AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene78380

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78380.t1 MTR_1g093095 75.000 36 9 0 135 170 99 134 4.27e-14 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78380.t1 AT1G51220 44.505 182 73 8 6 170 27 197 7.98e-35 124
MS.gene78380.t1 AT3G20880 43.478 161 62 6 36 170 118 275 2.49e-28 108
MS.gene78380.t1 AT3G57670 38.596 171 60 3 44 170 67 236 9.88e-26 101
MS.gene78380.t1 AT1G34790 46.341 82 43 1 90 170 83 164 8.48e-19 81.6
MS.gene78380.t1 AT1G13290 45.783 83 31 2 88 170 52 120 1.19e-17 78.6
MS.gene78380.t1 AT1G08290 48.276 58 24 1 113 170 148 199 2.57e-13 67.0

Find 39 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAATGACTTCAATGGTTAT+TGG 0.191789 2.3:-5171770 MS.gene78380:CDS
TATAGAATGGAGGGTTATTT+AGG 0.265203 2.3:+5171742 None:intergenic
GTTACTGTGGCTTTGCATCT+AGG 0.282488 2.3:-5171525 MS.gene78380:CDS
AAAGATATGTTGTTACTATA+AGG 0.326372 2.3:+5171714 None:intergenic
CATGTTGTTGTATCTATTGA+AGG 0.358064 2.3:+5171317 None:intergenic
CATCATTTCCATGGAACTAA+AGG 0.398872 2.3:+5171602 None:intergenic
CCAATAACCATTGAAGTCAT+TGG 0.409520 2.3:+5171770 None:intergenic
AGAATCTTCCTTTAGTTCCA+TGG 0.448392 2.3:-5171610 MS.gene78380:CDS
CTTCATATTCATCATTTCCA+TGG 0.449667 2.3:+5171593 None:intergenic
TTACTGTGGCTTTGCATCTA+GGG 0.458041 2.3:-5171524 MS.gene78380:CDS
GTCCACCAAATAAAATTAGC+AGG 0.460803 2.3:-5171416 MS.gene78380:CDS
ATTGAAGTCATTGGAGAAGT+AGG 0.466777 2.3:+5171779 None:intergenic
ACCCCTGCTCAGATTCTAAT+CGG 0.468227 2.3:-5171375 MS.gene78380:CDS
TCTCTTGGAGGTGGAGATGA+AGG 0.479256 2.3:+5171681 None:intergenic
AAAGGAAGAGCTTCTCTTGG+AGG 0.486389 2.3:+5171669 None:intergenic
AAATCAGATGAACTTATACT+TGG 0.487140 2.3:+5171498 None:intergenic
AGCAAAGGAAGAGCTTCTCT+TGG 0.490887 2.3:+5171666 None:intergenic
TACTTCTCCAATGACTTCAA+TGG 0.492298 2.3:-5171777 MS.gene78380:CDS
TTGAAGGTCTTGAAACAAAG+AGG 0.499110 2.3:+5171333 None:intergenic
AAATTAGCAGGGGTCAGTAT+TGG 0.506191 2.3:-5171404 MS.gene78380:CDS
TAAGGAAAATTATAGAATGG+AGG 0.508828 2.3:+5171732 None:intergenic
GGACCGATTAGAATCTGAGC+AGG 0.523985 2.3:+5171372 None:intergenic
CATGGAAATGATGAATATGA+AGG 0.524476 2.3:-5171592 MS.gene78380:CDS
GGAAGAGCTTCTCTTGGAGG+TGG 0.534319 2.3:+5171672 None:intergenic
CTATAAGGAAAATTATAGAA+TGG 0.547263 2.3:+5171729 None:intergenic
ATTAGAATCTGAGCAGGGGT+AGG 0.550899 2.3:+5171378 None:intergenic
AAGGAAAATTATAGAATGGA+GGG 0.551334 2.3:+5171733 None:intergenic
TTGAAGTCATTGGAGAAGTA+GGG 0.551474 2.3:+5171780 None:intergenic
AGAGGGCATGAAAACTGTGT+TGG 0.560971 2.3:+5171351 None:intergenic
TTAGAATCTGAGCAGGGGTA+GGG 0.569587 2.3:+5171379 None:intergenic
TCCACCAAATAAAATTAGCA+GGG 0.584942 2.3:-5171415 MS.gene78380:CDS
TGAAGGTCTTGAAACAAAGA+GGG 0.613383 2.3:+5171334 None:intergenic
GTAGGGCTTAGGTTAAGCAA+AGG 0.619991 2.3:+5171651 None:intergenic
GACCGATTAGAATCTGAGCA+GGG 0.623713 2.3:+5171373 None:intergenic
AGATGATGATGCCGTTACTG+TGG 0.634808 2.3:-5171538 MS.gene78380:CDS
CAATAGATACAACAACATGC+AGG 0.643534 2.3:-5171313 MS.gene78380:CDS
TAGATGCAAAGCCACAGTAA+CGG 0.646015 2.3:+5171527 None:intergenic
CCACCAAATAAAATTAGCAG+GGG 0.685279 2.3:-5171414 MS.gene78380:CDS
ACCGATTAGAATCTGAGCAG+GGG 0.690964 2.3:+5171374 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGATATGTTGTTACTATA+AGG + chr2.3:5171383-5171402 None:intergenic 20.0%
!! CTATAAGGAAAATTATAGAA+TGG + chr2.3:5171368-5171387 None:intergenic 20.0%
! AAATCAGATGAACTTATACT+TGG + chr2.3:5171599-5171618 None:intergenic 25.0%
! AAGGAAAATTATAGAATGGA+GGG + chr2.3:5171364-5171383 None:intergenic 25.0%
! TAAGGAAAATTATAGAATGG+AGG + chr2.3:5171365-5171384 None:intergenic 25.0%
CATGGAAATGATGAATATGA+AGG - chr2.3:5171502-5171521 MS.gene78380:CDS 30.0%
CATGTTGTTGTATCTATTGA+AGG + chr2.3:5171780-5171799 None:intergenic 30.0%
CTTCATATTCATCATTTCCA+TGG + chr2.3:5171504-5171523 None:intergenic 30.0%
TATAGAATGGAGGGTTATTT+AGG + chr2.3:5171355-5171374 None:intergenic 30.0%
TCCACCAAATAAAATTAGCA+GGG - chr2.3:5171679-5171698 MS.gene78380:CDS 30.0%
! AGAAGATCTTCATGTTTTGT+AGG + chr2.3:5171464-5171483 None:intergenic 30.0%
! GAAGATCTTCATGTTTTGTA+GGG + chr2.3:5171463-5171482 None:intergenic 30.0%
ATTGAAGTCATTGGAGAAGT+AGG + chr2.3:5171318-5171337 None:intergenic 35.0%
CAATAGATACAACAACATGC+AGG - chr2.3:5171781-5171800 MS.gene78380:CDS 35.0%
CATCATTTCCATGGAACTAA+AGG + chr2.3:5171495-5171514 None:intergenic 35.0%
CCAATAACCATTGAAGTCAT+TGG + chr2.3:5171327-5171346 None:intergenic 35.0%
CCAATGACTTCAATGGTTAT+TGG - chr2.3:5171324-5171343 MS.gene78380:CDS 35.0%
CCACCAAATAAAATTAGCAG+GGG - chr2.3:5171680-5171699 MS.gene78380:CDS 35.0%
GTCCACCAAATAAAATTAGC+AGG - chr2.3:5171678-5171697 MS.gene78380:CDS 35.0%
TACTTCTCCAATGACTTCAA+TGG - chr2.3:5171317-5171336 MS.gene78380:CDS 35.0%
TGAAGGTCTTGAAACAAAGA+GGG + chr2.3:5171763-5171782 None:intergenic 35.0%
TTGAAGGTCTTGAAACAAAG+AGG + chr2.3:5171764-5171783 None:intergenic 35.0%
TTGAAGTCATTGGAGAAGTA+GGG + chr2.3:5171317-5171336 None:intergenic 35.0%
! AGAATCTTCCTTTAGTTCCA+TGG - chr2.3:5171484-5171503 MS.gene78380:CDS 35.0%
! TGACCCCTGCTAATTTTATT+TGG + chr2.3:5171686-5171705 None:intergenic 35.0%
AAATTAGCAGGGGTCAGTAT+TGG - chr2.3:5171690-5171709 MS.gene78380:CDS 40.0%
TAGATGCAAAGCCACAGTAA+CGG + chr2.3:5171570-5171589 None:intergenic 40.0%
! CTTCATGTTTTGTAGGGCTT+AGG + chr2.3:5171457-5171476 None:intergenic 40.0%
! TTACTGTGGCTTTGCATCTA+GGG - chr2.3:5171570-5171589 MS.gene78380:CDS 40.0%
!! CCCCTGCTAATTTTATTTGG+TGG + chr2.3:5171683-5171702 None:intergenic 40.0%
AAAGGAAGAGCTTCTCTTGG+AGG + chr2.3:5171428-5171447 None:intergenic 45.0%
ACCCCTGCTCAGATTCTAAT+CGG - chr2.3:5171719-5171738 MS.gene78380:CDS 45.0%
ACCGATTAGAATCTGAGCAG+GGG + chr2.3:5171723-5171742 None:intergenic 45.0%
AGCAAAGGAAGAGCTTCTCT+TGG + chr2.3:5171431-5171450 None:intergenic 45.0%
ATTAGAATCTGAGCAGGGGT+AGG + chr2.3:5171719-5171738 None:intergenic 45.0%
GACCGATTAGAATCTGAGCA+GGG + chr2.3:5171724-5171743 None:intergenic 45.0%
GTAGGGCTTAGGTTAAGCAA+AGG + chr2.3:5171446-5171465 None:intergenic 45.0%
TTAGAATCTGAGCAGGGGTA+GGG + chr2.3:5171718-5171737 None:intergenic 45.0%
! AGAGGGCATGAAAACTGTGT+TGG + chr2.3:5171746-5171765 None:intergenic 45.0%
! AGATGATGATGCCGTTACTG+TGG - chr2.3:5171556-5171575 MS.gene78380:CDS 45.0%
! GTTACTGTGGCTTTGCATCT+AGG - chr2.3:5171569-5171588 MS.gene78380:CDS 45.0%
GGACCGATTAGAATCTGAGC+AGG + chr2.3:5171725-5171744 None:intergenic 50.0%
TCTCTTGGAGGTGGAGATGA+AGG + chr2.3:5171416-5171435 None:intergenic 50.0%
GGAAGAGCTTCTCTTGGAGG+TGG + chr2.3:5171425-5171444 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 5171302 5171814 5171302 ID=MS.gene78380
chr2.3 mRNA 5171302 5171814 5171302 ID=MS.gene78380.t1;Parent=MS.gene78380
chr2.3 exon 5171302 5171814 5171302 ID=MS.gene78380.t1.exon1;Parent=MS.gene78380.t1
chr2.3 CDS 5171302 5171814 5171302 ID=cds.MS.gene78380.t1;Parent=MS.gene78380.t1
Gene Sequence

>MS.gene78380

ATGAGTACTCATCCCTACTTCTCCAATGACTTCAATGGTTATTGGTTTGACCTAAATAACCCTCCATTCTATAATTTTCCTTATAGTAACAACATATCTTTTGCATCTTCTCCTTCATCTCCACCTCCAAGAGAAGCTCTTCCTTTGCTTAACCTAAGCCCTACAAAACATGAAGATCTTCTAGAATCTTCCTTTAGTTCCATGGAAATGATGAATATGAAGGAGAAAGAACTAAGCATATCATCAAATTCTTTAGATGATGATGCCGTTACTGTGGCTTTGCATCTAGGGCTTCCAAGTATAAGTTCATCTGATTTAGCTTCTTCAAATATTTACAAAGATGATGAAAAAGTAGTGACTGTTGATTCTTCTGAGTGTCCACCAAATAAAATTAGCAGGGGTCAGTATTGGATCCCTACCCCTGCTCAGATTCTAATCGGTCCAACACAGTTTTCATGCCCTCTTTGTTTCAAGACCTTCAATAGATACAACAACATGCAGGTATATATTTAA
Protein sequence

>MS.gene78380.t1

MSTHPYFSNDFNGYWFDLNNPPFYNFPYSNNISFASSPSSPPPREALPLLNLSPTKHEDLLESSFSSMEMMNMKEKELSISSNSLDDDAVTVALHLGLPSISSSDLASSNIYKDDEKVVTVDSSECPPNKISRGQYWIPTPAQILIGPTQFSCPLCFKTFNRYNNMQVYI