576919 6.1:-12255424 MS.gene019998:CDS
AACAAGGGCAGCTTAGAAAG+AGG 0.580040 6.1:-12255543 MS.gene019998:CDS
GGGTAGAGTTGGATGAAATG+TGG 0.588939 6.1:-12255375 MS.gene019998:CDS
CTTAGTGTGAAACCTAAACA+AGG 0.589654 6.1:-12255559 MS.gene019998:CDS
TTGCTTCTTTAAGGAAGAAG+AGG 0.590446 6.1:+12255720 None:intergenic
GGAATTGAAAGTTCAAGAGC+CGG 0.590503 6.1:-12255350 MS.gene019998:CDS
GATTTCGTCATCGAAAGTGA+AGG 0.607171 6.1:+12255675 None:intergenic
AGCTTAGAAAGAGGATCTGG+AGG 0.623043 6.1:-12255534 MS.gene019998:CDS
AGAGTTGGATGAAATGTGGA+GGG 0.623431 6.1:-12255371 MS.gene019998:CDS
TAGAGTTGGATGAAATGTGG+AGG 0.631386 6.1:-12255372 MS.gene019998:CDS
AGATCATTATAGAATCTAGG+AGG 0.675424 6.1:+12255463 None:intergenic
TTGGGGACAAGAGTTGACTG+AGG 0.693465 6.1:-12255407 MS.gene019998:CDS
TTAGTGTGAAACCTAAACAA+GGG 0.727599 6.1:-12255558 MS.gene019998:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAGATTTCAAATCCAAATT+GGG - chr6.1:12255411-12255430 MS.gene019998:CDS 20.0%
! CTTAGATTTCAAATCCAAAT+TGG - chr6.1:12255410-12255429 MS.gene019998:CDS 25.0%
! TCAAGATCATTATAGAATCT+AGG + chr6.1:12255588-12255607 None:intergenic 25.0%
!!! TTTCTCTTGTTTTGGATTTT+GGG + chr6.1:12255304-12255323 None:intergenic 25.0%
AGATCATTATAGAATCTAGG+AGG + chr6.1:12255585-12255604 None:intergenic 30.0%
ATATGAGAACATGAAGAAAG+AGG - chr6.1:12255545-12255564 MS.gene019998:CDS 30.0%
ATTCTATAATGATCTTGAGC+AGG - chr6.1:12255590-12255609 MS.gene019998:CDS 30.0%
GTCATTTCTAAGTTATTGCA+AGG - chr6.1:12255762-12255781 MS.gene019998:CDS 30.0%
GTTTGATGTTTGCTTCTTTA+AGG + chr6.1:12255337-12255356 None:intergenic 30.0%
TCCTTCACAGAGTTATAAAA+AGG + chr6.1:12255462-12255481 None:intergenic 30.0%
TTACCTTTCTCACAAGATTT+GGG - chr6.1:12255620-12255639 MS.gene019998:CDS 30.0%
TTAGTGTGAAACCTAAACAA+GGG - chr6.1:12255487-12255506 MS.gene019998:CDS 30.0%
TTTACCTTTCTCACAAGATT+TGG - chr6.1:12255619-12255638 MS.gene019998:CDS 30.0%
! AGAATCTAGGAGGAAATTTT+TGG + chr6.1:12255575-12255594 None:intergenic 30.0%
! TCCTTTTTATAACTCTGTGA+AGG - chr6.1:12255458-12255477 MS.gene019998:CDS 30.0%
!!! GTTTCTCTTGTTTTGGATTT+TGG + chr6.1:12255305-12255324 None:intergenic 30.0%
CTAAGAAGCCATTGAGAATA+AGG + chr6.1:12255395-12255414 None:intergenic 35.0%
CTTAGTGTGAAACCTAAACA+AGG - chr6.1:12255486-12255505 MS.gene019998:CDS 35.0%
GACGAAATCCTTATTCTCAA+TGG - chr6.1:12255384-12255403 MS.gene019998:CDS 35.0%
TACCTTTCTCACAAGATTTG+GGG - chr6.1:12255621-12255640 MS.gene019998:CDS 35.0%
! TGCTTCTTTAAGGAAGAAGA+GGG + chr6.1:12255327-12255346 None:intergenic 35.0%
! TTGCTTCTTTAAGGAAGAAG+AGG + chr6.1:12255328-12255347 None:intergenic 35.0%
!! CATTGCATTTTGACCCAATT+TGG + chr6.1:12255427-12255446 None:intergenic 35.0%
AGAGTTGGATGAAATGTGGA+GGG - chr6.1:12255674-12255693 MS.gene019998:CDS 40.0%
AGTTGACTGAGGAATCGAAT+CGG - chr6.1:12255649-12255668 MS.gene019998:CDS 40.0%
GATTTCGTCATCGAAAGTGA+AGG + chr6.1:12255373-12255392 None:intergenic 40.0%
GGAATTGAAAGTTCAAGAGC+CGG - chr6.1:12255695-12255714 MS.gene019998:CDS 40.0%
TAGAGTTGGATGAAATGTGG+AGG - chr6.1:12255673-12255692 MS.gene019998:CDS 40.0%
! TTTCTAAGCTGCCCTTGTTT+AGG + chr6.1:12255501-12255520 None:intergenic 40.0%
!! GAAGAGGGTTTCTCTTGTTT+TGG + chr6.1:12255312-12255331 None:intergenic 40.0%
AACAAGGGCAGCTTAGAAAG+AGG - chr6.1:12255502-12255521 MS.gene019998:CDS 45.0%
AGCTTAGAAAGAGGATCTGG+AGG - chr6.1:12255511-12255530 MS.gene019998:CDS 45.0%
GAAAGTTCAAGAGCCGGAAT+TGG - chr6.1:12255701-12255720 MS.gene019998:CDS 45.0%
GGGTAGAGTTGGATGAAATG+TGG - chr6.1:12255670-12255689 MS.gene019998:CDS 45.0%
GTCCCCAAATCTTGTGAGAA+AGG + chr6.1:12255626-12255645 None:intergenic 45.0%
GTTGACTGAGGAATCGAATC+GGG - chr6.1:12255650-12255669 MS.gene019998:CDS 45.0%
TCAAGAGCCGGAATTGGATT+TGG - chr6.1:12255707-12255726 MS.gene019998:CDS 45.0%
! AATTGGATTTGGAGCGTGCA+CGG - chr6.1:12255718-12255737 MS.gene019998:CDS 45.0%
GCACGCTCCAAATCCAATTC+CGG + chr6.1:12255717-12255736 None:intergenic 50.0%
GGAATCGAATCGGGTAGAGT+TGG - chr6.1:12255659-12255678 MS.gene019998:CDS 50.0%
GGAGCGTGCACGGTTAATTA+AGG - chr6.1:12255728-12255747 MS.gene019998:CDS 50.0%
GGCAGCTTAGAAAGAGGATC+TGG - chr6.1:12255508-12255527 MS.gene019998:CDS 50.0%
TTGGGGACAAGAGTTGACTG+AGG - chr6.1:12255638-12255657 MS.gene019998:CDS 50.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 12255267 12255800 12255267 ID=MS.gene019998
chr6.1 mRNA 12255267 12255800 12255267 ID=MS.gene019998.t1;Parent=MS.gene019998
chr6.1 exon 12255267 12255800 12255267 ID=MS.gene019998.t1.exon1;Parent=MS.gene019998.t1
chr6.1 CDS 12255267 12255800 12255267 ID=cds.MS.gene019998.t1;Parent=MS.gene019998.t1
Gene Sequence

>MS.gene019998

ATGGCAAAGAAATCAAGTTGTTCTTCTTCTTCATCCCAAAATCCAAAACAAGAGAAACCCTCTTCTTCCTTAAAGAAGCAAACATCAAACTCACGTAAGAAAACCTTCACTTTCGATGACGAAATCCTTATTCTCAATGGCTTCTTAGATTTCAAATCCAAATTGGGTCAAAATGCAATGACAGATTACACTCCTTTTTATAACTCTGTGAAGGATTTGCTTAGTGTGAAACCTAAACAAGGGCAGCTTAGAAAGAGGATCTGGAGGTTAACACAAAAATATGAGAACATGAAGAAAGAGGAAAACCAAAAATTTCCTCCTAGATTCTATAATGATCTTGAGCAGGAAATAATTTACCTTTCTCACAAGATTTGGGGACAAGAGTTGACTGAGGAATCGAATCGGGTAGAGTTGGATGAAATGTGGAGGGAATTGAAAGTTCAAGAGCCGGAATTGGATTTGGAGCGTGCACGGTTAATTAAGGACTCGATTGACGTCATTTCTAAGTTATTGCAAGGATCATCTTCGTCTTAG
Protein sequence

>MS.gene019998.t1

MAKKSSCSSSSSQNPKQEKPSSSLKKQTSNSRKKTFTFDDEILILNGFLDFKSKLGQNAMTDYTPFYNSVKDLLSVKPKQGQLRKRIWRLTQKYENMKKEENQKFPPRFYNDLEQEIIYLSHKIWGQELTEESNRVELDEMWRELKVQEPELDLERARLIKDSIDVISKLLQGSSSS