AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0874500


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0874500 MtrunA17_Chr6g0455241 95.402 87 4 0 20 106 56 142 7.72e-59 177
Msa0874500 MtrunA17_Chr6g0455271 95.876 97 4 0 1 97 1 97 1.14e-53 164
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 20 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACATGCAGCAAGAATGCTTT+TGG 0.267933 6_1:-10312036 Msa0874500:CDS
CTACGATAGGCTTGATCTAT+TGG 0.282742 6_1:+10311954 None:intergenic
AGTTGCTTGCCTTCTCAAAA+TGG 0.301353 6_1:-10311933 Msa0874500:CDS
AACAACATCATTGAAGATAA+AGG 0.308741 6_1:-10312123 Msa0874500:CDS
TTGTCTCATCAACAATGATT+TGG 0.352096 6_1:-10312084 Msa0874500:CDS
TAAGTACCACACCTATTGTT+AGG 0.400080 6_1:+10311903 None:intergenic
ACAACATCATTGAAGATAAA+GGG 0.430981 6_1:-10312122 Msa0874500:CDS
CAAACACAAACTGGTAGAAC+TGG 0.449515 6_1:-10312005 Msa0874500:CDS
GATTTGAGTCAAACACAAAC+TGG 0.464256 6_1:-10312014 Msa0874500:CDS
ATGGAGGTGGACCTAACAAT+AGG 0.486497 6_1:-10311914 Msa0874500:CDS
GTAATTGGATCAATAAGATA+AGG 0.536107 6_1:+10312156 None:intergenic
TTGCCTTCTCAAAATGGAGG+TGG 0.550109 6_1:-10311927 Msa0874500:CDS
AGAAGGCAAGCAACTACGAT+AGG 0.559482 6_1:+10311941 None:intergenic
TGCTTGCCTTCTCAAAATGG+AGG 0.624405 6_1:-10311930 Msa0874500:CDS
GGTAGAACTGGTAACAACAA+TGG 0.669601 6_1:-10311993 Msa0874500:CDS
GATAAAGGGTTGTACCTCAG+AGG 0.671194 6_1:-10312108 Msa0874500:CDS
GGTGGACCTAACAATAGGTG+TGG 0.694293 6_1:-10311909 Msa0874500:CDS
GTTGATGAGACAATCCTCTG+AGG 0.737752 6_1:+10312094 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GTAATTGGATCAATAAGATA+AGG + chr6_1:10311919-10311938 None:intergenic 25.0%
!!! TTGTTTTGCTTAGATGTAAT+TGG + chr6_1:10311934-10311953 None:intergenic 25.0%
! AACAACATCATTGAAGATAA+AGG - chr6_1:10311949-10311968 Msa0874500:CDS 25.0%
! ACAACATCATTGAAGATAAA+GGG - chr6_1:10311950-10311969 Msa0874500:CDS 25.0%
TTGTCTCATCAACAATGATT+TGG - chr6_1:10311988-10312007 Msa0874500:CDS 30.0%
GATTTGAGTCAAACACAAAC+TGG - chr6_1:10312058-10312077 Msa0874500:CDS 35.0%
TAAGTACCACACCTATTGTT+AGG + chr6_1:10312172-10312191 None:intergenic 35.0%
! ACATGCAGCAAGAATGCTTT+TGG - chr6_1:10312036-10312055 Msa0874500:CDS 40.0%
CAAACACAAACTGGTAGAAC+TGG - chr6_1:10312067-10312086 Msa0874500:CDS 40.0%
GGTAGAACTGGTAACAACAA+TGG - chr6_1:10312079-10312098 Msa0874500:CDS 40.0%
CTACGATAGGCTTGATCTAT+TGG + chr6_1:10312121-10312140 None:intergenic 40.0%
AGTTGCTTGCCTTCTCAAAA+TGG - chr6_1:10312139-10312158 Msa0874500:CDS 40.0%
GATAAAGGGTTGTACCTCAG+AGG - chr6_1:10311964-10311983 Msa0874500:CDS 45.0%
! GTTGATGAGACAATCCTCTG+AGG + chr6_1:10311981-10312000 None:intergenic 45.0%
AGAAGGCAAGCAACTACGAT+AGG + chr6_1:10312134-10312153 None:intergenic 45.0%
TGCTTGCCTTCTCAAAATGG+AGG - chr6_1:10312142-10312161 Msa0874500:CDS 45.0%
TTGCCTTCTCAAAATGGAGG+TGG - chr6_1:10312145-10312164 Msa0874500:CDS 45.0%
ATGGAGGTGGACCTAACAAT+AGG - chr6_1:10312158-10312177 Msa0874500:CDS 45.0%
!! GGTCCACCTCCATTTTGAGA+AGG + chr6_1:10312151-10312170 None:intergenic 50.0%
GGTGGACCTAACAATAGGTG+TGG - chr6_1:10312163-10312182 Msa0874500:CDS 50.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 10311887 10312207 10311887 ID=Msa0874500;Name=Msa0874500
chr6_1 mRNA 10311887 10312207 10311887 ID=Msa0874500-mRNA-1;Parent=Msa0874500;Name=Msa0874500-mRNA-1;_AED=0.27;_eAED=0.28;_QI=0|-1|0|1|-1|1|1|0|106
chr6_1 exon 10311887 10312207 10311887 ID=Msa0874500-mRNA-1:exon:3205;Parent=Msa0874500-mRNA-1
chr6_1 CDS 10311887 10312207 10311887 ID=Msa0874500-mRNA-1:cds;Parent=Msa0874500-mRNA-1
Gene Sequence

>Msa0874500

ATGATGAACAAGGGTGTATCACTATTGTTCCTTATCTTATTGATCCAATTACATCTAAGCAAAACAACATCATTGAAGATAAAGGGTTGTACCTCAGAGGATTGTCTCATCAACAATGATTTGGAATCAGAAGAATTTTCTATGAGTTCACATGCAGCAAGAATGCTTTTGGATTTGAGTCAAACACAAACTGGTAGAACTGGTAACAACAATGGTGCTGCTGTTAAGTGTCCAATAGATCAAGCCTATCGTAGTTGCTTGCCTTCTCAAAATGGAGGTGGACCTAACAATAGGTGTGGTACTTACAATAGAGTTTGCTAA

Protein sequence

>Msa0874500

MMNKGVSLLFLILLIQLHLSKTTSLKIKGCTSEDCLINNDLESEEFSMSSHAARMLLDLSQTQTGRTGNNNGAAVKCPIDQAYRSCLPSQNGGGPNNRCGTYNRVC*