AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene045330

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene045330.t1 MTR_3g084720 74.219 256 26 4 1 243 1 229 1.37e-99 290
MS.gene045330.t1 MTR_7g010470 55.000 80 35 1 168 246 1 80 1.37e-21 86.3
MS.gene045330.t1 MTR_6g055180 75.510 49 10 1 1 47 1 49 4.27e-16 71.6
MS.gene045330.t1 MTR_6g465230 45.865 133 59 6 1 133 98 217 3.65e-11 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene045330.t1 AT2G18490 55.714 70 31 0 122 191 142 211 2.28e-20 87.4
MS.gene045330.t1 AT2G18490 55.714 70 31 0 122 191 192 261 3.04e-20 87.8
MS.gene045330.t1 AT2G15740 51.899 79 34 1 122 200 217 291 2.61e-19 85.9
MS.gene045330.t1 AT5G22990 50.602 83 40 1 135 216 232 314 2.03e-18 83.2
MS.gene045330.t1 AT5G42640 41.414 99 54 1 93 191 191 285 1.08e-17 80.9

Find 29 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGAGTCTTGAAGCACAATT+TGG 0.219378 3.4:+79253973 MS.gene045330:CDS
TTAGTTGGTACCAATAATTT+TGG 0.312371 3.4:+79253919 MS.gene045330:CDS
AGCATGACTACCAAAATTAT+TGG 0.316188 3.4:-79253929 None:intergenic
AGCCTACCACACAAGAAATA+TGG 0.358104 3.4:+79254276 MS.gene045330:CDS
TATTAATAATAATTATTTGA+AGG 0.406891 3.4:-79254585 None:intergenic
TTATCAGCACAAGCAATAAC+AGG 0.430056 3.4:-79254480 None:intergenic
ACCCATTCATCATCATTAGT+TGG 0.445707 3.4:+79253904 MS.gene045330:CDS
ACAATCATAGATTGGTTCAA+TGG 0.452424 3.4:+79253863 MS.gene045330:CDS
TTCTAGGATTCGAAAGAGAC+CGG 0.465129 3.4:+79254413 MS.gene045330:CDS
AGCAATGAAAATATTGATGA+TGG 0.472887 3.4:+79254243 MS.gene045330:CDS
GATAAGCCTGCATGGAGATC+AGG 0.486979 3.4:-79254126 None:intergenic
AGAGTCTTGAAGCACAATTT+GGG 0.488266 3.4:+79253974 MS.gene045330:CDS
ATTTCTTGTGTGGTAGGCTG+TGG 0.491007 3.4:-79254272 None:intergenic
TAATATGAACAATCATAGAT+TGG 0.492110 3.4:+79253855 None:intergenic
TCACATCCTGATCTCCATGC+AGG 0.495288 3.4:+79254120 MS.gene045330:CDS
TACCAACTAATGATGATGAA+TGG 0.519642 3.4:-79253906 None:intergenic
ACCAACTAATGATGATGAAT+GGG 0.533514 3.4:-79253905 None:intergenic
GTCCATATTTCTTGTGTGGT+AGG 0.551362 3.4:-79254278 None:intergenic
CAAATTCAAAAGCTCAATGA+CGG 0.582932 3.4:+79254441 MS.gene045330:CDS
AGATTGGTTCAATGGATGCA+TGG 0.584866 3.4:+79253871 MS.gene045330:CDS
TATGGTCCATATTTCTTGTG+TGG 0.586966 3.4:-79254282 None:intergenic
CTCTCACCCCTCTTACAAGT+GGG 0.599620 3.4:+79254544 MS.gene045330:CDS
GCTCTCACCCCTCTTACAAG+TGG 0.621287 3.4:+79254543 MS.gene045330:CDS
TCTAGGATTCGAAAGAGACC+GGG 0.623769 3.4:+79254414 MS.gene045330:CDS
TCCGGGAATCATAAAAGCGA+TGG 0.628214 3.4:+79253951 MS.gene045330:CDS
AAGTGGGATAAAAGTCAAGT+CGG 0.629673 3.4:+79254560 MS.gene045330:CDS
GACGACGACGATGTTGATGT+AGG 0.650410 3.4:-79254003 None:intergenic
ATTGTGATGATAAGCCTGCA+TGG 0.664872 3.4:-79254134 None:intergenic
ATGTTAACAAGAACGATACG+AGG 0.702248 3.4:+79254208 MS.gene045330:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGCAATGAAAATATTGATGA+TGG + chr3.4:79254243-79254262 MS.gene045330:CDS 25.0%
! GAAAAAAGAGATACATTTCT+AGG + chr3.4:79254397-79254416 MS.gene045330:CDS 25.0%
!! ATTTTGTTGCATTTTGAACA+TGG - chr3.4:79254309-79254328 None:intergenic 25.0%
!!! CAAACGATTAATATTTTTGC+TGG + chr3.4:79254174-79254193 MS.gene045330:CDS 25.0%
!!! TTAGTTGGTACCAATAATTT+TGG + chr3.4:79253919-79253938 MS.gene045330:CDS 25.0%
AGCATGACTACCAAAATTAT+TGG - chr3.4:79253932-79253951 None:intergenic 30.0%
CAAATTCAAAAGCTCAATGA+CGG + chr3.4:79254441-79254460 MS.gene045330:CDS 30.0%
! ACAATCATAGATTGGTTCAA+TGG + chr3.4:79253863-79253882 MS.gene045330:CDS 30.0%
! ACCAACTAATGATGATGAAT+GGG - chr3.4:79253908-79253927 None:intergenic 30.0%
! TACCAACTAATGATGATGAA+TGG - chr3.4:79253909-79253928 None:intergenic 30.0%
! TTGCATTTTGAACATGGATA+TGG - chr3.4:79254303-79254322 None:intergenic 30.0%
AAGTGGGATAAAAGTCAAGT+CGG + chr3.4:79254560-79254579 MS.gene045330:CDS 35.0%
ACCCATTCATCATCATTAGT+TGG + chr3.4:79253904-79253923 MS.gene045330:CDS 35.0%
AGAGTCTTGAAGCACAATTT+GGG + chr3.4:79253974-79253993 MS.gene045330:CDS 35.0%
ATGTTAACAAGAACGATACG+AGG + chr3.4:79254208-79254227 MS.gene045330:CDS 35.0%
TATGGTCCATATTTCTTGTG+TGG - chr3.4:79254285-79254304 None:intergenic 35.0%
TTATCAGCACAAGCAATAAC+AGG - chr3.4:79254483-79254502 None:intergenic 35.0%
! ACTTTTATCCCACTTGTAAG+AGG - chr3.4:79254555-79254574 None:intergenic 35.0%
! AGCTTTTGAATTTGAAGACC+CGG - chr3.4:79254435-79254454 None:intergenic 35.0%
! CTTTTATCCCACTTGTAAGA+GGG - chr3.4:79254554-79254573 None:intergenic 35.0%
! TTTTATCCCACTTGTAAGAG+GGG - chr3.4:79254553-79254572 None:intergenic 35.0%
!! TAATTTTGGTAGTCATGCTC+CGG + chr3.4:79253933-79253952 MS.gene045330:CDS 35.0%
!! TATTTTTGCTGGTGATGTTG+AGG + chr3.4:79254185-79254204 MS.gene045330:CDS 35.0%
AGCCTACCACACAAGAAATA+TGG + chr3.4:79254276-79254295 MS.gene045330:CDS 40.0%
ATTGTGATGATAAGCCTGCA+TGG - chr3.4:79254137-79254156 None:intergenic 40.0%
GAGAGTCTTGAAGCACAATT+TGG + chr3.4:79253973-79253992 MS.gene045330:CDS 40.0%
GTCCATATTTCTTGTGTGGT+AGG - chr3.4:79254281-79254300 None:intergenic 40.0%
! AGATTGGTTCAATGGATGCA+TGG + chr3.4:79253871-79253890 MS.gene045330:CDS 40.0%
!! AATTTTGGTAGTCATGCTCC+GGG + chr3.4:79253934-79253953 MS.gene045330:CDS 40.0%
!! TCCATCGCTTTTATGATTCC+CGG - chr3.4:79253955-79253974 None:intergenic 40.0%
!! TTCTAGGATTCGAAAGAGAC+CGG + chr3.4:79254413-79254432 MS.gene045330:CDS 40.0%
ATTTCTTGTGTGGTAGGCTG+TGG - chr3.4:79254275-79254294 None:intergenic 45.0%
TCCGGGAATCATAAAAGCGA+TGG + chr3.4:79253951-79253970 MS.gene045330:CDS 45.0%
! TCTAGGATTCGAAAGAGACC+GGG + chr3.4:79254414-79254433 MS.gene045330:CDS 45.0%
CTCTCACCCCTCTTACAAGT+GGG + chr3.4:79254544-79254563 MS.gene045330:CDS 50.0%
GACGACGACGATGTTGATGT+AGG - chr3.4:79254006-79254025 None:intergenic 50.0%
GATAAGCCTGCATGGAGATC+AGG - chr3.4:79254129-79254148 None:intergenic 50.0%
TCACATCCTGATCTCCATGC+AGG + chr3.4:79254120-79254139 MS.gene045330:CDS 50.0%
GCTCTCACCCCTCTTACAAG+TGG + chr3.4:79254543-79254562 MS.gene045330:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 79253859 79254605 79253859 ID=MS.gene045330
chr3.4 mRNA 79253859 79254605 79253859 ID=MS.gene045330.t1;Parent=MS.gene045330
chr3.4 exon 79253859 79254605 79253859 ID=MS.gene045330.t1.exon1;Parent=MS.gene045330.t1
chr3.4 CDS 79253859 79254605 79253859 ID=cds.MS.gene045330.t1;Parent=MS.gene045330.t1
Gene Sequence

>MS.gene045330

ATGAACAATCATAGATTGGTTCAATGGATGCATGGCTACAACACAACCCATTCATCATCATTAGTTGGTACCAATAATTTTGGTAGTCATGCTCCGGGAATCATAAAAGCGATGGAGAGTCTTGAAGCACAATTTGGGCATTTGCCTACATCAACATCGTCGTCGTCATCAATTAATATCAATATTAATGATGACATCATCATCAATAACAACAAGAACAACAACATGATGATGACAATGAATACTTCTCTTGCTGCTTCTTCACATCCTGATCTCCATGCAGGCTTATCATCACAATCACAAGAACTGTCTTCTCAAACGATTAATATTTTTGCTGGTGATGTTGAGGATGTTAACAAGAACGATACGAGGAAGAAGAAGAAGAGCAATGAAAATATTGATGATGGAAGAATCCACAGCCTACCACACAAGAAATATGGACCATATCCATGTTCAAAATGCAACAAAATATTTGAAACATCACAAAAATTTGCTAATCATGTTTCAAGTCACTACAAGTTCGAAAGTGAAGAAGACAGAAAAAAGAGATACATTTCTAGGATTCGAAAGAGACCGGGTCTTCAAATTCAAAAGCTCAATGACGGAACAACTACTTTTGTTCCTGTTATTGCTTGTGCTGATAAGTCACATGCTTCAATCAATGATGATGATCATAATATGATTGCTCTCACCCCTCTTACAAGTGGGATAAAAGTCAAGTCGGAGCCTTCAAATAATTATTATTAA
Protein sequence

>MS.gene045330.t1

MNNHRLVQWMHGYNTTHSSSLVGTNNFGSHAPGIIKAMESLEAQFGHLPTSTSSSSSINININDDIIINNNKNNNMMMTMNTSLAASSHPDLHAGLSSQSQELSSQTINIFAGDVEDVNKNDTRKKKKSNENIDDGRIHSLPHKKYGPYPCSKCNKIFETSQKFANHVSSHYKFESEEDRKKRYISRIRKRPGLQIQKLNDGTTTFVPVIACADKSHASINDDDHNMIALTPLTSGIKVKSEPSNNYY