AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0275030


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0275030 MtrunA17_Chr2g0287711 98.113 159 3 0 1 159 1 159 3.32e-115 323
Msa0275030 MtrunA17_Chr4g0065681 69.753 162 45 3 1 159 1 161 1.11e-75 223
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0275030 AT3G06145.1 47.826 161 70 3 1 156 10 161 9.65e-46 147

Find 43 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATATCATGAATCCATATATA+AGG 0.244487 2_3:-6942150 None:intergenic
AGACTTGTCACCCTTATATA+TGG 0.279087 2_3:+6942139 Msa0275030:CDS
CAAACTCAAGCCTATGGATT+AGG 0.289594 2_3:+6941922 Msa0275030:CDS
ATGGATTAGGGACAAGGATT+TGG 0.306918 2_3:+6941935 Msa0275030:CDS
GGCCAGTGGAGCTACAAATA+AGG 0.312493 2_3:+6941971 Msa0275030:CDS
ATTCAAATTCAGCTTAAATC+AGG 0.334002 2_3:-6942300 None:intergenic
CATCTGAGATTAGGATCTTA+AGG 0.352876 2_3:+6942235 Msa0275030:CDS
CTGTTGCTTTACCATCCTTA+AGG 0.367149 2_3:-6942184 None:intergenic
TGAAGATGTCATCTGAGATT+AGG 0.401974 2_3:+6942226 Msa0275030:CDS
AAACTCAAGCCTATGGATTA+GGG 0.408249 2_3:+6941923 Msa0275030:CDS
TTATTGCTTCCACTTCTACT+AGG 0.419143 2_3:-6942081 None:intergenic
ATGACATCTTCAAATCTTCA+AGG 0.438998 2_3:-6942215 None:intergenic
ACCCTTATTTGTAGCTCCAC+TGG 0.442006 2_3:-6941973 None:intergenic
TTTCTGTTTGTAAGAGAACT+AGG 0.443516 2_3:+6942277 Msa0275030:CDS
GCCAGTGGAGCTACAAATAA+GGG 0.451437 2_3:+6941972 Msa0275030:CDS
TATCATGAATCCATATATAA+GGG 0.457032 2_3:-6942149 None:intergenic
GGTTTGAGCCTTCAATCTCT+TGG 0.462194 2_3:+6941874 Msa0275030:CDS
ATATAGAGGGTGATTCCTTA+AGG 0.467627 2_3:+6942169 Msa0275030:CDS
TATATGGATTCATGATATAG+AGG 0.471994 2_3:+6942155 Msa0275030:CDS
GGATTTGGAACCTCAGTGAT+AGG 0.472437 2_3:+6941950 Msa0275030:CDS
TTGAGCCTTCAATCTCTTGG+TGG 0.475841 2_3:+6941877 Msa0275030:CDS
ATCTGAGATTAGGATCTTAA+GGG 0.486868 2_3:+6942236 Msa0275030:CDS
TTCACTCTCTTTGAAGACCC+TGG 0.493195 2_3:-6942030 None:intergenic
ACATATATGCCTAGTAGAAG+TGG 0.519308 2_3:+6942072 Msa0275030:CDS
AGCAACCACCAAGAGATTGA+AGG 0.523461 2_3:-6941882 None:intergenic
GGTGGGATCAATACTGAAGA+AGG 0.524915 2_3:+6941993 Msa0275030:CDS
AAATCAGTTGGAGTCCCTCA+TGG 0.525222 2_3:+6941840 Msa0275030:CDS
TATGATCAAACTCAAGCCTA+TGG 0.536028 2_3:+6941916 Msa0275030:CDS
AATCAGTTGGAGTCCCTCAT+GGG 0.543483 2_3:+6941841 Msa0275030:CDS
TCCCTCATGGGGAAAATGAA+AGG 0.568471 2_3:+6941853 Msa0275030:CDS
TAGAAGTGGAAGCAATAATG+TGG 0.572091 2_3:+6942086 Msa0275030:CDS
AATCCTTGTCCCTAATCCAT+AGG 0.573051 2_3:-6941932 None:intergenic
AGAAGTGGAAGCAATAATGT+GGG 0.576987 2_3:+6942087 Msa0275030:CDS
AGAGGGTGATTCCTTAAGGA+TGG 0.612353 2_3:+6942173 Msa0275030:CDS
AAGCCTATGGATTAGGGACA+AGG 0.623725 2_3:+6941929 Msa0275030:CDS
ATATGGATTCATGATATAGA+GGG 0.626290 2_3:+6942156 Msa0275030:CDS
ATCAGTTGGAGTCCCTCATG+GGG 0.636488 2_3:+6941842 Msa0275030:CDS
AGTGGAGCTACAAATAAGGG+TGG 0.638187 2_3:+6941975 Msa0275030:CDS
GTGGAGCTACAAATAAGGGT+GGG 0.660257 2_3:+6941976 Msa0275030:CDS
GAACCTCAGTGATAGGCCAG+TGG 0.677138 2_3:+6941957 Msa0275030:CDS
GCTCCACTGGCCTATCACTG+AGG 0.684800 2_3:-6941960 None:intergenic
AAACAGAAATGCAACCTCTG+TGG 0.692206 2_3:-6942263 None:intergenic
ATCTTAAGGGATCACCACAG+AGG 0.749718 2_3:+6942249 Msa0275030:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATCATGAATCCATATATAA+GGG - chr2_3:6942152-6942171 None:intergenic 20.0%
!! ATATCATGAATCCATATATA+AGG - chr2_3:6942153-6942172 None:intergenic 20.0%
! TATATGGATTCATGATATAG+AGG + chr2_3:6942155-6942174 Msa0275030:CDS 25.0%
! ATATGGATTCATGATATAGA+GGG + chr2_3:6942156-6942175 Msa0275030:CDS 25.0%
ATGACATCTTCAAATCTTCA+AGG - chr2_3:6942218-6942237 None:intergenic 30.0%
! ATCTGAGATTAGGATCTTAA+GGG + chr2_3:6942236-6942255 Msa0275030:CDS 30.0%
TTTCTGTTTGTAAGAGAACT+AGG + chr2_3:6942277-6942296 Msa0275030:CDS 30.0%
TATGATCAAACTCAAGCCTA+TGG + chr2_3:6941916-6941935 Msa0275030:CDS 35.0%
! AAACTCAAGCCTATGGATTA+GGG + chr2_3:6941923-6941942 Msa0275030:CDS 35.0%
!!! AAGGTTCATATTTTGAAGCC+AGG + chr2_3:6942012-6942031 Msa0275030:CDS 35.0%
!!! AGGTTCATATTTTGAAGCCA+GGG + chr2_3:6942013-6942032 Msa0275030:CDS 35.0%
ACATATATGCCTAGTAGAAG+TGG + chr2_3:6942072-6942091 Msa0275030:CDS 35.0%
TTATTGCTTCCACTTCTACT+AGG - chr2_3:6942084-6942103 None:intergenic 35.0%
TAGAAGTGGAAGCAATAATG+TGG + chr2_3:6942086-6942105 Msa0275030:CDS 35.0%
AGAAGTGGAAGCAATAATGT+GGG + chr2_3:6942087-6942106 Msa0275030:CDS 35.0%
AGACTTGTCACCCTTATATA+TGG + chr2_3:6942139-6942158 Msa0275030:CDS 35.0%
ATATAGAGGGTGATTCCTTA+AGG + chr2_3:6942169-6942188 Msa0275030:CDS 35.0%
! TGAAGATGTCATCTGAGATT+AGG + chr2_3:6942226-6942245 Msa0275030:CDS 35.0%
! CATCTGAGATTAGGATCTTA+AGG + chr2_3:6942235-6942254 Msa0275030:CDS 35.0%
! ACCTTTCATTTTCCCCATGA+GGG - chr2_3:6941857-6941876 None:intergenic 40.0%
! AACCTTTCATTTTCCCCATG+AGG - chr2_3:6941858-6941877 None:intergenic 40.0%
CAAACTCAAGCCTATGGATT+AGG + chr2_3:6941922-6941941 Msa0275030:CDS 40.0%
AATCCTTGTCCCTAATCCAT+AGG - chr2_3:6941935-6941954 None:intergenic 40.0%
!! ATGGATTAGGGACAAGGATT+TGG + chr2_3:6941935-6941954 Msa0275030:CDS 40.0%
!! CTGTTGCTTTACCATCCTTA+AGG - chr2_3:6942187-6942206 None:intergenic 40.0%
AAACAGAAATGCAACCTCTG+TGG - chr2_3:6942266-6942285 None:intergenic 40.0%
AAATCAGTTGGAGTCCCTCA+TGG + chr2_3:6941840-6941859 Msa0275030:CDS 45.0%
AATCAGTTGGAGTCCCTCAT+GGG + chr2_3:6941841-6941860 Msa0275030:CDS 45.0%
TCCCTCATGGGGAAAATGAA+AGG + chr2_3:6941853-6941872 Msa0275030:CDS 45.0%
GGTTTGAGCCTTCAATCTCT+TGG + chr2_3:6941874-6941893 Msa0275030:CDS 45.0%
TTGAGCCTTCAATCTCTTGG+TGG + chr2_3:6941877-6941896 Msa0275030:CDS 45.0%
AGCAACCACCAAGAGATTGA+AGG - chr2_3:6941885-6941904 None:intergenic 45.0%
!! AAGCCTATGGATTAGGGACA+AGG + chr2_3:6941929-6941948 Msa0275030:CDS 45.0%
! GGATTTGGAACCTCAGTGAT+AGG + chr2_3:6941950-6941969 Msa0275030:CDS 45.0%
GCCAGTGGAGCTACAAATAA+GGG + chr2_3:6941972-6941991 Msa0275030:CDS 45.0%
! ACCCTTATTTGTAGCTCCAC+TGG - chr2_3:6941976-6941995 None:intergenic 45.0%
AGTGGAGCTACAAATAAGGG+TGG + chr2_3:6941975-6941994 Msa0275030:CDS 45.0%
GTGGAGCTACAAATAAGGGT+GGG + chr2_3:6941976-6941995 Msa0275030:CDS 45.0%
GGTGGGATCAATACTGAAGA+AGG + chr2_3:6941993-6942012 Msa0275030:CDS 45.0%
! TTCACTCTCTTTGAAGACCC+TGG - chr2_3:6942033-6942052 None:intergenic 45.0%
AGAGGGTGATTCCTTAAGGA+TGG + chr2_3:6942173-6942192 Msa0275030:CDS 45.0%
ATCTTAAGGGATCACCACAG+AGG + chr2_3:6942249-6942268 Msa0275030:CDS 45.0%
ATCAGTTGGAGTCCCTCATG+GGG + chr2_3:6941842-6941861 Msa0275030:CDS 50.0%
GGCCAGTGGAGCTACAAATA+AGG + chr2_3:6941971-6941990 Msa0275030:CDS 50.0%
GAACCTCAGTGATAGGCCAG+TGG + chr2_3:6941957-6941976 Msa0275030:CDS 55.0%
! GCTCCACTGGCCTATCACTG+AGG - chr2_3:6941963-6941982 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 6941832 6942314 6941832 ID=Msa0275030;Name=Msa0275030
chr2_3 mRNA 6941832 6942314 6941832 ID=Msa0275030-mRNA-1;Parent=Msa0275030;Name=Msa0275030-mRNA-1;_AED=0.01;_eAED=0.02;_QI=0|-1|0|1|-1|1|1|0|160
chr2_3 exon 6941832 6942314 6941832 ID=Msa0275030-mRNA-1:exon:3268;Parent=Msa0275030-mRNA-1
chr2_3 CDS 6941832 6942314 6941832 ID=Msa0275030-mRNA-1:cds;Parent=Msa0275030-mRNA-1
Gene Sequence

>Msa0275030

ATGACTAAAAATCAGTTGGAGTCCCTCATGGGGAAAATGAAAGGTTTGAGCCTTCAATCTCTTGGTGGTTGCTTTGATAGCTGCTATGATCAAACTCAAGCCTATGGATTAGGGACAAGGATTTGGAACCTCAGTGATAGGCCAGTGGAGCTACAAATAAGGGTGGGATCAATACTGAAGAAGGTTCATATTTTGAAGCCAGGGTCTTCAAAGAGAGTGAAAAGTAAACGCATATATAAGACATATATGCCTAGTAGAAGTGGAAGCAATAATGTGGGAATGAAGAGTTTGTTGTATTACTATGATGAGACTTGTCACCCTTATATATGGATTCATGATATAGAGGGTGATTCCTTAAGGATGGTAAAGCAACAGTATATTAGCCTTGAAGATTTGAAGATGTCATCTGAGATTAGGATCTTAAGGGATCACCACAGAGGTTGCATTTCTGTTTGTAAGAGAACTAGGCCTGATTTAAGCTGA

Protein sequence

>Msa0275030

MTKNQLESLMGKMKGLSLQSLGGCFDSCYDQTQAYGLGTRIWNLSDRPVELQIRVGSILKKVHILKPGSSKRVKSKRIYKTYMPSRSGSNNVGMKSLLYYYDETCHPYIWIHDIEGDSLRMVKQQYISLEDLKMSSEIRILRDHHRGCISVCKRTRPDLS*