AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1249870


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 21 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTATAGAATAAACTGATT+TGG 0.312344 8_2:+44983785 Msa1249870:three_prime_UTR
TGACGGGCACGCTGGACTTC+AGG 0.368255 8_2:+44983445 Msa1249870:five_prime_UTR
AAATAGCCCAACCGCAATTC+GGG 0.383989 8_2:+44983394 Msa1249870:five_prime_UTR
TTATGTCAATTATAGGAAAT+GGG 0.391046 8_2:+44983587 Msa1249870:intron
GAAATAGCCCAACCGCAATT+CGG 0.424489 8_2:+44983393 Msa1249870:five_prime_UTR
CATGTTAGTTTATTTGAGGC+TGG 0.445533 8_2:+44983818 Msa1249870:three_prime_UTR
AGTTCATGTTAGTTTATTTG+AGG 0.446503 8_2:+44983814 Msa1249870:three_prime_UTR
TTGAGAACCCGAATTGCGGT+TGG 0.473250 8_2:-44983401 None:intergenic
CTATTAATGCAGTGGATGAC+GGG 0.487601 8_2:+44983429 Msa1249870:five_prime_UTR
GCTATTAATGCAGTGGATGA+CGG 0.498064 8_2:+44983428 Msa1249870:five_prime_UTR
TGAGAACCCGAATTGCGGTT+GGG 0.503855 8_2:-44983400 None:intergenic
AAGAAACAATCAAATGGTGT+AGG 0.506674 8_2:+44983360 Msa1249870:five_prime_UTR
AACCGCAATTCGGGTTCTCA+AGG 0.543466 8_2:+44983403 Msa1249870:five_prime_UTR
AGAAACAATCAAATGGTGTA+GGG 0.550444 8_2:+44983361 Msa1249870:five_prime_UTR
GGCACTGAAGAAGCAAATGA+AGG 0.554741 8_2:+44983635 Msa1249870:CDS
TTTGTTATCAATTTGGGACA+TGG 0.585071 8_2:+44983755 Msa1249870:three_prime_UTR
CAAGGCAGCTATTAATGCAG+TGG 0.600034 8_2:+44983421 Msa1249870:five_prime_UTR
TGCCTTGAGAACCCGAATTG+CGG 0.609132 8_2:-44983405 None:intergenic
GCAGTGGATGACGGGCACGC+TGG 0.611049 8_2:+44983437 Msa1249870:five_prime_UTR
TGTCAATTATAGGAAATGGG+TGG 0.612210 8_2:+44983590 Msa1249870:intron
GCGTCTTCGCTCCATATATG+CGG 0.682881 8_2:-44983663 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAATTTTTGTTATCAATTT+GGG + chr8_2:44983749-44983768 Msa1249870:exon 10.0%
!!! AATTCAACATTGATATTTTA+TGG + chr8_2:44983614-44983633 Msa1249870:exon 15.0%
!! TATTAAACTTAGAAAAATCT+GGG - chr8_2:44983688-44983707 None:intergenic 15.0%
!!! TATAAATGCTTTTGAAATTA+TGG - chr8_2:44983716-44983735 None:intergenic 15.0%
!!! GTTAATTTTTGTTATCAATT+TGG + chr8_2:44983748-44983767 Msa1249870:exon 15.0%
!! TAGAAAAAGAAACAATCAAA+TGG + chr8_2:44983354-44983373 Msa1249870:five_prime_UTR 20.0%
!!! CATTATTAAACTTGTTTTAG+TGG + chr8_2:44983473-44983492 Msa1249870:intron 20.0%
!!! GTTGTTTTTATGTCAATTAT+AGG + chr8_2:44983580-44983599 Msa1249870:intron 20.0%
!! TTTATGTCAATTATAGGAAA+TGG + chr8_2:44983586-44983605 Msa1249870:intron 20.0%
!! TTATGTCAATTATAGGAAAT+GGG + chr8_2:44983587-44983606 Msa1249870:intron 20.0%
!! CTATTAAACTTAGAAAAATC+TGG - chr8_2:44983689-44983708 None:intergenic 20.0%
!! ATCTATAGAATAAACTGATT+TGG + chr8_2:44983785-44983804 Msa1249870:three_prime_UTR 20.0%
!! AGTTCATGTTAGTTTATTTG+AGG + chr8_2:44983814-44983833 Msa1249870:three_prime_UTR 25.0%
AAGAAACAATCAAATGGTGT+AGG + chr8_2:44983360-44983379 Msa1249870:five_prime_UTR 30.0%
AGAAACAATCAAATGGTGTA+GGG + chr8_2:44983361-44983380 Msa1249870:five_prime_UTR 30.0%
TATGCATACATATGCTCTAA+GGG - chr8_2:44983554-44983573 None:intergenic 30.0%
ATATGCATACATATGCTCTA+AGG - chr8_2:44983555-44983574 None:intergenic 30.0%
! TTTGTTATCAATTTGGGACA+TGG + chr8_2:44983755-44983774 Msa1249870:three_prime_UTR 30.0%
! ATTTTTCTGTGTGTATCAGT+CGG + chr8_2:44983900-44983919 Msa1249870:three_prime_UTR 30.0%
TGTCAATTATAGGAAATGGG+TGG + chr8_2:44983590-44983609 Msa1249870:intron 35.0%
TGAAGGAAAAACCGCATATA+TGG + chr8_2:44983652-44983671 Msa1249870:CDS 35.0%
! CATGTTAGTTTATTTGAGGC+TGG + chr8_2:44983818-44983837 Msa1249870:three_prime_UTR 35.0%
GCTATTAATGCAGTGGATGA+CGG + chr8_2:44983428-44983447 Msa1249870:five_prime_UTR 40.0%
CTATTAATGCAGTGGATGAC+GGG + chr8_2:44983429-44983448 Msa1249870:five_prime_UTR 40.0%
!! CATACATATGCTCTAAGGGA+AGG - chr8_2:44983550-44983569 None:intergenic 40.0%
GAAATAGCCCAACCGCAATT+CGG + chr8_2:44983393-44983412 Msa1249870:five_prime_UTR 45.0%
AAATAGCCCAACCGCAATTC+GGG + chr8_2:44983394-44983413 Msa1249870:five_prime_UTR 45.0%
CAAGGCAGCTATTAATGCAG+TGG + chr8_2:44983421-44983440 Msa1249870:five_prime_UTR 45.0%
! GGCACTGAAGAAGCAAATGA+AGG + chr8_2:44983635-44983654 Msa1249870:CDS 45.0%
TGAGAACCCGAATTGCGGTT+GGG - chr8_2:44983403-44983422 None:intergenic 50.0%
TTGAGAACCCGAATTGCGGT+TGG - chr8_2:44983404-44983423 None:intergenic 50.0%
! AACCGCAATTCGGGTTCTCA+AGG + chr8_2:44983403-44983422 Msa1249870:five_prime_UTR 50.0%
TGCCTTGAGAACCCGAATTG+CGG - chr8_2:44983408-44983427 None:intergenic 50.0%
GCGTCTTCGCTCCATATATG+CGG - chr8_2:44983666-44983685 None:intergenic 50.0%
! TGACGGGCACGCTGGACTTC+AGG + chr8_2:44983445-44983464 Msa1249870:five_prime_UTR 65.0%
!! GCAGTGGATGACGGGCACGC+TGG + chr8_2:44983437-44983456 Msa1249870:five_prime_UTR 70.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 44983336 44983939 44983336 ID=Msa1249870;Name=Msa1249870
chr8_2 mRNA 44983336 44983939 44983336 ID=Msa1249870-mRNA-1;Parent=Msa1249870;Name=Msa1249870-mRNA-1;_AED=0.00;_eAED=0.00;_QI=162|1|1|1|1|1|2|187|39
chr8_2 exon 44983336 44983466 44983336 ID=Msa1249870-mRNA-1:exon:13586;Parent=Msa1249870-mRNA-1
chr8_2 exon 44983602 44983939 44983602 ID=Msa1249870-mRNA-1:exon:13587;Parent=Msa1249870-mRNA-1
chr8_2 five_prime_UTR 44983336 44983466 44983336 ID=Msa1249870-mRNA-1:five_prime_utr;Parent=Msa1249870-mRNA-1
chr8_2 five_prime_UTR 44983602 44983632 44983602 ID=Msa1249870-mRNA-1:five_prime_utr;Parent=Msa1249870-mRNA-1
chr8_2 CDS 44983633 44983752 44983633 ID=Msa1249870-mRNA-1:cds;Parent=Msa1249870-mRNA-1
chr8_2 three_prime_UTR 44983753 44983939 44983753 ID=Msa1249870-mRNA-1:three_prime_utr;Parent=Msa1249870-mRNA-1
Gene Sequence

>Msa1249870

ATGGCACTGAAGAAGCAAATGAAGGAAAAACCGCATATATGGAGCGAAGACGCCCAGATTTTTCTAAGTTTAATAGAAGACCATAATTTCAAAAGCATTTATAAATTATATGTAAGTTAA

Protein sequence

>Msa1249870

MALKKQMKEKPHIWSEDAQIFLSLIEDHNFKSIYKLYVS*