AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1082500


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1082500 MtrunA17_Chr8g0368761 65.854 41 14 0 1 41 608 648 1.26e-12 60.8
Msa1082500 MtrunA17_Chr1g0179081 63.415 41 15 0 1 41 596 636 4.14e-12 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCCTGTAGAGGACAACTCTT+AGG 0.312720 7_2:-82581845 Msa1082500:CDS
GGCAAACAAATTCATAAGAT+TGG 0.384625 7_2:-82582497 Msa1082500:CDS
CCGGGGTGGGACAAACAAAC+TGG 0.410782 7_2:+82581809 None:intergenic
GTAGCAGACGTGGAGGAATC+TGG 0.429247 7_2:-82582434 Msa1082500:intron
CCCTAAGAGTTGTCCTCTAC+AGG 0.431074 7_2:+82581844 None:intergenic
CGGTTGCTTTAAACCGACTC+CGG 0.476303 7_2:+82581790 None:intergenic
AATATTGCATGCTTTGTAGC+TGG 0.484095 7_2:-82582518 Msa1082500:CDS
TGTTTGTCCCACCCCGGAGT+CGG 0.489285 7_2:-82581803 Msa1082500:CDS
AAACAAATTCATAAGATTGG+AGG 0.491683 7_2:-82582494 Msa1082500:CDS
GGTTGCTTTAAACCGACTCC+GGG 0.492322 7_2:+82581791 None:intergenic
CCAGTTTGTTTGTCCCACCC+CGG 0.527349 7_2:-82581809 Msa1082500:CDS
CCTGTAGAGGACAACTCTTA+GGG 0.537100 7_2:-82581844 Msa1082500:CDS
CTTTAAACCGACTCCGGGGT+GGG 0.547172 7_2:+82581796 None:intergenic
GCTTTAAACCGACTCCGGGG+TGG 0.559196 7_2:+82581795 None:intergenic
TTTAAAGCAACCGAGAGCTT+AGG 0.568948 7_2:-82581780 None:intergenic
GCTACTTCAACGACTACAGA+AGG 0.610128 7_2:+82582452 None:intergenic
TGTACATGAATAGCCTGTAG+AGG 0.665102 7_2:-82581857 Msa1082500:intron
AGTCGTTGAAGTAGCAGACG+TGG 0.666126 7_2:-82582444 Msa1082500:CDS
CGTTGAAGTAGCAGACGTGG+AGG 0.685057 7_2:-82582441 Msa1082500:CDS
GTTGCTTTAAACCGACTCCG+GGG 0.705236 7_2:+82581792 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATAAAAAAAAAACAGA+AGG + chr7_2:82581922-82581941 None:intergenic 10.0%
!! AGTAATTAAAAAAAAATGAA+AGG - chr7_2:82582276-82582295 Msa1082500:intron 10.0%
!! ATAATAATAAAATGAATAGA+AGG - chr7_2:82582301-82582320 Msa1082500:intron 10.0%
!! AAAAATAAAAAAAAAACAGA+AGG + chr7_2:82581922-82581941 None:intergenic 10.0%
!! AGTAATTAAAAAAAAATGAA+AGG - chr7_2:82582276-82582295 Msa1082500:intron 10.0%
!! ATAATAATAAAATGAATAGA+AGG - chr7_2:82582301-82582320 Msa1082500:intron 10.0%
!! AAGTAATTTGAAAAAATGAA+AGG + chr7_2:82581961-82581980 None:intergenic 15.0%
!! AAGTAATTTGAAAAAATGAA+AGG + chr7_2:82581961-82581980 None:intergenic 15.0%
! AAACAAATTCATAAGATTGG+AGG - chr7_2:82581826-82581845 Msa1082500:CDS 25.0%
! TCATTCATAGAAGTAGTATA+CGG + chr7_2:82582001-82582020 None:intergenic 25.0%
! AATTCAAATGGTACATACAT+TGG + chr7_2:82582080-82582099 None:intergenic 25.0%
! AATGTATGTACCATTTGAAT+TGG - chr7_2:82582079-82582098 Msa1082500:intron 25.0%
! ATATCAAACGAAATCTTACA+GGG + chr7_2:82582207-82582226 None:intergenic 25.0%
! AAACAAATTCATAAGATTGG+AGG - chr7_2:82581826-82581845 Msa1082500:CDS 25.0%
! TCATTCATAGAAGTAGTATA+CGG + chr7_2:82582001-82582020 None:intergenic 25.0%
! AATTCAAATGGTACATACAT+TGG + chr7_2:82582080-82582099 None:intergenic 25.0%
! AATGTATGTACCATTTGAAT+TGG - chr7_2:82582079-82582098 Msa1082500:intron 25.0%
! ATATCAAACGAAATCTTACA+GGG + chr7_2:82582207-82582226 None:intergenic 25.0%
GGCAAACAAATTCATAAGAT+TGG - chr7_2:82581823-82581842 Msa1082500:CDS 30.0%
GACATCAAACTGTATCTTAT+CGG - chr7_2:82582025-82582044 Msa1082500:intron 30.0%
ACATCAAACTGTATCTTATC+GGG - chr7_2:82582026-82582045 Msa1082500:intron 30.0%
TACAAGCTTGATCCAAAAAT+TGG - chr7_2:82582153-82582172 Msa1082500:intron 30.0%
! CCAAGTTATGTACCAATTTT+TGG + chr7_2:82582168-82582187 None:intergenic 30.0%
CCAAAAATTGGTACATAACT+TGG - chr7_2:82582165-82582184 Msa1082500:intron 30.0%
GATATCAAACGAAATCTTAC+AGG + chr7_2:82582208-82582227 None:intergenic 30.0%
TGCAAACAACTTCATAAGAT+TGG + chr7_2:82582400-82582419 None:intergenic 30.0%
GGCAAACAAATTCATAAGAT+TGG - chr7_2:82581823-82581842 Msa1082500:CDS 30.0%
GACATCAAACTGTATCTTAT+CGG - chr7_2:82582025-82582044 Msa1082500:intron 30.0%
ACATCAAACTGTATCTTATC+GGG - chr7_2:82582026-82582045 Msa1082500:intron 30.0%
TACAAGCTTGATCCAAAAAT+TGG - chr7_2:82582153-82582172 Msa1082500:intron 30.0%
! CCAAGTTATGTACCAATTTT+TGG + chr7_2:82582168-82582187 None:intergenic 30.0%
CCAAAAATTGGTACATAACT+TGG - chr7_2:82582165-82582184 Msa1082500:intron 30.0%
GATATCAAACGAAATCTTAC+AGG + chr7_2:82582208-82582227 None:intergenic 30.0%
TGCAAACAACTTCATAAGAT+TGG + chr7_2:82582400-82582419 None:intergenic 30.0%
AATATTGCATGCTTTGTAGC+TGG - chr7_2:82581802-82581821 Msa1082500:CDS 35.0%
! GTTGTTTGTTGCTCATCATA+TGG + chr7_2:82582058-82582077 None:intergenic 35.0%
ACACGATTCACCAATTCAAA+TGG + chr7_2:82582092-82582111 None:intergenic 35.0%
TGAATCGTGTATCAAACAAC+AGG - chr7_2:82582102-82582121 Msa1082500:intron 35.0%
AATCTTACAGGGAATGAATG+AGG + chr7_2:82582196-82582215 None:intergenic 35.0%
AATATTGCATGCTTTGTAGC+TGG - chr7_2:82581802-82581821 Msa1082500:CDS 35.0%
! GTTGTTTGTTGCTCATCATA+TGG + chr7_2:82582058-82582077 None:intergenic 35.0%
ACACGATTCACCAATTCAAA+TGG + chr7_2:82582092-82582111 None:intergenic 35.0%
TGAATCGTGTATCAAACAAC+AGG - chr7_2:82582102-82582121 Msa1082500:intron 35.0%
AATCTTACAGGGAATGAATG+AGG + chr7_2:82582196-82582215 None:intergenic 35.0%
CCATTCATAGACGTAGTAGA+CGG - chr7_2:82582232-82582251 Msa1082500:intron 40.0%
GCTTCTTCAACGACTATAGA+AGG - chr7_2:82582352-82582371 Msa1082500:intron 40.0%
CTACAGGCTATTCATGTACA+GGG + chr7_2:82582463-82582482 None:intergenic 40.0%
TCTACAGGCTATTCATGTAC+AGG + chr7_2:82582464-82582483 None:intergenic 40.0%
TGTACATGAATAGCCTGTAG+AGG - chr7_2:82582463-82582482 Msa1082500:CDS 40.0%
! TTTAAAGCAACCGAGAGCTT+AGG - chr7_2:82582540-82582559 Msa1082500:CDS 40.0%
TTAAAGCAACCGAGAGCTTA+GGG - chr7_2:82582541-82582560 Msa1082500:CDS 40.0%
CCATTCATAGACGTAGTAGA+CGG - chr7_2:82582232-82582251 Msa1082500:intron 40.0%
GCTTCTTCAACGACTATAGA+AGG - chr7_2:82582352-82582371 Msa1082500:intron 40.0%
CTACAGGCTATTCATGTACA+GGG + chr7_2:82582463-82582482 None:intergenic 40.0%
TCTACAGGCTATTCATGTAC+AGG + chr7_2:82582464-82582483 None:intergenic 40.0%
TGTACATGAATAGCCTGTAG+AGG - chr7_2:82582463-82582482 Msa1082500:CDS 40.0%
GCTACTTCAACGACTACAGA+AGG + chr7_2:82581871-82581890 None:intergenic 45.0%
CCGTCTACTACGTCTATGAA+TGG + chr7_2:82582235-82582254 None:intergenic 45.0%
CCTGTAGAGGACAACTCTTA+GGG - chr7_2:82582476-82582495 Msa1082500:CDS 45.0%
GCTACTTCAACGACTACAGA+AGG + chr7_2:82581871-82581890 None:intergenic 45.0%
CCGTCTACTACGTCTATGAA+TGG + chr7_2:82582235-82582254 None:intergenic 45.0%
CCTGTAGAGGACAACTCTTA+GGG - chr7_2:82582476-82582495 Msa1082500:CDS 45.0%
AGTCGTTGAAGTAGCAGACG+TGG - chr7_2:82581876-82581895 Msa1082500:intron 50.0%
GAAGCAGACGTGGAGGAATT+TGG + chr7_2:82582337-82582356 None:intergenic 50.0%
AGTCGTTGAAGAAGCAGACG+TGG + chr7_2:82582347-82582366 None:intergenic 50.0%
GCCTGTAGAGGACAACTCTT+AGG - chr7_2:82582475-82582494 Msa1082500:CDS 50.0%
CCCTAAGAGTTGTCCTCTAC+AGG + chr7_2:82582479-82582498 None:intergenic 50.0%
! GTTGCTTTAAACCGACTCCG+GGG + chr7_2:82582531-82582550 None:intergenic 50.0%
! GGTTGCTTTAAACCGACTCC+GGG + chr7_2:82582532-82582551 None:intergenic 50.0%
! CGGTTGCTTTAAACCGACTC+CGG + chr7_2:82582533-82582552 None:intergenic 50.0%
AGTCGTTGAAGTAGCAGACG+TGG - chr7_2:82581876-82581895 Msa1082500:intron 50.0%
GAAGCAGACGTGGAGGAATT+TGG + chr7_2:82582337-82582356 None:intergenic 50.0%
AGTCGTTGAAGAAGCAGACG+TGG + chr7_2:82582347-82582366 None:intergenic 50.0%
GCCTGTAGAGGACAACTCTT+AGG - chr7_2:82582475-82582494 Msa1082500:CDS 50.0%
CCCTAAGAGTTGTCCTCTAC+AGG + chr7_2:82582479-82582498 None:intergenic 50.0%
! GTTGCTTTAAACCGACTCCG+GGG + chr7_2:82582531-82582550 None:intergenic 50.0%
! GGTTGCTTTAAACCGACTCC+GGG + chr7_2:82582532-82582551 None:intergenic 50.0%
! CGGTTGCTTTAAACCGACTC+CGG + chr7_2:82582533-82582552 None:intergenic 50.0%
CGTTGAAGTAGCAGACGTGG+AGG - chr7_2:82581879-82581898 Msa1082500:intron 55.0%
GTAGCAGACGTGGAGGAATC+TGG - chr7_2:82581886-82581905 Msa1082500:intron 55.0%
CGTTGAAGAAGCAGACGTGG+AGG + chr7_2:82582344-82582363 None:intergenic 55.0%
! CCAGTTTGTTTGTCCCACCC+CGG - chr7_2:82582511-82582530 Msa1082500:CDS 55.0%
! CTTTAAACCGACTCCGGGGT+GGG + chr7_2:82582527-82582546 None:intergenic 55.0%
CGTTGAAGTAGCAGACGTGG+AGG - chr7_2:82581879-82581898 Msa1082500:intron 55.0%
GTAGCAGACGTGGAGGAATC+TGG - chr7_2:82581886-82581905 Msa1082500:intron 55.0%
CGTTGAAGAAGCAGACGTGG+AGG + chr7_2:82582344-82582363 None:intergenic 55.0%
! CCAGTTTGTTTGTCCCACCC+CGG - chr7_2:82582511-82582530 Msa1082500:CDS 55.0%
! CTTTAAACCGACTCCGGGGT+GGG + chr7_2:82582527-82582546 None:intergenic 55.0%
CCGGGGTGGGACAAACAAAC+TGG + chr7_2:82582514-82582533 None:intergenic 60.0%
TGTTTGTCCCACCCCGGAGT+CGG - chr7_2:82582517-82582536 Msa1082500:CDS 60.0%
! GCTTTAAACCGACTCCGGGG+TGG + chr7_2:82582528-82582547 None:intergenic 60.0%
CCGGGGTGGGACAAACAAAC+TGG + chr7_2:82582514-82582533 None:intergenic 60.0%
TGTTTGTCCCACCCCGGAGT+CGG - chr7_2:82582517-82582536 Msa1082500:CDS 60.0%
! GCTTTAAACCGACTCCGGGG+TGG + chr7_2:82582528-82582547 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 82581781 82582561 82581781 ID=Msa1082500;Name=Msa1082500
chr7_2 mRNA 82581781 82582561 82581781 ID=Msa1082500-mRNA-1;Parent=Msa1082500;Name=Msa1082500-mRNA-1;_AED=0.45;_eAED=1.00;_QI=0|0|0|1|0|0|2|0|70
chr7_2 exon 82582435 82582561 82582435 ID=Msa1082500-mRNA-1:exon:21446;Parent=Msa1082500-mRNA-1
chr7_2 exon 82581781 82581866 82581781 ID=Msa1082500-mRNA-1:exon:21445;Parent=Msa1082500-mRNA-1
chr7_2 CDS 82582435 82582561 82582435 ID=Msa1082500-mRNA-1:cds;Parent=Msa1082500-mRNA-1
chr7_2 CDS 82581781 82581866 82581781 ID=Msa1082500-mRNA-1:cds;Parent=Msa1082500-mRNA-1
Gene Sequence

>Msa1082500

GGCGACACAAAGTTCTTAAAGAATATTGCATGCTTTGTAGCTGGCAAACAAATTCATAAGATTGGAGGTTTGAGAGATAATCTCGTTCCTTCTGTAGTCGTTGAAGTAGCAGACGTGGAGGAATCTGCCTGTAGAGGACAACTCTTAGGGAGATACAATGTTCCAGTTTGTTTGTCCCACCCCGGAGTCGGTTTAAAGCAACCGAGAGCTTAG

Protein sequence

>Msa1082500

GDTKFLKNIACFVAGKQIHKIGGLRDNLVPSVVVEVADVEESACRGQLLGRYNVPVCLSHPGVGLKQPRA*