AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1342100


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1342100 MtrunA17_Chr7g0266361 93.939 132 3 1 1 127 1 132 6.73e-85 243
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1342100 AT3G10120.1 28.177 181 66 8 1 126 1 172 1.99e-12 61.2

Find 23 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTGTACATCTTGAACTTC+TGG 0.229795 tig0005162:-13245 Msa1342100:intergenic
CTCACCTTCTTGCGCTCTTT+TGG 0.237188 tig0005162:-13212 Msa1342100:intergenic
TCTCTTGTTCATGGTGAAAA+TGG 0.241059 tig0005162:+13359 Msa1342100:CDS
TCAGGTATGCTTTGCAATAC+TGG 0.263195 tig0005162:-13437 None:intergenic
AATAAACATGGGAAATTGTT+TGG 0.325749 tig0005162:+13079 None:intergenic
ATCTATTGCTAGATTACTTC+AGG 0.354532 tig0005162:-13455 Msa1342100:intergenic
TTGCAAGAGATGCTGGATAA+TGG 0.374576 tig0005162:+13311 Msa1342100:CDS
AAAACCTCTTCAGCTTTGAT+AGG 0.399855 tig0005162:-13173 Msa1342100:intergenic
GTGAAGATCATGAAAACAAA+TGG 0.479078 tig0005162:+13122 Msa1342100:CDS
AAGATGCTATCTCTTGTTCA+TGG 0.483231 tig0005162:+13350 Msa1342100:CDS
AAAAGTGATGATGCCTGTGC+AGG 0.529059 tig0005162:+13407 Msa1342100:CDS
TACAGAAAAGTAGTGCAGTT+AGG 0.532146 tig0005162:+13261 Msa1342100:CDS
TACTGGTTTCCACCCTGCAC+AGG 0.563255 tig0005162:-13420 Msa1342100:intergenic
TGTTCATGGTGAAAATGGAA+TGG 0.589839 tig0005162:+13364 Msa1342100:CDS
AACACCTATCAAAGCTGAAG+AGG 0.600750 tig0005162:+13169 Msa1342100:CDS
CAAGAGATGCTGGATAATGG+AGG 0.604501 tig0005162:+13314 Msa1342100:CDS
CAAAAGAGCGCAAGAAGGTG+AGG 0.614183 tig0005162:+13213 Msa1342100:CDS
CATGGTGAAAATGGAATGGA+TGG 0.619170 tig0005162:+13368 Msa1342100:CDS
ATCACCAAAAGAGCGCAAGA+AGG 0.623997 tig0005162:+13208 Msa1342100:CDS
AAGAGATGCTGGATAATGGA+GGG 0.645439 tig0005162:+13315 Msa1342100:CDS
AAAGTGATGATGCCTGTGCA+GGG 0.662931 tig0005162:+13408 Msa1342100:CDS
GGTGCTGCAACAAATTAATG+TGG 0.691279 tig0005162:+13100 Msa1342100:CDS
GTGATGATGCCTGTGCAGGG+TGG 0.757120 tig0005162:+13411 Msa1342100:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GTGAAGATCATGAAAACAAA+TGG + tig0005162:13122-13141 Msa1342100:CDS 30.0%
! AAAACCTCTTCAGCTTTGAT+AGG - tig0005162:13176-13195 Msa1342100:intergenic 35.0%
TTCTGTACATCTTGAACTTC+TGG - tig0005162:13248-13267 Msa1342100:intergenic 35.0%
TACAGAAAAGTAGTGCAGTT+AGG + tig0005162:13261-13280 Msa1342100:CDS 35.0%
AAGATGCTATCTCTTGTTCA+TGG + tig0005162:13350-13369 Msa1342100:CDS 35.0%
TCTCTTGTTCATGGTGAAAA+TGG + tig0005162:13359-13378 Msa1342100:CDS 35.0%
TGTTCATGGTGAAAATGGAA+TGG + tig0005162:13364-13383 Msa1342100:CDS 35.0%
! GGTGCTGCAACAAATTAATG+TGG + tig0005162:13100-13119 Msa1342100:CDS 40.0%
AACACCTATCAAAGCTGAAG+AGG + tig0005162:13169-13188 Msa1342100:CDS 40.0%
!!! TCTTTTGGTGATGATGGAAG+AGG - tig0005162:13200-13219 Msa1342100:intergenic 40.0%
GCAAAAATTGCAAGAGATGC+TGG + tig0005162:13304-13323 Msa1342100:CDS 40.0%
TTGCAAGAGATGCTGGATAA+TGG + tig0005162:13311-13330 Msa1342100:CDS 40.0%
!! AAGAGATGCTGGATAATGGA+GGG + tig0005162:13315-13334 Msa1342100:CDS 40.0%
CATGGTGAAAATGGAATGGA+TGG + tig0005162:13368-13387 Msa1342100:CDS 40.0%
TCAGGTATGCTTTGCAATAC+TGG - tig0005162:13440-13459 Msa1342100:intergenic 40.0%
!!! TTGCGCTCTTTTGGTGATGA+TGG - tig0005162:13206-13225 Msa1342100:intergenic 45.0%
! ATCACCAAAAGAGCGCAAGA+AGG + tig0005162:13208-13227 Msa1342100:CDS 45.0%
! CAAGAGATGCTGGATAATGG+AGG + tig0005162:13314-13333 Msa1342100:CDS 45.0%
! AAAAGTGATGATGCCTGTGC+AGG + tig0005162:13407-13426 Msa1342100:CDS 45.0%
! AAAGTGATGATGCCTGTGCA+GGG + tig0005162:13408-13427 Msa1342100:CDS 45.0%
! CTCACCTTCTTGCGCTCTTT+TGG - tig0005162:13215-13234 Msa1342100:intergenic 50.0%
! CAAAAGAGCGCAAGAAGGTG+AGG + tig0005162:13213-13232 Msa1342100:CDS 50.0%
!! TACTGGTTTCCACCCTGCAC+AGG - tig0005162:13423-13442 Msa1342100:intergenic 55.0%
! GTGATGATGCCTGTGCAGGG+TGG + tig0005162:13411-13430 Msa1342100:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0005162 gene 13086 13469 13086 ID=Msa1342100;Name=Msa1342100
tig0005162 mRNA 13086 13469 13086 ID=Msa1342100-mRNA-1;Parent=Msa1342100;Name=Msa1342100-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|127
tig0005162 exon 13086 13469 13086 ID=Msa1342100-mRNA-1:exon:3459;Parent=Msa1342100-mRNA-1
tig0005162 CDS 13086 13469 13086 ID=Msa1342100-mRNA-1:cds;Parent=Msa1342100-mRNA-1
Gene Sequence

>Msa1342100

ATGGGAAATTGTTTGGTGCTGCAACAAATTAATGTGGTGAAGATCATGAAAACAAATGGAAAAATTCTTGAATACAAAACACAAACACCTATCAAAGCTGAAGAGGTTTTGCCTCTTCCATCATCACCAAAAGAGCGCAAGAAGGTGAGGTTTGCAGATCCAGAAGTTCAAGATGTACAGAAAAGTAGTGCAGTTAGGATTAAGCTTGTTATTAGTAAGCAAAAATTGCAAGAGATGCTGGATAATGGAGGGATTTCAGTTGAAAAGATGCTATCTCTTGTTCATGGTGAAAATGGAATGGATGGTGAAGATTTGTGTAAAAAAAGTGATGATGCCTGTGCAGGGTGGAAACCAGTATTGCAAAGCATACCTGAAGTAATCTAG

Protein sequence

>Msa1342100

MGNCLVLQQINVVKIMKTNGKILEYKTQTPIKAEEVLPLPSSPKERKKVRFADPEVQDVQKSSAVRIKLVISKQKLQEMLDNGGISVEKMLSLVHGENGMDGEDLCKKSDDACAGWKPVLQSIPEVI*