AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0258850


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0258850 MtrunA17_Chr2g0321571 100.000 107 0 0 1 107 1 107 6.46e-75 216
Msa0258850 MtrunA17_Chr4g0035271 99.065 107 1 0 1 107 1 107 2.02e-74 215
Msa0258850 MtrunA17_Chr6g0455051 75.556 45 2 1 26 70 6 41 1.05e-16 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0258850 AT2G21580.1 91.667 108 8 1 1 107 1 108 2.42e-53 162
Msa0258850 AT4G39200.1 88.889 108 11 1 1 107 1 108 9.22e-52 158
Msa0258850 AT2G21580.2 87.963 108 11 2 1 107 1 107 1.09e-51 158
Msa0258850 AT4G39200.2 87.037 108 12 2 1 107 1 107 4.24e-50 154
Msa0258850 AT4G34555.1 88.785 107 11 1 1 106 1 107 9.74e-50 153
Msa0258850 AT2G16360.1 85.714 105 14 1 2 105 2 106 3.04e-46 144

Find 38 sgRNAs with CRISPR-Local

Find 117 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGAGTGATGAGTTTGTATT+TGG 0.207961 2_2:-55515879 None:intergenic
TGCTTGCCGCAGAGAAGATT+TGG 0.313854 2_2:-55515575 None:intergenic
GAAAGCAAAAGAAGAAGAAA+TGG 0.344636 2_2:+55515774 Msa0258850:CDS
GGGGTTGGTGGTTACCATTA+GGG 0.358777 2_2:-55515614 None:intergenic
CAGTCCTCTCTGATCGTCTC+AGG 0.361688 2_2:+55515903 Msa0258850:CDS
CGCAGAGAAGATTTGGAAGA+AGG 0.369919 2_2:-55515568 None:intergenic
TGATGGCAAGAGGATTGATT+AGG 0.387796 2_2:+55516047 Msa0258850:CDS
TCATCAAAGCCGGCGAAATC+AGG 0.410202 2_2:+55515746 Msa0258850:CDS
GGTGGTGGTGCTGCCTTCTT+CGG 0.414824 2_2:-55515722 None:intergenic
TCGTGCAATCAGAGATTTGA+TGG 0.416147 2_2:+55516030 Msa0258850:CDS
TCATCAACTCCAAACCCTAA+TGG 0.421313 2_2:+55515600 Msa0258850:exon
TGGTGGTTACCATTAGGGTT+TGG 0.424277 2_2:-55515609 None:intergenic
TGAAACCGCCTATGTATTAG+TGG 0.440250 2_2:-55516110 None:intergenic
CTAATACATAGGCGGTTTCA+AGG 0.473470 2_2:+55516113 Msa0258850:exon
AACATGGTCTTGTTTGATCA+AGG 0.477202 2_2:+55515827 Msa0258850:CDS
CAAAGGTAAACAAAAGGAAA+AGG 0.503611 2_2:+55515799 Msa0258850:CDS
TTCAGTGAGAAGCTTATCAT+AGG 0.513766 2_2:-55515852 None:intergenic
GATTTCGCCGGCTTTGATGA+CGG 0.516878 2_2:-55515743 None:intergenic
ATGGAGCAAAGGTAAACAAA+AGG 0.525529 2_2:+55515793 Msa0258850:CDS
ACCACCACCGTCATCAAAGC+CGG 0.527384 2_2:+55515736 Msa0258850:CDS
CACTAGAGCCACTAATACAT+AGG 0.531061 2_2:+55516102 Msa0258850:CDS
TTTGTTGTAGGCACCGAAGA+AGG 0.534954 2_2:+55515709 Msa0258850:intron
GGAGTGATGAGTTTGTATTT+GGG 0.540872 2_2:-55515878 None:intergenic
GCAGAGAAGATTTGGAAGAA+GGG 0.551616 2_2:-55515567 None:intergenic
ATCAGAGATTTGATGGCAAG+AGG 0.560553 2_2:+55516037 Msa0258850:CDS
TTTCCTCCTCCTGATTTCGC+CGG 0.569055 2_2:-55515755 None:intergenic
GCCGGCTTTGATGACGGTGG+TGG 0.569126 2_2:-55515737 None:intergenic
AGACGATCAGAGAGGACTGA+AGG 0.570313 2_2:-55515899 None:intergenic
GGCAAGAGGATTGATTAGGT+TGG 0.587429 2_2:+55516051 Msa0258850:CDS
AGTCCTCTCTGATCGTCTCA+GGG 0.592148 2_2:+55515904 Msa0258850:CDS
AAGAAGAAGAAATGGAGCAA+AGG 0.611863 2_2:+55515782 Msa0258850:CDS
AAGCCGGCGAAATCAGGAGG+AGG 0.614520 2_2:+55515752 Msa0258850:CDS
TCAAAGCCGGCGAAATCAGG+AGG 0.640955 2_2:+55515749 Msa0258850:CDS
AAAGGAAAAGGTTAACAACA+TGG 0.683005 2_2:+55515811 Msa0258850:CDS
CTTCTTCCAAATCTTCTCTG+CGG 0.690277 2_2:+55515569 Msa0258850:five_prime_UTR
TTCGCCGGCTTTGATGACGG+TGG 0.725481 2_2:-55515740 None:intergenic
TAGAGCCACTAATACATAGG+CGG 0.728751 2_2:+55516105 Msa0258850:exon
ATACCCTGAGACGATCAGAG+AGG 0.757534 2_2:-55515907 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTGTTTTTAATTTTATTATG+AGG + chr2_2:55516135-55516154 Msa0258850:three_prime_UTR 15.0%
!!! TATGTTTACATTATTGTTTT+TGG + chr2_2:55516262-55516281 Msa0258850:three_prime_UTR 15.0%
!!! ATGTTTACATTATTGTTTTT+GGG + chr2_2:55516263-55516282 Msa0258850:three_prime_UTR 15.0%
!!! TTGTATAATTGATTTGTTTT+AGG + chr2_2:55516290-55516309 Msa0258850:three_prime_UTR 15.0%
!!! GTGTTTTTAATTTTATTATG+AGG + chr2_2:55516135-55516154 Msa0258850:three_prime_UTR 15.0%
!!! TATGTTTACATTATTGTTTT+TGG + chr2_2:55516262-55516281 Msa0258850:three_prime_UTR 15.0%
!!! ATGTTTACATTATTGTTTTT+GGG + chr2_2:55516263-55516282 Msa0258850:three_prime_UTR 15.0%
!!! TTGTATAATTGATTTGTTTT+AGG + chr2_2:55516290-55516309 Msa0258850:three_prime_UTR 15.0%
!!! TTGTAATGTTTTCAGATTAA+TGG + chr2_2:55515995-55516014 Msa0258850:intron 20.0%
!!! TTGATTTTACTCTAAAGTTT+AGG + chr2_2:55516325-55516344 Msa0258850:three_prime_UTR 20.0%
!!! TTGTAATGTTTTCAGATTAA+TGG + chr2_2:55515995-55516014 Msa0258850:intron 20.0%
!!! TTGATTTTACTCTAAAGTTT+AGG + chr2_2:55516325-55516344 Msa0258850:three_prime_UTR 20.0%
!!! TTTTCAGATTAATGGATCTT+TGG + chr2_2:55516003-55516022 Msa0258850:intron 25.0%
!! TTTTATTATGAGGATGTGTT+TGG + chr2_2:55516145-55516164 Msa0258850:three_prime_UTR 25.0%
!!! TTTTCAGATTAATGGATCTT+TGG + chr2_2:55516003-55516022 Msa0258850:intron 25.0%
!! TTTTATTATGAGGATGTGTT+TGG + chr2_2:55516145-55516164 Msa0258850:three_prime_UTR 25.0%
!! GAATTTGATGATGGAAATTG+GGG - chr2_2:55515636-55515655 None:intergenic 30.0%
!! GGAATTTGATGATGGAAATT+GGG - chr2_2:55515637-55515656 None:intergenic 30.0%
!! AGGAATTTGATGATGGAAAT+TGG - chr2_2:55515638-55515657 None:intergenic 30.0%
TAAGGAAAGGAATTTGATGA+TGG - chr2_2:55515645-55515664 None:intergenic 30.0%
!! ACTTCCATTTTCTTTGTTGT+AGG + chr2_2:55515697-55515716 Msa0258850:intron 30.0%
GAAAGCAAAAGAAGAAGAAA+TGG + chr2_2:55515774-55515793 Msa0258850:CDS 30.0%
CAAAGGTAAACAAAAGGAAA+AGG + chr2_2:55515799-55515818 Msa0258850:CDS 30.0%
AAAGGAAAAGGTTAACAACA+TGG + chr2_2:55515811-55515830 Msa0258850:CDS 30.0%
!!! TTTTACTCTAAAGTTTAGGC+AGG + chr2_2:55516329-55516348 Msa0258850:three_prime_UTR 30.0%
!! GAATTTGATGATGGAAATTG+GGG - chr2_2:55515636-55515655 None:intergenic 30.0%
!! GGAATTTGATGATGGAAATT+GGG - chr2_2:55515637-55515656 None:intergenic 30.0%
!! AGGAATTTGATGATGGAAAT+TGG - chr2_2:55515638-55515657 None:intergenic 30.0%
TAAGGAAAGGAATTTGATGA+TGG - chr2_2:55515645-55515664 None:intergenic 30.0%
!! ACTTCCATTTTCTTTGTTGT+AGG + chr2_2:55515697-55515716 Msa0258850:intron 30.0%
GAAAGCAAAAGAAGAAGAAA+TGG + chr2_2:55515774-55515793 Msa0258850:CDS 30.0%
CAAAGGTAAACAAAAGGAAA+AGG + chr2_2:55515799-55515818 Msa0258850:CDS 30.0%
AAAGGAAAAGGTTAACAACA+TGG + chr2_2:55515811-55515830 Msa0258850:CDS 30.0%
CGAGATTTAGATCTAAGGAA+AGG - chr2_2:55515658-55515677 None:intergenic 35.0%
TGCAACGAGATTTAGATCTA+AGG - chr2_2:55515663-55515682 None:intergenic 35.0%
AAGAAGAAGAAATGGAGCAA+AGG + chr2_2:55515782-55515801 Msa0258850:CDS 35.0%
ATGGAGCAAAGGTAAACAAA+AGG + chr2_2:55515793-55515812 Msa0258850:CDS 35.0%
!! AACATGGTCTTGTTTGATCA+AGG + chr2_2:55515827-55515846 Msa0258850:CDS 35.0%
TTCAGTGAGAAGCTTATCAT+AGG - chr2_2:55515855-55515874 None:intergenic 35.0%
GGAGTGATGAGTTTGTATTT+GGG - chr2_2:55515881-55515900 None:intergenic 35.0%
AGGAGTGATGAGTTTGTATT+TGG - chr2_2:55515882-55515901 None:intergenic 35.0%
CGAGATTTAGATCTAAGGAA+AGG - chr2_2:55515658-55515677 None:intergenic 35.0%
TGCAACGAGATTTAGATCTA+AGG - chr2_2:55515663-55515682 None:intergenic 35.0%
AAGAAGAAGAAATGGAGCAA+AGG + chr2_2:55515782-55515801 Msa0258850:CDS 35.0%
ATGGAGCAAAGGTAAACAAA+AGG + chr2_2:55515793-55515812 Msa0258850:CDS 35.0%
!! AACATGGTCTTGTTTGATCA+AGG + chr2_2:55515827-55515846 Msa0258850:CDS 35.0%
TTCAGTGAGAAGCTTATCAT+AGG - chr2_2:55515855-55515874 None:intergenic 35.0%
GGAGTGATGAGTTTGTATTT+GGG - chr2_2:55515881-55515900 None:intergenic 35.0%
AGGAGTGATGAGTTTGTATT+TGG - chr2_2:55515882-55515901 None:intergenic 35.0%
GCAGAGAAGATTTGGAAGAA+GGG - chr2_2:55515570-55515589 None:intergenic 40.0%
CTTCTTCCAAATCTTCTCTG+CGG + chr2_2:55515569-55515588 Msa0258850:five_prime_UTR 40.0%
TCATCAACTCCAAACCCTAA+TGG + chr2_2:55515600-55515619 Msa0258850:exon 40.0%
!! TTGATGATGGAAATTGGGGT+TGG - chr2_2:55515632-55515651 None:intergenic 40.0%
GGTGCCTACAACAAAGAAAA+TGG - chr2_2:55515704-55515723 None:intergenic 40.0%
GAATTGAATCGAAGCGACAA+AGG - chr2_2:55515958-55515977 None:intergenic 40.0%
TCGTGCAATCAGAGATTTGA+TGG + chr2_2:55516030-55516049 Msa0258850:CDS 40.0%
! ATCAGAGATTTGATGGCAAG+AGG + chr2_2:55516037-55516056 Msa0258850:CDS 40.0%
TGATGGCAAGAGGATTGATT+AGG + chr2_2:55516047-55516066 Msa0258850:CDS 40.0%
CACTAGAGCCACTAATACAT+AGG + chr2_2:55516102-55516121 Msa0258850:CDS 40.0%
TAGAGCCACTAATACATAGG+CGG + chr2_2:55516105-55516124 Msa0258850:exon 40.0%
TGAAACCGCCTATGTATTAG+TGG - chr2_2:55516113-55516132 None:intergenic 40.0%
CTAATACATAGGCGGTTTCA+AGG + chr2_2:55516113-55516132 Msa0258850:exon 40.0%
GCAGAGAAGATTTGGAAGAA+GGG - chr2_2:55515570-55515589 None:intergenic 40.0%
CTTCTTCCAAATCTTCTCTG+CGG + chr2_2:55515569-55515588 Msa0258850:five_prime_UTR 40.0%
TCATCAACTCCAAACCCTAA+TGG + chr2_2:55515600-55515619 Msa0258850:exon 40.0%
!! TTGATGATGGAAATTGGGGT+TGG - chr2_2:55515632-55515651 None:intergenic 40.0%
GGTGCCTACAACAAAGAAAA+TGG - chr2_2:55515704-55515723 None:intergenic 40.0%
GAATTGAATCGAAGCGACAA+AGG - chr2_2:55515958-55515977 None:intergenic 40.0%
TCGTGCAATCAGAGATTTGA+TGG + chr2_2:55516030-55516049 Msa0258850:CDS 40.0%
! ATCAGAGATTTGATGGCAAG+AGG + chr2_2:55516037-55516056 Msa0258850:CDS 40.0%
TGATGGCAAGAGGATTGATT+AGG + chr2_2:55516047-55516066 Msa0258850:CDS 40.0%
CACTAGAGCCACTAATACAT+AGG + chr2_2:55516102-55516121 Msa0258850:CDS 40.0%
TAGAGCCACTAATACATAGG+CGG + chr2_2:55516105-55516124 Msa0258850:exon 40.0%
TGAAACCGCCTATGTATTAG+TGG - chr2_2:55516113-55516132 None:intergenic 40.0%
CTAATACATAGGCGGTTTCA+AGG + chr2_2:55516113-55516132 Msa0258850:exon 40.0%
CGCAGAGAAGATTTGGAAGA+AGG - chr2_2:55515571-55515590 None:intergenic 45.0%
TGGTGGTTACCATTAGGGTT+TGG - chr2_2:55515612-55515631 None:intergenic 45.0%
! ATGATGGAAATTGGGGTTGG+TGG - chr2_2:55515629-55515648 None:intergenic 45.0%
!! TTTGTTGTAGGCACCGAAGA+AGG + chr2_2:55515709-55515728 Msa0258850:intron 45.0%
GGCAAGAGGATTGATTAGGT+TGG + chr2_2:55516051-55516070 Msa0258850:CDS 45.0%
CGCAGAGAAGATTTGGAAGA+AGG - chr2_2:55515571-55515590 None:intergenic 45.0%
TGGTGGTTACCATTAGGGTT+TGG - chr2_2:55515612-55515631 None:intergenic 45.0%
! ATGATGGAAATTGGGGTTGG+TGG - chr2_2:55515629-55515648 None:intergenic 45.0%
!! TTTGTTGTAGGCACCGAAGA+AGG + chr2_2:55515709-55515728 Msa0258850:intron 45.0%
GGCAAGAGGATTGATTAGGT+TGG + chr2_2:55516051-55516070 Msa0258850:CDS 45.0%
TGCTTGCCGCAGAGAAGATT+TGG - chr2_2:55515578-55515597 None:intergenic 50.0%
!! GGGGTTGGTGGTTACCATTA+GGG - chr2_2:55515617-55515636 None:intergenic 50.0%
!! TGGGGTTGGTGGTTACCATT+AGG - chr2_2:55515618-55515637 None:intergenic 50.0%
!! GATTTCGCCGGCTTTGATGA+CGG - chr2_2:55515746-55515765 None:intergenic 50.0%
TCATCAAAGCCGGCGAAATC+AGG + chr2_2:55515746-55515765 Msa0258850:CDS 50.0%
TTTCCTCCTCCTGATTTCGC+CGG - chr2_2:55515758-55515777 None:intergenic 50.0%
AGACGATCAGAGAGGACTGA+AGG - chr2_2:55515902-55515921 None:intergenic 50.0%
AGTCCTCTCTGATCGTCTCA+GGG + chr2_2:55515904-55515923 Msa0258850:CDS 50.0%
ATACCCTGAGACGATCAGAG+AGG - chr2_2:55515910-55515929 None:intergenic 50.0%
TGCTTGCCGCAGAGAAGATT+TGG - chr2_2:55515578-55515597 None:intergenic 50.0%
!! GGGGTTGGTGGTTACCATTA+GGG - chr2_2:55515617-55515636 None:intergenic 50.0%
!! TGGGGTTGGTGGTTACCATT+AGG - chr2_2:55515618-55515637 None:intergenic 50.0%
!! GATTTCGCCGGCTTTGATGA+CGG - chr2_2:55515746-55515765 None:intergenic 50.0%
TCATCAAAGCCGGCGAAATC+AGG + chr2_2:55515746-55515765 Msa0258850:CDS 50.0%
TTTCCTCCTCCTGATTTCGC+CGG - chr2_2:55515758-55515777 None:intergenic 50.0%
AGACGATCAGAGAGGACTGA+AGG - chr2_2:55515902-55515921 None:intergenic 50.0%
AGTCCTCTCTGATCGTCTCA+GGG + chr2_2:55515904-55515923 Msa0258850:CDS 50.0%
ATACCCTGAGACGATCAGAG+AGG - chr2_2:55515910-55515929 None:intergenic 50.0%
ACCACCACCGTCATCAAAGC+CGG + chr2_2:55515736-55515755 Msa0258850:CDS 55.0%
TCAAAGCCGGCGAAATCAGG+AGG + chr2_2:55515749-55515768 Msa0258850:CDS 55.0%
CAGTCCTCTCTGATCGTCTC+AGG + chr2_2:55515903-55515922 Msa0258850:CDS 55.0%
ACCACCACCGTCATCAAAGC+CGG + chr2_2:55515736-55515755 Msa0258850:CDS 55.0%
TCAAAGCCGGCGAAATCAGG+AGG + chr2_2:55515749-55515768 Msa0258850:CDS 55.0%
CAGTCCTCTCTGATCGTCTC+AGG + chr2_2:55515903-55515922 Msa0258850:CDS 55.0%
!! GGTGGTGGTGCTGCCTTCTT+CGG - chr2_2:55515725-55515744 None:intergenic 60.0%
!! TTCGCCGGCTTTGATGACGG+TGG - chr2_2:55515743-55515762 None:intergenic 60.0%
AAGCCGGCGAAATCAGGAGG+AGG + chr2_2:55515752-55515771 Msa0258850:CDS 60.0%
!! GGTGGTGGTGCTGCCTTCTT+CGG - chr2_2:55515725-55515744 None:intergenic 60.0%
!! TTCGCCGGCTTTGATGACGG+TGG - chr2_2:55515743-55515762 None:intergenic 60.0%
AAGCCGGCGAAATCAGGAGG+AGG + chr2_2:55515752-55515771 Msa0258850:CDS 60.0%
!! GCCGGCTTTGATGACGGTGG+TGG - chr2_2:55515740-55515759 None:intergenic 65.0%
!! GCCGGCTTTGATGACGGTGG+TGG - chr2_2:55515740-55515759 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 55515555 55516351 55515555 ID=Msa0258850;Name=Msa0258850
chr2_2 mRNA 55515555 55516351 55515555 ID=Msa0258850-mRNA-1;Parent=Msa0258850;Name=Msa0258850-mRNA-1;_AED=0.06;_eAED=0.06;_QI=64|1|1|1|1|1|3|228|107
chr2_2 exon 55515555 55515621 55515555 ID=Msa0258850-mRNA-1:exon:16785;Parent=Msa0258850-mRNA-1
chr2_2 exon 55515719 55515925 55515719 ID=Msa0258850-mRNA-1:exon:16786;Parent=Msa0258850-mRNA-1
chr2_2 exon 55516010 55516351 55516010 ID=Msa0258850-mRNA-1:exon:16787;Parent=Msa0258850-mRNA-1
chr2_2 five_prime_UTR 55515555 55515618 55515555 ID=Msa0258850-mRNA-1:five_prime_utr;Parent=Msa0258850-mRNA-1
chr2_2 CDS 55515619 55515621 55515619 ID=Msa0258850-mRNA-1:cds;Parent=Msa0258850-mRNA-1
chr2_2 CDS 55515719 55515925 55515719 ID=Msa0258850-mRNA-1:cds;Parent=Msa0258850-mRNA-1
chr2_2 CDS 55516010 55516123 55516010 ID=Msa0258850-mRNA-1:cds;Parent=Msa0258850-mRNA-1
chr2_2 three_prime_UTR 55516124 55516351 55516124 ID=Msa0258850-mRNA-1:three_prime_utr;Parent=Msa0258850-mRNA-1
Gene Sequence

>Msa0258850

ATGGCACCGAAGAAGGCAGCACCACCACCGTCATCAAAGCCGGCGAAATCAGGAGGAGGAAAGCAAAAGAAGAAGAAATGGAGCAAAGGTAAACAAAAGGAAAAGGTTAACAACATGGTCTTGTTTGATCAAGGTACCTATGATAAGCTTCTCACTGAAGCTCCCAAATACAAACTCATCACTCCTTCAGTCCTCTCTGATCGTCTCAGGATTAATGGATCTTTGGCACGTCGTGCAATCAGAGATTTGATGGCAAGAGGATTGATTAGGTTGGTGTCTGCTCATTCTAGTCAGCAGATTTACACTAGAGCCACTAATACATAG

Protein sequence

>Msa0258850

MAPKKAAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQGTYDKLLTEAPKYKLITPSVLSDRLRINGSLARRAIRDLMARGLIRLVSAHSSQQIYTRATNT*