AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG006090


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG006090 MtrunA17_Chr2g0277381 98.933 375 4 0 1 375 1 375 0.0 780
MsaG006090 MtrunA17_Chr1g0164511 28.497 193 118 5 77 256 13 198 1.44e-12 67.4
MsaG006090 MtrunA17_Chr3g0082161 28.497 193 118 5 77 256 13 198 1.92e-12 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG006090 AT4G06634.1 68.407 364 99 7 10 361 12 371 9.17e-161 456
MsaG006090 AT4G06634.3 65.489 368 96 9 10 361 12 364 1.79e-148 425
MsaG006090 AT4G06634.2 65.964 332 97 7 42 361 6 333 9.30e-135 389
MsaG006090 AT3G48430.1 27.273 121 80 2 77 195 1243 1357 2.81e-11 65.9
MsaG006090 AT3G48430.2 27.273 121 80 2 77 195 884 998 3.53e-11 65.5

Find 96 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAAGGCTCCCGCTGTTAAA+TGG 0.155162 2:-1472739 MsaT006090.1:CDS
GTTTCTGTTGCAGAAATTTC+TGG 0.165103 2:-1470646 MsaT006090.1:intron
TCAGTAGTTGGCTCGGGTTC+TGG 0.253968 2:+1471200 None:intergenic
TACTTTATCGGCACATCTAT+TGG 0.312836 2:+1457492 None:intergenic
GCGTATCTCTTCCCACAATC+TGG 0.321481 2:+1469816 None:intergenic
TTACGCTGAGCAACTTTAGA+AGG 0.345270 2:+1457153 None:intergenic
CCTTTCCACACCCCTCATAA+TGG 0.376204 2:+1471075 None:intergenic
TTGCTGTTAAGATGGGTAAC+AGG 0.381864 2:-1472550 MsaT006090.1:intron
GCAGTTTGTTTGCCATTATG+AGG 0.386353 2:-1471087 MsaT006090.1:CDS
CTAAAGTTGCTCAGCGTAAA+GGG 0.392561 2:-1457149 MsaT006090.1:CDS
GGAGGAGTTGCATACTTTAT+CGG 0.401475 2:+1457480 None:intergenic
CCTTCATAAGGACATGCATA+TGG 0.405323 2:+1457390 None:intergenic
CTCTTCCCACAATCTGGGTA+TGG 0.407430 2:+1469822 None:intergenic
GGTTCTGGCTCAGGAGCTAA+TGG 0.412849 2:+1471215 None:intergenic
GTTGGCTCGGGTTCTGGCTC+AGG 0.414498 2:+1471206 None:intergenic
GGGAGCCTTGGACGTGAGAA+AGG 0.426315 2:+1472751 None:intergenic
GTTTCTTCTTTCACTGGCCA+AGG 0.432210 2:+1457087 None:intergenic
CCATTTAACAGCGGGAGCCT+TGG 0.434294 2:+1472739 None:intergenic
CAAGGCTCCCGCTGTTAAAT+GGG 0.434337 2:-1472738 MsaT006090.1:CDS
AAGACATTTCTTAATTCATA+CGG 0.439731 2:-1470607 MsaT006090.1:CDS
GCAAGTGATCACGATGCTTA+TGG 0.440454 2:-1457240 MsaT006090.1:CDS
AGACATTTCTTAATTCATAC+GGG 0.448713 2:-1470606 MsaT006090.1:CDS
TTATAGATGCTGGTGCTTTG+AGG 0.456478 2:-1471136 MsaT006090.1:CDS
TCTAAAGTTGCTCAGCGTAA+AGG 0.457185 2:-1457150 MsaT006090.1:CDS
TCGTAAGTTTCTTCTTTCAC+TGG 0.459248 2:+1457081 None:intergenic
CAATATGCAGGCCTTCTCCT+TGG 0.459806 2:-1469901 MsaT006090.1:intron
GGAAGTGTTTGCTGTTAAGA+TGG 0.461719 2:-1472558 MsaT006090.1:CDS
CAGTTTGTTTGCCATTATGA+GGG 0.471982 2:-1471086 MsaT006090.1:CDS
CATAAATGCCTTGAAAGAAA+AGG 0.473578 2:-1471246 MsaT006090.1:CDS
GAAGATGGTTGGAGATATGC+TGG 0.474493 2:-1457015 MsaT006090.1:CDS
CATTGCTTCCCATCATGAAA+AGG 0.475165 2:-1469769 MsaT006090.1:intron
TAATAATGCTGAAAATGAAA+TGG 0.485384 2:-1457268 MsaT006090.1:CDS
CCACAAGACGTTGTTGCCAC+TGG 0.487699 2:-1472583 MsaT006090.1:CDS
AGCTTAAACTGCATTTAAAG+AGG 0.494339 2:-1457338 MsaT006090.1:CDS
ATATTAAAAGTGGCAGGGGT+TGG 0.494716 2:+1457120 None:intergenic
TTAGCCATATTAAAAGTGGC+AGG 0.498748 2:+1457114 None:intergenic
CCATATGCATGTCCTTATGA+AGG 0.500362 2:-1457390 MsaT006090.1:CDS
CTTTGTAGCTATGAAGGCTG+TGG 0.501431 2:-1471167 MsaT006090.1:CDS
TCCTTATGAAGGGTGTGAAA+AGG 0.501607 2:-1457379 MsaT006090.1:CDS
TGAAAATGCTATGCATGCTC+TGG 0.502807 2:-1457292 MsaT006090.1:CDS
AAGTACTTCAGTAGTTGGCT+CGG 0.511218 2:+1471193 None:intergenic
AGGAAGCATTCCCACATCCA+TGG 0.515275 2:-1471116 MsaT006090.1:CDS
ACTGCCTCTCTCCATGGATG+TGG 0.516577 2:+1471105 None:intergenic
GGAGCCTTGGACGTGAGAAA+GGG 0.516870 2:+1472752 None:intergenic
CGTATCTCTTCCCACAATCT+GGG 0.520117 2:+1469817 None:intergenic
CTTCATAAGGACATGCATAT+GGG 0.522116 2:+1457391 None:intergenic
GTAAAAGTCAGAAGCAAAGC+AGG 0.525445 2:-1457200 MsaT006090.1:CDS
AGTACTTCAGTAGTTGGCTC+GGG 0.526508 2:+1471194 None:intergenic
TTCTGGAGCGACATACGGTT+CGG 0.536084 2:-1457427 MsaT006090.1:CDS
CAGCGAAGAAACTGAGGAGG+AGG 0.538145 2:-1457052 MsaT006090.1:CDS
AGACCTTCTGGAGCGACATA+CGG 0.541337 2:-1457432 MsaT006090.1:CDS
GTGTCTTCATGTGAGACCTC+AGG 0.542819 2:+1469871 None:intergenic
TCTTCCCACAATCTGGGTAT+GGG 0.550401 2:+1469823 None:intergenic
CGCTGAGCAACTTTAGAAGG+AGG 0.554525 2:+1457156 None:intergenic
TATGCCCATACCCAGATTGT+GGG 0.558178 2:-1469827 MsaT006090.1:CDS
CTGTTAAATGGGTCAAACAA+TGG 0.559100 2:-1472727 MsaT006090.1:intron
GTTTGCCATTATGAGGGGTG+TGG 0.559433 2:-1471080 MsaT006090.1:CDS
CAAGACGTTGTTGCCACTGG+TGG 0.559549 2:-1472580 MsaT006090.1:CDS
CCATTATGAGGGGTGTGGAA+AGG 0.561192 2:-1471075 MsaT006090.1:intron
GTGACAATGTTGAAGATGGT+TGG 0.563304 2:-1457026 MsaT006090.1:CDS
GCTTAAACTGCATTTAAAGA+GGG 0.566396 2:-1457337 MsaT006090.1:CDS
AGCCATATTAAAAGTGGCAG+GGG 0.567185 2:+1457116 None:intergenic
GTGTGTCCTCATGAAGGCTG+TGG 0.567957 2:-1470570 MsaT006090.1:CDS
CATTTAAAGAGGGAGCATCC+TGG 0.569801 2:-1457327 MsaT006090.1:CDS
GGAAAGACATTTATAGATGC+TGG 0.570125 2:-1471146 MsaT006090.1:CDS
TCCTCATGAAGGCTGTGGTA+AGG 0.574286 2:-1470565 MsaT006090.1:intron
TGTTTGACCCATTTAACAGC+GGG 0.574962 2:+1472731 None:intergenic
AAACAAACTGCCTCTCTCCA+TGG 0.576594 2:+1471099 None:intergenic
ACGCCCCTTTCTCACGTCCA+AGG 0.578019 2:-1472756 MsaT006090.1:CDS
ATATGCCCATACCCAGATTG+TGG 0.578913 2:-1469828 MsaT006090.1:CDS
AGACCTCAGGTTAAAATCCA+AGG 0.579184 2:+1469884 None:intergenic
CTGCCTCTCTCCATGGATGT+GGG 0.586666 2:+1471106 None:intergenic
TAGCCATATTAAAAGTGGCA+GGG 0.588156 2:+1457115 None:intergenic
AGTTTGTTTGCCATTATGAG+GGG 0.589676 2:-1471085 MsaT006090.1:CDS
GAAGTGTTTGCTGTTAAGAT+GGG 0.593955 2:-1472557 MsaT006090.1:CDS
CAGGTTAAAATCCAAGGAGA+AGG 0.604105 2:+1469890 None:intergenic
GAACCGTATGTCGCTCCAGA+AGG 0.605176 2:+1457429 None:intergenic
CATATGCATGTCCTTATGAA+GGG 0.608937 2:-1457389 MsaT006090.1:CDS
GAGCCTTGGACGTGAGAAAG+GGG 0.615789 2:+1472753 None:intergenic
GATCGTGACAATGTTGAAGA+TGG 0.616587 2:-1457030 MsaT006090.1:CDS
TATGGTGGAAAACGTTCCAA+TGG 0.620791 2:-1457222 MsaT006090.1:CDS
ACATGCATATGGGCGATCAG+AGG 0.622960 2:+1457401 None:intergenic
AGTGATCACGATGCTTATGG+TGG 0.628298 2:-1457237 MsaT006090.1:CDS
GAACAACGAAGATGATGATG+AGG 0.630489 2:-1456992 MsaT006090.1:CDS
GGCGTCTCTCAAAGAGAGAG+TGG 0.633941 2:+1472774 None:intergenic
ACCTTACCACAGCCTTCATG+AGG 0.637114 2:+1470564 None:intergenic
AAGACGTTGTTGCCACTGGT+GGG 0.637791 2:-1472579 MsaT006090.1:CDS
GACATTTCTTAATTCATACG+GGG 0.654030 2:-1470605 MsaT006090.1:CDS
CAGCAAACACTTCCCACCAG+TGG 0.655133 2:+1472567 None:intergenic
CCAGTGGCAACAACGTCTTG+TGG 0.655732 2:+1472583 None:intergenic
ATTCCCACATCCATGGAGAG+AGG 0.655979 2:-1471109 MsaT006090.1:CDS
TGAAGACAGCGAAGAAACTG+AGG 0.661243 2:-1457058 MsaT006090.1:CDS
AGACAGCGAAGAAACTGAGG+AGG 0.668007 2:-1457055 MsaT006090.1:CDS
ACATTTCTTAATTCATACGG+GGG 0.674154 2:-1470604 MsaT006090.1:CDS
TTGTTTGACCCATTTAACAG+CGG 0.696885 2:+1472730 None:intergenic
AAGATGGTTGGAGATATGCT+GGG 0.715505 2:-1457014 MsaT006090.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr2 gene 1456972 1472813 1456972 ID=MsaG006090
Chr2 mRNA 1456972 1472813 1456972 ID=MsaT006090.1;Parent=MsaG006090
Chr2 exon 1456972 1457520 1456972 ID=MsaT006090.1.exon6;Parent=MsaT006090.1
Chr2 CDS 1456972 1457520 1456972 ID=cds.MsaT006090.1;Parent=MsaT006090.1
Chr2 exon 1469770 1469913 1469770 ID=MsaT006090.1.exon5;Parent=MsaT006090.1
Chr2 CDS 1469770 1469913 1469770 ID=cds.MsaT006090.1;Parent=MsaT006090.1
Chr2 exon 1470566 1470655 1470566 ID=MsaT006090.1.exon4;Parent=MsaT006090.1
Chr2 CDS 1470566 1470655 1470566 ID=cds.MsaT006090.1;Parent=MsaT006090.1
Chr2 exon 1471076 1471275 1471076 ID=MsaT006090.1.exon3;Parent=MsaT006090.1
Chr2 CDS 1471076 1471275 1471076 ID=cds.MsaT006090.1;Parent=MsaT006090.1
Chr2 exon 1472551 1472609 1472551 ID=MsaT006090.1.exon2;Parent=MsaT006090.1
Chr2 CDS 1472551 1472609 1472551 ID=cds.MsaT006090.1;Parent=MsaT006090.1
Chr2 exon 1472728 1472813 1472728 ID=MsaT006090.1.exon1;Parent=MsaT006090.1
Chr2 CDS 1472728 1472813 1472728 ID=cds.MsaT006090.1;Parent=MsaT006090.1
Gene Sequence

>MsaT006090.1

ATGGAGACTCACTACAACCACTCTCTCTTTGAGAGACGCCCCTTTCTCACGTCCAAGGCTCCCGCTGTTAAATGGGTCAAACAATGGGTTCCACAAGACGTTGTTGCCACTGGTGGGAAGTGTTTGCTGTTAAGATGGGTAACAGAGGATACCATAAATGCCTTGAAAGAAAAGGAAAAAGAACCATTAGCTCCTGAGCCAGAACCCGAGCCAACTACTGAAGTACTTTTTCTTTGTAGCTATGAAGGCTGTGGAAAGACATTTATAGATGCTGGTGCTTTGAGGAAGCATTCCCACATCCATGGAGAGAGGCAGTTTGTTTGCCATTATGAGGGGTGTGGAAAGAAATTTCTGGACAGCTCAAAGTTAAAAAGACATTTCTTAATTCATACGGGGGAGAGGGATTTTGTGTGTCCTCATGAAGGCTGTGGTAAGGCCTTCTCCTTGGATTTTAACCTGAGGTCTCACATGAAGACACATTCACAAGAGAATTATCATATATGCCCATACCCAGATTGTGGGAAGAGATACGCTCATGAATACAAGCTAAAGAATCACATTGCTTCCCATCATGAAAAGAGTACACCAATAGATGTGCCGATAAAGTATGCAACTCCTCCTTCAGAAAAGCAAACAAAAACTGCTAGACCTTCTGGAGCGACATACGGTTCGGCATCCTCTGATCGCCCATATGCATGTCCTTATGAAGGGTGTGAAAAGGCTTACATTCATGAGTACAAGCTTAAACTGCATTTAAAGAGGGAGCATCCTGGCCACATAAATGATGAAAATGCTATGCATGCTCTGGCTAATAATGCTGAAAATGAAATGGATGAAGCAAGTGATCACGATGCTTATGGTGGAAAACGTTCCAATGGTAAAAGTCAGAAGCAAAGCAGGCCCAAGCCAAACTTGAAAATGCCTCCTTCTAAAGTTGCTCAGCGTAAAGGGTCTACTCCAACCCCTGCCACTTTTAATATGGCTAAAAAACCTTGGCCAGTGAAAGAAGAAACTTACGATGAAGACAGCGAAGAAACTGAGGAGGAGGATCGTGACAATGTTGAAGATGGTTGGAGATATGCTGGGAACAACGAAGATGATGATGAGGAAACAGAATATGAAGACTGA

Protein sequence

>MsaT006090.1

METHYNHSLFERRPFLTSKAPAVKWVKQWVPQDVVATGGKCLLLRWVTEDTINALKEKEKEPLAPEPEPEPTTEVLFLCSYEGCGKTFIDAGALRKHSHIHGERQFVCHYEGCGKKFLDSSKLKRHFLIHTGERDFVCPHEGCGKAFSLDFNLRSHMKTHSQENYHICPYPDCGKRYAHEYKLKNHIASHHEKSTPIDVPIKYATPPSEKQTKTARPSGATYGSASSDRPYACPYEGCEKAYIHEYKLKLHLKREHPGHINDENAMHALANNAENEMDEASDHDAYGGKRSNGKSQKQSRPKPNLKMPPSKVAQRKGSTPTPATFNMAKKPWPVKEETYDEDSEETEEEDRDNVEDGWRYAGNNEDDDEETEYED*