AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1013400


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 32 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAAACCCTAGCTGCATCTT+TGG 0.221573 7_1:+19969529 Msa1013400:five_prime_UTR
GCTGCATCTTTGGAAGAATT+AGG 0.286020 7_1:+19969539 Msa1013400:five_prime_UTR
AAACCCTACAGTTTATATTT+CGG 0.332398 7_1:-19970226 None:intergenic
GAAGTGTGACGATGCCTCTT+TGG 0.332537 7_1:-19969648 None:intergenic
CAATGCTTATGCCTGAGTTT+AGG 0.346762 7_1:+19970044 Msa1013400:exon
ACTTGTGACTTGATTTAGTT+TGG 0.352767 7_1:+19970203 Msa1013400:three_prime_UTR
AGTAAAGTGTCGATCTCTAA+TGG 0.363459 7_1:+19969853 Msa1013400:CDS
GTAAAGTGTCGATCTCTAAT+GGG 0.392517 7_1:+19969854 Msa1013400:CDS
CTCTGGTTCCTCAAGAACTT+TGG 0.404366 7_1:-19969783 None:intergenic
TCTTGTGAGCTTTGTAAGAC+TGG 0.419661 7_1:-19969611 None:intergenic
TATGCTTCCTTGCATACCTC+TGG 0.420261 7_1:-19969800 None:intergenic
AAGTGTTTGTTTGAAGTTGA+AGG 0.438744 7_1:+19970169 Msa1013400:three_prime_UTR
AGAGAGATATATATGTGTGT+TGG 0.462365 7_1:-19969503 None:intergenic
TTCTTCCAAAGATGCAGCTA+GGG 0.475876 7_1:-19969534 None:intergenic
ATCGTCACACTTCAACCAAA+GGG 0.488627 7_1:+19969658 Msa1013400:five_prime_UTR
ATGATGAATACATACCCCTT+TGG 0.493133 7_1:-19969673 None:intergenic
AGTGTTTGTTTGAAGTTGAA+GGG 0.501632 7_1:+19970170 Msa1013400:three_prime_UTR
ATTCTTCCAAAGATGCAGCT+AGG 0.530379 7_1:-19969535 None:intergenic
TCTTACAAAGCTCACAAGAA+TGG 0.532217 7_1:+19969615 Msa1013400:five_prime_UTR
GTGTTTGTTTGAAGTTGAAG+GGG 0.550371 7_1:+19970171 Msa1013400:three_prime_UTR
AGAATTGTGTGCCTAAACTC+AGG 0.570831 7_1:-19970055 None:intergenic
GGTTTATCGAATTTCAGAGA+TGG 0.592629 7_1:+19969560 Msa1013400:five_prime_UTR
CATCGTCACACTTCAACCAA+AGG 0.595920 7_1:+19969657 Msa1013400:five_prime_UTR
TGATGCTCAAAATGAGCCGT+GGG 0.596386 7_1:+19970092 Msa1013400:three_prime_UTR
AGATGGATCCAAAGTTCTTG+AGG 0.596761 7_1:+19969775 Msa1013400:intron
TTGATGCTCAAAATGAGCCG+TGG 0.600460 7_1:+19970091 Msa1013400:three_prime_UTR
TGAGGAACCAGAGGTATGCA+AGG 0.624057 7_1:+19969793 Msa1013400:exon
TGTTTGTTTGAAGTTGAAGG+GGG 0.627059 7_1:+19970172 Msa1013400:three_prime_UTR
CAAAGTTCTTGAGGAACCAG+AGG 0.651910 7_1:+19969784 Msa1013400:five_prime_UTR
TTTGTAAGACTGGTTGTGAG+CGG 0.659865 7_1:-19969601 None:intergenic
TAAAGTGTCGATCTCTAATG+GGG 0.672667 7_1:+19969855 Msa1013400:CDS
TCGTCACACTTCAACCAAAG+GGG 0.708509 7_1:+19969659 Msa1013400:five_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGAAAAATATAATCCCA+CGG - chr7_1:19970111-19970130 None:intergenic 20.0%
!!! TATGTTCGAAAGTATTTTGA+TGG + chr7_1:19969937-19969956 Msa1013400:CDS 25.0%
TTGTGATTGATTACTGTAGA+TGG + chr7_1:19969758-19969777 Msa1013400:intron 30.0%
! AGGAAGCATAACAAGAAAAA+TGG + chr7_1:19969813-19969832 Msa1013400:CDS 30.0%
! AGTACTCTGTTAGCATTTTT+GGG + chr7_1:19969983-19970002 Msa1013400:CDS 30.0%
! ATCATTTTCGATTGTGTGAT+TGG + chr7_1:19970135-19970154 Msa1013400:three_prime_UTR 30.0%
! AAGTGTTTGTTTGAAGTTGA+AGG + chr7_1:19970169-19970188 Msa1013400:three_prime_UTR 30.0%
! AGTGTTTGTTTGAAGTTGAA+GGG + chr7_1:19970170-19970189 Msa1013400:three_prime_UTR 30.0%
ACTTGTGACTTGATTTAGTT+TGG + chr7_1:19970203-19970222 Msa1013400:three_prime_UTR 30.0%
GGTTTATCGAATTTCAGAGA+TGG + chr7_1:19969560-19969579 Msa1013400:five_prime_UTR 35.0%
TCTTACAAAGCTCACAAGAA+TGG + chr7_1:19969615-19969634 Msa1013400:five_prime_UTR 35.0%
ATGATGAATACATACCCCTT+TGG - chr7_1:19969676-19969695 None:intergenic 35.0%
!! AGTAAAGTGTCGATCTCTAA+TGG + chr7_1:19969853-19969872 Msa1013400:CDS 35.0%
!! GTAAAGTGTCGATCTCTAAT+GGG + chr7_1:19969854-19969873 Msa1013400:CDS 35.0%
!! TAAAGTGTCGATCTCTAATG+GGG + chr7_1:19969855-19969874 Msa1013400:CDS 35.0%
! CAGTACTCTGTTAGCATTTT+TGG + chr7_1:19969982-19970001 Msa1013400:CDS 35.0%
! GTGTTTGTTTGAAGTTGAAG+GGG + chr7_1:19970171-19970190 Msa1013400:three_prime_UTR 35.0%
! TGTTTGTTTGAAGTTGAAGG+GGG + chr7_1:19970172-19970191 Msa1013400:three_prime_UTR 35.0%
TTCTTCCAAAGATGCAGCTA+GGG - chr7_1:19969537-19969556 None:intergenic 40.0%
ATTCTTCCAAAGATGCAGCT+AGG - chr7_1:19969538-19969557 None:intergenic 40.0%
! GCTGCATCTTTGGAAGAATT+AGG + chr7_1:19969539-19969558 Msa1013400:five_prime_UTR 40.0%
! TTTGTAAGACTGGTTGTGAG+CGG - chr7_1:19969604-19969623 None:intergenic 40.0%
! TCTTGTGAGCTTTGTAAGAC+TGG - chr7_1:19969614-19969633 None:intergenic 40.0%
ATGGCATCAAAAAGCCAAAG+AGG + chr7_1:19969634-19969653 Msa1013400:five_prime_UTR 40.0%
ATCGTCACACTTCAACCAAA+GGG + chr7_1:19969658-19969677 Msa1013400:five_prime_UTR 40.0%
AGATGGATCCAAAGTTCTTG+AGG + chr7_1:19969775-19969794 Msa1013400:intron 40.0%
CAATGCTTATGCCTGAGTTT+AGG + chr7_1:19970044-19970063 Msa1013400:exon 40.0%
AGAATTGTGTGCCTAAACTC+AGG - chr7_1:19970058-19970077 None:intergenic 40.0%
CAAAACCCTAGCTGCATCTT+TGG + chr7_1:19969529-19969548 Msa1013400:five_prime_UTR 45.0%
CATCGTCACACTTCAACCAA+AGG + chr7_1:19969657-19969676 Msa1013400:five_prime_UTR 45.0%
TCGTCACACTTCAACCAAAG+GGG + chr7_1:19969659-19969678 Msa1013400:five_prime_UTR 45.0%
! CTCTGGTTCCTCAAGAACTT+TGG - chr7_1:19969786-19969805 None:intergenic 45.0%
CAAAGTTCTTGAGGAACCAG+AGG + chr7_1:19969784-19969803 Msa1013400:five_prime_UTR 45.0%
TATGCTTCCTTGCATACCTC+TGG - chr7_1:19969803-19969822 None:intergenic 45.0%
TTGATGCTCAAAATGAGCCG+TGG + chr7_1:19970091-19970110 Msa1013400:three_prime_UTR 45.0%
TGATGCTCAAAATGAGCCGT+GGG + chr7_1:19970092-19970111 Msa1013400:three_prime_UTR 45.0%
! TTGTTTGAAGTTGAAGGGGG+AGG + chr7_1:19970175-19970194 Msa1013400:three_prime_UTR 45.0%
! TGTTTGAAGTTGAAGGGGGA+GGG + chr7_1:19970176-19970195 Msa1013400:three_prime_UTR 45.0%
GAAGTGTGACGATGCCTCTT+TGG - chr7_1:19969651-19969670 None:intergenic 50.0%
! TGAGGAACCAGAGGTATGCA+AGG + chr7_1:19969793-19969812 Msa1013400:exon 50.0%
! GTTTGAAGTTGAAGGGGGAG+GGG + chr7_1:19970177-19970196 Msa1013400:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 19969506 19970238 19969506 ID=Msa1013400;Name=Msa1013400
chr7_1 mRNA 19969506 19970238 19969506 ID=Msa1013400-mRNA-1;Parent=Msa1013400;Name=Msa1013400-mRNA-1;_AED=0.34;_eAED=0.34;_QI=206|1|1|1|1|1|2|179|83
chr7_1 exon 19969506 19969680 19969506 ID=Msa1013400-mRNA-1:exon:4817;Parent=Msa1013400-mRNA-1
chr7_1 exon 19969777 19970238 19969777 ID=Msa1013400-mRNA-1:exon:4818;Parent=Msa1013400-mRNA-1
chr7_1 five_prime_UTR 19969506 19969680 19969506 ID=Msa1013400-mRNA-1:five_prime_utr;Parent=Msa1013400-mRNA-1
chr7_1 five_prime_UTR 19969777 19969807 19969777 ID=Msa1013400-mRNA-1:five_prime_utr;Parent=Msa1013400-mRNA-1
chr7_1 CDS 19969808 19970059 19969808 ID=Msa1013400-mRNA-1:cds;Parent=Msa1013400-mRNA-1
chr7_1 three_prime_UTR 19970060 19970238 19970060 ID=Msa1013400-mRNA-1:three_prime_utr;Parent=Msa1013400-mRNA-1
Gene Sequence

>Msa1013400

ATGCAAGGAAGCATAACAAGAAAAATGGTGAAATTGCAGAAGAAGAGTAAAGTGTCGATCTCTAATGGGGCTTTTTGTATTTTGAATCTCAGATTTCTAATTCATGTTATGTATTGTTTATTTCAAATCTATGTTCGAAAGTATTTTGATGGATTATTTAATTTAGAGAAAATGCAGTACTCTGTTAGCATTTTTGGGTTTTCATTTCTGAATATTAAAACTGCTATAGTAATCTTCAATGCTTATGCCTGA

Protein sequence

>Msa1013400

MQGSITRKMVKLQKKSKVSISNGAFCILNLRFLIHVMYCLFQIYVRKYFDGLFNLEKMQYSVSIFGFSFLNIKTAIVIFNAYA*