AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG039308


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG039308 MtrunA17_Chr7g0256891 96.689 604 20 0 4 607 47 650 0.0 1221
MsaG039308 MtrunA17_Chr2g0286541 25.510 196 139 2 406 596 930 1123 6.43e-13 72.0
MsaG039308 MtrunA17_Chr7g0268571 23.558 208 151 3 406 607 729 934 5.58e-11 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG039308 AT2G41450.1 48.576 597 249 8 21 604 61 612 0.0 539
MsaG039308 AT2G41450.2 48.735 593 246 8 25 604 2 549 0.0 538
MsaG039308 AT4G03130.1 27.805 205 130 7 406 601 562 757 5.29e-14 75.9
MsaG039308 AT4G03130.2 27.805 205 130 7 406 601 566 761 5.69e-14 75.9
MsaG039308 AT3G21480.1 23.175 315 198 8 315 596 708 1011 1.43e-11 68.2
MsaG039308 AT4G03130.3 30.986 142 87 5 406 543 566 700 6.60e-11 65.9

Find 106 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTCCCCATTCTTTGTTTA+AGG 0.153944 7:+87372044 MsaT039308.1:CDS
ACAAAGAATCTGAAGGATTT+TGG 0.192159 7:+87368712 MsaT039308.1:CDS
TTCTGTACTGCTCTCTGTTC+CGG 0.211542 7:+87370671 MsaT039308.1:CDS
TCCAGTTTGGCTGGAGATTC+AGG 0.213380 7:+87367515 MsaT039308.1:CDS
CTGATAAGGACTCTGCAAAT+TGG 0.274898 7:-87373297 None:intergenic
CAAACAATTCCTTCTTTAGA+TGG 0.275506 7:-87369431 None:intergenic
TTTGACTTGTGTCTGTTCTA+TGG 0.278979 7:-87369578 None:intergenic
CGTAAAGCATTATGCTTTCC+TGG 0.295086 7:+87369387 MsaT039308.1:CDS
GTGTCATTGCAGCAGTTCTT+AGG 0.300365 7:-87369834 None:intergenic
AAGAAACTTTGATTGCTTTC+CGG 0.309803 7:-87367319 None:intergenic
GTTGATATCCTGCAGGGTTT+TGG 0.322827 7:+87368618 MsaT039308.1:intron
CTAAAGCATTGTTCAGTTGA+TGG 0.343270 7:-87370191 None:intergenic
TCTGTACTGCTCTCTGTTCC+GGG 0.344750 7:+87370672 MsaT039308.1:CDS
TGTCCCCATTCTTTGTTTAA+GGG 0.350626 7:+87372045 MsaT039308.1:CDS
TCCTGAATCTCCAGCCAAAC+TGG 0.360192 7:-87367516 None:intergenic
CCCAATGCTTTGGTAAAAGT+TGG 0.376995 7:+87369606 MsaT039308.1:CDS
CACTACCTGAAGGTATGATT+TGG 0.384485 7:-87367133 None:intergenic
TTCTTGTATTAGGTTATTAG+TGG 0.388331 7:+87373118 MsaT039308.1:intron
TTATTTGTTGAAGTATAAAT+CGG 0.396914 7:+87371990 MsaT039308.1:CDS
TCTGCTATTGTTAGGTCTGC+TGG 0.410098 7:+87372117 MsaT039308.1:CDS
TATAACCCTTAAACAAAGAA+TGG 0.415431 7:-87372050 None:intergenic
ACTACTTCTGAAATCCAGTT+TGG 0.417176 7:+87367502 MsaT039308.1:CDS
TTGAGAGATGTGTGACTAAT+GGG 0.419347 7:+87367340 MsaT039308.1:CDS
AAACTCTGTCTGCTATTGTT+AGG 0.420715 7:+87372109 MsaT039308.1:CDS
TGATAAGGACTCTGCAAATT+GGG 0.421166 7:-87373296 None:intergenic
ATGAATTATGCTGCAAATAC+CGG 0.424682 7:+87367300 MsaT039308.1:CDS
TGGCTGCAAAGAAAGGTATA+AGG 0.425240 7:+87373212 MsaT039308.1:CDS
CTTGAGAGATGTGTGACTAA+TGG 0.429713 7:+87367339 MsaT039308.1:CDS
TTGTCTGTCATCATTTGCTC+TGG 0.434845 7:-87369868 None:intergenic
ACTGTCGATCAGATTCTAGC+TGG 0.443148 7:+87370033 MsaT039308.1:CDS
TTCAACAATTGCAGGTGTAA+AGG 0.444936 7:-87369505 None:intergenic
ACCTCACATTCTGAATGATA+AGG 0.445474 7:+87371966 MsaT039308.1:CDS
TTGACTTGTGTCTGTTCTAT+GGG 0.445981 7:-87369577 None:intergenic
TTTCGACAAGGCAGATTTGT+TGG 0.448692 7:+87371859 MsaT039308.1:CDS
ATAACCCTTAAACAAAGAAT+GGG 0.449312 7:-87372049 None:intergenic
TCTGCATATTCTGTGTCTGC+AGG 0.453750 7:-87368064 None:intergenic
CGAGGATGAAGAGGCTTCCC+AGG 0.455925 7:-87369973 None:intergenic
TCAAAGTAAACCCAATGCTT+TGG 0.461826 7:+87369596 MsaT039308.1:CDS
CTTCTGAAATCCAGTTTGGC+TGG 0.468826 7:+87367506 MsaT039308.1:CDS
TTGTTAACTACACAGTGCTT+GGG 0.469784 7:+87371807 MsaT039308.1:intron
CTGATCGACAGTCAACAAAC+TGG 0.471082 7:-87370022 None:intergenic
TTTGATGACAATGCTAACTC+TGG 0.474813 7:+87369450 MsaT039308.1:CDS
TCGGAGCTTCTAAATGCATA+TGG 0.479623 7:-87370154 None:intergenic
AGATATTGTTTCTAGAGCTC+CGG 0.491665 7:+87368643 MsaT039308.1:CDS
GGCATGTTAACAATCTGATA+AGG 0.498089 7:-87373311 None:intergenic
CATGATTCTCCATCTAAAGA+AGG 0.505386 7:+87369422 MsaT039308.1:CDS
CTGTCGATCAGATTCTAGCT+GGG 0.506118 7:+87370034 MsaT039308.1:CDS
AGACATTGAAGAAGCAATGA+TGG 0.507527 7:+87373192 MsaT039308.1:CDS
GAATTCTGATGAGGCTGTGA+GGG 0.507711 7:-87369483 None:intergenic
CTTGGGTGGTCTCATCGACT+TGG 0.511542 7:+87371824 MsaT039308.1:CDS
GCAATGATGGCTGCAAAGAA+AGG 0.515441 7:+87373205 MsaT039308.1:CDS
ATGTATATGACAGAGCTACC+TGG 0.523476 7:+87367276 MsaT039308.1:CDS
GTTGGATCTTCTCGAGGACG+TGG 0.523707 7:+87369624 MsaT039308.1:CDS
TATTACCAAATCATACCTTC+AGG 0.525549 7:+87367128 MsaT039308.1:CDS
CGAGGACGTGGAAAACTCAA+TGG 0.537156 7:+87369636 MsaT039308.1:CDS
AGGATTGGCCCTACCAGCCT+CGG 0.539403 7:-87370066 None:intergenic
CGGAAGAGACTTCAAAATGT+TGG 0.539655 7:+87368663 MsaT039308.1:CDS
GGATTCCGCAGAACAAGGAT+TGG 0.544036 7:-87370081 None:intergenic
ATAGCACAGGTGGATACAAA+AGG 0.544150 7:+87369330 MsaT039308.1:CDS
TGACTTCAACGAGGATGAAG+AGG 0.545463 7:-87369982 None:intergenic
GGTGGAACTATTGCCTCTGA+TGG 0.550900 7:+87370599 MsaT039308.1:CDS
CGTAGAACATGAATTCATGC+TGG 0.551754 7:+87367083 MsaT039308.1:intron
TAATTGAAGTATCACAATGA+GGG 0.558462 7:-87370103 None:intergenic
AATGATGACAGACAAGCAAA+TGG 0.562041 7:+87369876 MsaT039308.1:CDS
ATACAAAAGGTAGAGCCCGC+AGG 0.578945 7:+87369343 MsaT039308.1:CDS
TGAGGGGATTCCGCAGAACA+AGG 0.583621 7:-87370086 None:intergenic
CTGCATATTCTGTGTCTGCA+GGG 0.585523 7:-87368063 None:intergenic
TTTGCAGCATAATTCATCCC+AGG 0.585813 7:-87367294 None:intergenic
TAAGGACTTTCGACAGTGAG+TGG 0.588593 7:+87373230 MsaT039308.1:CDS
TGTATATGACAGAGCTACCT+GGG 0.591959 7:+87367277 MsaT039308.1:CDS
TTAACTACACAGTGCTTGGG+TGG 0.593202 7:+87371810 MsaT039308.1:intron
AATTTCACTCCTGAAGAAAG+AGG 0.594165 7:+87366969 MsaT039308.1:CDS
TGTGGTTGAGCTTCCATCAG+AGG 0.594722 7:-87370612 None:intergenic
TCCTTATCATTCAGAATGTG+AGG 0.599269 7:-87371967 None:intergenic
GTAAAAGTTGGATCTTCTCG+AGG 0.601134 7:+87369618 MsaT039308.1:CDS
CGTTGAAGTCAAAGAGAGTG+AGG 0.602805 7:+87369994 MsaT039308.1:CDS
TCAACCACACATGTTGTCAC+AGG 0.605648 7:+87370626 MsaT039308.1:CDS
TAAGAAAACACAGCTTACAA+AGG 0.606148 7:+87370244 MsaT039308.1:CDS
TGTCGATCAGATTCTAGCTG+GGG 0.610722 7:+87370035 MsaT039308.1:CDS
TTGATGACAATGCTAACTCT+GGG 0.616144 7:+87369451 MsaT039308.1:CDS
CATGAGACAAGAGCTCGACA+TGG 0.620599 7:+87373267 MsaT039308.1:CDS
TTGAAGTCAAAGAGAGTGAG+GGG 0.624778 7:+87369996 MsaT039308.1:CDS
GTAATTGAAGTATCACAATG+AGG 0.625076 7:-87370104 None:intergenic
AATTGAAGTATCACAATGAG+GGG 0.625488 7:-87370102 None:intergenic
TGGGGAGACAAAGAATCTGA+AGG 0.626446 7:+87368705 MsaT039308.1:CDS
CAGAGGCAATAGTTCCACCT+AGG 0.629274 7:-87370595 None:intergenic
GTTGAAGTCAAAGAGAGTGA+GGG 0.634453 7:+87369995 MsaT039308.1:CDS
CAATGCAATCTATCAACGGA+AGG 0.636176 7:+87368105 MsaT039308.1:CDS
CTGTCAATGCAATCTATCAA+CGG 0.636846 7:+87368101 MsaT039308.1:CDS
ATTGCATTGACAGCTGCAAG+TGG 0.637300 7:-87368091 None:intergenic
ATCATGAGAGTCGAACCACC+AGG 0.638186 7:-87369405 None:intergenic
GGAATTCTGATGAGGCTGTG+AGG 0.653417 7:-87369484 None:intergenic
TTGCATTGACAGCTGCAAGT+GGG 0.654261 7:-87368090 None:intergenic
TAGGGCCAATCCTTGTTCTG+CGG 0.655927 7:+87370076 MsaT039308.1:CDS
AATTCTGATGAGGCTGTGAG+GGG 0.660055 7:-87369482 None:intergenic
TTTGGCTGGAGATTCAGGAA+AGG 0.669858 7:+87367520 MsaT039308.1:CDS
ATATAGGTGATTGAAGACCT+AGG 0.671284 7:+87370578 MsaT039308.1:intron
AAATGGTGCAGATTGTACCC+AGG 0.675885 7:+87369893 MsaT039308.1:CDS
AAAGCATTATGCTTTCCTGG+TGG 0.677104 7:+87369390 MsaT039308.1:CDS
TTGTCCTGTGACAACATGTG+TGG 0.679152 7:-87370630 None:intergenic
TAAGGACTCTGCAAATTGGG+AGG 0.680636 7:-87373293 None:intergenic
GCTATTGTTAGGTCTGCTGG+TGG 0.684582 7:+87372120 MsaT039308.1:CDS
TAACCCTTAAACAAAGAATG+GGG 0.687115 7:-87372048 None:intergenic
CACTCTCTTTGACTTCAACG+AGG 0.710470 7:-87369991 None:intergenic
GGTGTAAAGGAATTCTGATG+AGG 0.724005 7:-87369492 None:intergenic
TAGGTGATTGAAGACCTAGG+TGG 0.771557 7:+87370581 MsaT039308.1:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr7 gene 87366927 87373327 87366927 ID=MsaG039308
Chr7 mRNA 87366927 87373327 87366927 ID=MsaT039308.1;Parent=MsaG039308
Chr7 exon 87366927 87366990 87366927 ID=MsaT039308.1.exon1;Parent=MsaT039308.1
Chr7 CDS 87366927 87366990 87366927 ID=cds.MsaT039308.1;Parent=MsaT039308.1
Chr7 exon 87367088 87367149 87367088 ID=MsaT039308.1.exon2;Parent=MsaT039308.1
Chr7 CDS 87367088 87367149 87367088 ID=cds.MsaT039308.1;Parent=MsaT039308.1
Chr7 exon 87367264 87367361 87367264 ID=MsaT039308.1.exon3;Parent=MsaT039308.1
Chr7 CDS 87367264 87367361 87367264 ID=cds.MsaT039308.1;Parent=MsaT039308.1
Chr7 exon 87367490 87367541 87367490 ID=MsaT039308.1.exon4;Parent=MsaT039308.1
Chr7 CDS 87367490 87367541 87367490 ID=cds.MsaT039308.1;Parent=MsaT039308.1
Chr7 exon 87368034 87368126 87368034 ID=MsaT039308.1.exon5;Parent=MsaT039308.1
Chr7 CDS 87368034 87368126 87368034 ID=cds.MsaT039308.1;Parent=MsaT039308.1
Chr7 exon 87368633 87368743 87368633 ID=MsaT039308.1.exon6;Parent=MsaT039308.1
Chr7 CDS 87368633 87368743 87368633 ID=cds.MsaT039308.1;Parent=MsaT039308.1
Chr7 exon 87369318 87369657 87369318 ID=MsaT039308.1.exon7;Parent=MsaT039308.1
Chr7 CDS 87369318 87369657 87369318 ID=cds.MsaT039308.1;Parent=MsaT039308.1
Chr7 exon 87369817 87370265 87369817 ID=MsaT039308.1.exon8;Parent=MsaT039308.1
Chr7 CDS 87369817 87370265 87369817 ID=cds.MsaT039308.1;Parent=MsaT039308.1
Chr7 exon 87370584 87370693 87370584 ID=MsaT039308.1.exon9;Parent=MsaT039308.1
Chr7 CDS 87370584 87370693 87370584 ID=cds.MsaT039308.1;Parent=MsaT039308.1
Chr7 exon 87371822 87371880 87371822 ID=MsaT039308.1.exon10;Parent=MsaT039308.1
Chr7 CDS 87371822 87371880 87371822 ID=cds.MsaT039308.1;Parent=MsaT039308.1
Chr7 exon 87371959 87372146 87371959 ID=MsaT039308.1.exon11;Parent=MsaT039308.1
Chr7 CDS 87371959 87372146 87371959 ID=cds.MsaT039308.1;Parent=MsaT039308.1
Chr7 exon 87373130 87373327 87373130 ID=MsaT039308.1.exon12;Parent=MsaT039308.1
Chr7 CDS 87373130 87373327 87373130 ID=cds.MsaT039308.1;Parent=MsaT039308.1
Gene Sequence

>MsaT039308.1

ATGTTTCAAGATGTTTCTGCAAACCATAAAAACGCTTCTGGGAATTTCACTCCTGAAGAAAGAGAACATGAATTCATGCTGGTTAATACTAAAGATGATGATGATATTACCAAATCATACCTTCAGGAGGTATTACAGATGTATATGACAGAGCTACCTGGGATGAATTATGCTGCAAATACCGGAAAGCAATCAAAGTTTCTTGAGAGATGTGTGACTAATGGGAAATATCGAACACTACTTCTGAAATCCAGTTTGGCTGGAGATTCAGGAAAGGTTATAGCTGCAATTACTTATCAAATCGTCCCTGCAGACACAGAATATGCAGAGATCCCACTTGCAGCTGTCAATGCAATCTATCAACGGAAGGGTTTTGGTCAGATATTGTTTCTAGAGCTCCGGAAGAGACTTCAAAATGTTGGCATTCGCTCTATTTTCTGTTGGGGAGACAAAGAATCTGAAGGATTTTGGCTTAAACAGGGTTTTTCATCAATAGCACAGGTGGATACAAAAGGTAGAGCCCGCAGGTTACCTGTAAAAGCTGATATTCGTAAAGCATTATGCTTTCCTGGTGGTTCGACTCTCATGATTCTCCATCTAAAGAAGGAATTGTTTGATGACAATGCTAACTCTGGGAAGTGTCTCCCCTCACAGCCTCATCAGAATTCCTTTACACCTGCAATTGTTGAAAATGAGCAGCTCGAATTCTCAGATGAACTACTCATTAACTTGAAATCTTCCCATAGAACAGACACAAGTCAAAGTAAACCCAATGCTTTGGTAAAAGTTGGATCTTCTCGAGGACGTGGAAAACTCAATGGATTTGACAGTCAGAATCCTAAGAACTGCTGCAATGACACTGTTGATTTTGCCAGAGCAAATGATGACAGACAAGCAAATGGTGCAGATTGTACCCAGGATGAAAATTATGCTAATATAGCGCATTGTTCTCAATCTACAAAAGTTTTAAAGAGGGCCTGGGAAGCCTCTTCATCCTCGTTGAAGTCAAAGAGAGTGAGGGGAAGCCAGTTTGTTGACTGTCGATCAGATTCTAGCTGGGGTTTTGTCTCCGAGGCTGGTAGGGCCAATCCTTGTTCTGCGGAATCCCCTCATTGTGATACTTCAATTACAAAGAACTCTGAAAAATGTATTGGAGACCATATGCATTTAGAAGCTCCGATCAGCCTAAAACTGCCATCAACTGAACAATGCTTTAGAATCATGTTGATGAACATCACTGATGACGCTAAGAAAACACAGCTTACAAAGGTGATTGAAGACCTAGGTGGAACTATTGCCTCTGATGGAAGCTCAACCACACATGTTGTCACAGGACAAGTGAGAAAAACTCTGAATTTCTGTACTGCTCTCTGTTCCGGTGCTTGGGTGGTCTCATCGACTTGGTTAAAAGAAAGTTTTCGACAAGGCAGATTTGTTGATGAATTACCTCACATTCTGAATGATAAGGATTATTTGTTGAAGTATAAATCGGATTTAAGAAGTGCAGTTTTACGAGCAAAAGCTTGTCCCCATTCTTTGTTTAAGGGTTATAATATATGTATTGCAGCTAATGTTCAAACTTCTGCAAAAACTCTGTCTGCTATTGTTAGGTCTGCTGGTGGTAATGTTATTAGTGGACTAAGAAAAGTAAATGAAGCATCAACAACAATCTTTGTGACTCGCGAAGAAGACATTGAAGAAGCAATGATGGCTGCAAAGAAAGGTATAAGGACTTTCGACAGTGAGTGGTTTATGAACTGTGTCATGAGACAAGAGCTCGACATGGAAGCCTCCCAATTTGCAGAGTCCTTATCAGATTGTTAA

Protein sequence

>MsaT039308.1

MFQDVSANHKNASGNFTPEEREHEFMLVNTKDDDDITKSYLQEVLQMYMTELPGMNYAANTGKQSKFLERCVTNGKYRTLLLKSSLAGDSGKVIAAITYQIVPADTEYAEIPLAAVNAIYQRKGFGQILFLELRKRLQNVGIRSIFCWGDKESEGFWLKQGFSSIAQVDTKGRARRLPVKADIRKALCFPGGSTLMILHLKKELFDDNANSGKCLPSQPHQNSFTPAIVENEQLEFSDELLINLKSSHRTDTSQSKPNALVKVGSSRGRGKLNGFDSQNPKNCCNDTVDFARANDDRQANGADCTQDENYANIAHCSQSTKVLKRAWEASSSSLKSKRVRGSQFVDCRSDSSWGFVSEAGRANPCSAESPHCDTSITKNSEKCIGDHMHLEAPISLKLPSTEQCFRIMLMNITDDAKKTQLTKVIEDLGGTIASDGSSTTHVVTGQVRKTLNFCTALCSGAWVVSSTWLKESFRQGRFVDELPHILNDKDYLLKYKSDLRSAVLRAKACPHSLFKGYNICIAANVQTSAKTLSAIVRSAGGNVISGLRKVNEASTTIFVTREEDIEEAMMAAKKGIRTFDSEWFMNCVMRQELDMEASQFAESLSDC*