AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1125530

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1125530 MtrunA17_Chr7g0266341 80.682 88 17 0 1 88 45 132 1.52e-42 140
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1125530 AT3G10130.1 59.551 89 35 1 1 88 57 145 1.61e-29 107

Find 32 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGAATTACCATGTTTATTT+TGG 0.071500 7_3:+77026471 None:intergenic
TTTGAATTTCTGTTTGATTT+TGG 0.073218 7_3:+77026529 None:intergenic
GGATACTGGTGTGGTGGTTT+TGG 0.214876 7_3:+77026551 None:intergenic
GAAGGGACCAGTATGAAATT+AGG 0.242932 7_3:-77025945 Msa1125530:CDS
GCTTGTTCATTGTTATTCTT+TGG 0.247598 7_3:+77026504 None:intergenic
GATTTCTTCATGTTCTTACT+TGG 0.291596 7_3:-77025822 Msa1125530:CDS
ATAGATACAACTTTCTTGTT+AGG 0.296174 7_3:+77026397 None:intergenic
CTTGTTCATTGTTATTCTTT+GGG 0.358668 7_3:+77026505 None:intergenic
AAGGGACCAGTATGAAATTA+GGG 0.383324 7_3:-77025944 Msa1125530:CDS
AGTTCAAAGTTCTAACTAGA+AGG 0.388608 7_3:-77025963 Msa1125530:CDS
CAATTTCCCTAATTTCATAC+TGG 0.403074 7_3:+77025938 None:intergenic
ATTTCTTCATGTTCTTACTT+GGG 0.448254 7_3:-77025821 Msa1125530:CDS
AACTTGACAGTCTCAAGGTC+CGG 0.485073 7_3:+77025982 None:intergenic
CAATCAACCTCGATTCATCA+TGG 0.498247 7_3:-77026424 Msa1125530:five_prime_UTR
TGAACGCTTCTTCGAGAGTA+CGG 0.505095 7_3:+77026100 None:intergenic
CTCGAAGAAGCGTTCATGAC+AGG 0.512309 7_3:-77026093 Msa1125530:intron
AGGAGCTATATAAACTGTGC+CGG 0.516270 7_3:-77026579 None:intergenic
ATGCTGACATGGTTCTTCGC+TGG 0.534716 7_3:+77026339 None:intergenic
GGAGCTATATAAACTGTGCC+GGG 0.544814 7_3:-77026578 None:intergenic
GTTGCTAGAAGATGCAGAGT+TGG 0.547178 7_3:+77026372 None:intergenic
GTATGAAATTAGGGAAATTG+AGG 0.549915 7_3:-77025935 Msa1125530:intron
GTTGATTGAAATGAAATACA+AGG 0.552830 7_3:+77026439 None:intergenic
TGCAGTCTCAGTAACGGCAT+CGG 0.558896 7_3:+77026152 None:intergenic
TCGAGCTTCGAATGCTGACA+TGG 0.562557 7_3:+77026328 None:intergenic
GTTCAAAGTTCTAACTAGAA+GGG 0.562833 7_3:-77025962 Msa1125530:CDS
TTGATTGAAATGAAATACAA+GGG 0.593601 7_3:+77026440 None:intergenic
CTTTGAACTTGACAGTCTCA+AGG 0.599106 7_3:+77025977 None:intergenic
GAAATACAAGGGTTGCAAAG+AGG 0.619038 7_3:+77026451 None:intergenic
TTTACGTCGCTGTGAGAGAG+AGG 0.620129 7_3:+77026271 None:intergenic
GTACTTTGCAGTCTCAGTAA+CGG 0.640972 7_3:+77026146 None:intergenic
ACGTCGCTGTGAGAGAGAGG+TGG 0.646916 7_3:+77026274 None:intergenic
ATTCAATCCCAAAATAAACA+TGG 0.670563 7_3:-77026479 Msa1125530:five_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGTATATTGTTAATTATTT+CGG - chr7_3:77026354-77026373 Msa1125530:five_prime_UTR 10.0%
!!! CTATAATTATTCAAATATTT+TGG - chr7_3:77026477-77026496 Msa1125530:five_prime_UTR 10.0%
!! TTGTATATTGTTAATTATTT+CGG - chr7_3:77026354-77026373 Msa1125530:five_prime_UTR 10.0%
!!! CTATAATTATTCAAATATTT+TGG - chr7_3:77026477-77026496 Msa1125530:five_prime_UTR 10.0%
!!! TTGAATTTCTGTTTGATTTT+GGG + chr7_3:77025853-77025872 None:intergenic 20.0%
!!! TTTGAATTTCTGTTTGATTT+TGG + chr7_3:77025854-77025873 None:intergenic 20.0%
!! TTGATTGAAATGAAATACAA+GGG + chr7_3:77025943-77025962 None:intergenic 20.0%
!!! ATTTTCTTTTTGTTCACAAA+AGG - chr7_3:77026528-77026547 Msa1125530:five_prime_UTR 20.0%
!!! TTGAATTTCTGTTTGATTTT+GGG + chr7_3:77025853-77025872 None:intergenic 20.0%
!!! TTTGAATTTCTGTTTGATTT+TGG + chr7_3:77025854-77025873 None:intergenic 20.0%
!! TTGATTGAAATGAAATACAA+GGG + chr7_3:77025943-77025962 None:intergenic 20.0%
!!! ATTTTCTTTTTGTTCACAAA+AGG - chr7_3:77026528-77026547 Msa1125530:five_prime_UTR 20.0%
!! CTTGTTCATTGTTATTCTTT+GGG + chr7_3:77025878-77025897 None:intergenic 25.0%
! ATTCAATCCCAAAATAAACA+TGG - chr7_3:77025901-77025920 Msa1125530:intron 25.0%
!!! GGAATTACCATGTTTATTTT+GGG + chr7_3:77025911-77025930 None:intergenic 25.0%
!! AGGAATTACCATGTTTATTT+TGG + chr7_3:77025912-77025931 None:intergenic 25.0%
! GTTGATTGAAATGAAATACA+AGG + chr7_3:77025944-77025963 None:intergenic 25.0%
! ATAGATACAACTTTCTTGTT+AGG + chr7_3:77025986-77026005 None:intergenic 25.0%
!!! AAGAGATAAGTAGGATTTTT+TGG + chr7_3:77026147-77026166 None:intergenic 25.0%
! AAAATGATGAAGAGATAAGT+AGG + chr7_3:77026156-77026175 None:intergenic 25.0%
! ATTTCTTCATGTTCTTACTT+GGG - chr7_3:77026559-77026578 Msa1125530:five_prime_UTR 25.0%
!! CTTGTTCATTGTTATTCTTT+GGG + chr7_3:77025878-77025897 None:intergenic 25.0%
! ATTCAATCCCAAAATAAACA+TGG - chr7_3:77025901-77025920 Msa1125530:intron 25.0%
!!! GGAATTACCATGTTTATTTT+GGG + chr7_3:77025911-77025930 None:intergenic 25.0%
!! AGGAATTACCATGTTTATTT+TGG + chr7_3:77025912-77025931 None:intergenic 25.0%
! GTTGATTGAAATGAAATACA+AGG + chr7_3:77025944-77025963 None:intergenic 25.0%
! ATAGATACAACTTTCTTGTT+AGG + chr7_3:77025986-77026005 None:intergenic 25.0%
!!! AAGAGATAAGTAGGATTTTT+TGG + chr7_3:77026147-77026166 None:intergenic 25.0%
! AAAATGATGAAGAGATAAGT+AGG + chr7_3:77026156-77026175 None:intergenic 25.0%
! ATTTCTTCATGTTCTTACTT+GGG - chr7_3:77026559-77026578 Msa1125530:five_prime_UTR 25.0%
! GCTTGTTCATTGTTATTCTT+TGG + chr7_3:77025879-77025898 None:intergenic 30.0%
! AGTTCAAAGTTCTAACTAGA+AGG - chr7_3:77026417-77026436 Msa1125530:five_prime_UTR 30.0%
! GTTCAAAGTTCTAACTAGAA+GGG - chr7_3:77026418-77026437 Msa1125530:five_prime_UTR 30.0%
CAATTTCCCTAATTTCATAC+TGG + chr7_3:77026445-77026464 None:intergenic 30.0%
GTATGAAATTAGGGAAATTG+AGG - chr7_3:77026445-77026464 Msa1125530:five_prime_UTR 30.0%
GATTTCTTCATGTTCTTACT+TGG - chr7_3:77026558-77026577 Msa1125530:five_prime_UTR 30.0%
! GCTTGTTCATTGTTATTCTT+TGG + chr7_3:77025879-77025898 None:intergenic 30.0%
! AGTTCAAAGTTCTAACTAGA+AGG - chr7_3:77026417-77026436 Msa1125530:five_prime_UTR 30.0%
! GTTCAAAGTTCTAACTAGAA+GGG - chr7_3:77026418-77026437 Msa1125530:five_prime_UTR 30.0%
CAATTTCCCTAATTTCATAC+TGG + chr7_3:77026445-77026464 None:intergenic 30.0%
GTATGAAATTAGGGAAATTG+AGG - chr7_3:77026445-77026464 Msa1125530:five_prime_UTR 30.0%
GATTTCTTCATGTTCTTACT+TGG - chr7_3:77026558-77026577 Msa1125530:five_prime_UTR 30.0%
!!! TCTGTTTGATTTTGGGATAC+TGG + chr7_3:77025846-77025865 None:intergenic 35.0%
! GTACGGCTTTCAAATCTTTT+TGG + chr7_3:77026266-77026285 None:intergenic 35.0%
TTTGAGCTTTCTTGTAGTTC+CGG - chr7_3:77026379-77026398 Msa1125530:five_prime_UTR 35.0%
AAGGGACCAGTATGAAATTA+GGG - chr7_3:77026436-77026455 Msa1125530:five_prime_UTR 35.0%
!!! TCTGTTTGATTTTGGGATAC+TGG + chr7_3:77025846-77025865 None:intergenic 35.0%
! GTACGGCTTTCAAATCTTTT+TGG + chr7_3:77026266-77026285 None:intergenic 35.0%
TTTGAGCTTTCTTGTAGTTC+CGG - chr7_3:77026379-77026398 Msa1125530:five_prime_UTR 35.0%
AAGGGACCAGTATGAAATTA+GGG - chr7_3:77026436-77026455 Msa1125530:five_prime_UTR 35.0%
!!! TTGATTTTGGGATACTGGTG+TGG + chr7_3:77025841-77025860 None:intergenic 40.0%
GAAATACAAGGGTTGCAAAG+AGG + chr7_3:77025932-77025951 None:intergenic 40.0%
CAATCAACCTCGATTCATCA+TGG - chr7_3:77025956-77025975 Msa1125530:CDS 40.0%
! AGGTTTTCCATGATGAATCG+AGG + chr7_3:77025966-77025985 None:intergenic 40.0%
GTACTTTGCAGTCTCAGTAA+CGG + chr7_3:77026237-77026256 None:intergenic 40.0%
CTTTGAACTTGACAGTCTCA+AGG + chr7_3:77026406-77026425 None:intergenic 40.0%
GAAGGGACCAGTATGAAATT+AGG - chr7_3:77026435-77026454 Msa1125530:five_prime_UTR 40.0%
!!! TTGATTTTGGGATACTGGTG+TGG + chr7_3:77025841-77025860 None:intergenic 40.0%
GAAATACAAGGGTTGCAAAG+AGG + chr7_3:77025932-77025951 None:intergenic 40.0%
CAATCAACCTCGATTCATCA+TGG - chr7_3:77025956-77025975 Msa1125530:CDS 40.0%
! AGGTTTTCCATGATGAATCG+AGG + chr7_3:77025966-77025985 None:intergenic 40.0%
GTACTTTGCAGTCTCAGTAA+CGG + chr7_3:77026237-77026256 None:intergenic 40.0%
CTTTGAACTTGACAGTCTCA+AGG + chr7_3:77026406-77026425 None:intergenic 40.0%
GAAGGGACCAGTATGAAATT+AGG - chr7_3:77026435-77026454 Msa1125530:five_prime_UTR 40.0%
!!! TGTGGTGGTTTTGGTTTTCC+CGG + chr7_3:77025823-77025842 None:intergenic 45.0%
!!! ATTTTGGGATACTGGTGTGG+TGG + chr7_3:77025838-77025857 None:intergenic 45.0%
GTTGCTAGAAGATGCAGAGT+TGG + chr7_3:77026011-77026030 None:intergenic 45.0%
TGAACGCTTCTTCGAGAGTA+CGG + chr7_3:77026283-77026302 None:intergenic 45.0%
AACTTGACAGTCTCAAGGTC+CGG + chr7_3:77026401-77026420 None:intergenic 45.0%
!!! TGTGGTGGTTTTGGTTTTCC+CGG + chr7_3:77025823-77025842 None:intergenic 45.0%
!!! ATTTTGGGATACTGGTGTGG+TGG + chr7_3:77025838-77025857 None:intergenic 45.0%
GTTGCTAGAAGATGCAGAGT+TGG + chr7_3:77026011-77026030 None:intergenic 45.0%
TGAACGCTTCTTCGAGAGTA+CGG + chr7_3:77026283-77026302 None:intergenic 45.0%
AACTTGACAGTCTCAAGGTC+CGG + chr7_3:77026401-77026420 None:intergenic 45.0%
! GGATACTGGTGTGGTGGTTT+TGG + chr7_3:77025832-77025851 None:intergenic 50.0%
ATGCTGACATGGTTCTTCGC+TGG + chr7_3:77026044-77026063 None:intergenic 50.0%
TCGAGCTTCGAATGCTGACA+TGG + chr7_3:77026055-77026074 None:intergenic 50.0%
TTTACGTCGCTGTGAGAGAG+AGG + chr7_3:77026112-77026131 None:intergenic 50.0%
TGCAGTCTCAGTAACGGCAT+CGG + chr7_3:77026231-77026250 None:intergenic 50.0%
!! CTCGAAGAAGCGTTCATGAC+AGG - chr7_3:77026287-77026306 Msa1125530:CDS 50.0%
! GGATACTGGTGTGGTGGTTT+TGG + chr7_3:77025832-77025851 None:intergenic 50.0%
ATGCTGACATGGTTCTTCGC+TGG + chr7_3:77026044-77026063 None:intergenic 50.0%
TCGAGCTTCGAATGCTGACA+TGG + chr7_3:77026055-77026074 None:intergenic 50.0%
TTTACGTCGCTGTGAGAGAG+AGG + chr7_3:77026112-77026131 None:intergenic 50.0%
TGCAGTCTCAGTAACGGCAT+CGG + chr7_3:77026231-77026250 None:intergenic 50.0%
!! CTCGAAGAAGCGTTCATGAC+AGG - chr7_3:77026287-77026306 Msa1125530:CDS 50.0%
ACGTCGCTGTGAGAGAGAGG+TGG + chr7_3:77026109-77026128 None:intergenic 60.0%
ACGTCGCTGTGAGAGAGAGG+TGG + chr7_3:77026109-77026128 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 77025808 77026594 77025808 ID=Msa1125530;Name=Msa1125530
chr7_3 mRNA 77025808 77026594 77025808 ID=Msa1125530-mRNA-1;Parent=Msa1125530;Name=Msa1125530-mRNA-1;_AED=0.14;_eAED=0.14;_QI=246|0.33|0.25|0.5|1|1|4|0|91
chr7_3 exon 77025808 77025852 77025808 ID=Msa1125530-mRNA-1:exon:21189;Parent=Msa1125530-mRNA-1
chr7_3 exon 77025936 77026006 77025936 ID=Msa1125530-mRNA-1:exon:21188;Parent=Msa1125530-mRNA-1
chr7_3 exon 77026094 77026180 77026094 ID=Msa1125530-mRNA-1:exon:21187;Parent=Msa1125530-mRNA-1
chr7_3 exon 77026276 77026594 77026276 ID=Msa1125530-mRNA-1:exon:21186;Parent=Msa1125530-mRNA-1
chr7_3 five_prime_UTR 77026349 77026594 77026349 ID=Msa1125530-mRNA-1:five_prime_utr;Parent=Msa1125530-mRNA-1
chr7_3 CDS 77026276 77026348 77026276 ID=Msa1125530-mRNA-1:cds;Parent=Msa1125530-mRNA-1
chr7_3 CDS 77026094 77026180 77026094 ID=Msa1125530-mRNA-1:cds;Parent=Msa1125530-mRNA-1
chr7_3 CDS 77025936 77026006 77025936 ID=Msa1125530-mRNA-1:cds;Parent=Msa1125530-mRNA-1
chr7_3 CDS 77025808 77025852 77025808 ID=Msa1125530-mRNA-1:cds;Parent=Msa1125530-mRNA-1
Gene Sequence

>Msa1125530

ATGTCAGCATTCGAAGCTCGAATCTCACTCATTTTTGCTCTCGCTTCTCAATCCACCTCTCTCTCACAGCGACTTGTTGCCGATGCCGTTACTGAGACTGCAAAGTACTTGTTTCCAAAAAGATTTGAAAGCCGTACTCTCGAAGAAGCGTTCATGACAGTTCCGGACCTTGAGACTGTCAAGTTCAAAGTTCTAACTAGAAGGGACCAGTATGAAATTAGGGAAATTGAGGATAGTGTGATTTCTTCATGTTCTTACTTGGGCATGTGCCTGTAA
Protein sequence

>Msa1125530

MSAFEARISLIFALASQSTSLSQRLVADAVTETAKYLFPKRFESRTLEEAFMTVPDLETVKFKVLTRRDQYEIREIEDSVISSCSYLGMCL*