AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0031050


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0031050 MtrunA17_Chr1g0188931 97.183 71 2 0 4 74 31 101 1.26e-48 149
Msa0031050 MtrunA17_Chr3g0127211 76.056 71 17 0 4 74 31 101 7.14e-38 121
Msa0031050 MtrunA17_Chr8g0346501 67.606 71 23 0 4 74 31 101 4.45e-33 109
Msa0031050 MtrunA17_Chr1g0188951 65.517 58 20 0 17 74 1 58 1.72e-24 86.7
Msa0031050 MtrunA17_Chr2g0316921 47.826 69 36 0 6 74 37 105 1.22e-23 86.3
Msa0031050 MtrunA17_Chr8g0360291 46.269 67 36 0 8 74 39 105 7.44e-22 82.0
Msa0031050 MtrunA17_Chr5g0436971 46.479 71 38 0 4 74 35 105 1.37e-21 81.3
Msa0031050 MtrunA17_Chr4g0046851 46.269 67 36 0 8 74 39 105 1.80e-21 80.9
Msa0031050 MtrunA17_Chr3g0113291 45.070 71 39 0 4 74 58 128 8.60e-21 79.7
Msa0031050 MtrunA17_Chr7g0242231 47.826 69 36 0 6 74 37 105 2.01e-20 78.2
Msa0031050 MtrunA17_Chr2g0316891 45.161 62 34 0 13 74 42 103 6.07e-20 77.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0031050 AT4G27745.2 67.606 71 23 0 4 74 31 101 2.82e-35 115
Msa0031050 AT4G27745.3 67.606 71 23 0 4 74 31 101 2.82e-35 115
Msa0031050 AT4G27745.1 67.606 71 23 0 4 74 31 101 2.82e-35 115
Msa0031050 AT4G27745.4 67.606 71 23 0 4 74 31 101 2.82e-35 115
Msa0031050 AT5G53940.1 44.928 69 38 0 6 74 37 105 1.70e-22 84.0
Msa0031050 AT4G27740.1 45.714 70 38 0 5 74 32 101 3.00e-22 82.4
Msa0031050 AT3G11230.1 49.296 71 36 0 4 74 35 105 4.63e-22 82.8
Msa0031050 AT3G11230.2 49.296 71 36 0 4 74 68 138 1.01e-21 82.8
Msa0031050 AT3G11230.4 50.000 68 34 0 4 71 35 102 1.25e-21 80.9
Msa0031050 AT3G11230.3 50.000 68 34 0 4 71 68 135 2.77e-21 80.9
Msa0031050 AT3G08990.2 46.377 69 37 0 6 74 37 105 6.73e-21 79.7
Msa0031050 AT3G08990.1 46.377 69 37 0 6 74 37 105 6.73e-21 79.7
Msa0031050 AT3G08990.3 46.377 69 37 0 6 74 37 105 6.73e-21 79.7
Msa0031050 AT3G55890.4 47.887 71 37 0 4 74 35 105 1.62e-20 78.6
Msa0031050 AT3G55890.1 47.887 71 37 0 4 74 35 105 1.62e-20 78.6
Msa0031050 AT3G55890.3 47.761 67 35 0 4 70 35 101 4.13e-20 77.0
Msa0031050 AT3G55890.2 47.761 67 35 0 4 70 35 101 4.13e-20 77.0
Msa0031050 AT2G40110.1 46.377 69 37 0 6 74 37 105 1.09e-19 76.6
Msa0031050 AT2G40110.2 45.455 66 36 0 6 71 37 102 6.98e-19 73.9

Find 16 sgRNAs with CRISPR-Local

Find 90 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGCAATGAATGTCATAAT+AGG 0.240119 1_1:-57614269 Msa0031050:CDS
ATGAATTCCATGTCTACTTT+TGG 0.252538 1_1:+57614245 None:intergenic
ATATAATTTCAGGGAAGAAA+TGG 0.360217 1_1:-57614311 Msa0031050:intron
ATGCAATGAATGTCATAATA+GGG 0.414182 1_1:-57614268 Msa0031050:CDS
AGTAAACATCAGCAATTGTA+TGG 0.440083 1_1:+57614213 None:intergenic
TGTGACTGCAATCAAGTGCT+TGG 0.515226 1_1:-57614188 Msa0031050:CDS
ACTGCAATCAAGTGCTTGGT+TGG 0.543372 1_1:-57614184 Msa0031050:CDS
TTTCAGGGAAGAAATGGAAG+AGG 0.547363 1_1:-57614305 Msa0031050:intron
GAAGTTTGAGAGAGTCTATG+AGG 0.548405 1_1:-57614162 Msa0031050:CDS
GGATATTTGCTTGTTGTGTA+CGG 0.556397 1_1:+57615078 None:intergenic
AATAGGGCCAAAAGTAGACA+TGG 0.595301 1_1:-57614252 Msa0031050:CDS
GTAGACATGGAATTCATGAC+AGG 0.597395 1_1:-57614239 Msa0031050:CDS
TGAGGAAACTCAAAAGTACA+AGG 0.598867 1_1:-57614144 Msa0031050:CDS
GAAACTCAAAAGTACAAGGA+AGG 0.606538 1_1:-57614140 Msa0031050:CDS
TGAAGACAATCAATCATCAA+CGG 0.627656 1_1:-57615033 Msa0031050:five_prime_UTR
CAACGGCTACATGAACAAGC+AGG 0.647684 1_1:-57615016 Msa0031050:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAATTTGAAATTGAATTAT+TGG + chr1_1:57614215-57614234 None:intergenic 10.0%
!! AAATTATATATAAATGAACT+TGG + chr1_1:57614881-57614900 None:intergenic 10.0%
!! TTCATTTATATATAATTTCA+GGG - chr1_1:57614883-57614902 Msa0031050:intron 10.0%
!!! TAAATTTGAAATTGAATTAT+TGG + chr1_1:57614215-57614234 None:intergenic 10.0%
!! AAATTATATATAAATGAACT+TGG + chr1_1:57614881-57614900 None:intergenic 10.0%
!! TTCATTTATATATAATTTCA+GGG - chr1_1:57614883-57614902 Msa0031050:intron 10.0%
!! AAAGAATACAAATCAAATTT+AGG + chr1_1:57614540-57614559 None:intergenic 15.0%
!!! GTAACAAAAATTCTTTAAAA+TGG + chr1_1:57614598-57614617 None:intergenic 15.0%
!!! TATAAGAACGTTATATATTT+TGG - chr1_1:57614803-57614822 Msa0031050:intron 15.0%
!! TTGATCAATTTATAATAACA+TGG - chr1_1:57614834-57614853 Msa0031050:intron 15.0%
!! GTTCATTTATATATAATTTC+AGG - chr1_1:57614882-57614901 Msa0031050:intron 15.0%
!! AAAGAATACAAATCAAATTT+AGG + chr1_1:57614540-57614559 None:intergenic 15.0%
!!! GTAACAAAAATTCTTTAAAA+TGG + chr1_1:57614598-57614617 None:intergenic 15.0%
!!! TATAAGAACGTTATATATTT+TGG - chr1_1:57614803-57614822 Msa0031050:intron 15.0%
!! TTGATCAATTTATAATAACA+TGG - chr1_1:57614834-57614853 Msa0031050:intron 15.0%
!! GTTCATTTATATATAATTTC+AGG - chr1_1:57614882-57614901 Msa0031050:intron 15.0%
!! TGAAATAATATCATCATGAA+GGG + chr1_1:57614431-57614450 None:intergenic 20.0%
!! TTGAAATAATATCATCATGA+AGG + chr1_1:57614432-57614451 None:intergenic 20.0%
!! TATTATTTCAAAAACCTTTC+AGG - chr1_1:57614441-57614460 Msa0031050:intron 20.0%
!!! ATACAATGAAAGTATGAAAA+TGG + chr1_1:57614624-57614643 None:intergenic 20.0%
!! CAATTTATAATAACATGGTT+AGG - chr1_1:57614839-57614858 Msa0031050:intron 20.0%
!! TGAAATAATATCATCATGAA+GGG + chr1_1:57614431-57614450 None:intergenic 20.0%
!! TTGAAATAATATCATCATGA+AGG + chr1_1:57614432-57614451 None:intergenic 20.0%
!! TATTATTTCAAAAACCTTTC+AGG - chr1_1:57614441-57614460 Msa0031050:intron 20.0%
!!! ATACAATGAAAGTATGAAAA+TGG + chr1_1:57614624-57614643 None:intergenic 20.0%
!! CAATTTATAATAACATGGTT+AGG - chr1_1:57614839-57614858 Msa0031050:intron 20.0%
!!! TTATGCAAGTTTTTGTTTTG+AGG + chr1_1:57614149-57614168 None:intergenic 25.0%
! TTCCAAATCTTAATAGAGAA+AGG + chr1_1:57614481-57614500 None:intergenic 25.0%
! TCACAAAAGTTGTCTAAAAA+TGG - chr1_1:57614699-57614718 Msa0031050:intron 25.0%
! ATATAATTTCAGGGAAGAAA+TGG - chr1_1:57614892-57614911 Msa0031050:intron 25.0%
! ATGCAATGAATGTCATAATA+GGG - chr1_1:57614935-57614954 Msa0031050:intron 25.0%
!!! TTATGCAAGTTTTTGTTTTG+AGG + chr1_1:57614149-57614168 None:intergenic 25.0%
! TTCCAAATCTTAATAGAGAA+AGG + chr1_1:57614481-57614500 None:intergenic 25.0%
! TCACAAAAGTTGTCTAAAAA+TGG - chr1_1:57614699-57614718 Msa0031050:intron 25.0%
! ATATAATTTCAGGGAAGAAA+TGG - chr1_1:57614892-57614911 Msa0031050:intron 25.0%
! ATGCAATGAATGTCATAATA+GGG - chr1_1:57614935-57614954 Msa0031050:intron 25.0%
TGAAGACAATCAATCATCAA+CGG - chr1_1:57614170-57614189 Msa0031050:CDS 30.0%
AGATGATTATTATCTGCGTT+TGG - chr1_1:57614284-57614303 Msa0031050:CDS 30.0%
!! TTTTATAGCCACTTTGTGAA+GGG - chr1_1:57614325-57614344 Msa0031050:intron 30.0%
!! AGCTCATAAAAGCTTTGAAA+TGG - chr1_1:57614351-57614370 Msa0031050:intron 30.0%
! TTTGAAATGGAGAGTTTCAT+TGG - chr1_1:57614364-57614383 Msa0031050:intron 30.0%
CACCTTTCTCTATTAAGATT+TGG - chr1_1:57614476-57614495 Msa0031050:intron 30.0%
ATCAACACAGTATAAACATG+TGG - chr1_1:57614510-57614529 Msa0031050:intron 30.0%
! GCACATGTGTTAGAATTTTT+GGG + chr1_1:57614774-57614793 None:intergenic 30.0%
! TGCACATGTGTTAGAATTTT+TGG + chr1_1:57614775-57614794 None:intergenic 30.0%
CATGCAATGAATGTCATAAT+AGG - chr1_1:57614934-57614953 Msa0031050:intron 30.0%
! ATGAATTCCATGTCTACTTT+TGG + chr1_1:57614961-57614980 None:intergenic 30.0%
AGTAAACATCAGCAATTGTA+TGG + chr1_1:57614993-57615012 None:intergenic 30.0%
TGAAGACAATCAATCATCAA+CGG - chr1_1:57614170-57614189 Msa0031050:CDS 30.0%
AGATGATTATTATCTGCGTT+TGG - chr1_1:57614284-57614303 Msa0031050:CDS 30.0%
!! TTTTATAGCCACTTTGTGAA+GGG - chr1_1:57614325-57614344 Msa0031050:intron 30.0%
!! AGCTCATAAAAGCTTTGAAA+TGG - chr1_1:57614351-57614370 Msa0031050:intron 30.0%
! TTTGAAATGGAGAGTTTCAT+TGG - chr1_1:57614364-57614383 Msa0031050:intron 30.0%
CACCTTTCTCTATTAAGATT+TGG - chr1_1:57614476-57614495 Msa0031050:intron 30.0%
ATCAACACAGTATAAACATG+TGG - chr1_1:57614510-57614529 Msa0031050:intron 30.0%
! GCACATGTGTTAGAATTTTT+GGG + chr1_1:57614774-57614793 None:intergenic 30.0%
! TGCACATGTGTTAGAATTTT+TGG + chr1_1:57614775-57614794 None:intergenic 30.0%
CATGCAATGAATGTCATAAT+AGG - chr1_1:57614934-57614953 Msa0031050:intron 30.0%
! ATGAATTCCATGTCTACTTT+TGG + chr1_1:57614961-57614980 None:intergenic 30.0%
AGTAAACATCAGCAATTGTA+TGG + chr1_1:57614993-57615012 None:intergenic 30.0%
!! GGATATTTGCTTGTTGTGTA+CGG + chr1_1:57614128-57614147 None:intergenic 35.0%
TCACAAAGTGGCTATAAAAC+TGG + chr1_1:57614324-57614343 None:intergenic 35.0%
!! GTTTTATAGCCACTTTGTGA+AGG - chr1_1:57614324-57614343 Msa0031050:intron 35.0%
! TGAGGAAACTCAAAAGTACA+AGG - chr1_1:57615059-57615078 Msa0031050:five_prime_UTR 35.0%
! GAAACTCAAAAGTACAAGGA+AGG - chr1_1:57615063-57615082 Msa0031050:five_prime_UTR 35.0%
!! GGATATTTGCTTGTTGTGTA+CGG + chr1_1:57614128-57614147 None:intergenic 35.0%
TCACAAAGTGGCTATAAAAC+TGG + chr1_1:57614324-57614343 None:intergenic 35.0%
!! GTTTTATAGCCACTTTGTGA+AGG - chr1_1:57614324-57614343 Msa0031050:intron 35.0%
! TGAGGAAACTCAAAAGTACA+AGG - chr1_1:57615059-57615078 Msa0031050:five_prime_UTR 35.0%
! GAAACTCAAAAGTACAAGGA+AGG - chr1_1:57615063-57615082 Msa0031050:five_prime_UTR 35.0%
TATCATCATGAAGGGCAACA+TGG + chr1_1:57614423-57614442 None:intergenic 40.0%
TTTCAGGGAAGAAATGGAAG+AGG - chr1_1:57614898-57614917 Msa0031050:intron 40.0%
AATAGGGCCAAAAGTAGACA+TGG - chr1_1:57614951-57614970 Msa0031050:intron 40.0%
GTAGACATGGAATTCATGAC+AGG - chr1_1:57614964-57614983 Msa0031050:intron 40.0%
GAAGTTTGAGAGAGTCTATG+AGG - chr1_1:57615041-57615060 Msa0031050:five_prime_UTR 40.0%
TATCATCATGAAGGGCAACA+TGG + chr1_1:57614423-57614442 None:intergenic 40.0%
TTTCAGGGAAGAAATGGAAG+AGG - chr1_1:57614898-57614917 Msa0031050:intron 40.0%
AATAGGGCCAAAAGTAGACA+TGG - chr1_1:57614951-57614970 Msa0031050:intron 40.0%
GTAGACATGGAATTCATGAC+AGG - chr1_1:57614964-57614983 Msa0031050:intron 40.0%
GAAGTTTGAGAGAGTCTATG+AGG - chr1_1:57615041-57615060 Msa0031050:five_prime_UTR 40.0%
!! TGAGAGAGTGTTCACCTGAA+AGG + chr1_1:57614458-57614477 None:intergenic 45.0%
TGTGACTGCAATCAAGTGCT+TGG - chr1_1:57615015-57615034 Msa0031050:intron 45.0%
ACTGCAATCAAGTGCTTGGT+TGG - chr1_1:57615019-57615038 Msa0031050:exon 45.0%
!! TGAGAGAGTGTTCACCTGAA+AGG + chr1_1:57614458-57614477 None:intergenic 45.0%
TGTGACTGCAATCAAGTGCT+TGG - chr1_1:57615015-57615034 Msa0031050:intron 45.0%
ACTGCAATCAAGTGCTTGGT+TGG - chr1_1:57615019-57615038 Msa0031050:exon 45.0%
CAACGGCTACATGAACAAGC+AGG - chr1_1:57614187-57614206 Msa0031050:CDS 50.0%
GAGCTCAACCCTTCACAAAG+TGG + chr1_1:57614336-57614355 None:intergenic 50.0%
CAACGGCTACATGAACAAGC+AGG - chr1_1:57614187-57614206 Msa0031050:CDS 50.0%
GAGCTCAACCCTTCACAAAG+TGG + chr1_1:57614336-57614355 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 57614112 57615113 57614112 ID=Msa0031050;Name=Msa0031050
chr1_1 mRNA 57614112 57615113 57614112 ID=Msa0031050-mRNA-1;Parent=Msa0031050;Name=Msa0031050-mRNA-1;_AED=0.42;_eAED=0.42;_QI=85|0|0.5|1|0|0|2|0|74
chr1_1 exon 57614112 57614321 57614112 ID=Msa0031050-mRNA-1:exon:17453;Parent=Msa0031050-mRNA-1
chr1_1 exon 57615017 57615113 57615017 ID=Msa0031050-mRNA-1:exon:17452;Parent=Msa0031050-mRNA-1
chr1_1 five_prime_UTR 57615029 57615113 57615029 ID=Msa0031050-mRNA-1:five_prime_utr;Parent=Msa0031050-mRNA-1
chr1_1 CDS 57615017 57615028 57615017 ID=Msa0031050-mRNA-1:cds;Parent=Msa0031050-mRNA-1
chr1_1 CDS 57614112 57614321 57614112 ID=Msa0031050-mRNA-1:cds;Parent=Msa0031050-mRNA-1
Gene Sequence

>Msa0031050

ATGAACAAGCAGGGAAGAAATGGAAGAGGTTTTCTGTTTTCACATGCAATGAATGTCATAATAGGGCCAAAAGTAGACATGGAATTCATGACAGGTCTCCATACAATTGCTGATGTTTACTGTTGTGACTGCAATCAAGTGCTTGGTTGGAAGTTTGAGAGAGTCTATGAGGAAACTCAAAAGTACAAGGAAGGCAAATACATTCTTGAGAAGTCTAAAATT

Protein sequence

>Msa0031050

MNKQGRNGRGFLFSHAMNVIIGPKVDMEFMTGLHTIADVYCCDCNQVLGWKFERVYEETQKYKEGKYILEKSKI