AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0229380


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 31 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAACCCTAATTTAAAATT+TGG 0.114721 2_2:+1072075 None:intergenic
TAGTTACTATTGAAAATATT+TGG 0.211067 2_2:-1071592 Msa0229380:three_prime_UTR
AAATTAGGGTTTCTGAGATT+TGG 0.249611 2_2:-1072066 Msa0229380:five_prime_UTR
TTGACGTTCTCGGAAGGTTT+TGG 0.276388 2_2:+1072022 None:intergenic
AATTAGGGTTTCTGAGATTT+GGG 0.294104 2_2:-1072065 Msa0229380:five_prime_UTR
AAGAAATAAAACTATTTGTT+AGG 0.306769 2_2:-1071678 Msa0229380:exon
ACAACTCATTTGAGATGATA+AGG 0.388084 2_2:-1072157 Msa0229380:five_prime_UTR
CATAGTATCACTTGTGAGTA+TGG 0.389503 2_2:-1071507 Msa0229380:three_prime_UTR
CTCAGCAATGGGAAGATGAT+TGG 0.389575 2_2:-1071767 Msa0229380:CDS
CAACTCATTTGAGATGATAA+GGG 0.399945 2_2:-1072156 Msa0229380:five_prime_UTR
TCAGCTAAAGAGAGAGTTAG+AGG 0.407568 2_2:-1071712 Msa0229380:CDS
GAGATCAACCTTGACGTTCT+CGG 0.418361 2_2:+1072012 None:intergenic
AGACAAGGAGGAAGGGAGAG+AGG 0.431303 2_2:-1071793 Msa0229380:CDS
TGAAGACGACGACGAGTTCG+AGG 0.463513 2_2:-1071987 Msa0229380:CDS
TCAGCAATGGGAAGATGATT+GGG 0.477084 2_2:-1071766 Msa0229380:CDS
GAACGATTGTGGTTAAACTT+AGG 0.479254 2_2:-1071464 Msa0229380:three_prime_UTR
TGAGATTTGGGTTAATCCAA+TGG 0.503923 2_2:-1072053 Msa0229380:exon
GGAGAGAGGTAGCTCAGCAA+TGG 0.520450 2_2:-1071779 Msa0229380:CDS
GGTTGGGAAGACAAGGAGGA+AGG 0.522923 2_2:-1071801 Msa0229380:CDS
GAGAGAGGTAGCTCAGCAAT+GGG 0.525728 2_2:-1071778 Msa0229380:CDS
GTTGGGAAGACAAGGAGGAA+GGG 0.529450 2_2:-1071800 Msa0229380:CDS
TACACCACATCAAATTGTTG+TGG 0.549280 2_2:-1071530 Msa0229380:three_prime_UTR
ACGATAGTGATATGTCTTCG+AGG 0.550743 2_2:+1072115 None:intergenic
GTATCACTTGTGAGTATGGT+TGG 0.566274 2_2:-1071503 Msa0229380:three_prime_UTR
TCAACCTTGACGTTCTCGGA+AGG 0.583809 2_2:+1072016 None:intergenic
ACTTGCAGGTTGGGAAGACA+AGG 0.596138 2_2:-1071808 Msa0229380:intron
CAGCTAAAGAGAGAGTTAGA+GGG 0.638489 2_2:-1071711 Msa0229380:CDS
GAGGAGTTTGAAATCAACGA+AGG 0.657612 2_2:-1071968 Msa0229380:intron
TGCAGGTTGGGAAGACAAGG+AGG 0.659645 2_2:-1071805 Msa0229380:intron
AAAACCTTCCGAGAACGTCA+AGG 0.660047 2_2:-1072020 Msa0229380:CDS
TATGCCACAACAATTTGATG+TGG 0.714011 2_2:+1071526 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTCCAAATTTTAAATT+AGG - chr2_2:1071513-1071532 Msa0229380:three_prime_UTR 10.0%
!!! TTTTTCCAAATTTTAAATTA+GGG - chr2_2:1071514-1071533 Msa0229380:three_prime_UTR 10.0%
!! AAGAAATAAAACTATTTGTT+AGG - chr2_2:1071916-1071935 Msa0229380:intron 15.0%
!!! AAATATTTTCAATAGTAACT+AGG + chr2_2:1072003-1072022 None:intergenic 15.0%
!! TAGTTACTATTGAAAATATT+TGG - chr2_2:1072002-1072021 Msa0229380:CDS 15.0%
!!! AGAAACCCTAATTTAAAATT+TGG + chr2_2:1071522-1071541 None:intergenic 20.0%
!!! AGTTTTTGAATGTTTTCATT+TGG - chr2_2:1072028-1072047 Msa0229380:CDS 20.0%
! TACTAACATGAATTCAAATC+TGG + chr2_2:1071733-1071752 None:intergenic 25.0%
!! TTTTGCATCAAGAAATTTTG+TGG + chr2_2:1071965-1071984 None:intergenic 25.0%
!! TGAATGTTTTCATTTGGATT+TGG - chr2_2:1072034-1072053 Msa0229380:CDS 25.0%
!!! TTTTTTTCTATGAACGATTG+TGG - chr2_2:1072119-1072138 Msa0229380:five_prime_UTR 25.0%
! ACAACTCATTTGAGATGATA+AGG - chr2_2:1071437-1071456 Msa0229380:three_prime_UTR 30.0%
! CAACTCATTTGAGATGATAA+GGG - chr2_2:1071438-1071457 Msa0229380:three_prime_UTR 30.0%
!! AAATTAGGGTTTCTGAGATT+TGG - chr2_2:1071528-1071547 Msa0229380:three_prime_UTR 30.0%
!! AATTAGGGTTTCTGAGATTT+GGG - chr2_2:1071529-1071548 Msa0229380:three_prime_UTR 30.0%
AAATTGATTGCAACAACGAT+TGG + chr2_2:1071690-1071709 None:intergenic 30.0%
!!! TTGTTAGGTATTTTAGCTCT+AGG - chr2_2:1071931-1071950 Msa0229380:intron 30.0%
! TGAGATTTGGGTTAATCCAA+TGG - chr2_2:1071541-1071560 Msa0229380:three_prime_UTR 35.0%
AACAACGATTGGAATGAAGA+GGG + chr2_2:1071679-1071698 None:intergenic 35.0%
! TGCAATCTTATGTAACTTGC+AGG - chr2_2:1071772-1071791 Msa0229380:CDS 35.0%
! ATCTTATGTAACTTGCAGGT+TGG - chr2_2:1071776-1071795 Msa0229380:CDS 35.0%
! TCTTATGTAACTTGCAGGTT+GGG - chr2_2:1071777-1071796 Msa0229380:CDS 35.0%
TACACCACATCAAATTGTTG+TGG - chr2_2:1072064-1072083 Msa0229380:five_prime_UTR 35.0%
TATGCCACAACAATTTGATG+TGG + chr2_2:1072071-1072090 None:intergenic 35.0%
CATAGTATCACTTGTGAGTA+TGG - chr2_2:1072087-1072106 Msa0229380:five_prime_UTR 35.0%
GAACGATTGTGGTTAAACTT+AGG - chr2_2:1072130-1072149 Msa0229380:five_prime_UTR 35.0%
ACGATAGTGATATGTCTTCG+AGG + chr2_2:1071482-1071501 None:intergenic 40.0%
! GAGGAGTTTGAAATCAACGA+AGG - chr2_2:1071626-1071645 Msa0229380:three_prime_UTR 40.0%
AATGAAGAGGGGTTAAAGGT+TGG + chr2_2:1071667-1071686 None:intergenic 40.0%
TTGGAATGAAGAGGGGTTAA+AGG + chr2_2:1071671-1071690 None:intergenic 40.0%
ACAACGATTGGAATGAAGAG+GGG + chr2_2:1071678-1071697 None:intergenic 40.0%
CAACAACGATTGGAATGAAG+AGG + chr2_2:1071680-1071699 None:intergenic 40.0%
TCAGCAATGGGAAGATGATT+GGG - chr2_2:1071828-1071847 Msa0229380:intron 40.0%
TCAGCTAAAGAGAGAGTTAG+AGG - chr2_2:1071882-1071901 Msa0229380:intron 40.0%
CAGCTAAAGAGAGAGTTAGA+GGG - chr2_2:1071883-1071902 Msa0229380:intron 40.0%
GTATCACTTGTGAGTATGGT+TGG - chr2_2:1072091-1072110 Msa0229380:five_prime_UTR 40.0%
! TTGACGTTCTCGGAAGGTTT+TGG + chr2_2:1071575-1071594 None:intergenic 45.0%
AAAACCTTCCGAGAACGTCA+AGG - chr2_2:1071574-1071593 Msa0229380:three_prime_UTR 45.0%
GAGATCAACCTTGACGTTCT+CGG + chr2_2:1071585-1071604 None:intergenic 45.0%
CTCAGCAATGGGAAGATGAT+TGG - chr2_2:1071827-1071846 Msa0229380:intron 45.0%
!!! GTTCTCGGAAGGTTTTGGCT+CGG + chr2_2:1071570-1071589 None:intergenic 50.0%
TCAACCTTGACGTTCTCGGA+AGG + chr2_2:1071581-1071600 None:intergenic 50.0%
! ACTTGCAGGTTGGGAAGACA+AGG - chr2_2:1071786-1071805 Msa0229380:CDS 50.0%
GTTGGGAAGACAAGGAGGAA+GGG - chr2_2:1071794-1071813 Msa0229380:CDS 50.0%
GAGAGAGGTAGCTCAGCAAT+GGG - chr2_2:1071816-1071835 Msa0229380:intron 50.0%
!!! GGTTTTGGCTCGGTTGCCAT+TGG + chr2_2:1071560-1071579 None:intergenic 55.0%
TGAAGACGACGACGAGTTCG+AGG - chr2_2:1071607-1071626 Msa0229380:three_prime_UTR 55.0%
! TGCAGGTTGGGAAGACAAGG+AGG - chr2_2:1071789-1071808 Msa0229380:CDS 55.0%
GGTTGGGAAGACAAGGAGGA+AGG - chr2_2:1071793-1071812 Msa0229380:CDS 55.0%
AGACAAGGAGGAAGGGAGAG+AGG - chr2_2:1071801-1071820 Msa0229380:CDS 55.0%
GGAGAGAGGTAGCTCAGCAA+TGG - chr2_2:1071815-1071834 Msa0229380:intron 55.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 1071435 1072181 1071435 ID=Msa0229380;Name=Msa0229380
chr2_2 mRNA 1071435 1072181 1071435 ID=Msa0229380-mRNA-1;Parent=Msa0229380;Name=Msa0229380-mRNA-1;_AED=0.25;_eAED=0.25;_QI=125|1|1|1|1|1|2|257|72
chr2_2 exon 1071435 1071822 1071435 ID=Msa0229380-mRNA-1:exon:353;Parent=Msa0229380-mRNA-1
chr2_2 exon 1071969 1072181 1071969 ID=Msa0229380-mRNA-1:exon:352;Parent=Msa0229380-mRNA-1
chr2_2 five_prime_UTR 1072057 1072181 1072057 ID=Msa0229380-mRNA-1:five_prime_utr;Parent=Msa0229380-mRNA-1
chr2_2 CDS 1071969 1072056 1071969 ID=Msa0229380-mRNA-1:cds;Parent=Msa0229380-mRNA-1
chr2_2 CDS 1071692 1071822 1071692 ID=Msa0229380-mRNA-1:cds;Parent=Msa0229380-mRNA-1
chr2_2 three_prime_UTR 1071435 1071691 1071435 ID=Msa0229380-mRNA-1:three_prime_utr;Parent=Msa0229380-mRNA-1
Gene Sequence

>Msa0229380

ATGGCAACCGAGCCAAAACCTTCCGAGAACGTCAAGGTTGATCTCTTTGAAGACGACGACGAGTTCGAGGAGTTTGAAATCAACGAAGGTTGGGAAGACAAGGAGGAAGGGAGAGAGGTAGCTCAGCAATGGGAAGATGATTGGGATGATGATGATGTTAGTGATGATTTCTCTCTTCAGCTAAAGAGAGAGTTAGAGGGCAATGCTGAGAAGAAATAA

Protein sequence

>Msa0229380

MATEPKPSENVKVDLFEDDDEFEEFEINEGWEDKEEGREVAQQWEDDWDDDDVSDDFSLQLKRELEGNAEKK*