AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0565350

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0565350 MtrunA17_Chr8g0380241 69.725 109 18 2 1 109 1 94 2.90e-44 140
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0565350 AT5G14285.1 43.885 139 75 2 3 140 1 137 1.34e-30 110
Msa0565350 AT3G27270.1 44.361 133 66 4 15 142 10 139 4.07e-28 104
Msa0565350 AT3G27270.2 44.361 133 66 4 15 142 10 139 4.93e-28 104
Msa0565350 AT3G25950.1 35.593 118 74 2 17 133 18 134 7.05e-17 74.7

Find 38 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGTCTCCGTCTTCGTTT+TGG 0.312642 4_1:+66248538 Msa0565350:CDS
CGAAGAAAAGCATGGCTAAT+TGG 0.313315 4_1:-66248484 None:intergenic
GAATCTGCGGGGTTCGGTCT+TGG 0.333789 4_1:-66248241 None:intergenic
GCGGCTGATAAGCCACGGTT+GGG 0.356572 4_1:-66248353 None:intergenic
TTCTTAACCGCCACCATTCT+CGG 0.383303 4_1:+66248302 Msa0565350:CDS
TTCACTTGCCGTTTCATGAT+CGG 0.402390 4_1:+66248509 Msa0565350:CDS
TGACTCGAATCTGCGGGGTT+CGG 0.408816 4_1:-66248247 None:intergenic
GGGGTTGGTGTCGGAGAAGA+AGG 0.474258 4_1:-66248333 None:intergenic
GCGAAGTAGTGAACGTAGCT+TGG 0.479988 4_1:-66248458 None:intergenic
CAGCTATCTTTAGCAGAAGA+AGG 0.482080 4_1:+66248152 Msa0565350:CDS
GGCGGCTGATAAGCCACGGT+TGG 0.485636 4_1:-66248354 None:intergenic
GATATTCTGCAAGGTAGTAT+TGG 0.489793 4_1:-66248375 None:intergenic
CGAAGTAGTGAACGTAGCTT+GGG 0.489911 4_1:-66248457 None:intergenic
GAAGGCGATTACGCCGAGAA+TGG 0.509060 4_1:-66248315 None:intergenic
AACCGAAAAGGTAAAGAGAA+AGG 0.509233 4_1:-66248205 None:intergenic
AGAAGATGAAGTAACCGAAA+AGG 0.522301 4_1:-66248217 None:intergenic
TGCCGTTTCATGATCGGTAA+CGG 0.523712 4_1:+66248515 Msa0565350:CDS
TGATAAGCCACGGTTGGGGT+TGG 0.524167 4_1:-66248348 None:intergenic
CACCGTTACCGATCATGAAA+CGG 0.536378 4_1:-66248517 None:intergenic
TATCTTTAGCAGAAGAAGGT+TGG 0.536708 4_1:+66248156 Msa0565350:CDS
GCCACGGTTGGGGTTGGTGT+CGG 0.564451 4_1:-66248342 None:intergenic
TAACAGATCGGTGATGAAGT+AGG 0.567648 4_1:-66248417 None:intergenic
GAGTATGTGACTCGAATCTG+CGG 0.574331 4_1:-66248254 None:intergenic
AACAGCAACCAAAACGAAGA+CGG 0.574348 4_1:-66248546 None:intergenic
AGTATGTGACTCGAATCTGC+GGG 0.576710 4_1:-66248253 None:intergenic
ATTCTGCAAGGTAGTATTGG+CGG 0.587733 4_1:-66248372 None:intergenic
GAAAAGGTAAAGAGAAAGGA+AGG 0.588741 4_1:-66248201 None:intergenic
CGGCTGATAAGCCACGGTTG+GGG 0.593778 4_1:-66248352 None:intergenic
GGCGATTACGCCGAGAATGG+TGG 0.608266 4_1:-66248312 None:intergenic
AGTAGTGAACGTAGCTTGGG+AGG 0.609827 4_1:-66248454 None:intergenic
TCCGACACCAACCCCAACCG+TGG 0.612983 4_1:+66248341 Msa0565350:CDS
GTCAAGAACGATATTCTGCA+AGG 0.624929 4_1:-66248384 None:intergenic
AAAGACGCAAATCAAGACGC+TGG 0.625165 4_1:-66248276 None:intergenic
GATTACGCCGAGAATGGTGG+CGG 0.626615 4_1:-66248309 None:intergenic
TATTGGCGGCTGATAAGCCA+CGG 0.657192 4_1:-66248358 None:intergenic
AGTGAAGACGAAGAAAAGCA+TGG 0.669757 4_1:-66248492 None:intergenic
AACGACGAAATGTAACAGAT+CGG 0.672930 4_1:-66248429 None:intergenic
GTATGTGACTCGAATCTGCG+GGG 0.720046 4_1:-66248252 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAAGGAAGGTGAAGAAAAAT+GGG - chr4_1:66248190-66248209 None:intergenic 30.0%
! TTCCTTTCTCTTTACCTTTT+CGG + chr4_1:66248203-66248222 Msa0565350:CDS 30.0%
TATCTTTAGCAGAAGAAGGT+TGG + chr4_1:66248156-66248175 Msa0565350:CDS 35.0%
GAAAGGAAGGTGAAGAAAAA+TGG - chr4_1:66248191-66248210 None:intergenic 35.0%
GAAAAGGTAAAGAGAAAGGA+AGG - chr4_1:66248204-66248223 None:intergenic 35.0%
AACCGAAAAGGTAAAGAGAA+AGG - chr4_1:66248208-66248227 None:intergenic 35.0%
AGAAGATGAAGTAACCGAAA+AGG - chr4_1:66248220-66248239 None:intergenic 35.0%
GATATTCTGCAAGGTAGTAT+TGG - chr4_1:66248378-66248397 None:intergenic 35.0%
AACGACGAAATGTAACAGAT+CGG - chr4_1:66248432-66248451 None:intergenic 35.0%
CAGCTATCTTTAGCAGAAGA+AGG + chr4_1:66248152-66248171 Msa0565350:CDS 40.0%
! ATTCTGCAAGGTAGTATTGG+CGG - chr4_1:66248375-66248394 None:intergenic 40.0%
GTCAAGAACGATATTCTGCA+AGG - chr4_1:66248387-66248406 None:intergenic 40.0%
TAACAGATCGGTGATGAAGT+AGG - chr4_1:66248420-66248439 None:intergenic 40.0%
! CGAAGAAAAGCATGGCTAAT+TGG - chr4_1:66248487-66248506 None:intergenic 40.0%
AGTGAAGACGAAGAAAAGCA+TGG - chr4_1:66248495-66248514 None:intergenic 40.0%
! TTCACTTGCCGTTTCATGAT+CGG + chr4_1:66248509-66248528 Msa0565350:CDS 40.0%
AACAGCAACCAAAACGAAGA+CGG - chr4_1:66248549-66248568 None:intergenic 40.0%
AGTATGTGACTCGAATCTGC+GGG - chr4_1:66248256-66248275 None:intergenic 45.0%
GAGTATGTGACTCGAATCTG+CGG - chr4_1:66248257-66248276 None:intergenic 45.0%
AAAGACGCAAATCAAGACGC+TGG - chr4_1:66248279-66248298 None:intergenic 45.0%
TTCTTAACCGCCACCATTCT+CGG + chr4_1:66248302-66248321 Msa0565350:CDS 45.0%
CGAAGTAGTGAACGTAGCTT+GGG - chr4_1:66248460-66248479 None:intergenic 45.0%
! TGCCGTTTCATGATCGGTAA+CGG + chr4_1:66248515-66248534 Msa0565350:CDS 45.0%
CACCGTTACCGATCATGAAA+CGG - chr4_1:66248520-66248539 None:intergenic 45.0%
GTATGTGACTCGAATCTGCG+GGG - chr4_1:66248255-66248274 None:intergenic 50.0%
TATTGGCGGCTGATAAGCCA+CGG - chr4_1:66248361-66248380 None:intergenic 50.0%
AGTAGTGAACGTAGCTTGGG+AGG - chr4_1:66248457-66248476 None:intergenic 50.0%
GCGAAGTAGTGAACGTAGCT+TGG - chr4_1:66248461-66248480 None:intergenic 50.0%
! TGCTGTCTCCGTCTTCGTTT+TGG + chr4_1:66248538-66248557 Msa0565350:CDS 50.0%
TGACTCGAATCTGCGGGGTT+CGG - chr4_1:66248250-66248269 None:intergenic 55.0%
GATTACGCCGAGAATGGTGG+CGG - chr4_1:66248312-66248331 None:intergenic 55.0%
GAAGGCGATTACGCCGAGAA+TGG - chr4_1:66248318-66248337 None:intergenic 55.0%
TGATAAGCCACGGTTGGGGT+TGG - chr4_1:66248351-66248370 None:intergenic 55.0%
! GAATCTGCGGGGTTCGGTCT+TGG - chr4_1:66248244-66248263 None:intergenic 60.0%
GGCGATTACGCCGAGAATGG+TGG - chr4_1:66248315-66248334 None:intergenic 60.0%
!! GGGGTTGGTGTCGGAGAAGA+AGG - chr4_1:66248336-66248355 None:intergenic 60.0%
CGGCTGATAAGCCACGGTTG+GGG - chr4_1:66248355-66248374 None:intergenic 60.0%
GCGGCTGATAAGCCACGGTT+GGG - chr4_1:66248356-66248375 None:intergenic 60.0%
TCCGACACCAACCCCAACCG+TGG + chr4_1:66248341-66248360 Msa0565350:CDS 65.0%
!! GCCACGGTTGGGGTTGGTGT+CGG - chr4_1:66248345-66248364 None:intergenic 65.0%
GGCGGCTGATAAGCCACGGT+TGG - chr4_1:66248357-66248376 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 66248143 66248574 66248143 ID=Msa0565350;Name=Msa0565350
chr4_1 mRNA 66248143 66248574 66248143 ID=Msa0565350-mRNA-1;Parent=Msa0565350;Name=Msa0565350-mRNA-1;_AED=0.38;_eAED=0.45;_QI=0|-1|0|1|-1|1|1|0|143
chr4_1 exon 66248143 66248574 66248143 ID=Msa0565350-mRNA-1:exon:21423;Parent=Msa0565350-mRNA-1
chr4_1 CDS 66248143 66248574 66248143 ID=Msa0565350-mRNA-1:cds;Parent=Msa0565350-mRNA-1
Gene Sequence

>Msa0565350

ATGGGAATGCAGCTATCTTTAGCAGAAGAAGGTTGGTTCGTTATCCCATTTTTCTTCACCTTCCTTTCTCTTTACCTTTTCGGTTACTTCATCTTCTTCCAAGACCGAACCCCGCAGATTCGAGTCACATACTCCAGCGTCTTGATTTGCGTCTTTCACTTCTTAACCGCCACCATTCTCGGCGTAATCGCCTTCTTCTCCGACACCAACCCCAACCGTGGCTTATCAGCCGCCAATACTACCTTGCAGAATATCGTTCTTGACTTCAGCATCGCCTACTTCATCACCGATCTGTTACATTTCGTCGTTTTCCTCCCAAGCTACGTTCACTACTTCGCTCACCAATTAGCCATGCTTTTCTTCGTCTTCACTTGCCGTTTCATGATCGGTAACGGTGCTGTCTCCGTCTTCGTTTTGGTTGCTGTTTTCTGA
Protein sequence

>Msa0565350

MGMQLSLAEEGWFVIPFFFTFLSLYLFGYFIFFQDRTPQIRVTYSSVLICVFHFLTATILGVIAFFSDTNPNRGLSAANTTLQNIVLDFSIAYFITDLLHFVVFLPSYVHYFAHQLAMLFFVFTCRFMIGNGAVSVFVLVAVF*