AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1407020

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1407020 MtrunA17_Chr4g0055761 99.301 143 1 0 1 143 1 143 6.46e-101 290
Msa1407020 MtrunA17_Chr8g0335331 59.574 47 16 2 43 88 37 81 1.07e-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
Msa1407020 AT4G17500.1 43.902 123 47 3 1 101 1 123 1.12e-25 99.0
Msa1407020 AT5G47220.1 34.028 144 63 4 1 141 1 115 5.69e-16 72.8
Msa1407020 AT2G44840.1 52.830 53 23 1 38 90 12 62 2.66e-12 62.8

Find 59 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTTCACCGGAGCAGCTTT+TGG 0.272014 tig0023248:-92656 None:intergenic
CGGTGCTCCAACAAATGTTT+CGG 0.316905 tig0023248:+92340 Msa1407020:CDS
GGCGGCGAATAGAGTCTAAA+AGG 0.317517 tig0023248:-92289 None:intergenic
GGTGCTCCAACAAATGTTTC+GGG 0.321872 tig0023248:+92341 Msa1407020:CDS
CGGAATCCACCCAACATTTA+CGG 0.327835 tig0023248:-92495 None:intergenic
TCTATTCGCCGCCACTTGTT+AGG 0.348893 tig0023248:+92299 Msa1407020:CDS
TCTGAAGATATGGTACTTTA+CGG 0.355225 tig0023248:+92458 Msa1407020:CDS
ACCCATGTTTAAGTGACAAT+TGG 0.355880 tig0023248:+92408 Msa1407020:CDS
TGGGTATAAACTGCTGAAAC+TGG 0.370999 tig0023248:-92390 None:intergenic
GGAGAATCCGAATTTATATT+CGG 0.374846 tig0023248:+92320 Msa1407020:CDS
CCCATGTTTAAGTGACAATT+GGG 0.395679 tig0023248:+92409 Msa1407020:CDS
GTTAGAAATGACGGTGAAAC+CGG 0.397441 tig0023248:+92562 Msa1407020:CDS
AAAACCGATGAGACACTTTC+GGG 0.401330 tig0023248:-92536 None:intergenic
TGGATTCCGTCTCTTGAAGT+TGG 0.401436 tig0023248:+92509 Msa1407020:CDS
AGAAGATGATTCTGAAGATA+TGG 0.403547 tig0023248:+92448 Msa1407020:CDS
TGGAGCACCGAATATAAATT+CGG 0.409017 tig0023248:-92327 None:intergenic
GTATTACCCGAAACATTTGT+TGG 0.425227 tig0023248:-92347 None:intergenic
CTTCGCGACGCCGTAAATGT+TGG 0.442144 tig0023248:+92485 Msa1407020:CDS
TGGAGCTCCGAGAGAAAACC+CGG 0.459822 tig0023248:-92370 None:intergenic
GGATTCCGTCTCTTGAAGTT+GGG 0.482850 tig0023248:+92510 Msa1407020:CDS
CAAATGTTTCGGGTAATACC+CGG 0.491537 tig0023248:+92351 Msa1407020:CDS
TTCTCCACCGGCATAACATC+CGG 0.492162 tig0023248:-92587 None:intergenic
CCCCAATTGTCACTTAAACA+TGG 0.498682 tig0023248:-92410 None:intergenic
GGCTTCTACGGCGGAGCAAG+TGG 0.500398 tig0023248:+92622 Msa1407020:CDS
TGTCCTACCGGTGGCTTCTA+CGG 0.500889 tig0023248:+92610 Msa1407020:CDS
AGAGTCTAAAAGGGCAAGAT+CGG 0.504431 tig0023248:-92279 None:intergenic
CGGCGTGAGACAACGGCCAT+GGG 0.507993 tig0023248:+92692 Msa1407020:CDS
ACCGGAGCCGGATGTTATGC+CGG 0.509833 tig0023248:+92580 Msa1407020:CDS
CCAAAAGCTGCTCCGGTGAA+AGG 0.513655 tig0023248:+92656 Msa1407020:CDS
AGAGGGACCAAAAGCTGCTC+CGG 0.514715 tig0023248:+92649 Msa1407020:CDS
ACCGGCATAACATCCGGCTC+CGG 0.525114 tig0023248:-92581 None:intergenic
CCCAATTGTCACTTAAACAT+GGG 0.539909 tig0023248:-92409 None:intergenic
CCTACCGGTGGCTTCTACGG+CGG 0.539965 tig0023248:+92613 Msa1407020:CDS
GCGGCGTGAGACAACGGCCA+TGG 0.544485 tig0023248:+92691 Msa1407020:CDS
AATGACGGTGAAACCGGAGC+CGG 0.545739 tig0023248:+92568 Msa1407020:CDS
ACCAAAGGCCACAACATGTA+CGG 0.547777 tig0023248:+92239 None:intergenic
GCCGGTGGAGAATGTCCTAC+CGG 0.570540 tig0023248:+92598 Msa1407020:CDS
GTCACCCGAAAGTGTCTCAT+CGG 0.573926 tig0023248:+92532 Msa1407020:CDS
AAATGTTTCGGGTAATACCC+GGG 0.585648 tig0023248:+92352 Msa1407020:CDS
TCAGAATCATCTTCTTTGAG+TGG 0.586437 tig0023248:-92440 None:intergenic
GGTTTCACCGTCATTTCTAA+CGG 0.587508 tig0023248:-92560 None:intergenic
GCGGCGAATAGAGTCTAAAA+GGG 0.598260 tig0023248:-92288 None:intergenic
GCGACGCCGTAAATGTTGGG+TGG 0.600378 tig0023248:+92489 Msa1407020:CDS
ACCGGTAGGACATTCTCCAC+CGG 0.602856 tig0023248:-92599 None:intergenic
TGCTCCGCCGTAGAAGCCAC+CGG 0.616358 tig0023248:-92617 None:intergenic
CAACATTTACGGCGTCGCGA+AGG 0.618314 tig0023248:-92484 None:intergenic
GCGGAGCAAGTGGTTCCAGA+GGG 0.635382 tig0023248:+92632 Msa1407020:CDS
GGCGGAGCAAGTGGTTCCAG+AGG 0.637613 tig0023248:+92631 Msa1407020:CDS
GGTGACCCAACTTCAAGAGA+CGG 0.645113 tig0023248:-92515 None:intergenic
CGGATTCTCCTAACAAGTGG+CGG 0.646031 tig0023248:-92307 None:intergenic
ATTCGGATTCTCCTAACAAG+TGG 0.648497 tig0023248:-92310 None:intergenic
GGTGGAGAATGTCCTACCGG+TGG 0.649479 tig0023248:+92601 Msa1407020:CDS
GGAGCCGGATGTTATGCCGG+TGG 0.660925 tig0023248:+92583 Msa1407020:CDS
CCGCCGTAGAAGCCACCGGT+AGG 0.661007 tig0023248:-92613 None:intergenic
GGCGTGAGACAACGGCCATG+GGG 0.667710 tig0023248:+92693 Msa1407020:CDS
CCATGTTTAAGTGACAATTG+GGG 0.685913 tig0023248:+92410 Msa1407020:CDS
ATGGCCGTTGTCTCACGCCG+CGG 0.699050 tig0023248:-92689 None:intergenic
GCGTGAGACAACGGCCATGG+GGG 0.713016 tig0023248:+92694 Msa1407020:CDS
GGAGCTCCGAGAGAAAACCC+GGG 0.762071 tig0023248:-92369 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GGAGAATCCGAATTTATATT+CGG + tig0023248:92320-92339 Msa1407020:CDS 30.0%
! AGAAGATGATTCTGAAGATA+TGG + tig0023248:92448-92467 Msa1407020:CDS 30.0%
TCTGAAGATATGGTACTTTA+CGG + tig0023248:92458-92477 Msa1407020:CDS 30.0%
!! TGGAGCACCGAATATAAATT+CGG - tig0023248:92330-92349 None:intergenic 35.0%
GTATTACCCGAAACATTTGT+TGG - tig0023248:92350-92369 None:intergenic 35.0%
ACCCATGTTTAAGTGACAAT+TGG + tig0023248:92408-92427 Msa1407020:CDS 35.0%
! CCCAATTGTCACTTAAACAT+GGG - tig0023248:92412-92431 None:intergenic 35.0%
CCCATGTTTAAGTGACAATT+GGG + tig0023248:92409-92428 Msa1407020:CDS 35.0%
CCATGTTTAAGTGACAATTG+GGG + tig0023248:92410-92429 Msa1407020:CDS 35.0%
TCAGAATCATCTTCTTTGAG+TGG - tig0023248:92443-92462 None:intergenic 35.0%
AAAAACCGATGAGACACTTT+CGG - tig0023248:92540-92559 None:intergenic 35.0%
! GGTTTTTCCGTTAGAAATGA+CGG + tig0023248:92553-92572 Msa1407020:CDS 35.0%
AGAGTCTAAAAGGGCAAGAT+CGG - tig0023248:92282-92301 None:intergenic 40.0%
ATTCGGATTCTCCTAACAAG+TGG - tig0023248:92313-92332 None:intergenic 40.0%
! CAAATGTTTCGGGTAATACC+CGG + tig0023248:92351-92370 Msa1407020:CDS 40.0%
! AAATGTTTCGGGTAATACCC+GGG + tig0023248:92352-92371 Msa1407020:CDS 40.0%
TGGGTATAAACTGCTGAAAC+TGG - tig0023248:92393-92412 None:intergenic 40.0%
! CCCCAATTGTCACTTAAACA+TGG - tig0023248:92413-92432 None:intergenic 40.0%
AAAACCGATGAGACACTTTC+GGG - tig0023248:92539-92558 None:intergenic 40.0%
GGTTTCACCGTCATTTCTAA+CGG - tig0023248:92563-92582 None:intergenic 40.0%
GTTAGAAATGACGGTGAAAC+CGG + tig0023248:92562-92581 Msa1407020:CDS 40.0%
! GGTAGTGTTTTTCCTTTCAC+CGG - tig0023248:92671-92690 None:intergenic 40.0%
TGAAAGGAAAAACACTACCG+CGG + tig0023248:92672-92691 Msa1407020:CDS 40.0%
GCGGCGAATAGAGTCTAAAA+GGG - tig0023248:92291-92310 None:intergenic 45.0%
CGGTGCTCCAACAAATGTTT+CGG + tig0023248:92340-92359 Msa1407020:CDS 45.0%
GGTGCTCCAACAAATGTTTC+GGG + tig0023248:92341-92360 Msa1407020:CDS 45.0%
! GTAATACCCGGGTTTTCTCT+CGG + tig0023248:92363-92382 Msa1407020:CDS 45.0%
CGGAATCCACCCAACATTTA+CGG - tig0023248:92498-92517 None:intergenic 45.0%
TGGATTCCGTCTCTTGAAGT+TGG + tig0023248:92509-92528 Msa1407020:CDS 45.0%
GGATTCCGTCTCTTGAAGTT+GGG + tig0023248:92510-92529 Msa1407020:CDS 45.0%
GGCGGCGAATAGAGTCTAAA+AGG - tig0023248:92292-92311 None:intergenic 50.0%
TCTATTCGCCGCCACTTGTT+AGG + tig0023248:92299-92318 Msa1407020:CDS 50.0%
CGGATTCTCCTAACAAGTGG+CGG - tig0023248:92310-92329 None:intergenic 50.0%
TTCGCGACGCCGTAAATGTT+GGG + tig0023248:92486-92505 Msa1407020:CDS 50.0%
GGTGACCCAACTTCAAGAGA+CGG - tig0023248:92518-92537 None:intergenic 50.0%
!! GTCACCCGAAAGTGTCTCAT+CGG + tig0023248:92532-92551 Msa1407020:CDS 50.0%
TTCTCCACCGGCATAACATC+CGG - tig0023248:92590-92609 None:intergenic 50.0%
TGGAGCTCCGAGAGAAAACC+CGG - tig0023248:92373-92392 None:intergenic 55.0%
CAACATTTACGGCGTCGCGA+AGG - tig0023248:92487-92506 None:intergenic 55.0%
CTTCGCGACGCCGTAAATGT+TGG + tig0023248:92485-92504 Msa1407020:CDS 55.0%
AATGACGGTGAAACCGGAGC+CGG + tig0023248:92568-92587 Msa1407020:CDS 55.0%
ACCGGTAGGACATTCTCCAC+CGG - tig0023248:92602-92621 None:intergenic 55.0%
TGTCCTACCGGTGGCTTCTA+CGG + tig0023248:92610-92629 Msa1407020:CDS 55.0%
AGAGGGACCAAAAGCTGCTC+CGG + tig0023248:92649-92668 Msa1407020:CDS 55.0%
! CCTTTCACCGGAGCAGCTTT+TGG - tig0023248:92659-92678 None:intergenic 55.0%
CCAAAAGCTGCTCCGGTGAA+AGG + tig0023248:92656-92675 Msa1407020:CDS 55.0%
GGAGCTCCGAGAGAAAACCC+GGG - tig0023248:92372-92391 None:intergenic 60.0%
GCGACGCCGTAAATGTTGGG+TGG + tig0023248:92489-92508 Msa1407020:CDS 60.0%
ACCGGAGCCGGATGTTATGC+CGG + tig0023248:92580-92599 Msa1407020:CDS 60.0%
ACCGGCATAACATCCGGCTC+CGG - tig0023248:92584-92603 None:intergenic 60.0%
GCCGGTGGAGAATGTCCTAC+CGG + tig0023248:92598-92617 Msa1407020:CDS 60.0%
GGTGGAGAATGTCCTACCGG+TGG + tig0023248:92601-92620 Msa1407020:CDS 60.0%
GCGGAGCAAGTGGTTCCAGA+GGG + tig0023248:92632-92651 Msa1407020:CDS 60.0%
! GGAGCAGCTTTTGGTCCCTC+TGG - tig0023248:92650-92669 None:intergenic 60.0%
ACTACCGCGGCGTGAGACAA+CGG + tig0023248:92685-92704 Msa1407020:CDS 60.0%
ACGGCCATGGGGGAAATTCG+CGG + tig0023248:92704-92723 Msa1407020:CDS 60.0%
GGAGCCGGATGTTATGCCGG+TGG + tig0023248:92583-92602 Msa1407020:CDS 65.0%
CCTACCGGTGGCTTCTACGG+CGG + tig0023248:92613-92632 Msa1407020:CDS 65.0%
TGCTCCGCCGTAGAAGCCAC+CGG - tig0023248:92620-92639 None:intergenic 65.0%
GGCTTCTACGGCGGAGCAAG+TGG + tig0023248:92622-92641 Msa1407020:CDS 65.0%
GGCGGAGCAAGTGGTTCCAG+AGG + tig0023248:92631-92650 Msa1407020:CDS 65.0%
ATGGCCGTTGTCTCACGCCG+CGG - tig0023248:92692-92711 None:intergenic 65.0%
CGGCGTGAGACAACGGCCAT+GGG + tig0023248:92692-92711 Msa1407020:CDS 65.0%
GGCGTGAGACAACGGCCATG+GGG + tig0023248:92693-92712 Msa1407020:CDS 65.0%
GCGTGAGACAACGGCCATGG+GGG + tig0023248:92694-92713 Msa1407020:CDS 65.0%
GCCATGGGGGAAATTCGCGG+CGG + tig0023248:92707-92726 Msa1407020:CDS 65.0%
TCCGCCGCGAATTTCCCCCA+TGG - tig0023248:92711-92730 None:intergenic 65.0%
CCGCCGTAGAAGCCACCGGT+AGG - tig0023248:92616-92635 None:intergenic 70.0%
GCGGCGTGAGACAACGGCCA+TGG + tig0023248:92691-92710 Msa1407020:CDS 70.0%
Chromosome Type Strat End Strand Name
tig0023248 gene 92254 92733 92254 ID=Msa1407020;Name=Msa1407020
tig0023248 mRNA 92254 92733 92254 ID=Msa1407020-mRNA-1;Parent=Msa1407020;Name=Msa1407020-mRNA-1;_AED=0.04;_eAED=0.14;_QI=0|-1|0|1|-1|1|1|0|160
tig0023248 exon 92254 92733 92254 ID=Msa1407020-mRNA-1:exon:24836;Parent=Msa1407020-mRNA-1
tig0023248 CDS 92254 92733 92254 ID=Msa1407020-mRNA-1:cds;Parent=Msa1407020-mRNA-1
Gene Sequence

>Msa1407020

ATGTACGGAAATAGTAATTTTGATTCCGATCTTGCCCTTTTAGACTCTATTCGCCGCCACTTGTTAGGAGAATCCGAATTTATATTCGGTGCTCCAACAAATGTTTCGGGTAATACCCGGGTTTTCTCTCGGAGCTCCAGTTTCAGCAGTTTATACCCATGTTTAAGTGACAATTGGGGTGAACTACCACTCAAAGAAGATGATTCTGAAGATATGGTACTTTACGGCGTCCTTCGCGACGCCGTAAATGTTGGGTGGATTCCGTCTCTTGAAGTTGGGTCACCCGAAAGTGTCTCATCGGTTTTTCCGTTAGAAATGACGGTGAAACCGGAGCCGGATGTTATGCCGGTGGAGAATGTCCTACCGGTGGCTTCTACGGCGGAGCAAGTGGTTCCAGAGGGACCAAAAGCTGCTCCGGTGAAAGGAAAAACACTACCGCGGCGTGAGACAACGGCCATGGGGGAAATTCGCGGCGGAGAT
Protein sequence

>Msa1407020

MYGNSNFDSDLALLDSIRRHLLGESEFIFGAPTNVSGNTRVFSRSSSFSSLYPCLSDNWGELPLKEDDSEDMVLYGVLRDAVNVGWIPSLEVGSPESVSSVFPLEMTVKPEPDVMPVENVLPVASTAEQVVPEGPKAAPVKGKTLPRRETTAMGEIRGGD