AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0009870

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 27 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCTCAATCAATTGAATTA+TGG 0.220514 1_1:-14723223 Msa0009870:three_prime_UTR
CTTGAAAGATTATCGAGTTT+TGG 0.287971 1_1:-14723435 Msa0009870:three_prime_UTR
GACTCCAACTAGCAAATCTT+TGG 0.288947 1_1:-14723568 Msa0009870:CDS
TGTCTCACTCTGCATATAAT+TGG 0.299300 1_1:+14723995 None:intergenic
GTTTCCGTTAATGATTGTTT+TGG 0.312248 1_1:-14723268 Msa0009870:three_prime_UTR
CGAAGTTGCTGCTGCTGATT+CGG 0.386996 1_1:-14723751 Msa0009870:CDS
AATTCCAAAACAATCATTAA+CGG 0.403566 1_1:+14723264 None:intergenic
GCCTAAGCTTGTGCGTGTTA+AGG 0.403824 1_1:-14723480 Msa0009870:exon
GACTCCAACTAGCAAACCTT+TGG 0.409498 1_1:-14723724 Msa0009870:CDS
TGCGGCAACATCATCTTTGT+TGG 0.415154 1_1:+14723605 None:intergenic
TTTCCCAAAGATTTGCTAGT+TGG 0.458073 1_1:+14723564 None:intergenic
ACTCCAACTAGCAAATCTTT+GGG 0.491743 1_1:-14723567 Msa0009870:CDS
GTTGTTGTGCATAGTTCTGA+TGG 0.499773 1_1:-14723663 Msa0009870:CDS
TTTCCCAAAGGTTTGCTAGT+TGG 0.503027 1_1:+14723720 None:intergenic
AAATGAAAGGACAACAGACT+TGG 0.519997 1_1:+14723397 None:intergenic
ACTCCAACTAGCAAACCTTT+GGG 0.520423 1_1:-14723723 Msa0009870:CDS
TAGACTTTACATTTATCCCA+TGG 0.531503 1_1:+14724050 None:intergenic
TGCTACAAAAGAGCTAAAGC+TGG 0.538283 1_1:-14723637 Msa0009870:CDS
ACCTTAACACGCACAAGCTT+AGG 0.546106 1_1:+14723479 None:intergenic
TTTCAAGAGACTTCACTCAT+CGG 0.565680 1_1:+14723451 None:intergenic
CTAGCAAACCTTTGGGAAAG+CGG 0.578566 1_1:-14723716 Msa0009870:CDS
TCAGTAGACCGCTTTCCCAA+AGG 0.587701 1_1:+14723708 None:intergenic
AAAGCGGTCTACTGATAGTG+TGG 0.622760 1_1:-14723700 Msa0009870:CDS
CATGCAGGAAAATATTGAAG+TGG 0.661188 1_1:-14723793 Msa0009870:intron
ACTTTACATTTATCCCATGG+AGG 0.673211 1_1:+14724053 None:intergenic
GTTAGCTTATCAAAATCCTG+TGG 0.715142 1_1:-14723899 Msa0009870:intron
AGTCACAACTGAATCAACTG+CGG 0.772555 1_1:+14723587 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAACAAAACAAAATGAA+AGG + chr1_1:14723882-14723901 None:intergenic 15.0%
!! AAAAAACAAAACAAAATGAA+AGG + chr1_1:14723882-14723901 None:intergenic 15.0%
!! AATTCCAAAACAATCATTAA+CGG + chr1_1:14724002-14724021 None:intergenic 20.0%
!! TTTCTCAATCAATTGAATTA+TGG - chr1_1:14724040-14724059 Msa0009870:five_prime_UTR 20.0%
!! AATTCCAAAACAATCATTAA+CGG + chr1_1:14724002-14724021 None:intergenic 20.0%
!! TTTCTCAATCAATTGAATTA+TGG - chr1_1:14724040-14724059 Msa0009870:five_prime_UTR 20.0%
! GCTCAAAAAAAGAAATCAAA+AGG + chr1_1:14723298-14723317 None:intergenic 25.0%
!!! TTGATTTCTTTTTTTGAGCT+TGG - chr1_1:14723299-14723318 Msa0009870:three_prime_UTR 25.0%
! TGATCAAAAAAATATACCAC+AGG + chr1_1:14723383-14723402 None:intergenic 25.0%
! ATCATTTCTGCAGTTTATAA+AGG - chr1_1:14723399-14723418 Msa0009870:three_prime_UTR 25.0%
! GCTCAAAAAAAGAAATCAAA+AGG + chr1_1:14723298-14723317 None:intergenic 25.0%
!!! TTGATTTCTTTTTTTGAGCT+TGG - chr1_1:14723299-14723318 Msa0009870:three_prime_UTR 25.0%
! TGATCAAAAAAATATACCAC+AGG + chr1_1:14723383-14723402 None:intergenic 25.0%
! ATCATTTCTGCAGTTTATAA+AGG - chr1_1:14723399-14723418 Msa0009870:three_prime_UTR 25.0%
TAGACTTTACATTTATCCCA+TGG + chr1_1:14723216-14723235 None:intergenic 30.0%
! CTTGAAAGATTATCGAGTTT+TGG - chr1_1:14723828-14723847 Msa0009870:intron 30.0%
! GTTTCCGTTAATGATTGTTT+TGG - chr1_1:14723995-14724014 Msa0009870:exon 30.0%
!!! TGGTTTTGTGTTTTGAAAGA+TGG - chr1_1:14724060-14724079 Msa0009870:five_prime_UTR 30.0%
TAGACTTTACATTTATCCCA+TGG + chr1_1:14723216-14723235 None:intergenic 30.0%
! CTTGAAAGATTATCGAGTTT+TGG - chr1_1:14723828-14723847 Msa0009870:intron 30.0%
! GTTTCCGTTAATGATTGTTT+TGG - chr1_1:14723995-14724014 Msa0009870:exon 30.0%
ACTTTACATTTATCCCATGG+AGG + chr1_1:14723213-14723232 None:intergenic 35.0%
TGTCTCACTCTGCATATAAT+TGG + chr1_1:14723271-14723290 None:intergenic 35.0%
! GTTAGCTTATCAAAATCCTG+TGG - chr1_1:14723364-14723383 Msa0009870:three_prime_UTR 35.0%
CATGCAGGAAAATATTGAAG+TGG - chr1_1:14723470-14723489 Msa0009870:three_prime_UTR 35.0%
ACTCCAACTAGCAAATCTTT+GGG - chr1_1:14723696-14723715 Msa0009870:CDS 35.0%
!! TTTCCCAAAGATTTGCTAGT+TGG + chr1_1:14723702-14723721 None:intergenic 35.0%
TTTCAAGAGACTTCACTCAT+CGG + chr1_1:14723815-14723834 None:intergenic 35.0%
AAATGAAAGGACAACAGACT+TGG + chr1_1:14723869-14723888 None:intergenic 35.0%
GCATAAAAACACCATAAGTC+TGG + chr1_1:14723949-14723968 None:intergenic 35.0%
ACTTTACATTTATCCCATGG+AGG + chr1_1:14723213-14723232 None:intergenic 35.0%
TGTCTCACTCTGCATATAAT+TGG + chr1_1:14723271-14723290 None:intergenic 35.0%
! GTTAGCTTATCAAAATCCTG+TGG - chr1_1:14723364-14723383 Msa0009870:three_prime_UTR 35.0%
CATGCAGGAAAATATTGAAG+TGG - chr1_1:14723470-14723489 Msa0009870:three_prime_UTR 35.0%
ACTCCAACTAGCAAATCTTT+GGG - chr1_1:14723696-14723715 Msa0009870:CDS 35.0%
!! TTTCCCAAAGATTTGCTAGT+TGG + chr1_1:14723702-14723721 None:intergenic 35.0%
TTTCAAGAGACTTCACTCAT+CGG + chr1_1:14723815-14723834 None:intergenic 35.0%
AAATGAAAGGACAACAGACT+TGG + chr1_1:14723869-14723888 None:intergenic 35.0%
GCATAAAAACACCATAAGTC+TGG + chr1_1:14723949-14723968 None:intergenic 35.0%
!! ATCACTTTTCTCATGCATGC+AGG - chr1_1:14723455-14723474 Msa0009870:three_prime_UTR 40.0%
ACTCCAACTAGCAAACCTTT+GGG - chr1_1:14723540-14723559 Msa0009870:CDS 40.0%
!! TTTCCCAAAGGTTTGCTAGT+TGG + chr1_1:14723546-14723565 None:intergenic 40.0%
!! GTTGTTGTGCATAGTTCTGA+TGG - chr1_1:14723600-14723619 Msa0009870:CDS 40.0%
TGCTACAAAAGAGCTAAAGC+TGG - chr1_1:14723626-14723645 Msa0009870:CDS 40.0%
AGTCACAACTGAATCAACTG+CGG + chr1_1:14723679-14723698 None:intergenic 40.0%
GACTCCAACTAGCAAATCTT+TGG - chr1_1:14723695-14723714 Msa0009870:CDS 40.0%
!! ATCACTTTTCTCATGCATGC+AGG - chr1_1:14723455-14723474 Msa0009870:three_prime_UTR 40.0%
ACTCCAACTAGCAAACCTTT+GGG - chr1_1:14723540-14723559 Msa0009870:CDS 40.0%
!! TTTCCCAAAGGTTTGCTAGT+TGG + chr1_1:14723546-14723565 None:intergenic 40.0%
!! GTTGTTGTGCATAGTTCTGA+TGG - chr1_1:14723600-14723619 Msa0009870:CDS 40.0%
TGCTACAAAAGAGCTAAAGC+TGG - chr1_1:14723626-14723645 Msa0009870:CDS 40.0%
AGTCACAACTGAATCAACTG+CGG + chr1_1:14723679-14723698 None:intergenic 40.0%
GACTCCAACTAGCAAATCTT+TGG - chr1_1:14723695-14723714 Msa0009870:CDS 40.0%
!!! TTTTGAGCTTGGTAACGACG+AGG - chr1_1:14723310-14723329 Msa0009870:three_prime_UTR 45.0%
GACTCCAACTAGCAAACCTT+TGG - chr1_1:14723539-14723558 Msa0009870:CDS 45.0%
! CTAGCAAACCTTTGGGAAAG+CGG - chr1_1:14723547-14723566 Msa0009870:CDS 45.0%
! AAAGCGGTCTACTGATAGTG+TGG - chr1_1:14723563-14723582 Msa0009870:CDS 45.0%
TGCGGCAACATCATCTTTGT+TGG + chr1_1:14723661-14723680 None:intergenic 45.0%
ACCTTAACACGCACAAGCTT+AGG + chr1_1:14723787-14723806 None:intergenic 45.0%
! TTTTGCTGCTGCCAGACTTA+TGG - chr1_1:14723935-14723954 Msa0009870:CDS 45.0%
!!! TTTTGAGCTTGGTAACGACG+AGG - chr1_1:14723310-14723329 Msa0009870:three_prime_UTR 45.0%
GACTCCAACTAGCAAACCTT+TGG - chr1_1:14723539-14723558 Msa0009870:CDS 45.0%
! CTAGCAAACCTTTGGGAAAG+CGG - chr1_1:14723547-14723566 Msa0009870:CDS 45.0%
! AAAGCGGTCTACTGATAGTG+TGG - chr1_1:14723563-14723582 Msa0009870:CDS 45.0%
TGCGGCAACATCATCTTTGT+TGG + chr1_1:14723661-14723680 None:intergenic 45.0%
ACCTTAACACGCACAAGCTT+AGG + chr1_1:14723787-14723806 None:intergenic 45.0%
! TTTTGCTGCTGCCAGACTTA+TGG - chr1_1:14723935-14723954 Msa0009870:CDS 45.0%
! CGAAGTTGCTGCTGCTGATT+CGG - chr1_1:14723512-14723531 Msa0009870:CDS 50.0%
TCAGTAGACCGCTTTCCCAA+AGG + chr1_1:14723558-14723577 None:intergenic 50.0%
GCCTAAGCTTGTGCGTGTTA+AGG - chr1_1:14723783-14723802 Msa0009870:CDS 50.0%
! CGAAGTTGCTGCTGCTGATT+CGG - chr1_1:14723512-14723531 Msa0009870:CDS 50.0%
TCAGTAGACCGCTTTCCCAA+AGG + chr1_1:14723558-14723577 None:intergenic 50.0%
GCCTAAGCTTGTGCGTGTTA+AGG - chr1_1:14723783-14723802 Msa0009870:CDS 50.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 14723206 14724079 14723206 ID=Msa0009870;Name=Msa0009870
chr1_1 mRNA 14723206 14724079 14723206 ID=Msa0009870-mRNA-1;Parent=Msa0009870;Name=Msa0009870-mRNA-1;_AED=0.38;_eAED=0.38;_QI=84|1|1|1|1|1|2|291|135
chr1_1 exon 14723206 14723808 14723206 ID=Msa0009870-mRNA-1:exon:5475;Parent=Msa0009870-mRNA-1
chr1_1 exon 14723900 14724079 14723900 ID=Msa0009870-mRNA-1:exon:5474;Parent=Msa0009870-mRNA-1
chr1_1 five_prime_UTR 14723996 14724079 14723996 ID=Msa0009870-mRNA-1:five_prime_utr;Parent=Msa0009870-mRNA-1
chr1_1 CDS 14723900 14723995 14723900 ID=Msa0009870-mRNA-1:cds;Parent=Msa0009870-mRNA-1
chr1_1 CDS 14723497 14723808 14723497 ID=Msa0009870-mRNA-1:cds;Parent=Msa0009870-mRNA-1
chr1_1 three_prime_UTR 14723206 14723496 14723206 ID=Msa0009870-mRNA-1:three_prime_utr;Parent=Msa0009870-mRNA-1
Gene Sequence

>Msa0009870

ATGATCCTTTTGATTTCTTTTTTTGAGCTTGGTAACGACGAGGAGAATGCTGCATATGTTGAGACTGTTTATGAGTTAGCTTATCAAAATCCTGTGGAAAATATTGAAGTGGTTGATTCAAGCAACAAAGACGAAGTTGCTGCTGCTGATTCGGTTGTGACTCCAACTAGCAAACCTTTGGGAAAGCGGTCTACTGATAGTGTGGAATTACTTGATGATGTTGTTGTGCATAGTTCTGATGGATCTGCTACAAAAGAGCTAAAGCTGGTTGATTCAACCAACAAAGATGATGTTGCCGCAGTTGATTCAGTTGTGACTCCAACTAGCAAATCTTTGGGAAAGCGATCTGCTGATAGCGTCGAATCAGCAGATGATATTGTTTTGATTGATTGTGACAAAAGAGCCTAA
Protein sequence

>Msa0009870

MILLISFFELGNDEENAAYVETVYELAYQNPVENIEVVDSSNKDEVAAADSVVTPTSKPLGKRSTDSVELLDDVVVHSSDGSATKELKLVDSTNKDDVAAVDSVVTPTSKSLGKRSADSVESADDIVLIDCDKRA*