AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1191990

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 36 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCGTTCAGTACTGGGAATA+TGG 0.302089 8_1:-36891758 Msa1191990:CDS
TTATTGCTTTGAGCAAGATT+TGG 0.372290 8_1:-36891113 Msa1191990:three_prime_UTR
ATCTTGCTCAAAGCAATAAC+CGG 0.374503 8_1:+36891117 None:intergenic
TCCGGTTCGACCAGCCTGTT+TGG 0.390434 8_1:-36891448 Msa1191990:CDS
CAGTCTAGTAGCAACATAAC+CGG 0.395979 8_1:+36891055 None:intergenic
TCTCCCAACCCGTTCAGTAC+TGG 0.409727 8_1:-36891766 Msa1191990:CDS
ACCAAACAGGCTGGTCGAAC+CGG 0.411099 8_1:+36891447 None:intergenic
TCAAACTTACTTTCCATGTC+TGG 0.416082 8_1:+36891276 None:intergenic
GACCGGATTGTTTACCCCTC+CGG 0.424311 8_1:-36891466 Msa1191990:CDS
CTCCCAACCCGTTCAGTACT+GGG 0.443973 8_1:-36891765 Msa1191990:CDS
TTCCCAGTACTGAACGGGTT+GGG 0.465952 8_1:+36891763 None:intergenic
CCATATTCCCAGTACTGAAC+GGG 0.471927 8_1:+36891758 None:intergenic
AGAGTCTAATAGACATTGCA+TGG 0.507838 8_1:+36891027 None:intergenic
TTCGACCAGCCTGTTTGGTA+CGG 0.509013 8_1:-36891443 Msa1191990:intron
AACCGGAGGGGTAAACAATC+CGG 0.519027 8_1:+36891464 None:intergenic
CGTGTAATGTTGTATTAACC+CGG 0.530247 8_1:-36891074 Msa1191990:three_prime_UTR
CTTCTTATAATAAGAACGGA+AGG 0.533992 8_1:+36890945 None:intergenic
TCCATATTCCCAGTACTGAA+CGG 0.550792 8_1:+36891757 None:intergenic
GCTGCTTGTGATTACCAACC+CGG 0.560393 8_1:-36891136 Msa1191990:three_prime_UTR
AAATCTTCTTATAATAAGAA+CGG 0.561130 8_1:+36890941 None:intergenic
TTCAGTACTGGGAATATGGA+TGG 0.571027 8_1:-36891754 Msa1191990:intron
AACAGGCTGGTCGAACCGGA+GGG 0.587783 8_1:+36891451 None:intergenic
GCTCAAAGCAATAACCGGGT+TGG 0.593554 8_1:+36891122 None:intergenic
AACGCGTCGGTGAACACGCA+AGG 0.594274 8_1:+36891312 None:intergenic
ATTCCCAGTACTGAACGGGT+TGG 0.599227 8_1:+36891762 None:intergenic
AAACAGGCTGGTCGAACCGG+AGG 0.601388 8_1:+36891450 None:intergenic
TATTGCTGAGAAGCCAGACA+TGG 0.619519 8_1:-36891289 Msa1191990:CDS
AGTCTAGTAGCAACATAACC+GGG 0.635153 8_1:+36891056 None:intergenic
AAAACAATGAACAGAAGTTG+CGG 0.642478 8_1:-36891815 None:intergenic
GAGTCTAATAGACATTGCAT+GGG 0.644314 8_1:+36891028 None:intergenic
TCTTGCTCAAAGCAATAACC+GGG 0.645936 8_1:+36891118 None:intergenic
CTTCTCAGCAATAAACGCGT+CGG 0.647614 8_1:+36891299 None:intergenic
TTCTTATAATAAGAACGGAA+GGG 0.653893 8_1:+36890946 None:intergenic
ACAGGCTGGTCGAACCGGAG+GGG 0.658075 8_1:+36891452 None:intergenic
ACAATGAACAGATGTTACTG+AGG 0.694420 8_1:-36891179 Msa1191990:intron
ACAATGAACAGAAGTTGCGG+CGG 0.700063 8_1:-36891812 Msa1191990:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTCTAATACTTTTTAAAAAT+TGG - chr8_1:36891727-36891746 Msa1191990:intron 15.0%
!! AAATCTTCTTATAATAAGAA+CGG + chr8_1:36891797-36891816 None:intergenic 15.0%
!!! CTCTAATACTTTTTAAAAAT+TGG - chr8_1:36891727-36891746 Msa1191990:intron 15.0%
!! AAATCTTCTTATAATAAGAA+CGG + chr8_1:36891797-36891816 None:intergenic 15.0%
!! AAAATCTAAATCAGGATAAA+TGG + chr8_1:36891069-36891088 None:intergenic 20.0%
!! ATTGATCTGTTATGATTTAT+TGG - chr8_1:36891140-36891159 Msa1191990:three_prime_UTR 20.0%
!! AAAATCTAAATCAGGATAAA+TGG + chr8_1:36891069-36891088 None:intergenic 20.0%
!! ATTGATCTGTTATGATTTAT+TGG - chr8_1:36891140-36891159 Msa1191990:three_prime_UTR 20.0%
! AATCATAACAGATCAATCAT+GGG + chr8_1:36891137-36891156 None:intergenic 25.0%
! AAATCATAACAGATCAATCA+TGG + chr8_1:36891138-36891157 None:intergenic 25.0%
! ATTTGATCTAAACAATGAAC+AGG - chr8_1:36891369-36891388 Msa1191990:intron 25.0%
! TGATCAAATAAGAAACCAAA+GGG + chr8_1:36891534-36891553 None:intergenic 25.0%
! TTGATCAAATAAGAAACCAA+AGG + chr8_1:36891535-36891554 None:intergenic 25.0%
! TTCTTATAATAAGAACGGAA+GGG + chr8_1:36891792-36891811 None:intergenic 25.0%
! AATCATAACAGATCAATCAT+GGG + chr8_1:36891137-36891156 None:intergenic 25.0%
! AAATCATAACAGATCAATCA+TGG + chr8_1:36891138-36891157 None:intergenic 25.0%
! ATTTGATCTAAACAATGAAC+AGG - chr8_1:36891369-36891388 Msa1191990:intron 25.0%
! TGATCAAATAAGAAACCAAA+GGG + chr8_1:36891534-36891553 None:intergenic 25.0%
! TTGATCAAATAAGAAACCAA+AGG + chr8_1:36891535-36891554 None:intergenic 25.0%
! TTCTTATAATAAGAACGGAA+GGG + chr8_1:36891792-36891811 None:intergenic 25.0%
ACTCTCAATGTTGTATTAAC+TGG - chr8_1:36891012-36891031 Msa1191990:three_prime_UTR 30.0%
CTGAAGTCAAAATCTAAATC+AGG + chr8_1:36891077-36891096 None:intergenic 30.0%
AAAGAATTGTATCTCCACAT+GGG + chr8_1:36891102-36891121 None:intergenic 30.0%
AAAAGAATTGTATCTCCACA+TGG + chr8_1:36891103-36891122 None:intergenic 30.0%
ATATCAGAGAGATATGATTG+AGG + chr8_1:36891198-36891217 None:intergenic 30.0%
!! TTTTAAAAACCGTACCAAAC+AGG + chr8_1:36891304-36891323 None:intergenic 30.0%
AGATCAAATAAGAAACCGAA+GGG + chr8_1:36891358-36891377 None:intergenic 30.0%
TAGATCAAATAAGAAACCGA+AGG + chr8_1:36891359-36891378 None:intergenic 30.0%
!!! AGGGTGGAGATATTTTAATA+TGG + chr8_1:36891515-36891534 None:intergenic 30.0%
ATTAAAATATCTCCACCCTT+TGG - chr8_1:36891516-36891535 Msa1191990:intron 30.0%
! TTATTGCTTTGAGCAAGATT+TGG - chr8_1:36891622-36891641 Msa1191990:intron 30.0%
CTTCTTATAATAAGAACGGA+AGG + chr8_1:36891793-36891812 None:intergenic 30.0%
ACTCTCAATGTTGTATTAAC+TGG - chr8_1:36891012-36891031 Msa1191990:three_prime_UTR 30.0%
CTGAAGTCAAAATCTAAATC+AGG + chr8_1:36891077-36891096 None:intergenic 30.0%
AAAGAATTGTATCTCCACAT+GGG + chr8_1:36891102-36891121 None:intergenic 30.0%
AAAAGAATTGTATCTCCACA+TGG + chr8_1:36891103-36891122 None:intergenic 30.0%
ATATCAGAGAGATATGATTG+AGG + chr8_1:36891198-36891217 None:intergenic 30.0%
!! TTTTAAAAACCGTACCAAAC+AGG + chr8_1:36891304-36891323 None:intergenic 30.0%
AGATCAAATAAGAAACCGAA+GGG + chr8_1:36891358-36891377 None:intergenic 30.0%
TAGATCAAATAAGAAACCGA+AGG + chr8_1:36891359-36891378 None:intergenic 30.0%
!!! AGGGTGGAGATATTTTAATA+TGG + chr8_1:36891515-36891534 None:intergenic 30.0%
ATTAAAATATCTCCACCCTT+TGG - chr8_1:36891516-36891535 Msa1191990:intron 30.0%
! TTATTGCTTTGAGCAAGATT+TGG - chr8_1:36891622-36891641 Msa1191990:intron 30.0%
CTTCTTATAATAAGAACGGA+AGG + chr8_1:36891793-36891812 None:intergenic 30.0%
!! AGGGCGAGGATATTTTAAAA+TGG + chr8_1:36891339-36891358 None:intergenic 35.0%
! TTTAAAATATCCTCGCCCTT+CGG - chr8_1:36891340-36891359 Msa1191990:CDS 35.0%
TCAAACTTACTTTCCATGTC+TGG + chr8_1:36891462-36891481 None:intergenic 35.0%
TCAAATAAGAAACCAAAGGG+TGG + chr8_1:36891531-36891550 None:intergenic 35.0%
ACAATGAACAGATGTTACTG+AGG - chr8_1:36891556-36891575 Msa1191990:intron 35.0%
ATCTTGCTCAAAGCAATAAC+CGG + chr8_1:36891621-36891640 None:intergenic 35.0%
CGTGTAATGTTGTATTAACC+CGG - chr8_1:36891661-36891680 Msa1191990:intron 35.0%
GAGTCTAATAGACATTGCAT+GGG + chr8_1:36891710-36891729 None:intergenic 35.0%
AGAGTCTAATAGACATTGCA+TGG + chr8_1:36891711-36891730 None:intergenic 35.0%
!! AGGGCGAGGATATTTTAAAA+TGG + chr8_1:36891339-36891358 None:intergenic 35.0%
! TTTAAAATATCCTCGCCCTT+CGG - chr8_1:36891340-36891359 Msa1191990:CDS 35.0%
TCAAACTTACTTTCCATGTC+TGG + chr8_1:36891462-36891481 None:intergenic 35.0%
TCAAATAAGAAACCAAAGGG+TGG + chr8_1:36891531-36891550 None:intergenic 35.0%
ACAATGAACAGATGTTACTG+AGG - chr8_1:36891556-36891575 Msa1191990:intron 35.0%
ATCTTGCTCAAAGCAATAAC+CGG + chr8_1:36891621-36891640 None:intergenic 35.0%
CGTGTAATGTTGTATTAACC+CGG - chr8_1:36891661-36891680 Msa1191990:intron 35.0%
GAGTCTAATAGACATTGCAT+GGG + chr8_1:36891710-36891729 None:intergenic 35.0%
AGAGTCTAATAGACATTGCA+TGG + chr8_1:36891711-36891730 None:intergenic 35.0%
! TCCATATTCCCAGTACTGAA+CGG + chr8_1:36890981-36891000 None:intergenic 40.0%
! TTCAGTACTGGGAATATGGA+TGG - chr8_1:36890981-36891000 Msa1191990:three_prime_UTR 40.0%
!!! TTTTGACTTCAGAACCCATG+TGG - chr8_1:36891085-36891104 Msa1191990:three_prime_UTR 40.0%
TCAGAGAGATATGATTGAGG+TGG + chr8_1:36891195-36891214 None:intergenic 40.0%
! TCTCTTCAGTGTTTTCAGAC+CGG - chr8_1:36891252-36891271 Msa1191990:intron 40.0%
TCTTGCTCAAAGCAATAACC+GGG + chr8_1:36891620-36891639 None:intergenic 40.0%
AGTCTAGTAGCAACATAACC+GGG + chr8_1:36891682-36891701 None:intergenic 40.0%
CAGTCTAGTAGCAACATAAC+CGG + chr8_1:36891683-36891702 None:intergenic 40.0%
! TCCATATTCCCAGTACTGAA+CGG + chr8_1:36890981-36891000 None:intergenic 40.0%
! TTCAGTACTGGGAATATGGA+TGG - chr8_1:36890981-36891000 Msa1191990:three_prime_UTR 40.0%
!!! TTTTGACTTCAGAACCCATG+TGG - chr8_1:36891085-36891104 Msa1191990:three_prime_UTR 40.0%
TCAGAGAGATATGATTGAGG+TGG + chr8_1:36891195-36891214 None:intergenic 40.0%
! TCTCTTCAGTGTTTTCAGAC+CGG - chr8_1:36891252-36891271 Msa1191990:intron 40.0%
TCTTGCTCAAAGCAATAACC+GGG + chr8_1:36891620-36891639 None:intergenic 40.0%
AGTCTAGTAGCAACATAACC+GGG + chr8_1:36891682-36891701 None:intergenic 40.0%
CAGTCTAGTAGCAACATAAC+CGG + chr8_1:36891683-36891702 None:intergenic 40.0%
! CCATATTCCCAGTACTGAAC+GGG + chr8_1:36890980-36890999 None:intergenic 45.0%
AAAAACCGTACCAAACAGGC+TGG + chr8_1:36891300-36891319 None:intergenic 45.0%
AAATAAGAAACCGAAGGGCG+AGG + chr8_1:36891353-36891372 None:intergenic 45.0%
CTTCTCAGCAATAAACGCGT+CGG + chr8_1:36891439-36891458 None:intergenic 45.0%
TATTGCTGAGAAGCCAGACA+TGG - chr8_1:36891446-36891465 Msa1191990:CDS 45.0%
! CCATATTCCCAGTACTGAAC+GGG + chr8_1:36890980-36890999 None:intergenic 45.0%
AAAAACCGTACCAAACAGGC+TGG + chr8_1:36891300-36891319 None:intergenic 45.0%
AAATAAGAAACCGAAGGGCG+AGG + chr8_1:36891353-36891372 None:intergenic 45.0%
CTTCTCAGCAATAAACGCGT+CGG + chr8_1:36891439-36891458 None:intergenic 45.0%
TATTGCTGAGAAGCCAGACA+TGG - chr8_1:36891446-36891465 Msa1191990:CDS 45.0%
! TTCCCAGTACTGAACGGGTT+GGG + chr8_1:36890975-36890994 None:intergenic 50.0%
! ATTCCCAGTACTGAACGGGT+TGG + chr8_1:36890976-36890995 None:intergenic 50.0%
! CCCGTTCAGTACTGGGAATA+TGG - chr8_1:36890977-36890996 Msa1191990:three_prime_UTR 50.0%
AACCGGAGGGGTAAACAATC+CGG + chr8_1:36891274-36891293 None:intergenic 50.0%
TTCGACCAGCCTGTTTGGTA+CGG - chr8_1:36891292-36891311 Msa1191990:CDS 50.0%
GCTGCTTGTGATTACCAACC+CGG - chr8_1:36891599-36891618 Msa1191990:intron 50.0%
GCTCAAAGCAATAACCGGGT+TGG + chr8_1:36891616-36891635 None:intergenic 50.0%
! TTCCCAGTACTGAACGGGTT+GGG + chr8_1:36890975-36890994 None:intergenic 50.0%
! ATTCCCAGTACTGAACGGGT+TGG + chr8_1:36890976-36890995 None:intergenic 50.0%
! CCCGTTCAGTACTGGGAATA+TGG - chr8_1:36890977-36890996 Msa1191990:three_prime_UTR 50.0%
AACCGGAGGGGTAAACAATC+CGG + chr8_1:36891274-36891293 None:intergenic 50.0%
TTCGACCAGCCTGTTTGGTA+CGG - chr8_1:36891292-36891311 Msa1191990:CDS 50.0%
GCTGCTTGTGATTACCAACC+CGG - chr8_1:36891599-36891618 Msa1191990:intron 50.0%
GCTCAAAGCAATAACCGGGT+TGG + chr8_1:36891616-36891635 None:intergenic 50.0%
TCTCCCAACCCGTTCAGTAC+TGG - chr8_1:36890969-36890988 Msa1191990:three_prime_UTR 55.0%
CTCCCAACCCGTTCAGTACT+GGG - chr8_1:36890970-36890989 Msa1191990:three_prime_UTR 55.0%
GACCGGATTGTTTACCCCTC+CGG - chr8_1:36891269-36891288 Msa1191990:intron 55.0%
! ACCAAACAGGCTGGTCGAAC+CGG + chr8_1:36891291-36891310 None:intergenic 55.0%
TCTCCCAACCCGTTCAGTAC+TGG - chr8_1:36890969-36890988 Msa1191990:three_prime_UTR 55.0%
CTCCCAACCCGTTCAGTACT+GGG - chr8_1:36890970-36890989 Msa1191990:three_prime_UTR 55.0%
GACCGGATTGTTTACCCCTC+CGG - chr8_1:36891269-36891288 Msa1191990:intron 55.0%
! ACCAAACAGGCTGGTCGAAC+CGG + chr8_1:36891291-36891310 None:intergenic 55.0%
! AACAGGCTGGTCGAACCGGA+GGG + chr8_1:36891287-36891306 None:intergenic 60.0%
! AAACAGGCTGGTCGAACCGG+AGG + chr8_1:36891288-36891307 None:intergenic 60.0%
! TCCGGTTCGACCAGCCTGTT+TGG - chr8_1:36891287-36891306 Msa1191990:CDS 60.0%
! AACGCGTCGGTGAACACGCA+AGG + chr8_1:36891426-36891445 None:intergenic 60.0%
! AACAGGCTGGTCGAACCGGA+GGG + chr8_1:36891287-36891306 None:intergenic 60.0%
! AAACAGGCTGGTCGAACCGG+AGG + chr8_1:36891288-36891307 None:intergenic 60.0%
! TCCGGTTCGACCAGCCTGTT+TGG - chr8_1:36891287-36891306 Msa1191990:CDS 60.0%
! AACGCGTCGGTGAACACGCA+AGG + chr8_1:36891426-36891445 None:intergenic 60.0%
! ACAGGCTGGTCGAACCGGAG+GGG + chr8_1:36891286-36891305 None:intergenic 65.0%
! ACAGGCTGGTCGAACCGGAG+GGG + chr8_1:36891286-36891305 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 36890926 36891831 36890926 ID=Msa1191990;Name=Msa1191990
chr8_1 mRNA 36890926 36891831 36890926 ID=Msa1191990-mRNA-1;Parent=Msa1191990;Name=Msa1191990-mRNA-1;_AED=0.21;_eAED=0.21;_QI=0|0.33|0.5|1|1|1|4|242|77
chr8_1 exon 36890926 36891190 36890926 ID=Msa1191990-mRNA-1:exon:12249;Parent=Msa1191990-mRNA-1
chr8_1 exon 36891286 36891366 36891286 ID=Msa1191990-mRNA-1:exon:12248;Parent=Msa1191990-mRNA-1
chr8_1 exon 36891444 36891496 36891444 ID=Msa1191990-mRNA-1:exon:12247;Parent=Msa1191990-mRNA-1
chr8_1 exon 36891755 36891831 36891755 ID=Msa1191990-mRNA-1:exon:12246;Parent=Msa1191990-mRNA-1
chr8_1 CDS 36891755 36891831 36891755 ID=Msa1191990-mRNA-1:cds;Parent=Msa1191990-mRNA-1
chr8_1 CDS 36891444 36891496 36891444 ID=Msa1191990-mRNA-1:cds;Parent=Msa1191990-mRNA-1
chr8_1 CDS 36891286 36891366 36891286 ID=Msa1191990-mRNA-1:cds;Parent=Msa1191990-mRNA-1
chr8_1 CDS 36891168 36891190 36891168 ID=Msa1191990-mRNA-1:cds;Parent=Msa1191990-mRNA-1
chr8_1 three_prime_UTR 36890926 36891167 36890926 ID=Msa1191990-mRNA-1:three_prime_utr;Parent=Msa1191990-mRNA-1
Gene Sequence

>Msa1191990

ATGAACAGAAGTTGCGGCGGAGCGAAACATAGTGAGCGTACTGTCTCCCAACCCGTTCAGTACTGGGAATATGGATGTGTTTTCAGACCGGATTGTTTACCCCTCCGGTTCGACCAGCCTGTTTGGTACGGAGTTGCTAAGAAGAAAAAAGTAGAGAGCAAACCTTGCGTGTTCACCGACGCGTTTATTGCTGAGAAGCCAGACATGGAAAATGTTACTGAGGAGCAAGTGTAG
Protein sequence

>Msa1191990

MNRSCGGAKHSERTVSQPVQYWEYGCVFRPDCLPLRFDQPVWYGVAKKKKVESKPCVFTDAFIAEKPDMENVTEEQV*