AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1422860


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1422860 MtrunA17_Chr3g0135021 94.444 108 2 1 1 108 1 104 8.26e-70 203
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTTCGAGTCAAAGCTCTTC+TGG 0.318499 tig0025489:+64866 Msa1422860:CDS
CCTTCTCCTGCTGGTGGAAC+CGG 0.386344 tig0025489:-65068 None:intergenic
GGTTGCAGTGGAAAGCTTGA+TGG 0.410694 tig0025489:+64887 Msa1422860:CDS
CGCCATGACGGTGGTGTAGC+CGG 0.417162 tig0025489:+65049 Msa1422860:CDS
TTTACCGGTCCTTCTCCTGC+TGG 0.444782 tig0025489:-65077 None:intergenic
GCAGGAGAAGGACCGGTAAA+GGG 0.444911 tig0025489:+65080 Msa1422860:CDS
AGCAGGAGAAGGACCGGTAA+AGG 0.449501 tig0025489:+65079 Msa1422860:CDS
GAAACCACTGCAGGTGGAAG+AGG 0.474000 tig0025489:-64819 None:intergenic
TTCATCTAGATCATTGTTCG+TGG 0.475117 tig0025489:-65120 None:intergenic
GAACATCAATGGCAACTCAT+TGG 0.481610 tig0025489:-65011 None:intergenic
GTGTAGCCGGTTCCACCAGC+AGG 0.482386 tig0025489:+65062 Msa1422860:CDS
GTTGATCAATGGTGTCACTA+TGG 0.489333 tig0025489:+64922 Msa1422860:CDS
ACCGGTCCTTCTCCTGCTGG+TGG 0.523534 tig0025489:-65074 None:intergenic
TTACCATCGTTGAACATCAA+TGG 0.525954 tig0025489:-65022 None:intergenic
ATCTTCTCCGTCTTCTTCTG+TGG 0.526120 tig0025489:-64987 None:intergenic
ACTACCTCTTCCACCTGCAG+TGG 0.560557 tig0025489:+64815 Msa1422860:CDS
CAAAGCTCTTCTGGTTGCAG+TGG 0.566167 tig0025489:+64875 Msa1422860:CDS
TCCACCAGCAGGAGAAGGAC+CGG 0.569119 tig0025489:+65073 Msa1422860:CDS
CCGGTTCCACCAGCAGGAGA+AGG 0.578852 tig0025489:+65068 Msa1422860:CDS
TCGAAGTATTCGATGATGAT+CGG 0.586920 tig0025489:-64850 None:intergenic
GTAGCTATGTGGTTGATCAA+TGG 0.596285 tig0025489:+64911 Msa1422860:CDS
GAAGTTGAAGAAACCACTGC+AGG 0.609331 tig0025489:-64828 None:intergenic
GTTGAAGAAACCACTGCAGG+TGG 0.625992 tig0025489:-64825 None:intergenic
GGTAATCTCCGCCATGACGG+TGG 0.628227 tig0025489:+65040 Msa1422860:CDS
CGCATCGCCACAGAAGAAGA+CGG 0.672339 tig0025489:+64980 Msa1422860:CDS
GATGGTAATCTCCGCCATGA+CGG 0.678032 tig0025489:+65037 Msa1422860:CDS
AGCTTGATGGAGTAGCTATG+TGG 0.699449 tig0025489:+64900 Msa1422860:CDS
CGGCTACACCACCGTCATGG+CGG 0.715775 tig0025489:-65048 None:intergenic
TTGCCATTGATGTTCAACGA+TGG 0.744804 tig0025489:+65019 Msa1422860:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TCGAAGTATTCGATGATGAT+CGG - tig0025489:64853-64872 None:intergenic 35.0%
TTACCATCGTTGAACATCAA+TGG - tig0025489:65025-65044 None:intergenic 35.0%
! TACACTTTTCTTCCCTTTAC+CGG - tig0025489:65095-65114 None:intergenic 35.0%
GTAGCTATGTGGTTGATCAA+TGG + tig0025489:64911-64930 Msa1422860:CDS 40.0%
!! GTTGATCAATGGTGTCACTA+TGG + tig0025489:64922-64941 Msa1422860:CDS 40.0%
GAACATCAATGGCAACTCAT+TGG - tig0025489:65014-65033 None:intergenic 40.0%
TTGCCATTGATGTTCAACGA+TGG + tig0025489:65019-65038 Msa1422860:CDS 40.0%
GAAGTTGAAGAAACCACTGC+AGG - tig0025489:64831-64850 None:intergenic 45.0%
ACTTCGAGTCAAAGCTCTTC+TGG + tig0025489:64866-64885 Msa1422860:CDS 45.0%
AGCTTGATGGAGTAGCTATG+TGG + tig0025489:64900-64919 Msa1422860:CDS 45.0%
ATCTTCTCCGTCTTCTTCTG+TGG - tig0025489:64990-65009 None:intergenic 45.0%
GTTGAAGAAACCACTGCAGG+TGG - tig0025489:64828-64847 None:intergenic 50.0%
! CAAAGCTCTTCTGGTTGCAG+TGG + tig0025489:64875-64894 Msa1422860:CDS 50.0%
GGTTGCAGTGGAAAGCTTGA+TGG + tig0025489:64887-64906 Msa1422860:CDS 50.0%
GATGGTAATCTCCGCCATGA+CGG + tig0025489:65037-65056 Msa1422860:CDS 50.0%
ACTACCTCTTCCACCTGCAG+TGG + tig0025489:64815-64834 Msa1422860:CDS 55.0%
GAAACCACTGCAGGTGGAAG+AGG - tig0025489:64822-64841 None:intergenic 55.0%
CGCATCGCCACAGAAGAAGA+CGG + tig0025489:64980-64999 Msa1422860:CDS 55.0%
TTTACCGGTCCTTCTCCTGC+TGG - tig0025489:65080-65099 None:intergenic 55.0%
AGCAGGAGAAGGACCGGTAA+AGG + tig0025489:65079-65098 Msa1422860:CDS 55.0%
GCAGGAGAAGGACCGGTAAA+GGG + tig0025489:65080-65099 Msa1422860:CDS 55.0%
GGTAATCTCCGCCATGACGG+TGG + tig0025489:65040-65059 Msa1422860:CDS 60.0%
AACCGGCTACACCACCGTCA+TGG - tig0025489:65054-65073 None:intergenic 60.0%
CCTTCTCCTGCTGGTGGAAC+CGG - tig0025489:65071-65090 None:intergenic 60.0%
TCCACCAGCAGGAGAAGGAC+CGG + tig0025489:65073-65092 Msa1422860:CDS 60.0%
CGGCTACACCACCGTCATGG+CGG - tig0025489:65051-65070 None:intergenic 65.0%
CGCCATGACGGTGGTGTAGC+CGG + tig0025489:65049-65068 Msa1422860:CDS 65.0%
! GTGTAGCCGGTTCCACCAGC+AGG + tig0025489:65062-65081 Msa1422860:CDS 65.0%
CCGGTTCCACCAGCAGGAGA+AGG + tig0025489:65068-65087 Msa1422860:CDS 65.0%
ACCGGTCCTTCTCCTGCTGG+TGG - tig0025489:65077-65096 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0025489 gene 64806 65132 64806 ID=Msa1422860;Name=Msa1422860
tig0025489 mRNA 64806 65132 64806 ID=Msa1422860-mRNA-1;Parent=Msa1422860;Name=Msa1422860-mRNA-1;_AED=0.00;_eAED=0.04;_QI=0|-1|0|1|-1|1|1|0|108
tig0025489 exon 64806 65132 64806 ID=Msa1422860-mRNA-1:exon:2863;Parent=Msa1422860-mRNA-1
tig0025489 CDS 64806 65132 64806 ID=Msa1422860-mRNA-1:cds;Parent=Msa1422860-mRNA-1
Gene Sequence

>Msa1422860

ATGGCAGCTACTACCTCTTCCACCTGCAGTGGTTTCTTCAACTTCCGATCATCATCGAATACTTCGAGTCAAAGCTCTTCTGGTTGCAGTGGAAAGCTTGATGGAGTAGCTATGTGGTTGATCAATGGTGTCACTATGGCTTTTTTTTCATCTTTAAATCGTTGCTCTTGCATTCGCATCGCCACAGAAGAAGACGGAGAAGATGCCAATGAGTTGCCATTGATGTTCAACGATGGTAATCTCCGCCATGACGGTGGTGTAGCCGGTTCCACCAGCAGGAGAAGGACCGGTAAAGGGAAGAAAAGTGTACTTGTCCACGAACAATGA

Protein sequence

>Msa1422860

MAATTSSTCSGFFNFRSSSNTSSQSSSGCSGKLDGVAMWLINGVTMAFFSSLNRCSCIRIATEEDGEDANELPLMFNDGNLRHDGGVAGSTSRRRTGKGKKSVLVHEQ*