AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1298510


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 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAACCCTAATTTAAAATT+TGG 0.114721 8_3:+59371041 None:intergenic
TAGTTACTATTGAAAATATT+TGG 0.211067 8_3:-59370558 Msa1298510:three_prime_UTR
AAATTAGGGTTTCTGAGATT+TGG 0.249611 8_3:-59371032 Msa1298510:five_prime_UTR
TTGACGTTCTCGGAAGGTTT+TGG 0.276388 8_3:+59370988 None:intergenic
AATTAGGGTTTCTGAGATTT+GGG 0.294104 8_3:-59371031 Msa1298510:five_prime_UTR
AAGAAATAAAACTATTTGTT+AGG 0.306769 8_3:-59370644 Msa1298510:exon
ACAACTCATTTGAGATGATA+AGG 0.388084 8_3:-59371123 Msa1298510:five_prime_UTR
CATAGTATCACTTGTGAGTA+TGG 0.389503 8_3:-59370473 Msa1298510:three_prime_UTR
CTCAGCAATGGGAAGATGAT+TGG 0.389575 8_3:-59370733 Msa1298510:CDS
CAACTCATTTGAGATGATAA+GGG 0.399945 8_3:-59371122 Msa1298510:five_prime_UTR
TCAGCTAAAGAGAGAGTTAG+AGG 0.407568 8_3:-59370678 Msa1298510:CDS
GAGATCAACCTTGACGTTCT+CGG 0.418361 8_3:+59370978 None:intergenic
AGACAAGGAGGAAGGGAGAG+AGG 0.431303 8_3:-59370759 Msa1298510:CDS
TGAAGACGACGACGAGTTCG+AGG 0.463513 8_3:-59370953 Msa1298510:CDS
TCAGCAATGGGAAGATGATT+GGG 0.477084 8_3:-59370732 Msa1298510:CDS
GAACGATTGTGGTTAAACTT+AGG 0.479254 8_3:-59370430 Msa1298510:three_prime_UTR
TGAGATTTGGGTTAATCCAA+TGG 0.503923 8_3:-59371019 Msa1298510:exon
GGAGAGAGGTAGCTCAGCAA+TGG 0.520450 8_3:-59370745 Msa1298510:CDS
GGTTGGGAAGACAAGGAGGA+AGG 0.522923 8_3:-59370767 Msa1298510:CDS
GAGAGAGGTAGCTCAGCAAT+GGG 0.525728 8_3:-59370744 Msa1298510:CDS
GTTGGGAAGACAAGGAGGAA+GGG 0.529450 8_3:-59370766 Msa1298510:CDS
TACACCACATCAAATTGTTG+TGG 0.549280 8_3:-59370496 Msa1298510:three_prime_UTR
ACGATAGTGATATGTCTTCG+AGG 0.550743 8_3:+59371081 None:intergenic
GTATCACTTGTGAGTATGGT+TGG 0.566274 8_3:-59370469 Msa1298510:three_prime_UTR
TCAACCTTGACGTTCTCGGA+AGG 0.583809 8_3:+59370982 None:intergenic
ACTTGCAGGTTGGGAAGACA+AGG 0.596138 8_3:-59370774 Msa1298510:intron
CAGCTAAAGAGAGAGTTAGA+GGG 0.638489 8_3:-59370677 Msa1298510:CDS
GAGGAGTTTGAAATCAACGA+AGG 0.657612 8_3:-59370934 Msa1298510:intron
TGCAGGTTGGGAAGACAAGG+AGG 0.659645 8_3:-59370771 Msa1298510:intron
AAAACCTTCCGAGAACGTCA+AGG 0.660047 8_3:-59370986 Msa1298510:CDS
TATGCCACAACAATTTGATG+TGG 0.714011 8_3:+59370492 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTTCCAAATTTTAAATT+AGG - chr8_3:59370479-59370498 Msa1298510:three_prime_UTR 10.0%
!!! TTTTTCCAAATTTTAAATTA+GGG - chr8_3:59370480-59370499 Msa1298510:three_prime_UTR 10.0%
!!! ATTTTTCCAAATTTTAAATT+AGG - chr8_3:59370479-59370498 Msa1298510:three_prime_UTR 10.0%
!!! TTTTTCCAAATTTTAAATTA+GGG - chr8_3:59370480-59370499 Msa1298510:three_prime_UTR 10.0%
!! AAGAAATAAAACTATTTGTT+AGG - chr8_3:59370882-59370901 Msa1298510:intron 15.0%
!!! AAATATTTTCAATAGTAACT+AGG + chr8_3:59370969-59370988 None:intergenic 15.0%
!! TAGTTACTATTGAAAATATT+TGG - chr8_3:59370968-59370987 Msa1298510:CDS 15.0%
!! AAGAAATAAAACTATTTGTT+AGG - chr8_3:59370882-59370901 Msa1298510:intron 15.0%
!!! AAATATTTTCAATAGTAACT+AGG + chr8_3:59370969-59370988 None:intergenic 15.0%
!! TAGTTACTATTGAAAATATT+TGG - chr8_3:59370968-59370987 Msa1298510:CDS 15.0%
!!! AGAAACCCTAATTTAAAATT+TGG + chr8_3:59370488-59370507 None:intergenic 20.0%
!!! AGTTTTTGAATGTTTTCATT+TGG - chr8_3:59370994-59371013 Msa1298510:CDS 20.0%
!!! AGAAACCCTAATTTAAAATT+TGG + chr8_3:59370488-59370507 None:intergenic 20.0%
!!! AGTTTTTGAATGTTTTCATT+TGG - chr8_3:59370994-59371013 Msa1298510:CDS 20.0%
! TACTAACATGAATTCAAATC+TGG + chr8_3:59370699-59370718 None:intergenic 25.0%
!! TTTTGCATCAAGAAATTTTG+TGG + chr8_3:59370931-59370950 None:intergenic 25.0%
!! TGAATGTTTTCATTTGGATT+TGG - chr8_3:59371000-59371019 Msa1298510:CDS 25.0%
!!! TTTTTTTCTATGAACGATTG+TGG - chr8_3:59371085-59371104 Msa1298510:five_prime_UTR 25.0%
! TACTAACATGAATTCAAATC+TGG + chr8_3:59370699-59370718 None:intergenic 25.0%
!! TTTTGCATCAAGAAATTTTG+TGG + chr8_3:59370931-59370950 None:intergenic 25.0%
!! TGAATGTTTTCATTTGGATT+TGG - chr8_3:59371000-59371019 Msa1298510:CDS 25.0%
!!! TTTTTTTCTATGAACGATTG+TGG - chr8_3:59371085-59371104 Msa1298510:five_prime_UTR 25.0%
! ACAACTCATTTGAGATGATA+AGG - chr8_3:59370403-59370422 Msa1298510:three_prime_UTR 30.0%
! CAACTCATTTGAGATGATAA+GGG - chr8_3:59370404-59370423 Msa1298510:three_prime_UTR 30.0%
!! AAATTAGGGTTTCTGAGATT+TGG - chr8_3:59370494-59370513 Msa1298510:three_prime_UTR 30.0%
!! AATTAGGGTTTCTGAGATTT+GGG - chr8_3:59370495-59370514 Msa1298510:three_prime_UTR 30.0%
AAATTGATTGCAACAACGAT+TGG + chr8_3:59370656-59370675 None:intergenic 30.0%
!!! TTGTTAGGTATTTTAGCTCT+AGG - chr8_3:59370897-59370916 Msa1298510:intron 30.0%
! ACAACTCATTTGAGATGATA+AGG - chr8_3:59370403-59370422 Msa1298510:three_prime_UTR 30.0%
! CAACTCATTTGAGATGATAA+GGG - chr8_3:59370404-59370423 Msa1298510:three_prime_UTR 30.0%
!! AAATTAGGGTTTCTGAGATT+TGG - chr8_3:59370494-59370513 Msa1298510:three_prime_UTR 30.0%
!! AATTAGGGTTTCTGAGATTT+GGG - chr8_3:59370495-59370514 Msa1298510:three_prime_UTR 30.0%
AAATTGATTGCAACAACGAT+TGG + chr8_3:59370656-59370675 None:intergenic 30.0%
!!! TTGTTAGGTATTTTAGCTCT+AGG - chr8_3:59370897-59370916 Msa1298510:intron 30.0%
! TGAGATTTGGGTTAATCCAA+TGG - chr8_3:59370507-59370526 Msa1298510:three_prime_UTR 35.0%
AACAACGATTGGAATGAAGA+GGG + chr8_3:59370645-59370664 None:intergenic 35.0%
! TGCAATCTTATGTAACTTGC+AGG - chr8_3:59370738-59370757 Msa1298510:CDS 35.0%
! ATCTTATGTAACTTGCAGGT+TGG - chr8_3:59370742-59370761 Msa1298510:CDS 35.0%
! TCTTATGTAACTTGCAGGTT+GGG - chr8_3:59370743-59370762 Msa1298510:CDS 35.0%
TACACCACATCAAATTGTTG+TGG - chr8_3:59371030-59371049 Msa1298510:five_prime_UTR 35.0%
TATGCCACAACAATTTGATG+TGG + chr8_3:59371037-59371056 None:intergenic 35.0%
CATAGTATCACTTGTGAGTA+TGG - chr8_3:59371053-59371072 Msa1298510:five_prime_UTR 35.0%
GAACGATTGTGGTTAAACTT+AGG - chr8_3:59371096-59371115 Msa1298510:five_prime_UTR 35.0%
! TGAGATTTGGGTTAATCCAA+TGG - chr8_3:59370507-59370526 Msa1298510:three_prime_UTR 35.0%
AACAACGATTGGAATGAAGA+GGG + chr8_3:59370645-59370664 None:intergenic 35.0%
! TGCAATCTTATGTAACTTGC+AGG - chr8_3:59370738-59370757 Msa1298510:CDS 35.0%
! ATCTTATGTAACTTGCAGGT+TGG - chr8_3:59370742-59370761 Msa1298510:CDS 35.0%
! TCTTATGTAACTTGCAGGTT+GGG - chr8_3:59370743-59370762 Msa1298510:CDS 35.0%
TACACCACATCAAATTGTTG+TGG - chr8_3:59371030-59371049 Msa1298510:five_prime_UTR 35.0%
TATGCCACAACAATTTGATG+TGG + chr8_3:59371037-59371056 None:intergenic 35.0%
CATAGTATCACTTGTGAGTA+TGG - chr8_3:59371053-59371072 Msa1298510:five_prime_UTR 35.0%
GAACGATTGTGGTTAAACTT+AGG - chr8_3:59371096-59371115 Msa1298510:five_prime_UTR 35.0%
ACGATAGTGATATGTCTTCG+AGG + chr8_3:59370448-59370467 None:intergenic 40.0%
! GAGGAGTTTGAAATCAACGA+AGG - chr8_3:59370592-59370611 Msa1298510:three_prime_UTR 40.0%
AATGAAGAGGGGTTAAAGGT+TGG + chr8_3:59370633-59370652 None:intergenic 40.0%
TTGGAATGAAGAGGGGTTAA+AGG + chr8_3:59370637-59370656 None:intergenic 40.0%
ACAACGATTGGAATGAAGAG+GGG + chr8_3:59370644-59370663 None:intergenic 40.0%
CAACAACGATTGGAATGAAG+AGG + chr8_3:59370646-59370665 None:intergenic 40.0%
TCAGCAATGGGAAGATGATT+GGG - chr8_3:59370794-59370813 Msa1298510:intron 40.0%
TCAGCTAAAGAGAGAGTTAG+AGG - chr8_3:59370848-59370867 Msa1298510:intron 40.0%
CAGCTAAAGAGAGAGTTAGA+GGG - chr8_3:59370849-59370868 Msa1298510:intron 40.0%
GTATCACTTGTGAGTATGGT+TGG - chr8_3:59371057-59371076 Msa1298510:five_prime_UTR 40.0%
ACGATAGTGATATGTCTTCG+AGG + chr8_3:59370448-59370467 None:intergenic 40.0%
! GAGGAGTTTGAAATCAACGA+AGG - chr8_3:59370592-59370611 Msa1298510:three_prime_UTR 40.0%
AATGAAGAGGGGTTAAAGGT+TGG + chr8_3:59370633-59370652 None:intergenic 40.0%
TTGGAATGAAGAGGGGTTAA+AGG + chr8_3:59370637-59370656 None:intergenic 40.0%
ACAACGATTGGAATGAAGAG+GGG + chr8_3:59370644-59370663 None:intergenic 40.0%
CAACAACGATTGGAATGAAG+AGG + chr8_3:59370646-59370665 None:intergenic 40.0%
TCAGCAATGGGAAGATGATT+GGG - chr8_3:59370794-59370813 Msa1298510:intron 40.0%
TCAGCTAAAGAGAGAGTTAG+AGG - chr8_3:59370848-59370867 Msa1298510:intron 40.0%
CAGCTAAAGAGAGAGTTAGA+GGG - chr8_3:59370849-59370868 Msa1298510:intron 40.0%
GTATCACTTGTGAGTATGGT+TGG - chr8_3:59371057-59371076 Msa1298510:five_prime_UTR 40.0%
! TTGACGTTCTCGGAAGGTTT+TGG + chr8_3:59370541-59370560 None:intergenic 45.0%
AAAACCTTCCGAGAACGTCA+AGG - chr8_3:59370540-59370559 Msa1298510:three_prime_UTR 45.0%
GAGATCAACCTTGACGTTCT+CGG + chr8_3:59370551-59370570 None:intergenic 45.0%
CTCAGCAATGGGAAGATGAT+TGG - chr8_3:59370793-59370812 Msa1298510:intron 45.0%
! TTGACGTTCTCGGAAGGTTT+TGG + chr8_3:59370541-59370560 None:intergenic 45.0%
AAAACCTTCCGAGAACGTCA+AGG - chr8_3:59370540-59370559 Msa1298510:three_prime_UTR 45.0%
GAGATCAACCTTGACGTTCT+CGG + chr8_3:59370551-59370570 None:intergenic 45.0%
CTCAGCAATGGGAAGATGAT+TGG - chr8_3:59370793-59370812 Msa1298510:intron 45.0%
!!! GTTCTCGGAAGGTTTTGGCT+CGG + chr8_3:59370536-59370555 None:intergenic 50.0%
TCAACCTTGACGTTCTCGGA+AGG + chr8_3:59370547-59370566 None:intergenic 50.0%
! ACTTGCAGGTTGGGAAGACA+AGG - chr8_3:59370752-59370771 Msa1298510:CDS 50.0%
GTTGGGAAGACAAGGAGGAA+GGG - chr8_3:59370760-59370779 Msa1298510:CDS 50.0%
GAGAGAGGTAGCTCAGCAAT+GGG - chr8_3:59370782-59370801 Msa1298510:intron 50.0%
!!! GTTCTCGGAAGGTTTTGGCT+CGG + chr8_3:59370536-59370555 None:intergenic 50.0%
TCAACCTTGACGTTCTCGGA+AGG + chr8_3:59370547-59370566 None:intergenic 50.0%
! ACTTGCAGGTTGGGAAGACA+AGG - chr8_3:59370752-59370771 Msa1298510:CDS 50.0%
GTTGGGAAGACAAGGAGGAA+GGG - chr8_3:59370760-59370779 Msa1298510:CDS 50.0%
GAGAGAGGTAGCTCAGCAAT+GGG - chr8_3:59370782-59370801 Msa1298510:intron 50.0%
!!! GGTTTTGGCTCGGTTGCCAT+TGG + chr8_3:59370526-59370545 None:intergenic 55.0%
TGAAGACGACGACGAGTTCG+AGG - chr8_3:59370573-59370592 Msa1298510:three_prime_UTR 55.0%
! TGCAGGTTGGGAAGACAAGG+AGG - chr8_3:59370755-59370774 Msa1298510:CDS 55.0%
GGTTGGGAAGACAAGGAGGA+AGG - chr8_3:59370759-59370778 Msa1298510:CDS 55.0%
AGACAAGGAGGAAGGGAGAG+AGG - chr8_3:59370767-59370786 Msa1298510:CDS 55.0%
GGAGAGAGGTAGCTCAGCAA+TGG - chr8_3:59370781-59370800 Msa1298510:intron 55.0%
!!! GGTTTTGGCTCGGTTGCCAT+TGG + chr8_3:59370526-59370545 None:intergenic 55.0%
TGAAGACGACGACGAGTTCG+AGG - chr8_3:59370573-59370592 Msa1298510:three_prime_UTR 55.0%
! TGCAGGTTGGGAAGACAAGG+AGG - chr8_3:59370755-59370774 Msa1298510:CDS 55.0%
GGTTGGGAAGACAAGGAGGA+AGG - chr8_3:59370759-59370778 Msa1298510:CDS 55.0%
AGACAAGGAGGAAGGGAGAG+AGG - chr8_3:59370767-59370786 Msa1298510:CDS 55.0%
GGAGAGAGGTAGCTCAGCAA+TGG - chr8_3:59370781-59370800 Msa1298510:intron 55.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 59370401 59371147 59370401 ID=Msa1298510;Name=Msa1298510
chr8_3 mRNA 59370401 59371147 59370401 ID=Msa1298510-mRNA-1;Parent=Msa1298510;Name=Msa1298510-mRNA-1;_AED=0.25;_eAED=0.25;_QI=125|1|1|1|1|1|2|257|72
chr8_3 exon 59370401 59370788 59370401 ID=Msa1298510-mRNA-1:exon:17136;Parent=Msa1298510-mRNA-1
chr8_3 exon 59370935 59371147 59370935 ID=Msa1298510-mRNA-1:exon:17135;Parent=Msa1298510-mRNA-1
chr8_3 five_prime_UTR 59371023 59371147 59371023 ID=Msa1298510-mRNA-1:five_prime_utr;Parent=Msa1298510-mRNA-1
chr8_3 CDS 59370935 59371022 59370935 ID=Msa1298510-mRNA-1:cds;Parent=Msa1298510-mRNA-1
chr8_3 CDS 59370658 59370788 59370658 ID=Msa1298510-mRNA-1:cds;Parent=Msa1298510-mRNA-1
chr8_3 three_prime_UTR 59370401 59370657 59370401 ID=Msa1298510-mRNA-1:three_prime_utr;Parent=Msa1298510-mRNA-1
Gene Sequence

>Msa1298510

ATGGCAACCGAGCCAAAACCTTCCGAGAACGTCAAGGTTGATCTCTTTGAAGACGACGACGAGTTCGAGGAGTTTGAAATCAACGAAGGTTGGGAAGACAAGGAGGAAGGGAGAGAGGTAGCTCAGCAATGGGAAGATGATTGGGATGATGATGATGTTAGTGATGATTTCTCTCTTCAGCTAAAGAGAGAGTTAGAGGGCAATGCTGAGAAGAAATAA

Protein sequence

>Msa1298510

MATEPKPSENVKVDLFEDDDEFEEFEINEGWEDKEEGREVAQQWEDDWDDDDVSDDFSLQLKRELEGNAEKK*