AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG003682


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG003682 MtrunA17_Chr1g0188461 95.775 497 21 0 1 497 1 497 0.0 915
MsaG003682 MtrunA17_Chr4g0042701 30.303 198 124 6 6 197 55 244 1.25e-13 73.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG003682 AT3G56570.1 54.307 534 201 8 1 495 1 530 0.0 532
MsaG003682 AT3G56570.2 54.206 535 201 9 1 495 1 531 0.0 527
MsaG003682 AT3G07670.1 23.582 335 188 10 64 394 135 405 4.83e-11 65.5

Find 103 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTTGTTTGGGTGGTTATT+TGG 0.196021 1:-60494124 MsaT003682.1:CDS
TTAACGGATATTCCTTCTTC+TGG 0.208879 1:+60494246 None:intergenic
CTACTGATACGTCTAATTTA+TGG 0.220381 1:+60490127 None:intergenic
ATTTAATACTTACGGGATAT+TGG 0.228032 1:-60490415 MsaT003682.1:CDS
ATTGTAAGACAAGCTTTCTT+TGG 0.277640 1:+60494180 None:intergenic
ATAGATGATTACCATGGTTT+TGG 0.280289 1:-60492917 MsaT003682.1:CDS
GCTTGTTTGGGTGGTTATTT+GGG 0.283926 1:-60494123 MsaT003682.1:CDS
GATTTCACACAATGCTTTAA+CGG 0.292015 1:+60494230 None:intergenic
CAAAGCATCACAAACTTCTT+TGG 0.300506 1:+60490002 None:intergenic
GATCATTGAGAATGCTTGTT+TGG 0.315901 1:-60494136 MsaT003682.1:CDS
AAGCTTAACCCGGAATTCTT+TGG 0.317812 1:-60492992 MsaT003682.1:CDS
TGATATTGTGAACATTGATT+TGG 0.318688 1:-60490340 MsaT003682.1:CDS
GCCGCTTTGCTACATAGATA+TGG 0.324543 1:-60490387 MsaT003682.1:CDS
TCGAGAAGAAATAAGACTTT+TGG 0.326128 1:+60492949 None:intergenic
TTTAATACTTACGGGATATT+GGG 0.328807 1:-60490414 MsaT003682.1:CDS
TAACGGATATTCCTTCTTCT+GGG 0.338446 1:+60494247 None:intergenic
TATTATGTATGAGAGGAGTT+TGG 0.351233 1:-60494088 MsaT003682.1:CDS
TCAACAGGAATGTTTGCCTT+TGG 0.352496 1:-60494025 MsaT003682.1:CDS
TACAGGTATTTAATACTTAC+GGG 0.360220 1:-60490422 MsaT003682.1:intron
ATATGATGTATAATAAAATA+AGG 0.361591 1:+60490169 None:intergenic
TGTTCCACACCAAAGAATTC+CGG 0.362959 1:+60492983 None:intergenic
ACTAGCTCAAAATTCCTCTT+TGG 0.365519 1:-60490791 MsaT003682.1:CDS
AGGAATGTTTGCCTTTGGTT+TGG 0.382903 1:-60494020 MsaT003682.1:CDS
TCCAGCTTCAATCATAAAAC+TGG 0.383775 1:-60490898 MsaT003682.1:intron
TATTTCGAGATATCATTTGA+TGG 0.393572 1:-60490210 MsaT003682.1:CDS
ATACAGGTATTTAATACTTA+CGG 0.399560 1:-60490423 MsaT003682.1:intron
TTGTGATGCTTTGTTGTCAC+TGG 0.403340 1:-60489992 MsaT003682.1:CDS
TTGAAGGTTCTGAATCCAAC+AGG 0.407785 1:+60493014 None:intergenic
GTGTGGTACTGAGCTTCATC+AGG 0.410493 1:-60493971 MsaT003682.1:intron
ATCATTGAGAATGCTTGTTT+GGG 0.415985 1:-60494135 MsaT003682.1:CDS
ATTATGTATGAGAGGAGTTT+GGG 0.425077 1:-60494087 MsaT003682.1:CDS
AATTCCGGGTTAAGCTTTGA+AGG 0.427673 1:+60492998 None:intergenic
GTCTCCCTTTGGAGAAGGTT+AGG 0.432291 1:-60490261 MsaT003682.1:CDS
GATATGAGGGAGAGTCTCTA+TGG 0.435839 1:-60489967 MsaT003682.1:CDS
TGTTGTCACTGGCTGATATG+AGG 0.437422 1:-60489981 MsaT003682.1:CDS
GACGTATCAGTAGCAGTTGC+TGG 0.438103 1:-60490117 MsaT003682.1:CDS
GTTCCACACCAAAGAATTCC+GGG 0.439461 1:+60492984 None:intergenic
ATCAATGTTCACAATATCAT+AGG 0.441709 1:+60490344 None:intergenic
TGGAAAGCTGTATCATTCTT+CGG 0.452010 1:-60489887 MsaT003682.1:CDS
GAGCAACACATTGCACTTTG+TGG 0.469836 1:-60494274 MsaT003682.1:CDS
TCTTGATCTGCTGTGGCGGT+TGG 0.477152 1:+60490284 None:intergenic
TGTGAACATTGATTTGGAAC+TGG 0.477397 1:-60490334 MsaT003682.1:CDS
AGAGAATATTCTACCCCTGT+TGG 0.478060 1:-60493029 MsaT003682.1:CDS
GCAGATCAAGAGTCTCCCTT+TGG 0.480598 1:-60490272 MsaT003682.1:CDS
TTTGGGCGAGGAATCTCCTT+GGG 0.486078 1:-60494070 MsaT003682.1:CDS
TCTTTGGATAAAACTGAGAA+AGG 0.499954 1:-60490775 MsaT003682.1:CDS
AATTTATGGTAAACATCATC+CGG 0.501826 1:+60490141 None:intergenic
AGACAAAGCTCTTGTCTATG+AGG 0.503563 1:-60493059 MsaT003682.1:CDS
CTGCTAGGAAGAAGTTGAAA+AGG 0.505819 1:-60489783 MsaT003682.1:CDS
TCTCTGTGGCAATGGCCACC+AGG 0.510589 1:-60494441 None:intergenic
GTTGCTCCATTCGAATCCAT+TGG 0.527285 1:+60494290 None:intergenic
GCTCAGTACCACACAAAAGC+TGG 0.530815 1:+60493980 None:intergenic
TGAGGATGATACTTCAATGC+TGG 0.532383 1:-60490719 MsaT003682.1:CDS
AAGCTCTTGTCTATGAGGAC+TGG 0.532918 1:-60493054 MsaT003682.1:CDS
GTATGAGAGGAGTTTGGGCG+AGG 0.534677 1:-60494082 MsaT003682.1:CDS
ATAGCCTAACCTTCTCCAAA+GGG 0.535931 1:+60490257 None:intergenic
CAAGAGTCTCCCTTTGGAGA+AGG 0.539649 1:-60490266 MsaT003682.1:CDS
GTTGTCACTGGCTGATATGA+GGG 0.545553 1:-60489980 MsaT003682.1:CDS
GGCGAGGAATCTCCTTGGGA+GGG 0.548860 1:-60494066 MsaT003682.1:CDS
TTTGTGGACACCCCAGAAGA+AGG 0.549481 1:-60494258 MsaT003682.1:CDS
GCTTCACTTACAGATCTGCC+AGG 0.550005 1:+60492885 None:intergenic
GGGCGAGGAATCTCCTTGGG+AGG 0.554610 1:-60494067 MsaT003682.1:CDS
ATTGAGAATGCTTGTTTGGG+TGG 0.555502 1:-60494132 MsaT003682.1:CDS
TGATACTTCAATGCTGGAGA+TGG 0.557586 1:-60490713 MsaT003682.1:CDS
GTTTGCGTGCATTCAAGCGA+TGG 0.559316 1:-60494320 MsaT003682.1:CDS
AACGGATATTCCTTCTTCTG+GGG 0.559930 1:+60494248 None:intergenic
GTTTGGGCGAGGAATCTCCT+TGG 0.560202 1:-60494071 MsaT003682.1:CDS
TAACCCGGAATTCTTTGGTG+TGG 0.569437 1:-60492987 MsaT003682.1:CDS
GTCTTCTAACAACGAATCTG+AGG 0.572955 1:-60490848 MsaT003682.1:CDS
CGGTTCTGCGTATCAGTGAA+AGG 0.574157 1:-60489867 MsaT003682.1:CDS
GTTGAAAAGGACAACAAAGA+GGG 0.577396 1:-60489770 MsaT003682.1:CDS
GGATTATTCTTCAATTACTG+AGG 0.579159 1:-60490737 MsaT003682.1:CDS
GGTTTGGAGTGTTGAAGAAG+TGG 0.580380 1:-60494004 MsaT003682.1:CDS
ATGATATCGAGGCATTAGAA+AGG 0.589395 1:-60489927 MsaT003682.1:CDS
AGAACCTTCAAAGCTTAACC+CGG 0.596675 1:-60493002 MsaT003682.1:CDS
GGGAGACTCTTGATCTGCTG+TGG 0.600462 1:+60490277 None:intergenic
AATAGCCTAACCTTCTCCAA+AGG 0.600517 1:+60490256 None:intergenic
TGAAGTCCAATGGATTCGAA+TGG 0.603454 1:-60494296 MsaT003682.1:CDS
CTTCACTTACAGATCTGCCA+GGG 0.605599 1:+60492886 None:intergenic
AGATGTTAGCAGTGGAGCTG+AGG 0.607643 1:-60490680 MsaT003682.1:intron
TTACTAATCTTAGCTCTGCT+AGG 0.608261 1:-60489798 MsaT003682.1:CDS
AAAGGCAAACATTCCTGTTG+AGG 0.608468 1:+60494027 None:intergenic
AGTTGAAAAGGACAACAAAG+AGG 0.608977 1:-60489771 MsaT003682.1:CDS
ATGATAAAAGATGTTAGCAG+TGG 0.610343 1:-60490688 MsaT003682.1:CDS
AAGCGATGGATGAAGTCCAA+TGG 0.611498 1:-60494306 MsaT003682.1:CDS
ATCAATAGAAGATGATATCG+AGG 0.613024 1:-60489938 MsaT003682.1:CDS
CTGTTGCTATTATGTATGAG+AGG 0.614081 1:-60494095 MsaT003682.1:CDS
CTTCAATCATAAAACTGGTG+AGG 0.621851 1:-60490893 MsaT003682.1:CDS
ATTTGGAACTGGTACTTCAG+TGG 0.622999 1:-60490323 MsaT003682.1:CDS
AGACTCTTGATCTGCTGTGG+CGG 0.628471 1:+60490280 None:intergenic
AGCTGAAGATAACCCTCCCA+AGG 0.629647 1:+60494054 None:intergenic
TCTTCAACACTCCAAACCAA+AGG 0.644717 1:+60494009 None:intergenic
GCATTGTGTGAAATCAATGC+AGG 0.646675 1:-60494222 MsaT003682.1:CDS
TGAAATCAATGCAGGTGATG+TGG 0.648395 1:-60494214 MsaT003682.1:CDS
TTCGAGATAGATGATTACCA+TGG 0.653774 1:-60492923 MsaT003682.1:CDS
TGTCTTACAATCAAGACTAG+TGG 0.657502 1:-60494168 MsaT003682.1:CDS
TCCATATCTATGTAGCAAAG+CGG 0.658059 1:+60490386 None:intergenic
TGAAGGTTCTGAATCCAACA+GGG 0.663792 1:+60493015 None:intergenic
AAAATAAGGAGTTCAATCTG+TGG 0.668743 1:+60490183 None:intergenic
GGGGAACCATGCCAAAACCA+TGG 0.671012 1:+60492906 None:intergenic
GAAAGGCGTTGATAGCGACA+TGG 0.674161 1:-60490758 MsaT003682.1:CDS
TTCACTTACAGATCTGCCAG+GGG 0.708708 1:+60492887 None:intergenic
GAAGGTTCTGAATCCAACAG+GGG 0.712164 1:+60493016 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 60489762 60494452 60489762 ID=MsaG003682
Chr1 mRNA 60489762 60494452 60489762 ID=MsaT003682.1;Parent=MsaG003682
Chr1 exon 60489762 60490439 60489762 ID=MsaT003682.1.exon5;Parent=MsaT003682.1
Chr1 CDS 60489762 60490439 60489762 ID=cds.MsaT003682.1;Parent=MsaT003682.1
Chr1 exon 60490681 60490915 60490681 ID=MsaT003682.1.exon4;Parent=MsaT003682.1
Chr1 CDS 60490681 60490915 60490681 ID=cds.MsaT003682.1;Parent=MsaT003682.1
Chr1 exon 60492896 60493092 60492896 ID=MsaT003682.1.exon3;Parent=MsaT003682.1
Chr1 CDS 60492896 60493092 60492896 ID=cds.MsaT003682.1;Parent=MsaT003682.1
Chr1 exon 60493972 60494344 60493972 ID=MsaT003682.1.exon2;Parent=MsaT003682.1
Chr1 CDS 60493972 60494344 60493972 ID=cds.MsaT003682.1;Parent=MsaT003682.1
Chr1 exon 60494442 60494452 60494442 ID=MsaT003682.1.exon1;Parent=MsaT003682.1
Chr1 CDS 60494442 60494452 60494442 ID=cds.MsaT003682.1;Parent=MsaT003682.1
Gene Sequence

>MsaT003682.1

ATGGCCACCAGACGTTTGCGTGCATTCAAGCGATGGATGAAGTCCAATGGATTCGAATGGAGCAACACATTGCACTTTGTGGACACCCCAGAAGAAGGAATATCCGTTAAAGCATTGTGTGAAATCAATGCAGGTGATGTGGTTGCAAAAATGCCAAAGAAAGCTTGTCTTACAATCAAGACTAGTGGTGCTTGTGAGATCATTGAGAATGCTTGTTTGGGTGGTTATTTGGGTTTAGCTGTTGCTATTATGTATGAGAGGAGTTTGGGCGAGGAATCTCCTTGGGAGGGTTATCTTCAGCTTTTGCCTCAACAGGAATGTTTGCCTTTGGTTTGGAGTGTTGAAGAAGTGGACCAGCTTTTGTGTGGTACTGAGCTTCATCAGACAGTGCAAGAAGACAAAGCTCTTGTCTATGAGGACTGGAAAGAGAATATTCTACCCCTGTTGGATTCAGAACCTTCAAAGCTTAACCCGGAATTCTTTGGTGTGGAACAGTACTTTGCAGCCAAAAGTCTTATTTCTTCTCGATCTTTCGAGATAGATGATTACCATGGTTTTGGCATGGTTCCCCTGGCAGATCTCTTCAATCATAAAACTGGTGAGGAAGATGTGCATTTCACTGCTTTGTCTTCTAACAACGAATCTGAGGATGACACTGATGACGAAATTGTTGATGAAGAAGCACTAGCTCAAAATTCCTCTTTGGATAAAACTGAGAAAGGCGTTGATAGCGACATGGATTATTCTTCAATTACTGAGGATGATACTTCAATGCTGGAGATGGTTATGATAAAAGATGTTAGCAGTGGAGCTGAGGTATTTAATACTTACGGGATATTGGGTAATGCCGCTTTGCTACATAGATATGGATTTACTGAGCAAGATAACACCTATGATATTGTGAACATTGATTTGGAACTGGTACTTCAGTGGTGTTCTTCTTTGTTCTCCAACCGCCACAGCAGATCAAGAGTCTCCCTTTGGAGAAGGTTAGGCTATTCCAGTGACACCGAAAACTCTGAATATTTCGAGATATCATTTGATGGAGAACCACAGATTGAACTCCTTATTTTATTATACATCATATTTTTACCGGATGATGTTTACCATAAATTAGACGTATCAGTAGCAGTTGCTGGAAATTGTCATGAATCAAGTGAAAAAACCACTTTTTTGAATGATGATATCTTTCTAAAGAAGCTGTCTAATATGAGCAAGAAAACTTTGATGACCAAAGAAGTTTGTGATGCTTTGTTGTCACTGGCTGATATGAGGGAGAGTCTCTATGGTTTGAAATCAATAGAAGATGATATCGAGGCATTAGAAAGGTGTAGTTTTGTTAGAGATGGAAAGCTGTATCATTCTTCGGTTCTGCGTATCAGTGAAAGGAAGATCCTTCAAAAACTCAGAAATTATGCTTCAAAGTCGTGTAAGATTACTAATCTTAGCTCTGCTAGGAAGAAGTTGAAAAGGACAACAAAGAGGGAGAGTTGA

Protein sequence

>MsaT003682.1

MATRRLRAFKRWMKSNGFEWSNTLHFVDTPEEGISVKALCEINAGDVVAKMPKKACLTIKTSGACEIIENACLGGYLGLAVAIMYERSLGEESPWEGYLQLLPQQECLPLVWSVEEVDQLLCGTELHQTVQEDKALVYEDWKENILPLLDSEPSKLNPEFFGVEQYFAAKSLISSRSFEIDDYHGFGMVPLADLFNHKTGEEDVHFTALSSNNESEDDTDDEIVDEEALAQNSSLDKTEKGVDSDMDYSSITEDDTSMLEMVMIKDVSSGAEVFNTYGILGNAALLHRYGFTEQDNTYDIVNIDLELVLQWCSSLFSNRHSRSRVSLWRRLGYSSDTENSEYFEISFDGEPQIELLILLYIIFLPDDVYHKLDVSVAVAGNCHESSEKTTFLNDDIFLKKLSNMSKKTLMTKEVCDALLSLADMRESLYGLKSIEDDIEALERCSFVRDGKLYHSSVLRISERKILQKLRNYASKSCKITNLSSARKKLKRTTKRES*