AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1262380

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1262380 MtrunA17_Chr4g0063791 94.915 177 1 3 1 170 1 176 3.91e-118 331
Msa1262380 MtrunA17_Chr2g0333051 38.889 144 63 4 32 165 5 133 2.10e-19 79.3
Msa1262380 MtrunA17_Chr4g0003391 38.462 143 63 6 32 170 5 126 1.75e-14 66.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1262380 AT3G15760.1 39.568 139 66 5 35 169 9 133 3.29e-16 71.6
Msa1262380 AT1G52565.1 41.353 133 57 5 32 162 8 121 2.90e-15 68.9

Find 35 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGATCTACTATATTATTT+TGG 0.176418 8_2:-65063162 None:intergenic
GATTGGCTTATTGTTGAATT+TGG 0.199091 8_2:+65062769 Msa1262380:exon
TCTATTCTGTTAGGTGAATT+AGG 0.199380 8_2:+65062962 Msa1262380:three_prime_UTR
TACAAAGCTGCTCTGTTTGC+AGG 0.285163 8_2:-65062714 None:intergenic
CTACGTTCTTGTTTATCTTC+TGG 0.298024 8_2:+65062403 Msa1262380:CDS
GTTATTACCTCTATTCTGTT+AGG 0.313498 8_2:+65062953 Msa1262380:three_prime_UTR
AACAGAGCAGCTTTGTATAA+TGG 0.334899 8_2:+65062720 Msa1262380:CDS
TCTCTTCATAACTCTAATAA+AGG 0.367080 8_2:+65063071 Msa1262380:three_prime_UTR
AAACATGGTGAAGAGAGAAT+TGG 0.390105 8_2:-65062354 None:intergenic
AACATGGTGAAGAGAGAATT+GGG 0.400815 8_2:-65062353 None:intergenic
GATAAACAAGAACGTAGAAT+AGG 0.427062 8_2:-65062397 None:intergenic
CCGAACTAAAATTTGAACAT+TGG 0.462032 8_2:-65063110 None:intergenic
GAAAGGAAAGAAGAGAGGTT+TGG 0.473786 8_2:-65062220 None:intergenic
TTTGAAGAAAAGTGAGAAAG+TGG 0.480831 8_2:-65062195 None:intergenic
GAAATTGAATTCAAGATCAA+AGG 0.482344 8_2:+65062650 Msa1262380:CDS
TCTAGAAGTACAGTAAAAGT+AGG 0.512331 8_2:+65062887 Msa1262380:three_prime_UTR
AAGGTTCAAAAGAATTGTAA+TGG 0.522701 8_2:+65062669 Msa1262380:CDS
GTTGTGGATTCATGTAAAGA+TGG 0.540155 8_2:+65062564 Msa1262380:CDS
GCAACCGCCATGGCTGTCTC+CGG 0.543566 8_2:+65062295 Msa1262380:CDS
AGATCGTGTGAATCAACGAT+TGG 0.545757 8_2:+65062752 Msa1262380:CDS
AAGAAGAAAGGAAAGAAGAG+AGG 0.550576 8_2:-65062225 None:intergenic
TAATTCACCTAACAGAATAG+AGG 0.559773 8_2:-65062960 None:intergenic
GTTCAAAAGAATTGTAATGG+TGG 0.561934 8_2:+65062672 Msa1262380:CDS
TGCTGTCTTTGCAACCGCCA+TGG 0.563392 8_2:+65062285 Msa1262380:CDS
AGCAAGGATGATGACTGTGC+CGG 0.571426 8_2:-65062314 None:intergenic
TAGGAAATAGAAGTTGATGA+AGG 0.571660 8_2:+65062906 Msa1262380:three_prime_UTR
ATTTCTGAAGACGGAGAGCA+AGG 0.583155 8_2:-65062330 None:intergenic
AGAATTGGGATTTCTGAAGA+CGG 0.611480 8_2:-65062339 None:intergenic
GACTGTGCCGGAGACAGCCA+TGG 0.611754 8_2:-65062302 None:intergenic
TGCAAAGACAGCACCTTGTG+AGG 0.629596 8_2:-65062275 None:intergenic
CTCTAATAAAGGAAATTATG+CGG 0.638575 8_2:+65063082 Msa1262380:three_prime_UTR
TCTTCAATGATTACCTCACA+AGG 0.650992 8_2:+65062262 Msa1262380:CDS
AATGGTGGAAACGAGAACAG+AGG 0.717333 8_2:+65062687 Msa1262380:CDS
GAGTACAGAAAACAACAACA+TGG 0.720965 8_2:+65062591 Msa1262380:CDS
TGTGCCGGAGACAGCCATGG+CGG 0.736789 8_2:-65062299 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTGTTAACATAATTCT+TGG + chr8_2:65062480-65062499 Msa1262380:intron 15.0%
!!! ATTATTTTGTTCATAGTTTT+AGG + chr8_2:65062997-65063016 Msa1262380:three_prime_UTR 15.0%
!!! TAATCTTGTTCATATTTTTT+AGG + chr8_2:65063021-65063040 Msa1262380:three_prime_UTR 15.0%
!!! AATCTTGTTCATATTTTTTA+GGG + chr8_2:65063022-65063041 Msa1262380:three_prime_UTR 15.0%
!!! TTTTTTGTTAACATAATTCT+TGG + chr8_2:65062480-65062499 Msa1262380:intron 15.0%
!!! ATTATTTTGTTCATAGTTTT+AGG + chr8_2:65062997-65063016 Msa1262380:three_prime_UTR 15.0%
!!! TAATCTTGTTCATATTTTTT+AGG + chr8_2:65063021-65063040 Msa1262380:three_prime_UTR 15.0%
!!! AATCTTGTTCATATTTTTTA+GGG + chr8_2:65063022-65063041 Msa1262380:three_prime_UTR 15.0%
!!! TGTTTTGAAGAAAAGAAGAA+AGG - chr8_2:65062240-65062259 None:intergenic 25.0%
!! AACAAGGTTTTTCTCTTTTT+AGG + chr8_2:65062452-65062471 Msa1262380:intron 25.0%
!! ACAAGGTTTTTCTCTTTTTA+GGG + chr8_2:65062453-65062472 Msa1262380:intron 25.0%
!!! TTCTTTGTTTTCTTTTCATC+TGG - chr8_2:65062513-65062532 None:intergenic 25.0%
! GAAATTGAATTCAAGATCAA+AGG + chr8_2:65062650-65062669 Msa1262380:CDS 25.0%
! AAGGTTCAAAAGAATTGTAA+TGG + chr8_2:65062669-65062688 Msa1262380:CDS 25.0%
!!! TTAGGGTAATTTTGTTATGT+TGG + chr8_2:65063039-65063058 Msa1262380:three_prime_UTR 25.0%
! TCTCTTCATAACTCTAATAA+AGG + chr8_2:65063071-65063090 Msa1262380:three_prime_UTR 25.0%
! CTCTAATAAAGGAAATTATG+CGG + chr8_2:65063082-65063101 Msa1262380:three_prime_UTR 25.0%
!!! CCAATGTTCAAATTTTAGTT+CGG + chr8_2:65063110-65063129 Msa1262380:three_prime_UTR 25.0%
!!! TGTTTTGAAGAAAAGAAGAA+AGG - chr8_2:65062240-65062259 None:intergenic 25.0%
!! AACAAGGTTTTTCTCTTTTT+AGG + chr8_2:65062452-65062471 Msa1262380:intron 25.0%
!! ACAAGGTTTTTCTCTTTTTA+GGG + chr8_2:65062453-65062472 Msa1262380:intron 25.0%
!!! TTCTTTGTTTTCTTTTCATC+TGG - chr8_2:65062513-65062532 None:intergenic 25.0%
! GAAATTGAATTCAAGATCAA+AGG + chr8_2:65062650-65062669 Msa1262380:CDS 25.0%
! AAGGTTCAAAAGAATTGTAA+TGG + chr8_2:65062669-65062688 Msa1262380:CDS 25.0%
!!! TTAGGGTAATTTTGTTATGT+TGG + chr8_2:65063039-65063058 Msa1262380:three_prime_UTR 25.0%
! TCTCTTCATAACTCTAATAA+AGG + chr8_2:65063071-65063090 Msa1262380:three_prime_UTR 25.0%
! CTCTAATAAAGGAAATTATG+CGG + chr8_2:65063082-65063101 Msa1262380:three_prime_UTR 25.0%
!!! CCAATGTTCAAATTTTAGTT+CGG + chr8_2:65063110-65063129 Msa1262380:three_prime_UTR 25.0%
TTTGAAGAAAAGTGAGAAAG+TGG - chr8_2:65062198-65062217 None:intergenic 30.0%
AAGAAGAAGAAGAAGAAACA+TGG - chr8_2:65062372-65062391 None:intergenic 30.0%
GATAAACAAGAACGTAGAAT+AGG - chr8_2:65062400-65062419 None:intergenic 30.0%
TTTACTACACACATTCAACA+AGG + chr8_2:65062436-65062455 Msa1262380:intron 30.0%
!!! GAAAAGAGTTAGTTTTGCTA+AGG + chr8_2:65062539-65062558 Msa1262380:CDS 30.0%
GTTCAAAAGAATTGTAATGG+TGG + chr8_2:65062672-65062691 Msa1262380:CDS 30.0%
!! GATTGGCTTATTGTTGAATT+TGG + chr8_2:65062769-65062788 Msa1262380:exon 30.0%
! TCTAGAAGTACAGTAAAAGT+AGG + chr8_2:65062887-65062906 Msa1262380:three_prime_UTR 30.0%
!! TAGGAAATAGAAGTTGATGA+AGG + chr8_2:65062906-65062925 Msa1262380:three_prime_UTR 30.0%
!! TAACTGCAACTATGTTTTTG+TGG - chr8_2:65062937-65062956 None:intergenic 30.0%
GTTATTACCTCTATTCTGTT+AGG + chr8_2:65062953-65062972 Msa1262380:three_prime_UTR 30.0%
TAATTCACCTAACAGAATAG+AGG - chr8_2:65062963-65062982 None:intergenic 30.0%
TCTATTCTGTTAGGTGAATT+AGG + chr8_2:65062962-65062981 Msa1262380:three_prime_UTR 30.0%
CCGAACTAAAATTTGAACAT+TGG - chr8_2:65063113-65063132 None:intergenic 30.0%
TTTGAAGAAAAGTGAGAAAG+TGG - chr8_2:65062198-65062217 None:intergenic 30.0%
AAGAAGAAGAAGAAGAAACA+TGG - chr8_2:65062372-65062391 None:intergenic 30.0%
GATAAACAAGAACGTAGAAT+AGG - chr8_2:65062400-65062419 None:intergenic 30.0%
TTTACTACACACATTCAACA+AGG + chr8_2:65062436-65062455 Msa1262380:intron 30.0%
!!! GAAAAGAGTTAGTTTTGCTA+AGG + chr8_2:65062539-65062558 Msa1262380:CDS 30.0%
GTTCAAAAGAATTGTAATGG+TGG + chr8_2:65062672-65062691 Msa1262380:CDS 30.0%
!! GATTGGCTTATTGTTGAATT+TGG + chr8_2:65062769-65062788 Msa1262380:exon 30.0%
! TCTAGAAGTACAGTAAAAGT+AGG + chr8_2:65062887-65062906 Msa1262380:three_prime_UTR 30.0%
!! TAGGAAATAGAAGTTGATGA+AGG + chr8_2:65062906-65062925 Msa1262380:three_prime_UTR 30.0%
!! TAACTGCAACTATGTTTTTG+TGG - chr8_2:65062937-65062956 None:intergenic 30.0%
GTTATTACCTCTATTCTGTT+AGG + chr8_2:65062953-65062972 Msa1262380:three_prime_UTR 30.0%
TAATTCACCTAACAGAATAG+AGG - chr8_2:65062963-65062982 None:intergenic 30.0%
TCTATTCTGTTAGGTGAATT+AGG + chr8_2:65062962-65062981 Msa1262380:three_prime_UTR 30.0%
CCGAACTAAAATTTGAACAT+TGG - chr8_2:65063113-65063132 None:intergenic 30.0%
AAGAAGAAAGGAAAGAAGAG+AGG - chr8_2:65062228-65062247 None:intergenic 35.0%
TCTTCAATGATTACCTCACA+AGG + chr8_2:65062262-65062281 Msa1262380:CDS 35.0%
! AGAATTGGGATTTCTGAAGA+CGG - chr8_2:65062342-65062361 None:intergenic 35.0%
AACATGGTGAAGAGAGAATT+GGG - chr8_2:65062356-65062375 None:intergenic 35.0%
AAACATGGTGAAGAGAGAAT+TGG - chr8_2:65062357-65062376 None:intergenic 35.0%
! CTACGTTCTTGTTTATCTTC+TGG + chr8_2:65062403-65062422 Msa1262380:CDS 35.0%
!! TAGTTTTGCTAAGGATGTTG+TGG + chr8_2:65062548-65062567 Msa1262380:CDS 35.0%
GTTGTGGATTCATGTAAAGA+TGG + chr8_2:65062564-65062583 Msa1262380:CDS 35.0%
GAGTACAGAAAACAACAACA+TGG + chr8_2:65062591-65062610 Msa1262380:CDS 35.0%
! AACAGAGCAGCTTTGTATAA+TGG + chr8_2:65062720-65062739 Msa1262380:CDS 35.0%
!! TGCAACTATGTTTTTGTGGT+GGG - chr8_2:65062933-65062952 None:intergenic 35.0%
AAGAAGAAAGGAAAGAAGAG+AGG - chr8_2:65062228-65062247 None:intergenic 35.0%
TCTTCAATGATTACCTCACA+AGG + chr8_2:65062262-65062281 Msa1262380:CDS 35.0%
! AGAATTGGGATTTCTGAAGA+CGG - chr8_2:65062342-65062361 None:intergenic 35.0%
AACATGGTGAAGAGAGAATT+GGG - chr8_2:65062356-65062375 None:intergenic 35.0%
AAACATGGTGAAGAGAGAAT+TGG - chr8_2:65062357-65062376 None:intergenic 35.0%
! CTACGTTCTTGTTTATCTTC+TGG + chr8_2:65062403-65062422 Msa1262380:CDS 35.0%
!! TAGTTTTGCTAAGGATGTTG+TGG + chr8_2:65062548-65062567 Msa1262380:CDS 35.0%
GTTGTGGATTCATGTAAAGA+TGG + chr8_2:65062564-65062583 Msa1262380:CDS 35.0%
GAGTACAGAAAACAACAACA+TGG + chr8_2:65062591-65062610 Msa1262380:CDS 35.0%
! AACAGAGCAGCTTTGTATAA+TGG + chr8_2:65062720-65062739 Msa1262380:CDS 35.0%
!! TGCAACTATGTTTTTGTGGT+GGG - chr8_2:65062933-65062952 None:intergenic 35.0%
GAAAGGAAAGAAGAGAGGTT+TGG - chr8_2:65062223-65062242 None:intergenic 40.0%
AGATCGTGTGAATCAACGAT+TGG + chr8_2:65062752-65062771 Msa1262380:CDS 40.0%
!! CTGCAACTATGTTTTTGTGG+TGG - chr8_2:65062934-65062953 None:intergenic 40.0%
CATATTAGAAGCAGCCAACA+AGG - chr8_2:65062167-65062186 None:intergenic 40.0%
GAAAGGAAAGAAGAGAGGTT+TGG - chr8_2:65062223-65062242 None:intergenic 40.0%
AGATCGTGTGAATCAACGAT+TGG + chr8_2:65062752-65062771 Msa1262380:CDS 40.0%
!! CTGCAACTATGTTTTTGTGG+TGG - chr8_2:65062934-65062953 None:intergenic 40.0%
! ATTTCTGAAGACGGAGAGCA+AGG - chr8_2:65062333-65062352 None:intergenic 45.0%
! AATGGTGGAAACGAGAACAG+AGG + chr8_2:65062687-65062706 Msa1262380:CDS 45.0%
TACAAAGCTGCTCTGTTTGC+AGG - chr8_2:65062717-65062736 None:intergenic 45.0%
! ATTTCTGAAGACGGAGAGCA+AGG - chr8_2:65062333-65062352 None:intergenic 45.0%
! AATGGTGGAAACGAGAACAG+AGG + chr8_2:65062687-65062706 Msa1262380:CDS 45.0%
TACAAAGCTGCTCTGTTTGC+AGG - chr8_2:65062717-65062736 None:intergenic 45.0%
TGCAAAGACAGCACCTTGTG+AGG - chr8_2:65062278-65062297 None:intergenic 50.0%
AGCAAGGATGATGACTGTGC+CGG - chr8_2:65062317-65062336 None:intergenic 50.0%
TGCAAAGACAGCACCTTGTG+AGG - chr8_2:65062278-65062297 None:intergenic 50.0%
AGCAAGGATGATGACTGTGC+CGG - chr8_2:65062317-65062336 None:intergenic 50.0%
TGCTGTCTTTGCAACCGCCA+TGG + chr8_2:65062285-65062304 Msa1262380:CDS 55.0%
TGCTGTCTTTGCAACCGCCA+TGG + chr8_2:65062285-65062304 Msa1262380:CDS 55.0%
GCAACCGCCATGGCTGTCTC+CGG + chr8_2:65062295-65062314 Msa1262380:CDS 65.0%
TGTGCCGGAGACAGCCATGG+CGG - chr8_2:65062302-65062321 None:intergenic 65.0%
GACTGTGCCGGAGACAGCCA+TGG - chr8_2:65062305-65062324 None:intergenic 65.0%
GCAACCGCCATGGCTGTCTC+CGG + chr8_2:65062295-65062314 Msa1262380:CDS 65.0%
TGTGCCGGAGACAGCCATGG+CGG - chr8_2:65062302-65062321 None:intergenic 65.0%
GACTGTGCCGGAGACAGCCA+TGG - chr8_2:65062305-65062324 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 65062165 65063181 65062165 ID=Msa1262380;Name=Msa1262380
chr8_2 mRNA 65062165 65063181 65062165 ID=Msa1262380-mRNA-1;Parent=Msa1262380;Name=Msa1262380-mRNA-1;_AED=0.00;_eAED=0.00;_QI=19|1|1|1|1|1|2|396|170
chr8_2 exon 65062165 65062424 65062165 ID=Msa1262380-mRNA-1:exon:21037;Parent=Msa1262380-mRNA-1
chr8_2 exon 65062514 65063181 65062514 ID=Msa1262380-mRNA-1:exon:21038;Parent=Msa1262380-mRNA-1
chr8_2 five_prime_UTR 65062165 65062183 65062165 ID=Msa1262380-mRNA-1:five_prime_utr;Parent=Msa1262380-mRNA-1
chr8_2 CDS 65062184 65062424 65062184 ID=Msa1262380-mRNA-1:cds;Parent=Msa1262380-mRNA-1
chr8_2 CDS 65062514 65062785 65062514 ID=Msa1262380-mRNA-1:cds;Parent=Msa1262380-mRNA-1
chr8_2 three_prime_UTR 65062786 65063181 65062786 ID=Msa1262380-mRNA-1:three_prime_utr;Parent=Msa1262380-mRNA-1
Gene Sequence

>Msa1262380

ATGAGACTATACCACTTTCTCACTTTTCTTCAAAGACCAAACCTCTCTTCTTTCCTTTCTTCTTTTCTTCAAAACATGTCTTCAATGATTACCTCACAAGGTGCTGTCTTTGCAACCGCCATGGCTGTCTCCGGCACAGTCATCATCCTTGCTCTCCGTCTTCAGAAATCCCAATTCTCTCTTCACCATGTTTCTTCTTCTTCTTCTTCAACTCCTATTCTACGTTCTTGTTTATCTTCTGATGAAAAGAAAACAAAGAAACTGAAGAAAAGAGTTAGTTTTGCTAAGGATGTTGTGGATTCATGTAAAGATGGAGAAGAGTACAGAAAACAACAACATGGTACTAGTACTATGAATAATACTACTAAACATTCTTTGAAATTGAATTCAAGATCAAAGGTTCAAAAGAATTGTAATGGTGGAAACGAGAACAGAGGAATGCCTGCAAACAGAGCAGCTTTGTATAATGGAATTCTTAGAGATCGTGTGAATCAACGATTGGCTTATTGTTGA
Protein sequence

>Msa1262380

MRLYHFLTFLQRPNLSSFLSSFLQNMSSMITSQGAVFATAMAVSGTVIILALRLQKSQFSLHHVSSSSSSTPILRSCLSSDEKKTKKLKKRVSFAKDVVDSCKDGEEYRKQQHGTSTMNNTTKHSLKLNSRSKVQKNCNGGNENRGMPANRAALYNGILRDRVNQRLAYC*