AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0417630


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0417630 MtrunA17_Chr3g0115121 98.795 166 2 0 1 166 1 166 1.36e-119 334
Msa0417630 MtrunA17_Chr4g0041831 47.727 132 69 0 21 152 6 137 2.83e-35 120
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0417630 AT5G14320.1 70.513 156 41 2 1 153 1 154 1.48e-76 226
Msa0417630 AT5G14320.2 62.069 116 39 2 1 113 1 114 3.02e-44 142
Msa0417630 AT1G77750.1 48.387 124 64 0 42 165 27 150 1.72e-37 126

Find 47 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATGTCCTGCAATTATTCT+TGG 0.215118 3_2:+64888312 None:intergenic
AATTCAATTCTCTTGTTGTT+TGG 0.264258 3_2:+64888674 None:intergenic
CAGAGGAATAAGGCATATTC+AGG 0.285946 3_2:-64888359 Msa0417630:CDS
AATTGTGTTACCTTTGACTT+TGG 0.293488 3_2:+64888805 None:intergenic
GACTTTGGAGTGTTGAGAAC+TGG 0.363379 3_2:+64888820 None:intergenic
GGTAAGAAGGTTACTGTTGC+TGG 0.372364 3_2:-64888286 Msa0417630:CDS
TTCAATGTTACAGAGGAATA+AGG 0.374673 3_2:-64888369 Msa0417630:CDS
AAGAAGAGCTTATTAGTCTC+AGG 0.387619 3_2:-64888556 Msa0417630:CDS
ATACATGACTGAAGGAGATT+TGG 0.390225 3_2:-64888519 Msa0417630:intron
GGGAGATAATGATAAGGATA+TGG 0.401243 3_2:-64888968 Msa0417630:five_prime_UTR
GATTCTAACTGATATCAGTA+TGG 0.462554 3_2:-64888606 Msa0417630:CDS
TTGCAGTACATTCATGGAGT+TGG 0.465952 3_2:-64888647 Msa0417630:CDS
TATGGAGAATAAAGTTACTA+AGG 0.474154 3_2:-64888588 Msa0417630:CDS
CAGGACATTGAAGGGTAAGA+AGG 0.478630 3_2:-64888299 Msa0417630:CDS
TTAATGCACTTAATATAAAG+AGG 0.487114 3_2:-64888402 Msa0417630:CDS
AGCGTACCAAGAATAATTGC+AGG 0.496459 3_2:-64888318 Msa0417630:CDS
ATTGAATTGTATAGGTTCAA+AGG 0.511797 3_2:-64888736 Msa0417630:intron
GAATAATTGCAGGACATTGA+AGG 0.513496 3_2:-64888308 Msa0417630:CDS
AACTGGGAAGGAAACTCGAT+TGG 0.516558 3_2:+64888837 None:intergenic
ATATCATGTGAACTTCTGCT+TGG 0.523221 3_2:-64888119 Msa0417630:three_prime_UTR
AGGAGAAAACACCAACTCTC+GGG 0.523730 3_2:-64888988 None:intergenic
TAGGAGAAAACACCAACTCT+CGG 0.533211 3_2:-64888989 None:intergenic
ATTGTGTGCGTTCGTGTTGG+TGG 0.534997 3_2:-64888707 Msa0417630:CDS
AATAATTGCAGGACATTGAA+GGG 0.549157 3_2:-64888307 Msa0417630:CDS
ATTGAGAGTGAAGGTGCCAC+AGG 0.552065 3_2:+64888886 None:intergenic
TATCATTATCTCCCGAGAGT+TGG 0.556639 3_2:+64888977 None:intergenic
ACTTAATATAAAGAGGTTGA+AGG 0.557426 3_2:-64888395 Msa0417630:CDS
TTCACTCTCAATCATCTCCA+AGG 0.561178 3_2:-64888875 Msa0417630:CDS
TCAATCATCTCCAAGGGTCA+TGG 0.561269 3_2:-64888868 Msa0417630:CDS
TAATGATAAGGATATGGCTA+TGG 0.563231 3_2:-64888962 Msa0417630:five_prime_UTR
AACATTGTGTGCGTTCGTGT+TGG 0.564683 3_2:-64888710 Msa0417630:CDS
GGAGAAGTGACCATGACCCT+TGG 0.564855 3_2:+64888858 None:intergenic
GTGCGTTCGTGTTGGTGGTG+TGG 0.576835 3_2:-64888702 Msa0417630:CDS
TTGGTACGCTGTCCTCTACA+AGG 0.578588 3_2:+64888331 None:intergenic
ACTCTCGGGAGATAATGATA+AGG 0.580530 3_2:-64888974 Msa0417630:five_prime_UTR
AGAGGAATAAGGCATATTCA+GGG 0.580912 3_2:-64888358 Msa0417630:CDS
ACTTTGGAGTGTTGAGAACT+GGG 0.582387 3_2:+64888821 None:intergenic
TCTCAACACTCCAAAGTCAA+AGG 0.589008 3_2:-64888815 Msa0417630:intron
TGGAGTGTTGAGAACTGGGA+AGG 0.596347 3_2:+64888825 None:intergenic
GTTAACAAATACATGACTGA+AGG 0.596392 3_2:-64888527 Msa0417630:CDS
TCACTCTCAATCATCTCCAA+GGG 0.616522 3_2:-64888874 Msa0417630:CDS
ATTCAGGGACTTCCTTGTAG+AGG 0.621863 3_2:-64888343 Msa0417630:CDS
AGTACATTCATGGAGTTGGA+AGG 0.622828 3_2:-64888643 Msa0417630:CDS
AGAAGAGCTTATTAGTCTCA+GGG 0.625713 3_2:-64888555 Msa0417630:CDS
AAGGAGATTCAATGTTACAG+AGG 0.654230 3_2:-64888376 Msa0417630:CDS
ACAAACACTCTCAATGCCTG+TGG 0.676701 3_2:-64888902 Msa0417630:CDS
TTGGAGATGATTGAGAGTGA+AGG 0.701686 3_2:+64888877 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTGTTTTGTAATTGTAA+TGG - chr3_2:64888589-64888608 Msa0417630:CDS 15.0%
!!! ATTTTGTTTTGTAATTGTAA+TGG - chr3_2:64888589-64888608 Msa0417630:CDS 15.0%
!! TTAATGCACTTAATATAAAG+AGG - chr3_2:64888642-64888661 Msa0417630:CDS 20.0%
!!! AGAGAAAAAAGAAAATGTTT+TGG - chr3_2:64888838-64888857 Msa0417630:CDS 20.0%
!! TTAATGCACTTAATATAAAG+AGG - chr3_2:64888642-64888661 Msa0417630:CDS 20.0%
!!! AGAGAAAAAAGAAAATGTTT+TGG - chr3_2:64888838-64888857 Msa0417630:CDS 20.0%
! TGATTCTGATTGAATTGTAT+AGG - chr3_2:64888300-64888319 Msa0417630:CDS 25.0%
! ATTGAATTGTATAGGTTCAA+AGG - chr3_2:64888308-64888327 Msa0417630:CDS 25.0%
!!! AATTCAATTCTCTTGTTGTT+TGG + chr3_2:64888373-64888392 None:intergenic 25.0%
! TATGGAGAATAAAGTTACTA+AGG - chr3_2:64888456-64888475 Msa0417630:intron 25.0%
! ACTTAATATAAAGAGGTTGA+AGG - chr3_2:64888649-64888668 Msa0417630:CDS 25.0%
!!! TGCGATTGTTTTGATTAAAT+TGG - chr3_2:64888865-64888884 Msa0417630:CDS 25.0%
! TGATTCTGATTGAATTGTAT+AGG - chr3_2:64888300-64888319 Msa0417630:CDS 25.0%
! ATTGAATTGTATAGGTTCAA+AGG - chr3_2:64888308-64888327 Msa0417630:CDS 25.0%
!!! AATTCAATTCTCTTGTTGTT+TGG + chr3_2:64888373-64888392 None:intergenic 25.0%
! TATGGAGAATAAAGTTACTA+AGG - chr3_2:64888456-64888475 Msa0417630:intron 25.0%
! ACTTAATATAAAGAGGTTGA+AGG - chr3_2:64888649-64888668 Msa0417630:CDS 25.0%
!!! TGCGATTGTTTTGATTAAAT+TGG - chr3_2:64888865-64888884 Msa0417630:CDS 25.0%
TAATGATAAGGATATGGCTA+TGG - chr3_2:64888082-64888101 Msa0417630:three_prime_UTR 30.0%
! AATTGTGTTACCTTTGACTT+TGG + chr3_2:64888242-64888261 None:intergenic 30.0%
AAGTCAAAGGTAACACAATT+AGG - chr3_2:64888242-64888261 Msa0417630:three_prime_UTR 30.0%
AGTCAAAGGTAACACAATTA+GGG - chr3_2:64888243-64888262 Msa0417630:three_prime_UTR 30.0%
ATCAGAATCAGAATGGAATT+TGG + chr3_2:64888290-64888309 None:intergenic 30.0%
CAATTCAATCAGAATCAGAA+TGG + chr3_2:64888297-64888316 None:intergenic 30.0%
GATTCTAACTGATATCAGTA+TGG - chr3_2:64888438-64888457 Msa0417630:intron 30.0%
GTTAACAAATACATGACTGA+AGG - chr3_2:64888517-64888536 Msa0417630:intron 30.0%
TTGTTTGTGAATTTCAGAGA+AGG - chr3_2:64888618-64888637 Msa0417630:CDS 30.0%
TTCAATGTTACAGAGGAATA+AGG - chr3_2:64888675-64888694 Msa0417630:CDS 30.0%
AATAATTGCAGGACATTGAA+GGG - chr3_2:64888737-64888756 Msa0417630:intron 30.0%
TAATGATAAGGATATGGCTA+TGG - chr3_2:64888082-64888101 Msa0417630:three_prime_UTR 30.0%
! AATTGTGTTACCTTTGACTT+TGG + chr3_2:64888242-64888261 None:intergenic 30.0%
AAGTCAAAGGTAACACAATT+AGG - chr3_2:64888242-64888261 Msa0417630:three_prime_UTR 30.0%
AGTCAAAGGTAACACAATTA+GGG - chr3_2:64888243-64888262 Msa0417630:three_prime_UTR 30.0%
ATCAGAATCAGAATGGAATT+TGG + chr3_2:64888290-64888309 None:intergenic 30.0%
CAATTCAATCAGAATCAGAA+TGG + chr3_2:64888297-64888316 None:intergenic 30.0%
GATTCTAACTGATATCAGTA+TGG - chr3_2:64888438-64888457 Msa0417630:intron 30.0%
GTTAACAAATACATGACTGA+AGG - chr3_2:64888517-64888536 Msa0417630:intron 30.0%
TTGTTTGTGAATTTCAGAGA+AGG - chr3_2:64888618-64888637 Msa0417630:CDS 30.0%
TTCAATGTTACAGAGGAATA+AGG - chr3_2:64888675-64888694 Msa0417630:CDS 30.0%
AATAATTGCAGGACATTGAA+GGG - chr3_2:64888737-64888756 Msa0417630:intron 30.0%
GGGAGATAATGATAAGGATA+TGG - chr3_2:64888076-64888095 Msa0417630:three_prime_UTR 35.0%
TCGCAGTTGAACAGAAAAAA+TGG - chr3_2:64888118-64888137 Msa0417630:three_prime_UTR 35.0%
! TTTTCGTTGCAGTACATTCA+TGG - chr3_2:64888391-64888410 Msa0417630:CDS 35.0%
! AAGAAGAGCTTATTAGTCTC+AGG - chr3_2:64888488-64888507 Msa0417630:intron 35.0%
! AGAAGAGCTTATTAGTCTCA+GGG - chr3_2:64888489-64888508 Msa0417630:intron 35.0%
ATACATGACTGAAGGAGATT+TGG - chr3_2:64888525-64888544 Msa0417630:CDS 35.0%
AAGGAGATTCAATGTTACAG+AGG - chr3_2:64888668-64888687 Msa0417630:CDS 35.0%
AGAGGAATAAGGCATATTCA+GGG - chr3_2:64888686-64888705 Msa0417630:CDS 35.0%
CAATGTCCTGCAATTATTCT+TGG + chr3_2:64888735-64888754 None:intergenic 35.0%
GAATAATTGCAGGACATTGA+AGG - chr3_2:64888736-64888755 Msa0417630:intron 35.0%
ATATCATGTGAACTTCTGCT+TGG - chr3_2:64888925-64888944 Msa0417630:exon 35.0%
GGGAGATAATGATAAGGATA+TGG - chr3_2:64888076-64888095 Msa0417630:three_prime_UTR 35.0%
TCGCAGTTGAACAGAAAAAA+TGG - chr3_2:64888118-64888137 Msa0417630:three_prime_UTR 35.0%
! TTTTCGTTGCAGTACATTCA+TGG - chr3_2:64888391-64888410 Msa0417630:CDS 35.0%
! AAGAAGAGCTTATTAGTCTC+AGG - chr3_2:64888488-64888507 Msa0417630:intron 35.0%
! AGAAGAGCTTATTAGTCTCA+GGG - chr3_2:64888489-64888508 Msa0417630:intron 35.0%
ATACATGACTGAAGGAGATT+TGG - chr3_2:64888525-64888544 Msa0417630:CDS 35.0%
AAGGAGATTCAATGTTACAG+AGG - chr3_2:64888668-64888687 Msa0417630:CDS 35.0%
AGAGGAATAAGGCATATTCA+GGG - chr3_2:64888686-64888705 Msa0417630:CDS 35.0%
CAATGTCCTGCAATTATTCT+TGG + chr3_2:64888735-64888754 None:intergenic 35.0%
GAATAATTGCAGGACATTGA+AGG - chr3_2:64888736-64888755 Msa0417630:intron 35.0%
ATATCATGTGAACTTCTGCT+TGG - chr3_2:64888925-64888944 Msa0417630:exon 35.0%
ACTCTCGGGAGATAATGATA+AGG - chr3_2:64888070-64888089 Msa0417630:three_prime_UTR 40.0%
TTGGAGATGATTGAGAGTGA+AGG + chr3_2:64888170-64888189 None:intergenic 40.0%
TTCACTCTCAATCATCTCCA+AGG - chr3_2:64888169-64888188 Msa0417630:three_prime_UTR 40.0%
TCACTCTCAATCATCTCCAA+GGG - chr3_2:64888170-64888189 Msa0417630:three_prime_UTR 40.0%
!! ACTTTGGAGTGTTGAGAACT+GGG + chr3_2:64888226-64888245 None:intergenic 40.0%
TCTCAACACTCCAAAGTCAA+AGG - chr3_2:64888229-64888248 Msa0417630:three_prime_UTR 40.0%
TTGCAGTACATTCATGGAGT+TGG - chr3_2:64888397-64888416 Msa0417630:CDS 40.0%
AGTACATTCATGGAGTTGGA+AGG - chr3_2:64888401-64888420 Msa0417630:CDS 40.0%
CAGAGGAATAAGGCATATTC+AGG - chr3_2:64888685-64888704 Msa0417630:CDS 40.0%
AGCGTACCAAGAATAATTGC+AGG - chr3_2:64888726-64888745 Msa0417630:intron 40.0%
ACTCTCGGGAGATAATGATA+AGG - chr3_2:64888070-64888089 Msa0417630:three_prime_UTR 40.0%
TTGGAGATGATTGAGAGTGA+AGG + chr3_2:64888170-64888189 None:intergenic 40.0%
TTCACTCTCAATCATCTCCA+AGG - chr3_2:64888169-64888188 Msa0417630:three_prime_UTR 40.0%
TCACTCTCAATCATCTCCAA+GGG - chr3_2:64888170-64888189 Msa0417630:three_prime_UTR 40.0%
!! ACTTTGGAGTGTTGAGAACT+GGG + chr3_2:64888226-64888245 None:intergenic 40.0%
TCTCAACACTCCAAAGTCAA+AGG - chr3_2:64888229-64888248 Msa0417630:three_prime_UTR 40.0%
TTGCAGTACATTCATGGAGT+TGG - chr3_2:64888397-64888416 Msa0417630:CDS 40.0%
AGTACATTCATGGAGTTGGA+AGG - chr3_2:64888401-64888420 Msa0417630:CDS 40.0%
CAGAGGAATAAGGCATATTC+AGG - chr3_2:64888685-64888704 Msa0417630:CDS 40.0%
AGCGTACCAAGAATAATTGC+AGG - chr3_2:64888726-64888745 Msa0417630:intron 40.0%
ACAAACACTCTCAATGCCTG+TGG - chr3_2:64888142-64888161 Msa0417630:three_prime_UTR 45.0%
TCAATCATCTCCAAGGGTCA+TGG - chr3_2:64888176-64888195 Msa0417630:three_prime_UTR 45.0%
AACTGGGAAGGAAACTCGAT+TGG + chr3_2:64888210-64888229 None:intergenic 45.0%
!! GACTTTGGAGTGTTGAGAAC+TGG + chr3_2:64888227-64888246 None:intergenic 45.0%
AACATTGTGTGCGTTCGTGT+TGG - chr3_2:64888334-64888353 Msa0417630:CDS 45.0%
ATTCAGGGACTTCCTTGTAG+AGG - chr3_2:64888701-64888720 Msa0417630:CDS 45.0%
CAGGACATTGAAGGGTAAGA+AGG - chr3_2:64888745-64888764 Msa0417630:intron 45.0%
GGTAAGAAGGTTACTGTTGC+TGG - chr3_2:64888758-64888777 Msa0417630:intron 45.0%
ACAAACACTCTCAATGCCTG+TGG - chr3_2:64888142-64888161 Msa0417630:three_prime_UTR 45.0%
TCAATCATCTCCAAGGGTCA+TGG - chr3_2:64888176-64888195 Msa0417630:three_prime_UTR 45.0%
AACTGGGAAGGAAACTCGAT+TGG + chr3_2:64888210-64888229 None:intergenic 45.0%
!! GACTTTGGAGTGTTGAGAAC+TGG + chr3_2:64888227-64888246 None:intergenic 45.0%
AACATTGTGTGCGTTCGTGT+TGG - chr3_2:64888334-64888353 Msa0417630:CDS 45.0%
ATTCAGGGACTTCCTTGTAG+AGG - chr3_2:64888701-64888720 Msa0417630:CDS 45.0%
CAGGACATTGAAGGGTAAGA+AGG - chr3_2:64888745-64888764 Msa0417630:intron 45.0%
GGTAAGAAGGTTACTGTTGC+TGG - chr3_2:64888758-64888777 Msa0417630:intron 45.0%
!! ATTGAGAGTGAAGGTGCCAC+AGG + chr3_2:64888161-64888180 None:intergenic 50.0%
!! TGGAGTGTTGAGAACTGGGA+AGG + chr3_2:64888222-64888241 None:intergenic 50.0%
ATTGTGTGCGTTCGTGTTGG+TGG - chr3_2:64888337-64888356 Msa0417630:CDS 50.0%
TTGGTACGCTGTCCTCTACA+AGG + chr3_2:64888716-64888735 None:intergenic 50.0%
!! ATTGAGAGTGAAGGTGCCAC+AGG + chr3_2:64888161-64888180 None:intergenic 50.0%
!! TGGAGTGTTGAGAACTGGGA+AGG + chr3_2:64888222-64888241 None:intergenic 50.0%
ATTGTGTGCGTTCGTGTTGG+TGG - chr3_2:64888337-64888356 Msa0417630:CDS 50.0%
TTGGTACGCTGTCCTCTACA+AGG + chr3_2:64888716-64888735 None:intergenic 50.0%
GGAGAAGTGACCATGACCCT+TGG + chr3_2:64888189-64888208 None:intergenic 55.0%
GGAGAAGTGACCATGACCCT+TGG + chr3_2:64888189-64888208 None:intergenic 55.0%
!! GTGCGTTCGTGTTGGTGGTG+TGG - chr3_2:64888342-64888361 Msa0417630:CDS 60.0%
!! GTGCGTTCGTGTTGGTGGTG+TGG - chr3_2:64888342-64888361 Msa0417630:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 64888069 64888997 64888069 ID=Msa0417630;Name=Msa0417630
chr3_2 mRNA 64888069 64888997 64888069 ID=Msa0417630-mRNA-1;Parent=Msa0417630;Name=Msa0417630-mRNA-1;_AED=0.01;_eAED=0.01;_QI=68|1|1|1|1|1|3|201|166
chr3_2 exon 64888069 64888431 64888069 ID=Msa0417630-mRNA-1:exon:14498;Parent=Msa0417630-mRNA-1
chr3_2 exon 64888520 64888744 64888520 ID=Msa0417630-mRNA-1:exon:14497;Parent=Msa0417630-mRNA-1
chr3_2 exon 64888816 64888997 64888816 ID=Msa0417630-mRNA-1:exon:14496;Parent=Msa0417630-mRNA-1
chr3_2 five_prime_UTR 64888930 64888997 64888930 ID=Msa0417630-mRNA-1:five_prime_utr;Parent=Msa0417630-mRNA-1
chr3_2 CDS 64888816 64888929 64888816 ID=Msa0417630-mRNA-1:cds;Parent=Msa0417630-mRNA-1
chr3_2 CDS 64888520 64888744 64888520 ID=Msa0417630-mRNA-1:cds;Parent=Msa0417630-mRNA-1
chr3_2 CDS 64888270 64888431 64888270 ID=Msa0417630-mRNA-1:cds;Parent=Msa0417630-mRNA-1
chr3_2 three_prime_UTR 64888069 64888269 64888069 ID=Msa0417630-mRNA-1:three_prime_utr;Parent=Msa0417630-mRNA-1
Gene Sequence

>Msa0417630

ATGGTACAAACACTCTCAATGCCTGTGGCACCTTCACTCTCAATCATCTCCAAGGGTCATGGTCACTTCTCCAATCGAGTTTCCTTCCCAGTTCTCAACACTCCAAAGTCAAAGGTTCAAAGGCTAAACATTGTGTGCGTTCGTGTTGGTGGTGTGGAAATTCCAAACAACAAGAGAATTGAATTTTCGTTGCAGTACATTCATGGAGTTGGAAGGAACAGAGCTAGACAGATTCTAACTGATATCAGTATGGAGAATAAAGTTACTAAGGAATTGAGTGAAGAAGAGCTTATTAGTCTCAGGGATGAAGTTAACAAATACATGACTGAAGGAGATTTGAGAAGGTTTAATGCACTTAATATAAAGAGGTTGAAGGAGATTCAATGTTACAGAGGAATAAGGCATATTCAGGGACTTCCTTGTAGAGGACAGCGTACCAAGAATAATTGCAGGACATTGAAGGGTAAGAAGGTTACTGTTGCTGGCAAGAAGAAAAAGTAA

Protein sequence

>Msa0417630

MVQTLSMPVAPSLSIISKGHGHFSNRVSFPVLNTPKSKVQRLNIVCVRVGGVEIPNNKRIEFSLQYIHGVGRNRARQILTDISMENKVTKELSEEELISLRDEVNKYMTEGDLRRFNALNIKRLKEIQCYRGIRHIQGLPCRGQRTKNNCRTLKGKKVTVAGKKKK*