AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0908170


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0908170 MtrunA17_Chr2g0305631 71.667 120 31 2 5 122 47 165 3.11e-49 154
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0908170 AT1G31200.1 39.370 127 62 5 8 120 3 128 7.59e-19 76.6
Msa0908170 AT1G10155.1 39.062 128 62 5 8 120 55 181 2.34e-18 76.6

Find 32 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGGAAAAGGAACTTCATTT+TGG 0.223452 6_2:+9295050 Msa0908170:CDS
GATGGCTAAAGTTGGGAAAA+AGG 0.285093 6_2:+9294932 Msa0908170:CDS
TCAAGCTTAGCCTCATCTTT+TGG 0.301147 6_2:-9295011 None:intergenic
CAGAGCTGACACAAGTTTCA+TGG 0.313789 6_2:+9294796 Msa0908170:CDS
GTTTCATGGTTGGAGGTATC+TGG 0.319576 6_2:+9294810 Msa0908170:CDS
GTTCCCCAACCGAAACCTTC+TGG 0.324475 6_2:-9294891 None:intergenic
AAAGTAAAAGTAGTAGATAA+AGG 0.334874 6_2:+9294834 Msa0908170:CDS
ATGAAGTATGGAGTGGAAAA+TGG 0.336655 6_2:+9295078 Msa0908170:CDS
AAGTAAAAGTAGTAGATAAA+GGG 0.432345 6_2:+9294835 Msa0908170:CDS
AAGCCAGAAGGTTTCGGTTG+GGG 0.447465 6_2:+9294888 Msa0908170:CDS
TGAAGTGTCAGGTGAGGAAA+AGG 0.454863 6_2:+9295037 Msa0908170:CDS
TAAGCCAGAAGGTTTCGGTT+GGG 0.457218 6_2:+9294887 Msa0908170:CDS
GAAGTTAAGCCAGAAGGTTT+CGG 0.458947 6_2:+9294882 Msa0908170:CDS
GGGAACCAGCACAGATGTAC+TGG 0.493026 6_2:+9294908 Msa0908170:CDS
AAGCTTGAAATTGAAGTGTC+AGG 0.504703 6_2:+9295026 Msa0908170:CDS
GAAATATACAGTGAAATTTG+AGG 0.518771 6_2:+9294857 Msa0908170:CDS
AAAGGGAACATATAAATATG+AGG 0.525864 6_2:+9294950 Msa0908170:CDS
GACACAAGTTTCATGGTTGG+AGG 0.541826 6_2:+9294803 Msa0908170:CDS
GCTGACACAAGTTTCATGGT+TGG 0.548605 6_2:+9294800 Msa0908170:CDS
CATCACCAGTACATCTGTGC+TGG 0.558599 6_2:-9294913 None:intergenic
TACTGGTGATGGCTAAAGTT+GGG 0.572904 6_2:+9294925 Msa0908170:CDS
TGGAGTGGAAAATGGAAAGG+AGG 0.576113 6_2:+9295086 Msa0908170:CDS
TTAAGCCAGAAGGTTTCGGT+TGG 0.579224 6_2:+9294886 Msa0908170:CDS
GTACTGGTGATGGCTAAAGT+TGG 0.597259 6_2:+9294924 Msa0908170:CDS
CAGCACAGATGTACTGGTGA+TGG 0.597825 6_2:+9294914 Msa0908170:CDS
GTATGGAGTGGAAAATGGAA+AGG 0.608777 6_2:+9295083 Msa0908170:CDS
ATATACAGTGAAATTTGAGG+TGG 0.617992 6_2:+9294860 Msa0908170:CDS
GACAACCATTCCAAAAGATG+AGG 0.618532 6_2:+9295001 Msa0908170:CDS
GAGGTGGAAGTTAAGCCAGA+AGG 0.632622 6_2:+9294876 Msa0908170:CDS
TGAAATTGAAGTGTCAGGTG+AGG 0.650518 6_2:+9295031 Msa0908170:CDS
GGATTGTATGAAGTATGGAG+TGG 0.655368 6_2:+9295071 Msa0908170:CDS
GAGGTAGTGCATCTAGAGTG+TGG 0.663909 6_2:+9294969 Msa0908170:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGTAAAAGTAGTAGATAA+AGG + chr6_2:9294834-9294853 Msa0908170:CDS 20.0%
!! AAGTAAAAGTAGTAGATAAA+GGG + chr6_2:9294835-9294854 Msa0908170:CDS 20.0%
! GAAATATACAGTGAAATTTG+AGG + chr6_2:9294857-9294876 Msa0908170:CDS 25.0%
! AAAGGGAACATATAAATATG+AGG + chr6_2:9294950-9294969 Msa0908170:CDS 25.0%
!! ATTTTGGATTGTATGAAGTA+TGG + chr6_2:9295066-9295085 Msa0908170:CDS 25.0%
ATATACAGTGAAATTTGAGG+TGG + chr6_2:9294860-9294879 Msa0908170:CDS 30.0%
ATGGCTAAAGTTGGGAAAAA+GGG + chr6_2:9294933-9294952 Msa0908170:CDS 35.0%
!!! TCTTTTGGAATGGTTGTCTT+AGG - chr6_2:9294999-9295018 None:intergenic 35.0%
! AAGCTTGAAATTGAAGTGTC+AGG + chr6_2:9295026-9295045 Msa0908170:CDS 35.0%
! GAGGAAAAGGAACTTCATTT+TGG + chr6_2:9295050-9295069 Msa0908170:CDS 35.0%
ATGAAGTATGGAGTGGAAAA+TGG + chr6_2:9295078-9295097 Msa0908170:CDS 35.0%
GAAGTTAAGCCAGAAGGTTT+CGG + chr6_2:9294882-9294901 Msa0908170:CDS 40.0%
!! TACTGGTGATGGCTAAAGTT+GGG + chr6_2:9294925-9294944 Msa0908170:CDS 40.0%
GATGGCTAAAGTTGGGAAAA+AGG + chr6_2:9294932-9294951 Msa0908170:CDS 40.0%
GACAACCATTCCAAAAGATG+AGG + chr6_2:9295001-9295020 Msa0908170:CDS 40.0%
!! CTTAGCCTCATCTTTTGGAA+TGG - chr6_2:9295009-9295028 None:intergenic 40.0%
! TCAAGCTTAGCCTCATCTTT+TGG - chr6_2:9295014-9295033 None:intergenic 40.0%
! TGAAATTGAAGTGTCAGGTG+AGG + chr6_2:9295031-9295050 Msa0908170:CDS 40.0%
GGATTGTATGAAGTATGGAG+TGG + chr6_2:9295071-9295090 Msa0908170:CDS 40.0%
GTATGGAGTGGAAAATGGAA+AGG + chr6_2:9295083-9295102 Msa0908170:CDS 40.0%
CAGAGCTGACACAAGTTTCA+TGG + chr6_2:9294796-9294815 Msa0908170:CDS 45.0%
GCTGACACAAGTTTCATGGT+TGG + chr6_2:9294800-9294819 Msa0908170:CDS 45.0%
GACACAAGTTTCATGGTTGG+AGG + chr6_2:9294803-9294822 Msa0908170:CDS 45.0%
!! GTTTCATGGTTGGAGGTATC+TGG + chr6_2:9294810-9294829 Msa0908170:CDS 45.0%
TTAAGCCAGAAGGTTTCGGT+TGG + chr6_2:9294886-9294905 Msa0908170:CDS 45.0%
TAAGCCAGAAGGTTTCGGTT+GGG + chr6_2:9294887-9294906 Msa0908170:CDS 45.0%
!! GTACTGGTGATGGCTAAAGT+TGG + chr6_2:9294924-9294943 Msa0908170:CDS 45.0%
! TGAAGTGTCAGGTGAGGAAA+AGG + chr6_2:9295037-9295056 Msa0908170:CDS 45.0%
TGGAGTGGAAAATGGAAAGG+AGG + chr6_2:9295086-9295105 Msa0908170:CDS 45.0%
GAGGTGGAAGTTAAGCCAGA+AGG + chr6_2:9294876-9294895 Msa0908170:CDS 50.0%
AAGCCAGAAGGTTTCGGTTG+GGG + chr6_2:9294888-9294907 Msa0908170:CDS 50.0%
CATCACCAGTACATCTGTGC+TGG - chr6_2:9294916-9294935 None:intergenic 50.0%
! CAGCACAGATGTACTGGTGA+TGG + chr6_2:9294914-9294933 Msa0908170:CDS 50.0%
! GAGGTAGTGCATCTAGAGTG+TGG + chr6_2:9294969-9294988 Msa0908170:CDS 50.0%
GTTCCCCAACCGAAACCTTC+TGG - chr6_2:9294894-9294913 None:intergenic 55.0%
GGGAACCAGCACAGATGTAC+TGG + chr6_2:9294908-9294927 Msa0908170:CDS 55.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 9294774 9295148 9294774 ID=Msa0908170;Name=Msa0908170
chr6_2 mRNA 9294774 9295148 9294774 ID=Msa0908170-mRNA-1;Parent=Msa0908170;Name=Msa0908170-mRNA-1;_AED=0.11;_eAED=0.12;_QI=0|-1|0|1|-1|1|1|0|124
chr6_2 exon 9294774 9295148 9294774 ID=Msa0908170-mRNA-1:exon:2257;Parent=Msa0908170-mRNA-1
chr6_2 CDS 9294774 9295148 9294774 ID=Msa0908170-mRNA-1:cds;Parent=Msa0908170-mRNA-1
Gene Sequence

>Msa0908170

ATGCATTATTTCAGCGAAGTTGCAGAGCTGACACAAGTTTCATGGTTGGAGGTATCTGGTAAAGTAAAAGTAGTAGATAAAGGGAAATATACAGTGAAATTTGAGGTGGAAGTTAAGCCAGAAGGTTTCGGTTGGGGAACCAGCACAGATGTACTGGTGATGGCTAAAGTTGGGAAAAAGGGAACATATAAATATGAGGTAGTGCATCTAGAGTGTGGTACTCCTAAGACAACCATTCCAAAAGATGAGGCTAAGCTTGAAATTGAAGTGTCAGGTGAGGAAAAGGAACTTCATTTTGGATTGTATGAAGTATGGAGTGGAAAATGGAAAGGAGGTTTGAAAATCTACAATGCAGTAGTTGCTAAGACGCCTTAA

Protein sequence

>Msa0908170

MHYFSEVAELTQVSWLEVSGKVKVVDKGKYTVKFEVEVKPEGFGWGTSTDVLVMAKVGKKGTYKYEVVHLECGTPKTTIPKDEAKLEIEVSGEEKELHFGLYEVWSGKWKGGLKIYNAVVAKTP*