AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0840820


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0840820 MtrunA17_Chr5g0410041 91.538 130 10 1 1 130 570 698 3.96e-70 223
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0840820 AT5G45610.1 50.427 117 57 1 12 128 529 644 2.77e-22 91.3

Find 31 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGCAGCTCATTGTCTGCTT+TGG 0.305196 5_4:+16651889 None:intergenic
TCTCTACCCTATTCTTGAAT+TGG 0.359195 5_4:+16651510 None:intergenic
TTGCTTGCCAATTCAAGAAT+AGG 0.364017 5_4:-16651517 Msa0840820:CDS
TGCTTGCCAATTCAAGAATA+GGG 0.377875 5_4:-16651516 Msa0840820:CDS
CATTCTACGCCGGTAGGAAC+TGG 0.430988 5_4:-16651406 Msa0840820:three_prime_UTR
AATGGCTACTTTGACATTTG+AGG 0.441826 5_4:-16651630 Msa0840820:CDS
AGACTTCATCCCAAGTGATC+TGG 0.477375 5_4:+16651479 None:intergenic
TTGAAATCTTTATGGGCCAT+AGG 0.479672 5_4:-16651985 Msa0840820:exon
AGGAAATGAAAACGAGCAGC+AGG 0.502080 5_4:-16651585 Msa0840820:CDS
GACGCACATACCAGATCACT+TGG 0.519231 5_4:-16651489 Msa0840820:CDS
TACGCGATTTAACAGAAAAG+AGG 0.525701 5_4:-16651655 Msa0840820:CDS
TTTAACAGAAAAGAGGGTAA+TGG 0.527317 5_4:-16651648 Msa0840820:CDS
AGGTCGCAACCAACTTGTCT+CGG 0.537834 5_4:-16651610 Msa0840820:CDS
ATTCAGGACATTTCTTATGC+GGG 0.543878 5_4:-16651735 Msa0840820:intron
ATAACGATGGCAGAATATGA+TGG 0.552624 5_4:+16651677 None:intergenic
CCCATAAAGATTTCAAAACC+AGG 0.555988 5_4:+16651992 None:intergenic
CATTCAGGACATTTCTTATG+CGG 0.556472 5_4:-16651736 Msa0840820:intron
TTATTGCAATAGAAAGCCTA+TGG 0.563884 5_4:+16651969 None:intergenic
GATGGCAGAATATGATGGAC+TGG 0.565546 5_4:+16651682 None:intergenic
TATTCTTGAATTGGCAAGCA+AGG 0.566030 5_4:+16651519 None:intergenic
ATTTAGGCACCAGTTCCTAC+CGG 0.566087 5_4:+16651397 None:intergenic
ACGCGATTTAACAGAAAAGA+GGG 0.567311 5_4:-16651654 Msa0840820:CDS
ATTTCCTTTCCGAGACAAGT+TGG 0.573669 5_4:+16651601 None:intergenic
AAGAAAACAAGGGAATTGGA+AGG 0.578949 5_4:+16651456 None:intergenic
TGTTAAATCGCGTATAACGA+TGG 0.589287 5_4:+16651664 None:intergenic
AAATGAAAACGAGCAGCAGG+AGG 0.599916 5_4:-16651582 Msa0840820:CDS
CGAGCAGCAGGAGGACAGCA+TGG 0.611280 5_4:-16651573 Msa0840820:CDS
GCAACCAACTTGTCTCGGAA+AGG 0.612395 5_4:-16651605 Msa0840820:CDS
ATGTATCATTCTACGCCGGT+AGG 0.655072 5_4:-16651412 Msa0840820:three_prime_UTR
ACGCACATACCAGATCACTT+GGG 0.716433 5_4:-16651488 Msa0840820:CDS
ATGCATGTATCATTCTACGC+CGG 0.732948 5_4:-16651416 Msa0840820:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGTACAGAAAAAGAAAACAA+GGG + chr5_4:16651952-16651971 None:intergenic 25.0%
! ATGTACAGAAAAAGAAAACA+AGG + chr5_4:16651953-16651972 None:intergenic 25.0%
TTATTGCAATAGAAAGCCTA+TGG + chr5_4:16651429-16651448 None:intergenic 30.0%
TTGCTTTAATCACAATGCTA+AGG + chr5_4:16651602-16651621 None:intergenic 30.0%
TTTAACAGAAAAGAGGGTAA+TGG - chr5_4:16651747-16651766 Msa0840820:intron 30.0%
GAAAAAGAAAACAAGGGAAT+TGG + chr5_4:16651946-16651965 None:intergenic 30.0%
TTGAAATCTTTATGGGCCAT+AGG - chr5_4:16651410-16651429 Msa0840820:three_prime_UTR 35.0%
! ATGAGCTGCCAGAAATTTTT+AGG - chr5_4:16651518-16651537 Msa0840820:CDS 35.0%
! TGAGCTGCCAGAAATTTTTA+GGG - chr5_4:16651519-16651538 Msa0840820:CDS 35.0%
TACCTCTCCCTAAAAATTTC+TGG + chr5_4:16651529-16651548 None:intergenic 35.0%
ATCCTGAACAATTTGCATTC+AGG - chr5_4:16651644-16651663 Msa0840820:CDS 35.0%
CATTCAGGACATTTCTTATG+CGG - chr5_4:16651659-16651678 Msa0840820:CDS 35.0%
ATTCAGGACATTTCTTATGC+GGG - chr5_4:16651660-16651679 Msa0840820:CDS 35.0%
ATAACGATGGCAGAATATGA+TGG + chr5_4:16651721-16651740 None:intergenic 35.0%
TGTTAAATCGCGTATAACGA+TGG + chr5_4:16651734-16651753 None:intergenic 35.0%
TACGCGATTTAACAGAAAAG+AGG - chr5_4:16651740-16651759 Msa0840820:intron 35.0%
ACGCGATTTAACAGAAAAGA+GGG - chr5_4:16651741-16651760 Msa0840820:intron 35.0%
! AATGGCTACTTTGACATTTG+AGG - chr5_4:16651765-16651784 Msa0840820:intron 35.0%
TATTCTTGAATTGGCAAGCA+AGG + chr5_4:16651879-16651898 None:intergenic 35.0%
TTGCTTGCCAATTCAAGAAT+AGG - chr5_4:16651878-16651897 Msa0840820:CDS 35.0%
TGCTTGCCAATTCAAGAATA+GGG - chr5_4:16651879-16651898 Msa0840820:CDS 35.0%
TCTCTACCCTATTCTTGAAT+TGG + chr5_4:16651888-16651907 None:intergenic 35.0%
AAGAAAACAAGGGAATTGGA+AGG + chr5_4:16651942-16651961 None:intergenic 35.0%
!! TGCCAGAAATTTTTAGGGAG+AGG - chr5_4:16651524-16651543 Msa0840820:CDS 40.0%
GTCCTGAATGCAAATTGTTC+AGG + chr5_4:16651649-16651668 None:intergenic 40.0%
ATTTCCTTTCCGAGACAAGT+TGG + chr5_4:16651797-16651816 None:intergenic 40.0%
ATGCATGTATCATTCTACGC+CGG - chr5_4:16651979-16651998 Msa0840820:exon 40.0%
!! GATGGCAGAATATGATGGAC+TGG + chr5_4:16651716-16651735 None:intergenic 45.0%
AGGAAATGAAAACGAGCAGC+AGG - chr5_4:16651810-16651829 Msa0840820:intron 45.0%
AAATGAAAACGAGCAGCAGG+AGG - chr5_4:16651813-16651832 Msa0840820:intron 45.0%
ACGCACATACCAGATCACTT+GGG - chr5_4:16651907-16651926 Msa0840820:CDS 45.0%
AGACTTCATCCCAAGTGATC+TGG + chr5_4:16651919-16651938 None:intergenic 45.0%
ATGTATCATTCTACGCCGGT+AGG - chr5_4:16651983-16652002 Msa0840820:exon 45.0%
TGGCAGCTCATTGTCTGCTT+TGG + chr5_4:16651509-16651528 None:intergenic 50.0%
AGGTCGCAACCAACTTGTCT+CGG - chr5_4:16651785-16651804 Msa0840820:intron 50.0%
GCAACCAACTTGTCTCGGAA+AGG - chr5_4:16651790-16651809 Msa0840820:intron 50.0%
GACGCACATACCAGATCACT+TGG - chr5_4:16651906-16651925 Msa0840820:CDS 50.0%
CGAGCAGCAGGAGGACAGCA+TGG - chr5_4:16651822-16651841 Msa0840820:intron 65.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 16651406 16652011 16651406 ID=Msa0840820;Name=Msa0840820
chr5_4 mRNA 16651406 16652011 16651406 ID=Msa0840820-mRNA-1;Parent=Msa0840820;Name=Msa0840820-mRNA-1;_AED=0.05;_eAED=0.05;_QI=15|1|1|1|1|1|2|78|130
chr5_4 exon 16651406 16651751 16651406 ID=Msa0840820-mRNA-1:exon:7177;Parent=Msa0840820-mRNA-1
chr5_4 exon 16651872 16652011 16651872 ID=Msa0840820-mRNA-1:exon:7176;Parent=Msa0840820-mRNA-1
chr5_4 five_prime_UTR 16651997 16652011 16651997 ID=Msa0840820-mRNA-1:five_prime_utr;Parent=Msa0840820-mRNA-1
chr5_4 CDS 16651872 16651996 16651872 ID=Msa0840820-mRNA-1:cds;Parent=Msa0840820-mRNA-1
chr5_4 CDS 16651484 16651751 16651484 ID=Msa0840820-mRNA-1:cds;Parent=Msa0840820-mRNA-1
chr5_4 three_prime_UTR 16651406 16651483 16651406 ID=Msa0840820-mRNA-1:three_prime_utr;Parent=Msa0840820-mRNA-1
Gene Sequence

>Msa0840820

ATGGGCCATAGGCTTTCTATTGCAATAAGTGTAAACTATCTTATGTCAATTTTGCAATTACTGTTATCTGAGAATCTCTTTGAAGCCAAAGCAGACAATGAGCTGCCAGAAATTTTTAGGGAGAGGACATTTCTTATGCGGGAGATATTGATATTACTTAATAGACTAGTATCCAGTCCATCATATTCTGCCATCGTTATACGCGATTTAACAGAAAAGAGGGTAATGGCTACTTTGACATTTGAGGTCGCAACCAACTTGTCTCGGAAAGGAAATGAAAACGAGCAGCAGGAGGACAGCATGGTGAAGCAAATAAGACGAACTGAAATAGTTGACCTTGCTTGCCAATTCAAGAATAGGGTAGAGACGCACATACCAGATCACTTGGGATGA

Protein sequence

>Msa0840820

MGHRLSIAISVNYLMSILQLLLSENLFEAKADNELPEIFRERTFLMREILILLNRLVSSPSYSAIVIRDLTEKRVMATLTFEVATNLSRKGNENEQQEDSMVKQIRRTEIVDLACQFKNRVETHIPDHLG*