AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0727020


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0727020 MtrunA17_CPg0492991 94.915 236 6 1 1 230 1 236 1.75e-168 463
Msa0727020 MtrunA17_Chr4g0015601 94.915 236 6 1 1 230 1 236 2.00e-168 463
Msa0727020 MtrunA17_Chr4g0016691 98.496 133 2 0 98 230 1 133 6.92e-95 273
Msa0727020 MtrunA17_Chr7g0275161 90.722 97 9 0 134 230 1 97 4.22e-60 184
Msa0727020 MtrunA17_Chr4g0016681 96.000 75 3 0 1 75 1 75 8.38e-50 157
Msa0727020 MtrunA17_Chr7g0275171 77.778 99 6 2 1 93 1 89 1.20e-48 155
Msa0727020 MtrunA17_Chr1g0178511 97.143 35 1 0 98 132 1 35 2.27e-16 74.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0727020 ATCG00160.1 87.234 235 24 1 1 229 1 235 9.78e-152 421

Find 38 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTCATTTGGAAACATATC+TGG 0.181531 5_1:+28921183 Msa0727020:CDS
ATGGAAGCTGGAGTTCATTT+TGG 0.255790 5_1:+28920789 Msa0727020:CDS
CAAGAGACAATTATCTCATT+TGG 0.294663 5_1:+28921171 Msa0727020:CDS
ATCAACGATTATTACAATAT+CGG 0.341941 5_1:-28921233 None:intergenic
TTTATCAGAAGCTTGTGATT+TGG 0.358806 5_1:+28920908 Msa0727020:CDS
CTAATTTGTTAAGAATTAAT+CGG 0.359442 5_1:-28921390 None:intergenic
ATCGAAATATCTGCTAGATC+TGG 0.363586 5_1:-28921337 None:intergenic
TCGAATGGCACCGTTTATAT+CGG 0.367963 5_1:+28920836 Msa0727020:CDS
TTACGCTTTGCCGATATAAA+CGG 0.369497 5_1:-28920846 None:intergenic
CTTCGAGAATGTATCACTTT+GGG 0.388824 5_1:+28921277 Msa0727020:CDS
GGAAAACAATTCTTAATTGT+TGG 0.390734 5_1:+28920951 Msa0727020:CDS
AAACGAGACTTCGTAAGTTC+AGG 0.412190 5_1:+28921083 Msa0727020:CDS
TGCAGCCCGTGTTACTGAAT+CGG 0.431042 5_1:-28920990 None:intergenic
TGATCAGCAAGAAGAATATA+CGG 0.437056 5_1:+28921252 Msa0727020:CDS
TCGGAGGTATGTTAACGAAT+TGG 0.448395 5_1:+28921050 Msa0727020:CDS
TTGGCCATGATACTCGGAAA+TGG 0.459897 5_1:+28920808 Msa0727020:CDS
TCTTCGAGAATGTATCACTT+TGG 0.477646 5_1:+28921276 Msa0727020:CDS
AACGAGACTTCGTAAGTTCA+GGG 0.478021 5_1:+28921084 Msa0727020:CDS
TCAACGATTATTACAATATC+GGG 0.480431 5_1:-28921232 None:intergenic
TTGAGAACGGAGCAAAAGAC+AGG 0.482432 5_1:+28921109 Msa0727020:CDS
GATTCCATTTCCGAGTATCA+TGG 0.488914 5_1:-28920812 None:intergenic
TTTGAAGAGATGATGGAAGC+TGG 0.489132 5_1:+28920777 Msa0727020:CDS
GATATAAACGGTGCCATTCG+AGG 0.490606 5_1:-28920834 None:intergenic
GTATCGATTAAACAAATCGT+TGG 0.491426 5_1:-28921304 None:intergenic
TTTATATCGGCAAAGCGTAA+AGG 0.502509 5_1:+28920849 Msa0727020:CDS
GCTATAGCATCATCATTAGC+TGG 0.518853 5_1:-28921361 None:intergenic
TCGAAATATCTGCTAGATCT+GGG 0.525094 5_1:-28921336 None:intergenic
TCTCATTTGGAAACATATCT+GGG 0.550552 5_1:+28921184 Msa0727020:CDS
GGGTGGCATAAAATATATGA+CGG 0.585418 5_1:+28921204 Msa0727020:CDS
TAAGTTCAGGGACTTGAGAA+CGG 0.589134 5_1:+28921096 Msa0727020:CDS
GGTGGCATAAAATATATGAC+GGG 0.610359 5_1:+28921205 Msa0727020:CDS
AGCAGCCGATTCAGTAACAC+GGG 0.610911 5_1:+28920985 Msa0727020:intron
TCGGAAATGGAATCCTCGAA+TGG 0.635386 5_1:+28920821 Msa0727020:CDS
AAGCAGCCGATTCAGTAACA+CGG 0.653513 5_1:+28920984 Msa0727020:intron
TGAGAACGGAGCAAAAGACA+GGG 0.670658 5_1:+28921110 Msa0727020:CDS
CATTTGGAAACATATCTGGG+TGG 0.732935 5_1:+28921187 Msa0727020:CDS
GTGGCATAAAATATATGACG+GGG 0.737363 5_1:+28921206 Msa0727020:CDS
TAATTGTCTCTTGAACATAG+CGG 0.783646 5_1:-28921161 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTCATTATGTTAATAAAAAA+TGG + chr5_1:28921026-28921045 Msa0727020:CDS 15.0%
!!! CTAATTTGTTAAGAATTAAT+CGG - chr5_1:28921393-28921412 None:intergenic 15.0%
!! TATGTTAATAAAAAATGGCT+CGG + chr5_1:28921031-28921050 Msa0727020:CDS 20.0%
!! ATCAACGATTATTACAATAT+CGG - chr5_1:28921236-28921255 None:intergenic 20.0%
! GGAAAACAATTCTTAATTGT+TGG + chr5_1:28920951-28920970 Msa0727020:CDS 25.0%
! TCAACGATTATTACAATATC+GGG - chr5_1:28921235-28921254 None:intergenic 25.0%
!!! ATTAGTTTTTGCAATTTGTG+AGG + chr5_1:28921408-28921427 Msa0727020:CDS 25.0%
!!! TTAGTTTTTGCAATTTGTGA+GGG + chr5_1:28921409-28921428 Msa0727020:CDS 25.0%
!! CATAACTTTTGAAGAGATGA+TGG + chr5_1:28920770-28920789 Msa0727020:CDS 30.0%
TTTATCAGAAGCTTGTGATT+TGG + chr5_1:28920908-28920927 Msa0727020:CDS 30.0%
TAATTGTCTCTTGAACATAG+CGG - chr5_1:28921164-28921183 None:intergenic 30.0%
CAAGAGACAATTATCTCATT+TGG + chr5_1:28921171-28921190 Msa0727020:CDS 30.0%
ATCTCATTTGGAAACATATC+TGG + chr5_1:28921183-28921202 Msa0727020:CDS 30.0%
TCTCATTTGGAAACATATCT+GGG + chr5_1:28921184-28921203 Msa0727020:CDS 30.0%
TGATCAGCAAGAAGAATATA+CGG + chr5_1:28921252-28921271 Msa0727020:CDS 30.0%
!! GTATCGATTAAACAAATCGT+TGG - chr5_1:28921307-28921326 None:intergenic 30.0%
!! TTCATTTTGGCCATGATACT+CGG + chr5_1:28920802-28920821 Msa0727020:CDS 35.0%
TTACGCTTTGCCGATATAAA+CGG - chr5_1:28920849-28920868 None:intergenic 35.0%
TTTATATCGGCAAAGCGTAA+AGG + chr5_1:28920849-28920868 Msa0727020:CDS 35.0%
! GTTAATAAAAAATGGCTCGG+AGG + chr5_1:28921034-28921053 Msa0727020:CDS 35.0%
GGGTGGCATAAAATATATGA+CGG + chr5_1:28921204-28921223 Msa0727020:CDS 35.0%
GGTGGCATAAAATATATGAC+GGG + chr5_1:28921205-28921224 Msa0727020:CDS 35.0%
GTGGCATAAAATATATGACG+GGG + chr5_1:28921206-28921225 Msa0727020:CDS 35.0%
TCTTCGAGAATGTATCACTT+TGG + chr5_1:28921276-28921295 Msa0727020:CDS 35.0%
CTTCGAGAATGTATCACTTT+GGG + chr5_1:28921277-28921296 Msa0727020:CDS 35.0%
TCGAAATATCTGCTAGATCT+GGG - chr5_1:28921339-28921358 None:intergenic 35.0%
ATCGAAATATCTGCTAGATC+TGG - chr5_1:28921340-28921359 None:intergenic 35.0%
!! TTTGAAGAGATGATGGAAGC+TGG + chr5_1:28920777-28920796 Msa0727020:CDS 40.0%
! ATGGAAGCTGGAGTTCATTT+TGG + chr5_1:28920789-28920808 Msa0727020:CDS 40.0%
GATTCCATTTCCGAGTATCA+TGG - chr5_1:28920815-28920834 None:intergenic 40.0%
TCGAATGGCACCGTTTATAT+CGG + chr5_1:28920836-28920855 Msa0727020:CDS 40.0%
! GTTTTTGATGCAGCAAGCAT+GGG + chr5_1:28920930-28920949 Msa0727020:CDS 40.0%
! TCGGAGGTATGTTAACGAAT+TGG + chr5_1:28921050-28921069 Msa0727020:CDS 40.0%
AAACGAGACTTCGTAAGTTC+AGG + chr5_1:28921083-28921102 Msa0727020:CDS 40.0%
AACGAGACTTCGTAAGTTCA+GGG + chr5_1:28921084-28921103 Msa0727020:CDS 40.0%
TAAGTTCAGGGACTTGAGAA+CGG + chr5_1:28921096-28921115 Msa0727020:CDS 40.0%
! AACATAGCGGCATCTCTTTT+TGG - chr5_1:28921151-28921170 None:intergenic 40.0%
CATTTGGAAACATATCTGGG+TGG + chr5_1:28921187-28921206 Msa0727020:CDS 40.0%
GCTATAGCATCATCATTAGC+TGG - chr5_1:28921364-28921383 None:intergenic 40.0%
TTGGCCATGATACTCGGAAA+TGG + chr5_1:28920808-28920827 Msa0727020:CDS 45.0%
TCGGAAATGGAATCCTCGAA+TGG + chr5_1:28920821-28920840 Msa0727020:CDS 45.0%
!! GATATAAACGGTGCCATTCG+AGG - chr5_1:28920837-28920856 None:intergenic 45.0%
! GGTTTTTGATGCAGCAAGCA+TGG + chr5_1:28920929-28920948 Msa0727020:CDS 45.0%
! AAGCAGCCGATTCAGTAACA+CGG + chr5_1:28920984-28921003 Msa0727020:intron 45.0%
TTGAGAACGGAGCAAAAGAC+AGG + chr5_1:28921109-28921128 Msa0727020:CDS 45.0%
TGAGAACGGAGCAAAAGACA+GGG + chr5_1:28921110-28921129 Msa0727020:CDS 45.0%
! AGCAGCCGATTCAGTAACAC+GGG + chr5_1:28920985-28921004 Msa0727020:intron 50.0%
! TGCAGCCCGTGTTACTGAAT+CGG - chr5_1:28920993-28921012 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 28920750 28921459 28920750 ID=Msa0727020;Name=Msa0727020
chr5_1 mRNA 28920750 28921459 28920750 ID=Msa0727020-mRNA-1;Parent=Msa0727020;Name=Msa0727020-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|0|0|1|0|0.5|2|0|230
chr5_1 exon 28920750 28920972 28920750 ID=Msa0727020-mRNA-1:exon:9954;Parent=Msa0727020-mRNA-1
chr5_1 exon 28920990 28921459 28920990 ID=Msa0727020-mRNA-1:exon:9955;Parent=Msa0727020-mRNA-1
chr5_1 CDS 28920750 28920972 28920750 ID=Msa0727020-mRNA-1:cds;Parent=Msa0727020-mRNA-1
chr5_1 CDS 28920990 28921459 28920990 ID=Msa0727020-mRNA-1:cds;Parent=Msa0727020-mRNA-1
Gene Sequence

>Msa0727020

ATGACAAAAAGATATTGGAACATAACTTTTGAAGAGATGATGGAAGCTGGAGTTCATTTTGGCCATGATACTCGGAAATGGAATCCTCGAATGGCACCGTTTATATCGGCAAAGCGTAAAGGTATTCATATTACAAATCTTACTCGAACTGCTCGTTTTTTATCAGAAGCTTGTGATTTGGTTTTTGATGCAGCAAGCATGGGAAAACAATTCTTAATTGTTGCCGATTCAGTAACACGGGCTGCAATAAGAGCTCGATGTCATTATGTTAATAAAAAATGGCTCGGAGGTATGTTAACGAATTGGTATACTACAGAAACGAGACTTCGTAAGTTCAGGGACTTGAGAACGGAGCAAAAGACAGGGAAACTGAACTCTCTTCCAAAAAGAGATGCCGCTATGTTCAAGAGACAATTATCTCATTTGGAAACATATCTGGGTGGCATAAAATATATGACGGGGTTACCCGATATTGTAATAATCGTTGATCAGCAAGAAGAATATACGGCTCTTCGAGAATGTATCACTTTGGGAATTCCAACGATTTGTTTAATCGATACAAATTGTGACCCAGATCTAGCAGATATTTCGATTCCAGCTAATGATGATGCTATAGCTTCAATCCGATTAATTCTTAACAAATTAGTTTTTGCAATTTGTGAGGGTCGTTCTAGCTATATACGAAATTTTTGA

Protein sequence

>Msa0727020

MTKRYWNITFEEMMEAGVHFGHDTRKWNPRMAPFISAKRKGIHITNLTRTARFLSEACDLVFDAASMGKQFLIVADSVTRAAIRARCHYVNKKWLGGMLTNWYTTETRLRKFRDLRTEQKTGKLNSLPKRDAAMFKRQLSHLETYLGGIKYMTGLPDIVIIVDQQEEYTALRECITLGIPTICLIDTNCDPDLADISIPANDDAIASIRLILNKLVFAICEGRSSYIRNF*