AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1204120


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1204120 MtrunA17_Chr4g0063301 96.262 107 4 0 1 107 1 107 7.81e-74 214
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1204120 AT1G75125.1 60.638 94 37 0 13 106 11 104 1.20e-39 128

Find 30 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTGGAAATCGCCTTGGAAT+TGG 0.320897 8_1:-59643501 None:intergenic
AATCATCACAGTCTAAATTA+AGG 0.339781 8_1:-59644040 None:intergenic
GTCCTACTTGCGATGGAAAC+AGG 0.354255 8_1:+59643843 Msa1204120:CDS
ACTTTGTGTCCGAGAATAAA+CGG 0.396004 8_1:+59643604 Msa1204120:CDS
AATCTTTACCCGTTTATTCT+CGG 0.396090 8_1:-59643613 None:intergenic
CGATTTCCAACATGGATTAC+CGG 0.398072 8_1:+59643513 Msa1204120:CDS
ACAACGTTGTCTGAATTGTC+TGG 0.418889 8_1:+59643984 Msa1204120:CDS
ACACATGGGTTAATTGCAAC+AGG 0.458488 8_1:-59643818 None:intergenic
CTTTGTGTCCGAGAATAAAC+GGG 0.475435 8_1:+59643605 Msa1204120:CDS
TGTCTGAATTGTCTGGGAAA+AGG 0.496121 8_1:+59643991 Msa1204120:CDS
TTCCAAGGCGATTTCCAACA+TGG 0.513408 8_1:+59643505 Msa1204120:CDS
ATCCATGTTGGAAATCGCCT+TGG 0.531843 8_1:-59643507 None:intergenic
ATATATGCAAGTTATGCAGC+GGG 0.546291 8_1:+59643762 Msa1204120:CDS
TGTAAAAGTTGTAGAGGGAA+AGG 0.556567 8_1:+59643734 Msa1204120:CDS
GTAAAAGTTGTAGAGGGAAA+GGG 0.562827 8_1:+59643735 Msa1204120:CDS
CAACGTTGTCTGAATTGTCT+GGG 0.565752 8_1:+59643985 Msa1204120:CDS
GCGGGAATTCAACCATAGCT+TGG 0.577529 8_1:+59643780 Msa1204120:CDS
CCCCAGTATTACAAAAGCAC+CGG 0.584681 8_1:-59643532 None:intergenic
AAAGCACCGGTAATCCATGT+TGG 0.590454 8_1:-59643519 None:intergenic
TGTGTTTGTCCTACTTGCGA+TGG 0.598415 8_1:+59643836 Msa1204120:CDS
TTGCCGTGTAAAAGTTGTAG+AGG 0.598560 8_1:+59643728 Msa1204120:CDS
ATTGCAACAGGATCATACAT+TGG 0.599710 8_1:-59643806 None:intergenic
AAGAAATGAATCCAATTCCA+AGG 0.602574 8_1:+59643490 Msa1204120:exon
ATACATTGGAGACCAAGCTA+TGG 0.629079 8_1:-59643792 None:intergenic
TCGCAAGTAGGACAAACACA+TGG 0.629902 8_1:-59643833 None:intergenic
GGGAATTGCAACTCTGAACG+TGG 0.644672 8_1:+59643554 Msa1204120:CDS
TATATATGCAAGTTATGCAG+CGG 0.648101 8_1:+59643761 Msa1204120:CDS
TGCCGTGTAAAAGTTGTAGA+GGG 0.654823 8_1:+59643729 Msa1204120:CDS
CGCAAGTAGGACAAACACAT+GGG 0.656170 8_1:-59643832 None:intergenic
AACCTGTTTCCATCGCAAGT+AGG 0.668457 8_1:-59643845 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTGCTTTCATTTGAATAT+TGG + chr8_1:59643894-59643913 Msa1204120:intron 20.0%
!! TTTGCTTTCATTTGAATATT+GGG + chr8_1:59643895-59643914 Msa1204120:intron 20.0%
!! GAAATTATAGTAACTGATAA+TGG + chr8_1:59643947-59643966 Msa1204120:intron 20.0%
!! TTTTCTATGTCACGTATTTT+GGG + chr8_1:59643408-59643427 Msa1204120:five_prime_UTR 25.0%
!! TAAATTGTCTCTGAGAAAAA+AGG + chr8_1:59643457-59643476 Msa1204120:five_prime_UTR 25.0%
! TTGCTTTCATTTGAATATTG+GGG + chr8_1:59643896-59643915 Msa1204120:intron 25.0%
! AATCATCACAGTCTAAATTA+AGG - chr8_1:59644043-59644062 None:intergenic 25.0%
!!! TGATTATTTTAGTGCTTATG+AGG + chr8_1:59644058-59644077 Msa1204120:three_prime_UTR 25.0%
! GTTTTCTATGTCACGTATTT+TGG + chr8_1:59643407-59643426 Msa1204120:five_prime_UTR 30.0%
AAGAAATGAATCCAATTCCA+AGG + chr8_1:59643490-59643509 Msa1204120:exon 30.0%
AATCTTTACCCGTTTATTCT+CGG - chr8_1:59643616-59643635 None:intergenic 30.0%
GATAATATTGATGTGCTTTC+TGG + chr8_1:59643672-59643691 Msa1204120:intron 30.0%
TATATATGCAAGTTATGCAG+CGG + chr8_1:59643761-59643780 Msa1204120:CDS 30.0%
TGTCTTGAAATTGAATTGCA+AGG + chr8_1:59643925-59643944 Msa1204120:intron 30.0%
!! TTCGTTGTCAACTTTTTCTT+TGG + chr8_1:59644089-59644108 Msa1204120:three_prime_UTR 30.0%
ACTTTGTGTCCGAGAATAAA+CGG + chr8_1:59643604-59643623 Msa1204120:CDS 35.0%
! TTGATGTGCTTTCTGGAAAT+TGG + chr8_1:59643679-59643698 Msa1204120:intron 35.0%
! TTCCCTCTACAACTTTTACA+CGG - chr8_1:59643734-59643753 None:intergenic 35.0%
TGTAAAAGTTGTAGAGGGAA+AGG + chr8_1:59643734-59643753 Msa1204120:CDS 35.0%
GTAAAAGTTGTAGAGGGAAA+GGG + chr8_1:59643735-59643754 Msa1204120:CDS 35.0%
ATATATGCAAGTTATGCAGC+GGG + chr8_1:59643762-59643781 Msa1204120:CDS 35.0%
ATTGCAACAGGATCATACAT+TGG - chr8_1:59643809-59643828 None:intergenic 35.0%
!!! ACTGATAATGGTTTTGTTGC+AGG + chr8_1:59643959-59643978 Msa1204120:intron 35.0%
!!! CTGATAATGGTTTTGTTGCA+GGG + chr8_1:59643960-59643979 Msa1204120:intron 35.0%
! CGATTTCCAACATGGATTAC+CGG + chr8_1:59643513-59643532 Msa1204120:CDS 40.0%
! TACCGGTGCTTTTGTAATAC+TGG + chr8_1:59643530-59643549 Msa1204120:CDS 40.0%
! ACCGGTGCTTTTGTAATACT+GGG + chr8_1:59643531-59643550 Msa1204120:CDS 40.0%
CTTTGTGTCCGAGAATAAAC+GGG + chr8_1:59643605-59643624 Msa1204120:CDS 40.0%
TTGCCGTGTAAAAGTTGTAG+AGG + chr8_1:59643728-59643747 Msa1204120:CDS 40.0%
TGCCGTGTAAAAGTTGTAGA+GGG + chr8_1:59643729-59643748 Msa1204120:CDS 40.0%
ATACATTGGAGACCAAGCTA+TGG - chr8_1:59643795-59643814 None:intergenic 40.0%
! ACACATGGGTTAATTGCAAC+AGG - chr8_1:59643821-59643840 None:intergenic 40.0%
ACAACGTTGTCTGAATTGTC+TGG + chr8_1:59643984-59644003 Msa1204120:CDS 40.0%
CAACGTTGTCTGAATTGTCT+GGG + chr8_1:59643985-59644004 Msa1204120:CDS 40.0%
TGTCTGAATTGTCTGGGAAA+AGG + chr8_1:59643991-59644010 Msa1204120:CDS 40.0%
GTTGGAAATCGCCTTGGAAT+TGG - chr8_1:59643504-59643523 None:intergenic 45.0%
TTCCAAGGCGATTTCCAACA+TGG + chr8_1:59643505-59643524 Msa1204120:CDS 45.0%
ATCCATGTTGGAAATCGCCT+TGG - chr8_1:59643510-59643529 None:intergenic 45.0%
!! AAAGCACCGGTAATCCATGT+TGG - chr8_1:59643522-59643541 None:intergenic 45.0%
! CCCCAGTATTACAAAAGCAC+CGG - chr8_1:59643535-59643554 None:intergenic 45.0%
! CCGGTGCTTTTGTAATACTG+GGG + chr8_1:59643532-59643551 Msa1204120:CDS 45.0%
! CGGTGCTTTTGTAATACTGG+GGG + chr8_1:59643533-59643552 Msa1204120:CDS 45.0%
! GGTGCTTTTGTAATACTGGG+GGG + chr8_1:59643534-59643553 Msa1204120:CDS 45.0%
CGCAAGTAGGACAAACACAT+GGG - chr8_1:59643835-59643854 None:intergenic 45.0%
TCGCAAGTAGGACAAACACA+TGG - chr8_1:59643836-59643855 None:intergenic 45.0%
TGTGTTTGTCCTACTTGCGA+TGG + chr8_1:59643836-59643855 Msa1204120:CDS 45.0%
AACCTGTTTCCATCGCAAGT+AGG - chr8_1:59643848-59643867 None:intergenic 45.0%
GGGAATTGCAACTCTGAACG+TGG + chr8_1:59643554-59643573 Msa1204120:CDS 50.0%
GCGGGAATTCAACCATAGCT+TGG + chr8_1:59643780-59643799 Msa1204120:CDS 50.0%
GTCCTACTTGCGATGGAAAC+AGG + chr8_1:59643843-59643862 Msa1204120:CDS 50.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 59643407 59644151 59643407 ID=Msa1204120;Name=Msa1204120
chr8_1 mRNA 59643407 59644151 59643407 ID=Msa1204120-mRNA-1;Parent=Msa1204120;Name=Msa1204120-mRNA-1;_AED=0.09;_eAED=0.09;_QI=88|1|1|1|1|1|3|128|107
chr8_1 exon 59643407 59643626 59643407 ID=Msa1204120-mRNA-1:exon:19264;Parent=Msa1204120-mRNA-1
chr8_1 exon 59643716 59643864 59643716 ID=Msa1204120-mRNA-1:exon:19265;Parent=Msa1204120-mRNA-1
chr8_1 exon 59643981 59644151 59643981 ID=Msa1204120-mRNA-1:exon:19266;Parent=Msa1204120-mRNA-1
chr8_1 five_prime_UTR 59643407 59643494 59643407 ID=Msa1204120-mRNA-1:five_prime_utr;Parent=Msa1204120-mRNA-1
chr8_1 CDS 59643495 59643626 59643495 ID=Msa1204120-mRNA-1:cds;Parent=Msa1204120-mRNA-1
chr8_1 CDS 59643716 59643864 59643716 ID=Msa1204120-mRNA-1:cds;Parent=Msa1204120-mRNA-1
chr8_1 CDS 59643981 59644023 59643981 ID=Msa1204120-mRNA-1:cds;Parent=Msa1204120-mRNA-1
chr8_1 three_prime_UTR 59644024 59644151 59644024 ID=Msa1204120-mRNA-1:three_prime_utr;Parent=Msa1204120-mRNA-1
Gene Sequence

>Msa1204120

ATGAATCCAATTCCAAGGCGATTTCCAACATGGATTACCGGTGCTTTTGTAATACTGGGGGGAATTGCAACTCTGAACGTGGCTTCTACACTTACACTCAAAACACTTCACTTTGTGTCCGAGAATAAACGGAAAAAAACAGCGTTGCCGTGTAAAAGTTGTAGAGGGAAAGGGTTTTATATATGCAAGTTATGCAGCGGGAATTCAACCATAGCTTGGTCTCCAATGTATGATCCTGTTGCAATTAACCCATGTGTTTGTCCTACTTGCGATGGAAACAGGGTACAACGTTGTCTGAATTGTCTGGGAAAAGGCTATGACTAA

Protein sequence

>Msa1204120

MNPIPRRFPTWITGAFVILGGIATLNVASTLTLKTLHFVSENKRKKTALPCKSCRGKGFYICKLCSGNSTIAWSPMYDPVAINPCVCPTCDGNRVQRCLNCLGKGYD*