AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1169270

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1169270 MtrunA17_Chr7g0263831 92.857 84 6 0 1 84 1 84 1.03e-29 100
Msa1169270 MtrunA17_Chr7g0263871 89.474 76 3 1 9 84 3 73 1.59e-16 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1169270 AT2G37120.1 78.689 61 13 0 24 84 16 76 6.03e-15 63.5
Msa1169270 AT3G53370.1 80.000 60 12 0 25 84 17 76 7.50e-13 58.2

Find 35 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAATAGTTCTCCTGGTTAT+TGG 0.281375 7_4:-62206572 Msa1169270:CDS
TTATGTAAGTATAATCAATT+AGG 0.364072 7_4:+62206225 None:intergenic
CAATGGACTCAAATGTTCTA+TGG 0.367098 7_4:-62206398 Msa1169270:three_prime_UTR
ACAAACCGTGGTGCAAACTT+TGG 0.386650 7_4:-62207026 Msa1169270:five_prime_UTR
GTTTAGAAAGCTGGATCTCT+AGG 0.416187 7_4:-62206608 Msa1169270:intron
TGGGGAAATGTTTAGAAAGC+TGG 0.417081 7_4:-62206617 Msa1169270:intron
GTCTCTGCACCTGGAGAGTA+GGG 0.431630 7_4:-62206422 Msa1169270:exon
TACTTTAGCAATATATTTCG+TGG 0.434438 7_4:-62206268 Msa1169270:three_prime_UTR
GTCCATTGCCCCTACTCTCC+AGG 0.446840 7_4:+62206413 None:intergenic
ATGGCCGATGACTTTGAATT+CGG 0.448197 7_4:-62206956 Msa1169270:CDS
ACCAGGAGAACTATTAAGCC+TGG 0.450176 7_4:+62206578 None:intergenic
TTGCTGTTGACATTCCTCAT+AGG 0.463310 7_4:-62206545 Msa1169270:CDS
CCCAGGCTTAATAGTTCTCC+TGG 0.470539 7_4:-62206579 Msa1169270:CDS
ATAGTTCTCCTGGTTATTGG+TGG 0.478741 7_4:-62206569 Msa1169270:CDS
TCCTCCTTCCTTTGATCGCA+TGG 0.481901 7_4:-62206924 Msa1169270:intron
TAGTTCTCCTGGTTATTGGT+GGG 0.495632 7_4:-62206568 Msa1169270:CDS
AAGCAAGGAGTCTCTGCACC+TGG 0.523372 7_4:-62206431 Msa1169270:CDS
AGTCTCTGCACCTGGAGAGT+AGG 0.526480 7_4:-62206423 Msa1169270:exon
GAAGAGTACCATGCGATCAA+AGG 0.548062 7_4:+62206916 None:intergenic
TTTAGAAAGCTGGATCTCTA+GGG 0.566106 7_4:-62206607 Msa1169270:intron
GAATTCAAAGTCATCGGCCA+TGG 0.568004 7_4:+62206958 None:intergenic
CACCTGGAGAGTAGGGGCAA+TGG 0.575695 7_4:-62206415 Msa1169270:exon
ATCACTCACATCTTCAACCA+TGG 0.576797 7_4:-62206975 Msa1169270:exon
AGAGTGCATAATTTCCTATG+AGG 0.578802 7_4:+62206531 None:intergenic
ATCACCGAATTCAAAGTCAT+CGG 0.579370 7_4:+62206952 None:intergenic
CCAGGAGAACTATTAAGCCT+GGG 0.597197 7_4:+62206579 None:intergenic
CTCAAATGTTCTATGGAATG+TGG 0.598269 7_4:-62206391 Msa1169270:three_prime_UTR
ACAGCAACCCACCAATAACC+AGG 0.598951 7_4:+62206561 None:intergenic
AGTACCATGCGATCAAAGGA+AGG 0.619049 7_4:+62206920 None:intergenic
CGAATCCAAAGTTTGCACCA+CGG 0.626371 7_4:+62207021 None:intergenic
AATCTATTTAAAACAAACCG+TGG 0.654277 7_4:-62207038 Msa1169270:five_prime_UTR
GGATCTCTAGGGTTCAACCC+AGG 0.683092 7_4:-62206596 Msa1169270:CDS
ACCATGCGATCAAAGGAAGG+AGG 0.683503 7_4:+62206923 None:intergenic
TCTCTGCACCTGGAGAGTAG+GGG 0.689358 7_4:-62206421 Msa1169270:exon
ACTTTCTGTCAATAACACAC+AGG 0.703987 7_4:+62206308 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATGTAAGTATAATCAATT+AGG + chr7_4:62207017-62207036 None:intergenic 15.0%
!! TTATGTAAGTATAATCAATT+AGG + chr7_4:62207017-62207036 None:intergenic 15.0%
!! TTAAGTTTAACTATATGTGT+TGG + chr7_4:62206468-62206487 None:intergenic 20.0%
!!! AGAATTGTTTAAAAAGTACA+AGG + chr7_4:62206878-62206897 None:intergenic 20.0%
!! TTAAGTTTAACTATATGTGT+TGG + chr7_4:62206468-62206487 None:intergenic 20.0%
!!! AGAATTGTTTAAAAAGTACA+AGG + chr7_4:62206878-62206897 None:intergenic 20.0%
!! AATCTATTTAAAACAAACCG+TGG - chr7_4:62206201-62206220 Msa1169270:three_prime_UTR 25.0%
! ATGAGATGTAAGAAAAGAAA+AGG + chr7_4:62206348-62206367 None:intergenic 25.0%
! TTCAAATTATTATGCTAGCT+CGG - chr7_4:62206500-62206519 Msa1169270:CDS 25.0%
! ATAACACAGAGCAATTAAAT+CGG + chr7_4:62206572-62206591 None:intergenic 25.0%
!! TTAATCAAGTTTTTGCTCTT+GGG - chr7_4:62206603-62206622 Msa1169270:CDS 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG - chr7_4:62206777-62206796 Msa1169270:intron 25.0%
! TACTTTAGCAATATATTTCG+TGG - chr7_4:62206971-62206990 Msa1169270:exon 25.0%
!! AATCTATTTAAAACAAACCG+TGG - chr7_4:62206201-62206220 Msa1169270:three_prime_UTR 25.0%
! ATGAGATGTAAGAAAAGAAA+AGG + chr7_4:62206348-62206367 None:intergenic 25.0%
! TTCAAATTATTATGCTAGCT+CGG - chr7_4:62206500-62206519 Msa1169270:CDS 25.0%
! ATAACACAGAGCAATTAAAT+CGG + chr7_4:62206572-62206591 None:intergenic 25.0%
!! TTAATCAAGTTTTTGCTCTT+GGG - chr7_4:62206603-62206622 Msa1169270:CDS 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG - chr7_4:62206777-62206796 Msa1169270:intron 25.0%
! TACTTTAGCAATATATTTCG+TGG - chr7_4:62206971-62206990 Msa1169270:exon 25.0%
TCTTTAGATTAGACATGTCT+TGG - chr7_4:62206416-62206435 Msa1169270:exon 30.0%
! TTAACTATATGTGTTGGTGT+CGG + chr7_4:62206462-62206481 None:intergenic 30.0%
CAAGAGCAAAAACTTGATTA+AGG + chr7_4:62206604-62206623 None:intergenic 30.0%
! CTTAATCAAGTTTTTGCTCT+TGG - chr7_4:62206602-62206621 Msa1169270:CDS 30.0%
! TAATCAAGTTTTTGCTCTTG+GGG - chr7_4:62206604-62206623 Msa1169270:CDS 30.0%
TTAATAGTTCTCCTGGTTAT+TGG - chr7_4:62206667-62206686 Msa1169270:intron 30.0%
!!! TTCATCTTCTTTTTTGAGAC+TGG + chr7_4:62206775-62206794 None:intergenic 30.0%
TCTTTAGATTAGACATGTCT+TGG - chr7_4:62206416-62206435 Msa1169270:exon 30.0%
! TTAACTATATGTGTTGGTGT+CGG + chr7_4:62206462-62206481 None:intergenic 30.0%
CAAGAGCAAAAACTTGATTA+AGG + chr7_4:62206604-62206623 None:intergenic 30.0%
! CTTAATCAAGTTTTTGCTCT+TGG - chr7_4:62206602-62206621 Msa1169270:CDS 30.0%
! TAATCAAGTTTTTGCTCTTG+GGG - chr7_4:62206604-62206623 Msa1169270:CDS 30.0%
TTAATAGTTCTCCTGGTTAT+TGG - chr7_4:62206667-62206686 Msa1169270:intron 30.0%
!!! TTCATCTTCTTTTTTGAGAC+TGG + chr7_4:62206775-62206794 None:intergenic 30.0%
ATCACCGAATTCAAAGTCAT+CGG + chr7_4:62206290-62206309 None:intergenic 35.0%
TTTAGAAAGCTGGATCTCTA+GGG - chr7_4:62206632-62206651 Msa1169270:intron 35.0%
AGAGTGCATAATTTCCTATG+AGG + chr7_4:62206711-62206730 None:intergenic 35.0%
! CAATGGACTCAAATGTTCTA+TGG - chr7_4:62206841-62206860 Msa1169270:intron 35.0%
CTCAAATGTTCTATGGAATG+TGG - chr7_4:62206848-62206867 Msa1169270:intron 35.0%
ACTTTCTGTCAATAACACAC+AGG + chr7_4:62206934-62206953 None:intergenic 35.0%
ATCACCGAATTCAAAGTCAT+CGG + chr7_4:62206290-62206309 None:intergenic 35.0%
TTTAGAAAGCTGGATCTCTA+GGG - chr7_4:62206632-62206651 Msa1169270:intron 35.0%
AGAGTGCATAATTTCCTATG+AGG + chr7_4:62206711-62206730 None:intergenic 35.0%
! CAATGGACTCAAATGTTCTA+TGG - chr7_4:62206841-62206860 Msa1169270:intron 35.0%
CTCAAATGTTCTATGGAATG+TGG - chr7_4:62206848-62206867 Msa1169270:intron 35.0%
ACTTTCTGTCAATAACACAC+AGG + chr7_4:62206934-62206953 None:intergenic 35.0%
ATCACTCACATCTTCAACCA+TGG - chr7_4:62206264-62206283 Msa1169270:three_prime_UTR 40.0%
ATGGCCGATGACTTTGAATT+CGG - chr7_4:62206283-62206302 Msa1169270:three_prime_UTR 40.0%
! GATTAGACATGTCTTGGTGT+AGG - chr7_4:62206422-62206441 Msa1169270:exon 40.0%
! ATTATTATGCTAGCTCGGTG+TGG - chr7_4:62206505-62206524 Msa1169270:CDS 40.0%
TGGGGAAATGTTTAGAAAGC+TGG - chr7_4:62206622-62206641 Msa1169270:intron 40.0%
GTTTAGAAAGCTGGATCTCT+AGG - chr7_4:62206631-62206650 Msa1169270:intron 40.0%
ATAGTTCTCCTGGTTATTGG+TGG - chr7_4:62206670-62206689 Msa1169270:intron 40.0%
TAGTTCTCCTGGTTATTGGT+GGG - chr7_4:62206671-62206690 Msa1169270:intron 40.0%
! TTGCTGTTGACATTCCTCAT+AGG - chr7_4:62206694-62206713 Msa1169270:intron 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG + chr7_4:62206752-62206771 None:intergenic 40.0%
!!! CTGGCTTCTTTTTTCTAGGA+GGG + chr7_4:62206756-62206775 None:intergenic 40.0%
!!! ACTGGCTTCTTTTTTCTAGG+AGG + chr7_4:62206757-62206776 None:intergenic 40.0%
!!! GAGACTGGCTTCTTTTTTCT+AGG + chr7_4:62206760-62206779 None:intergenic 40.0%
AAAAAGGAGAGACTGAAGCA+AGG - chr7_4:62206793-62206812 Msa1169270:intron 40.0%
ATCACTCACATCTTCAACCA+TGG - chr7_4:62206264-62206283 Msa1169270:three_prime_UTR 40.0%
ATGGCCGATGACTTTGAATT+CGG - chr7_4:62206283-62206302 Msa1169270:three_prime_UTR 40.0%
! GATTAGACATGTCTTGGTGT+AGG - chr7_4:62206422-62206441 Msa1169270:exon 40.0%
! ATTATTATGCTAGCTCGGTG+TGG - chr7_4:62206505-62206524 Msa1169270:CDS 40.0%
TGGGGAAATGTTTAGAAAGC+TGG - chr7_4:62206622-62206641 Msa1169270:intron 40.0%
GTTTAGAAAGCTGGATCTCT+AGG - chr7_4:62206631-62206650 Msa1169270:intron 40.0%
ATAGTTCTCCTGGTTATTGG+TGG - chr7_4:62206670-62206689 Msa1169270:intron 40.0%
TAGTTCTCCTGGTTATTGGT+GGG - chr7_4:62206671-62206690 Msa1169270:intron 40.0%
! TTGCTGTTGACATTCCTCAT+AGG - chr7_4:62206694-62206713 Msa1169270:intron 40.0%
!!! CTTCTTTTTTCTAGGAGGGA+GGG + chr7_4:62206752-62206771 None:intergenic 40.0%
!!! CTGGCTTCTTTTTTCTAGGA+GGG + chr7_4:62206756-62206775 None:intergenic 40.0%
!!! ACTGGCTTCTTTTTTCTAGG+AGG + chr7_4:62206757-62206776 None:intergenic 40.0%
!!! GAGACTGGCTTCTTTTTTCT+AGG + chr7_4:62206760-62206779 None:intergenic 40.0%
AAAAAGGAGAGACTGAAGCA+AGG - chr7_4:62206793-62206812 Msa1169270:intron 40.0%
ACAAACCGTGGTGCAAACTT+TGG - chr7_4:62206213-62206232 Msa1169270:three_prime_UTR 45.0%
CGAATCCAAAGTTTGCACCA+CGG + chr7_4:62206221-62206240 None:intergenic 45.0%
GAATTCAAAGTCATCGGCCA+TGG + chr7_4:62206284-62206303 None:intergenic 45.0%
AGTACCATGCGATCAAAGGA+AGG + chr7_4:62206322-62206341 None:intergenic 45.0%
!! GAAGAGTACCATGCGATCAA+AGG + chr7_4:62206326-62206345 None:intergenic 45.0%
!! CTATATGTGTTGGTGTCGGA+CGG + chr7_4:62206458-62206477 None:intergenic 45.0%
CCAGGAGAACTATTAAGCCT+GGG + chr7_4:62206663-62206682 None:intergenic 45.0%
ACCAGGAGAACTATTAAGCC+TGG + chr7_4:62206664-62206683 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG + chr7_4:62206753-62206772 None:intergenic 45.0%
ACAAACCGTGGTGCAAACTT+TGG - chr7_4:62206213-62206232 Msa1169270:three_prime_UTR 45.0%
CGAATCCAAAGTTTGCACCA+CGG + chr7_4:62206221-62206240 None:intergenic 45.0%
GAATTCAAAGTCATCGGCCA+TGG + chr7_4:62206284-62206303 None:intergenic 45.0%
AGTACCATGCGATCAAAGGA+AGG + chr7_4:62206322-62206341 None:intergenic 45.0%
!! GAAGAGTACCATGCGATCAA+AGG + chr7_4:62206326-62206345 None:intergenic 45.0%
!! CTATATGTGTTGGTGTCGGA+CGG + chr7_4:62206458-62206477 None:intergenic 45.0%
CCAGGAGAACTATTAAGCCT+GGG + chr7_4:62206663-62206682 None:intergenic 45.0%
ACCAGGAGAACTATTAAGCC+TGG + chr7_4:62206664-62206683 None:intergenic 45.0%
!!! GCTTCTTTTTTCTAGGAGGG+AGG + chr7_4:62206753-62206772 None:intergenic 45.0%
TCCTCCTTCCTTTGATCGCA+TGG - chr7_4:62206315-62206334 Msa1169270:three_prime_UTR 50.0%
ACCATGCGATCAAAGGAAGG+AGG + chr7_4:62206319-62206338 None:intergenic 50.0%
!! AAGAGTGTCTGCGTGTGAGA+TGG + chr7_4:62206400-62206419 None:intergenic 50.0%
CCCAGGCTTAATAGTTCTCC+TGG - chr7_4:62206660-62206679 Msa1169270:intron 50.0%
ACAGCAACCCACCAATAACC+AGG + chr7_4:62206681-62206700 None:intergenic 50.0%
TCCTCCTTCCTTTGATCGCA+TGG - chr7_4:62206315-62206334 Msa1169270:three_prime_UTR 50.0%
ACCATGCGATCAAAGGAAGG+AGG + chr7_4:62206319-62206338 None:intergenic 50.0%
!! AAGAGTGTCTGCGTGTGAGA+TGG + chr7_4:62206400-62206419 None:intergenic 50.0%
CCCAGGCTTAATAGTTCTCC+TGG - chr7_4:62206660-62206679 Msa1169270:intron 50.0%
ACAGCAACCCACCAATAACC+AGG + chr7_4:62206681-62206700 None:intergenic 50.0%
!! GGATCTCTAGGGTTCAACCC+AGG - chr7_4:62206643-62206662 Msa1169270:intron 55.0%
AAGCAAGGAGTCTCTGCACC+TGG - chr7_4:62206808-62206827 Msa1169270:intron 55.0%
AGTCTCTGCACCTGGAGAGT+AGG - chr7_4:62206816-62206835 Msa1169270:intron 55.0%
GTCTCTGCACCTGGAGAGTA+GGG - chr7_4:62206817-62206836 Msa1169270:intron 55.0%
TCTCTGCACCTGGAGAGTAG+GGG - chr7_4:62206818-62206837 Msa1169270:intron 55.0%
!! GGATCTCTAGGGTTCAACCC+AGG - chr7_4:62206643-62206662 Msa1169270:intron 55.0%
AAGCAAGGAGTCTCTGCACC+TGG - chr7_4:62206808-62206827 Msa1169270:intron 55.0%
AGTCTCTGCACCTGGAGAGT+AGG - chr7_4:62206816-62206835 Msa1169270:intron 55.0%
GTCTCTGCACCTGGAGAGTA+GGG - chr7_4:62206817-62206836 Msa1169270:intron 55.0%
TCTCTGCACCTGGAGAGTAG+GGG - chr7_4:62206818-62206837 Msa1169270:intron 55.0%
CACCTGGAGAGTAGGGGCAA+TGG - chr7_4:62206824-62206843 Msa1169270:intron 60.0%
GTCCATTGCCCCTACTCTCC+AGG + chr7_4:62206829-62206848 None:intergenic 60.0%
CACCTGGAGAGTAGGGGCAA+TGG - chr7_4:62206824-62206843 Msa1169270:intron 60.0%
GTCCATTGCCCCTACTCTCC+AGG + chr7_4:62206829-62206848 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 62206192 62207069 62206192 ID=Msa1169270;Name=Msa1169270
chr7_4 mRNA 62206192 62207069 62206192 ID=Msa1169270-mRNA-1;Parent=Msa1169270;Name=Msa1169270-mRNA-1;_AED=0.02;_eAED=0.02;_QI=91|1|1|1|1|1|2|232|84
chr7_4 exon 62206192 62206624 62206192 ID=Msa1169270-mRNA-1:exon:19717;Parent=Msa1169270-mRNA-1
chr7_4 exon 62206925 62207069 62206925 ID=Msa1169270-mRNA-1:exon:19716;Parent=Msa1169270-mRNA-1
chr7_4 five_prime_UTR 62206979 62207069 62206979 ID=Msa1169270-mRNA-1:five_prime_utr;Parent=Msa1169270-mRNA-1
chr7_4 CDS 62206925 62206978 62206925 ID=Msa1169270-mRNA-1:cds;Parent=Msa1169270-mRNA-1
chr7_4 CDS 62206424 62206624 62206424 ID=Msa1169270-mRNA-1:cds;Parent=Msa1169270-mRNA-1
chr7_4 three_prime_UTR 62206192 62206423 62206192 ID=Msa1169270-mRNA-1:three_prime_utr;Parent=Msa1169270-mRNA-1
Gene Sequence

>Msa1169270

ATGGCCGATGACTTTGAATTCGGTGATAAAGTTCCTCCTTCCTTTGATCGCATGAAAGCTGGATCTCTAGGGTTCAACCCAGGCTTAATAGTTCTCCTGGTTATTGGTGGGTTGCTGTTGACATTCCTCATAGGAAATTATGCACTCTACGTTTATGCACAGAAGACCCTCCCTCCTAGAAAAAAGAAGCCAGTCTCAAAAAAGAAGATGAAAAAGGAGAGACTGAAGCAAGGAGTCTCTGCACCTGGAGAGTAG
Protein sequence

>Msa1169270

MADDFEFGDKVPPSFDRMKAGSLGFNPGLIVLLVIGGLLLTFLIGNYALYVYAQKTLPPRKKKPVSKKKMKKERLKQGVSAPGE*