AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0562680


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0562680 MtrunA17_Chr8g0376171 97.436 78 2 0 32 109 1 78 7.83e-48 151
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 27 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGAGAACGTGATGAATAAT+AGG 0.212099 4_1:-62672031 None:intergenic
CCAATGGGCAGTGCCAAATT+TGG 0.221494 4_1:-62672307 None:intergenic
GGAAGAGGAGGTAGAGCTTT+TGG 0.286436 4_1:-62672009 None:intergenic
CAGTCTAAAGAAACCAAATT+TGG 0.296905 4_1:+62672294 Msa0562680:CDS
TGATAGGATCATTTGCCTTC+TGG 0.313169 4_1:-62672273 None:intergenic
TTTGGTTTCTTTAGACTGAT+AGG 0.318596 4_1:-62672289 None:intergenic
TGGAGCACTTCTCTTGGCCT+TGG 0.343783 4_1:+62672327 Msa0562680:CDS
TAATTATTACATGTAGTGAT+TGG 0.389402 4_1:-62672110 None:intergenic
GCCCATTGGAGCACTTCTCT+TGG 0.394201 4_1:+62672321 Msa0562680:CDS
CACTCACTCTTTCATTGCCA+TGG 0.400180 4_1:+62671904 Msa0562680:CDS
TATTACATGTAGTGATTGGT+TGG 0.418115 4_1:-62672106 None:intergenic
GTTGTGGAATGGTTTGTGTT+TGG 0.449224 4_1:-62672064 None:intergenic
AGAGAACGTGATGAATAATA+GGG 0.463254 4_1:-62672030 None:intergenic
CCAAATTTGGCACTGCCCAT+TGG 0.471352 4_1:+62672307 Msa0562680:CDS
TTAGAGCTGATCTCTCGGTT+TGG 0.472692 4_1:-62671952 None:intergenic
CCATGGAACAAAAGAAGAAA+AGG 0.474776 4_1:+62671921 Msa0562680:CDS
CGTGATGAATAATAGGGAAG+AGG 0.487139 4_1:-62672024 None:intergenic
GGCCAAGAGAAGTGCTCCAA+TGG 0.507470 4_1:-62672323 None:intergenic
AACAAAAGAAGAAAAGGATA+AGG 0.518763 4_1:+62671927 Msa0562680:CDS
AGTAAAATGCAGCAGCCAGA+AGG 0.537147 4_1:+62672258 Msa0562680:CDS
GAAGTAGTGTTGTTGTGGAA+TGG 0.541076 4_1:-62672075 None:intergenic
GCCAAGAGAAGTGCTCCAAT+GGG 0.543924 4_1:-62672322 None:intergenic
TTTGGTTAGAGCTGATCTCT+CGG 0.550203 4_1:-62671957 None:intergenic
GTGTAGAAGTAGTGTTGTTG+TGG 0.556287 4_1:-62672080 None:intergenic
GATGAATAATAGGGAAGAGG+AGG 0.559231 4_1:-62672021 None:intergenic
ATAAAATTCATAATTACACG+TGG 0.684458 4_1:-62671877 None:intergenic
AGAGTATAATAATCTCACCA+AGG 0.690310 4_1:-62672344 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATATAATATACAATGAA+AGG - chr4_1:62672192-62672211 None:intergenic 10.0%
!! CAATTGGATAATTAATTAAT+GGG - chr4_1:62672233-62672252 None:intergenic 15.0%
!! ATAAAATTCATAATTACACG+TGG - chr4_1:62671880-62671899 None:intergenic 20.0%
!! TAATTATTACATGTAGTGAT+TGG - chr4_1:62672113-62672132 None:intergenic 20.0%
!! AAAATATTACTAGAGAGAAT+TGG - chr4_1:62672159-62672178 None:intergenic 20.0%
!!! GATAATTAATTAATGGGTTA+AGG - chr4_1:62672227-62672246 None:intergenic 20.0%
!! GCAATTGGATAATTAATTAA+TGG - chr4_1:62672234-62672253 None:intergenic 20.0%
! AACAAAAGAAGAAAAGGATA+AGG + chr4_1:62671927-62671946 Msa0562680:CDS 25.0%
AGAGAACGTGATGAATAATA+GGG - chr4_1:62672033-62672052 None:intergenic 30.0%
TATTACATGTAGTGATTGGT+TGG - chr4_1:62672109-62672128 None:intergenic 30.0%
TATTACTAGAGAGAATTGGT+TGG - chr4_1:62672155-62672174 None:intergenic 30.0%
! TGCATTTTACTATCTGCAAT+TGG - chr4_1:62672249-62672268 None:intergenic 30.0%
! TTTGGTTTCTTTAGACTGAT+AGG - chr4_1:62672292-62672311 None:intergenic 30.0%
CAGTCTAAAGAAACCAAATT+TGG + chr4_1:62672294-62672313 Msa0562680:CDS 30.0%
! CCTTTTCTTCTTTTGTTCCA+TGG - chr4_1:62671924-62671943 None:intergenic 35.0%
CCATGGAACAAAAGAAGAAA+AGG + chr4_1:62671921-62671940 Msa0562680:CDS 35.0%
!!! TCAATGAGCAGCTCATTTTT+TGG - chr4_1:62671978-62671997 None:intergenic 35.0%
GAGAGAACGTGATGAATAAT+AGG - chr4_1:62672034-62672053 None:intergenic 35.0%
TTTGGTTAGAGCTGATCTCT+CGG - chr4_1:62671960-62671979 None:intergenic 40.0%
GATGAATAATAGGGAAGAGG+AGG - chr4_1:62672024-62672043 None:intergenic 40.0%
CGTGATGAATAATAGGGAAG+AGG - chr4_1:62672027-62672046 None:intergenic 40.0%
! GTTGTGGAATGGTTTGTGTT+TGG - chr4_1:62672067-62672086 None:intergenic 40.0%
! GAAGTAGTGTTGTTGTGGAA+TGG - chr4_1:62672078-62672097 None:intergenic 40.0%
! GTGTAGAAGTAGTGTTGTTG+TGG - chr4_1:62672083-62672102 None:intergenic 40.0%
TACTAGAGAGAATTGGTTGG+TGG - chr4_1:62672152-62672171 None:intergenic 40.0%
TGATAGGATCATTTGCCTTC+TGG - chr4_1:62672276-62672295 None:intergenic 40.0%
CACTCACTCTTTCATTGCCA+TGG + chr4_1:62671904-62671923 Msa0562680:CDS 45.0%
TTAGAGCTGATCTCTCGGTT+TGG - chr4_1:62671955-62671974 None:intergenic 45.0%
!!! GTAGAGCTTTTGGAACATGG+AGG - chr4_1:62672002-62672021 None:intergenic 45.0%
!!! GAGGTAGAGCTTTTGGAACA+TGG - chr4_1:62672005-62672024 None:intergenic 45.0%
AGTAAAATGCAGCAGCCAGA+AGG + chr4_1:62672258-62672277 Msa0562680:CDS 45.0%
! GGAAGAGGAGGTAGAGCTTT+TGG - chr4_1:62672012-62672031 None:intergenic 50.0%
CCAATGGGCAGTGCCAAATT+TGG - chr4_1:62672310-62672329 None:intergenic 50.0%
CCAAATTTGGCACTGCCCAT+TGG + chr4_1:62672307-62672326 Msa0562680:CDS 50.0%
!! GCCAAGAGAAGTGCTCCAAT+GGG - chr4_1:62672325-62672344 None:intergenic 50.0%
! GCCCATTGGAGCACTTCTCT+TGG + chr4_1:62672321-62672340 Msa0562680:CDS 55.0%
!! GGCCAAGAGAAGTGCTCCAA+TGG - chr4_1:62672326-62672345 None:intergenic 55.0%
! TGGAGCACTTCTCTTGGCCT+TGG + chr4_1:62672327-62672346 Msa0562680:CDS 55.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 62671860 62672351 62671860 ID=Msa0562680;Name=Msa0562680
chr4_1 mRNA 62671860 62672351 62671860 ID=Msa0562680-mRNA-1;Parent=Msa0562680;Name=Msa0562680-mRNA-1;_AED=0.00;_eAED=0.00;_QI=29|1|0.5|1|0|0.5|2|0|110
chr4_1 exon 62671860 62672122 62671860 ID=Msa0562680-mRNA-1:exon:19783;Parent=Msa0562680-mRNA-1
chr4_1 exon 62672256 62672351 62672256 ID=Msa0562680-mRNA-1:exon:19784;Parent=Msa0562680-mRNA-1
chr4_1 five_prime_UTR 62671860 62671888 62671860 ID=Msa0562680-mRNA-1:five_prime_utr;Parent=Msa0562680-mRNA-1
chr4_1 CDS 62671889 62672122 62671889 ID=Msa0562680-mRNA-1:cds;Parent=Msa0562680-mRNA-1
chr4_1 CDS 62672256 62672351 62672256 ID=Msa0562680-mRNA-1:cds;Parent=Msa0562680-mRNA-1
Gene Sequence

>Msa0562680

ATGAATTTTATCATTCACTCACTCTTTCATTGCCATGGAACAAAAGAAGAAAAGGATAAGGAACCAAACCGAGAGATCAGCTCTAACCAAAAAATGAGCTGCTCATTGAGCCTCCATGTTCCAAAAGCTCTACCTCCTCTTCCCTATTATTCATCACGTTCTCTCTTCATTGCTTCCAAACACAAACCATTCCACAACAACACTACTTCTACACTTTCCAACCAATCACTACATATAGTAAAATGCAGCAGCCAGAAGGCAAATGATCCTATCAGTCTAAAGAAACCAAATTTGGCACTGCCCATTGGAGCACTTCTCTTGGCCTTGGTG

Protein sequence

>Msa0562680

MNFIIHSLFHCHGTKEEKDKEPNREISSNQKMSCSLSLHVPKALPPLPYYSSRSLFIASKHKPFHNNTTSTLSNQSLHIVKCSSQKANDPISLKKPNLALPIGALLLALV