AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0370180


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0370180 MtrunA17_Chr3g0115121 98.795 166 2 0 1 166 1 166 1.79e-119 334
Msa0370180 MtrunA17_Chr4g0041831 47.692 130 68 0 23 152 8 137 7.69e-35 119
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0370180 AT5G14320.1 70.513 156 41 2 1 153 1 154 1.23e-76 226
Msa0370180 AT5G14320.2 58.268 127 48 2 1 124 1 125 1.64e-44 143
Msa0370180 AT1G77750.1 48.387 124 64 0 42 165 27 150 1.20e-37 127

Find 47 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATGTCCTGCAGTTATTCT+TGG 0.227656 3_1:+67717171 None:intergenic
AATTCAATTCTCTTGTTGTT+TGG 0.264258 3_1:+67717541 None:intergenic
CAGAGGAATAAGGCATATTC+AGG 0.285946 3_1:-67717218 Msa0370180:CDS
AATTGTGTTACCTTTGACTT+TGG 0.293488 3_1:+67717672 None:intergenic
ATCAAGTAACTAAATTAAAA+AGG 0.325206 3_1:+67717096 None:intergenic
GGTAAGAAGGTTACTGTTGC+TGG 0.360552 3_1:-67717145 Msa0370180:CDS
GACTTTGGAGTGTTGAGAAC+TGG 0.363379 3_1:+67717687 None:intergenic
TTCAGTGTTACAGAGGAATA+AGG 0.379843 3_1:-67717228 Msa0370180:CDS
AAGAAGAGCTTATTAGTCTC+AGG 0.387619 3_1:-67717423 Msa0370180:CDS
ATACATGACTGAAGGAGATT+TGG 0.390225 3_1:-67717386 Msa0370180:intron
GGGAGATAATGATAAGGATA+TGG 0.401243 3_1:-67717835 Msa0370180:five_prime_UTR
GGAGAAGTTAGCATGGCCTT+TGG 0.412794 3_1:+67717725 None:intergenic
GATTCTAACTGATATCAGTA+TGG 0.462554 3_1:-67717473 Msa0370180:CDS
TTGCAGTACATTCATGGAGT+TGG 0.465952 3_1:-67717514 Msa0370180:CDS
TTGAGCTGACAAATGCTAAG+AGG 0.469959 3_1:+67716915 None:intergenic
TTAATGCACTTAATATAAAG+AGG 0.487114 3_1:-67717261 Msa0370180:CDS
ATTGAATTGTATAGGTTCAA+AGG 0.511797 3_1:-67717603 Msa0370180:intron
AACTGGGAAGGAAACTCGAT+TGG 0.516558 3_1:+67717704 None:intergenic
AGGAGAAAACACCAACTCTC+GGG 0.523730 3_1:-67717855 None:intergenic
GAATAACTGCAGGACATTGA+AGG 0.525777 3_1:-67717167 Msa0370180:CDS
TAGGAGAAAACACCAACTCT+CGG 0.533211 3_1:-67717856 None:intergenic
CAGGACATTGAAGGGTAAGA+AGG 0.533951 3_1:-67717158 Msa0370180:CDS
ATTGTGTGCGTTCGTGTTGG+TGG 0.534997 3_1:-67717574 Msa0370180:CDS
ATATTATGTGAACTACTGCT+TGG 0.543434 3_1:-67716970 Msa0370180:three_prime_UTR
AATAACTGCAGGACATTGAA+GGG 0.550619 3_1:-67717166 Msa0370180:CDS
ATTGAGAGTGAAGGTGCCAC+AGG 0.552065 3_1:+67717753 None:intergenic
TATCATTATCTCCCGAGAGT+TGG 0.556639 3_1:+67717844 None:intergenic
TAATGATAAGGATATGGCTA+TGG 0.563231 3_1:-67717829 Msa0370180:five_prime_UTR
AACATTGTGTGCGTTCGTGT+TGG 0.564683 3_1:-67717577 Msa0370180:CDS
GTGCGTTCGTGTTGGTGGTG+TGG 0.576835 3_1:-67717569 Msa0370180:CDS
TTGGTACGCTGTCCTCTACA+AGG 0.578588 3_1:+67717190 None:intergenic
ACTCTCGGGAGATAATGATA+AGG 0.580530 3_1:-67717841 Msa0370180:five_prime_UTR
AGAGGAATAAGGCATATTCA+GGG 0.580912 3_1:-67717217 Msa0370180:CDS
ACTTTGGAGTGTTGAGAACT+GGG 0.582387 3_1:+67717688 None:intergenic
TCTCAACACTCCAAAGTCAA+AGG 0.589008 3_1:-67717682 Msa0370180:intron
TGGAGTGTTGAGAACTGGGA+AGG 0.596347 3_1:+67717692 None:intergenic
GTTAACAAATACATGACTGA+AGG 0.596392 3_1:-67717394 Msa0370180:CDS
TATGGAGAATAAAGTTACAA+AGG 0.597785 3_1:-67717455 Msa0370180:CDS
AAAGAAATTCAGTGTTACAG+AGG 0.605461 3_1:-67717235 Msa0370180:CDS
CTCGATTGGAGAAGTTAGCA+TGG 0.611741 3_1:+67717718 None:intergenic
TCACTCTCAATCATCTCCAA+AGG 0.619107 3_1:-67717741 Msa0370180:CDS
ATTCAGGGACTTCCTTGTAG+AGG 0.621863 3_1:-67717202 Msa0370180:CDS
AGTACATTCATGGAGTTGGA+AGG 0.622828 3_1:-67717510 Msa0370180:CDS
AGCGTACCAAGAATAACTGC+AGG 0.623820 3_1:-67717177 Msa0370180:CDS
AGAAGAGCTTATTAGTCTCA+GGG 0.625713 3_1:-67717422 Msa0370180:CDS
TTGGAGATGATTGAGAGTGA+AGG 0.661623 3_1:+67717744 None:intergenic
ACAAACACTCTCAATGCCTG+TGG 0.676701 3_1:-67717769 Msa0370180:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTGTTTTGTAATTGTAA+TGG - chr3_1:67717451-67717470 Msa0370180:CDS 15.0%
!! ATCAAGTAACTAAATTAAAA+AGG + chr3_1:67717672-67717691 None:intergenic 15.0%
!!! ATTGAGAAAAAAAAATGTTT+TGG - chr3_1:67717699-67717718 Msa0370180:CDS 15.0%
!!! ATTTTGTTTTGTAATTGTAA+TGG - chr3_1:67717451-67717470 Msa0370180:CDS 15.0%
!! ATCAAGTAACTAAATTAAAA+AGG + chr3_1:67717672-67717691 None:intergenic 15.0%
!!! ATTGAGAAAAAAAAATGTTT+TGG - chr3_1:67717699-67717718 Msa0370180:CDS 15.0%
!! TTAATGCACTTAATATAAAG+AGG - chr3_1:67717504-67717523 Msa0370180:CDS 20.0%
!! TTAATGCACTTAATATAAAG+AGG - chr3_1:67717504-67717523 Msa0370180:CDS 20.0%
! TGATTCTGATTGAATTGTAT+AGG - chr3_1:67717154-67717173 Msa0370180:CDS 25.0%
! ATTGAATTGTATAGGTTCAA+AGG - chr3_1:67717162-67717181 Msa0370180:CDS 25.0%
!!! AATTCAATTCTCTTGTTGTT+TGG + chr3_1:67717227-67717246 None:intergenic 25.0%
! TATGGAGAATAAAGTTACAA+AGG - chr3_1:67717310-67717329 Msa0370180:intron 25.0%
!!! TGCGATTGTTTTTGTTAAAT+TGG - chr3_1:67717726-67717745 Msa0370180:CDS 25.0%
! TGATTCTGATTGAATTGTAT+AGG - chr3_1:67717154-67717173 Msa0370180:CDS 25.0%
! ATTGAATTGTATAGGTTCAA+AGG - chr3_1:67717162-67717181 Msa0370180:CDS 25.0%
!!! AATTCAATTCTCTTGTTGTT+TGG + chr3_1:67717227-67717246 None:intergenic 25.0%
! TATGGAGAATAAAGTTACAA+AGG - chr3_1:67717310-67717329 Msa0370180:intron 25.0%
!!! TGCGATTGTTTTTGTTAAAT+TGG - chr3_1:67717726-67717745 Msa0370180:CDS 25.0%
TAATGATAAGGATATGGCTA+TGG - chr3_1:67716936-67716955 Msa0370180:three_prime_UTR 30.0%
! AATTGTGTTACCTTTGACTT+TGG + chr3_1:67717096-67717115 None:intergenic 30.0%
AAGTCAAAGGTAACACAATT+AGG - chr3_1:67717096-67717115 Msa0370180:three_prime_UTR 30.0%
AGTCAAAGGTAACACAATTA+GGG - chr3_1:67717097-67717116 Msa0370180:three_prime_UTR 30.0%
ATCAGAATCAGAATGGAATT+TGG + chr3_1:67717144-67717163 None:intergenic 30.0%
CAATTCAATCAGAATCAGAA+TGG + chr3_1:67717151-67717170 None:intergenic 30.0%
GATTCTAACTGATATCAGTA+TGG - chr3_1:67717292-67717311 Msa0370180:intron 30.0%
GTTAACAAATACATGACTGA+AGG - chr3_1:67717371-67717390 Msa0370180:intron 30.0%
TTGTTTGTGAATTTCAGAGA+AGG - chr3_1:67717480-67717499 Msa0370180:CDS 30.0%
AAAGAAATTCAGTGTTACAG+AGG - chr3_1:67717530-67717549 Msa0370180:CDS 30.0%
ATATTATGTGAACTACTGCT+TGG - chr3_1:67717795-67717814 Msa0370180:exon 30.0%
TAATGATAAGGATATGGCTA+TGG - chr3_1:67716936-67716955 Msa0370180:three_prime_UTR 30.0%
! AATTGTGTTACCTTTGACTT+TGG + chr3_1:67717096-67717115 None:intergenic 30.0%
AAGTCAAAGGTAACACAATT+AGG - chr3_1:67717096-67717115 Msa0370180:three_prime_UTR 30.0%
AGTCAAAGGTAACACAATTA+GGG - chr3_1:67717097-67717116 Msa0370180:three_prime_UTR 30.0%
ATCAGAATCAGAATGGAATT+TGG + chr3_1:67717144-67717163 None:intergenic 30.0%
CAATTCAATCAGAATCAGAA+TGG + chr3_1:67717151-67717170 None:intergenic 30.0%
GATTCTAACTGATATCAGTA+TGG - chr3_1:67717292-67717311 Msa0370180:intron 30.0%
GTTAACAAATACATGACTGA+AGG - chr3_1:67717371-67717390 Msa0370180:intron 30.0%
TTGTTTGTGAATTTCAGAGA+AGG - chr3_1:67717480-67717499 Msa0370180:CDS 30.0%
AAAGAAATTCAGTGTTACAG+AGG - chr3_1:67717530-67717549 Msa0370180:CDS 30.0%
ATATTATGTGAACTACTGCT+TGG - chr3_1:67717795-67717814 Msa0370180:exon 30.0%
GGGAGATAATGATAAGGATA+TGG - chr3_1:67716930-67716949 Msa0370180:three_prime_UTR 35.0%
TCGCTGTTGAACAGAAAAAA+TGG - chr3_1:67716972-67716991 Msa0370180:three_prime_UTR 35.0%
! TTTTCGTTGCAGTACATTCA+TGG - chr3_1:67717245-67717264 Msa0370180:CDS 35.0%
! AAGAAGAGCTTATTAGTCTC+AGG - chr3_1:67717342-67717361 Msa0370180:intron 35.0%
! AGAAGAGCTTATTAGTCTCA+GGG - chr3_1:67717343-67717362 Msa0370180:intron 35.0%
ATACATGACTGAAGGAGATT+TGG - chr3_1:67717379-67717398 Msa0370180:intron 35.0%
TTCAGTGTTACAGAGGAATA+AGG - chr3_1:67717537-67717556 Msa0370180:CDS 35.0%
AGAGGAATAAGGCATATTCA+GGG - chr3_1:67717548-67717567 Msa0370180:CDS 35.0%
AATAACTGCAGGACATTGAA+GGG - chr3_1:67717599-67717618 Msa0370180:intron 35.0%
GGGAGATAATGATAAGGATA+TGG - chr3_1:67716930-67716949 Msa0370180:three_prime_UTR 35.0%
TCGCTGTTGAACAGAAAAAA+TGG - chr3_1:67716972-67716991 Msa0370180:three_prime_UTR 35.0%
! TTTTCGTTGCAGTACATTCA+TGG - chr3_1:67717245-67717264 Msa0370180:CDS 35.0%
! AAGAAGAGCTTATTAGTCTC+AGG - chr3_1:67717342-67717361 Msa0370180:intron 35.0%
! AGAAGAGCTTATTAGTCTCA+GGG - chr3_1:67717343-67717362 Msa0370180:intron 35.0%
ATACATGACTGAAGGAGATT+TGG - chr3_1:67717379-67717398 Msa0370180:intron 35.0%
TTCAGTGTTACAGAGGAATA+AGG - chr3_1:67717537-67717556 Msa0370180:CDS 35.0%
AGAGGAATAAGGCATATTCA+GGG - chr3_1:67717548-67717567 Msa0370180:CDS 35.0%
AATAACTGCAGGACATTGAA+GGG - chr3_1:67717599-67717618 Msa0370180:intron 35.0%
ACTCTCGGGAGATAATGATA+AGG - chr3_1:67716924-67716943 Msa0370180:three_prime_UTR 40.0%
TTGGAGATGATTGAGAGTGA+AGG + chr3_1:67717024-67717043 None:intergenic 40.0%
TCACTCTCAATCATCTCCAA+AGG - chr3_1:67717024-67717043 Msa0370180:three_prime_UTR 40.0%
!! ACTTTGGAGTGTTGAGAACT+GGG + chr3_1:67717080-67717099 None:intergenic 40.0%
TCTCAACACTCCAAAGTCAA+AGG - chr3_1:67717083-67717102 Msa0370180:three_prime_UTR 40.0%
TTGCAGTACATTCATGGAGT+TGG - chr3_1:67717251-67717270 Msa0370180:CDS 40.0%
AGTACATTCATGGAGTTGGA+AGG - chr3_1:67717255-67717274 Msa0370180:CDS 40.0%
CAGAGGAATAAGGCATATTC+AGG - chr3_1:67717547-67717566 Msa0370180:CDS 40.0%
CAATGTCCTGCAGTTATTCT+TGG + chr3_1:67717597-67717616 None:intergenic 40.0%
GAATAACTGCAGGACATTGA+AGG - chr3_1:67717598-67717617 Msa0370180:intron 40.0%
ACTCTCGGGAGATAATGATA+AGG - chr3_1:67716924-67716943 Msa0370180:three_prime_UTR 40.0%
TTGGAGATGATTGAGAGTGA+AGG + chr3_1:67717024-67717043 None:intergenic 40.0%
TCACTCTCAATCATCTCCAA+AGG - chr3_1:67717024-67717043 Msa0370180:three_prime_UTR 40.0%
!! ACTTTGGAGTGTTGAGAACT+GGG + chr3_1:67717080-67717099 None:intergenic 40.0%
TCTCAACACTCCAAAGTCAA+AGG - chr3_1:67717083-67717102 Msa0370180:three_prime_UTR 40.0%
TTGCAGTACATTCATGGAGT+TGG - chr3_1:67717251-67717270 Msa0370180:CDS 40.0%
AGTACATTCATGGAGTTGGA+AGG - chr3_1:67717255-67717274 Msa0370180:CDS 40.0%
CAGAGGAATAAGGCATATTC+AGG - chr3_1:67717547-67717566 Msa0370180:CDS 40.0%
CAATGTCCTGCAGTTATTCT+TGG + chr3_1:67717597-67717616 None:intergenic 40.0%
GAATAACTGCAGGACATTGA+AGG - chr3_1:67717598-67717617 Msa0370180:intron 40.0%
ACAAACACTCTCAATGCCTG+TGG - chr3_1:67716996-67717015 Msa0370180:three_prime_UTR 45.0%
CTCGATTGGAGAAGTTAGCA+TGG + chr3_1:67717050-67717069 None:intergenic 45.0%
AACTGGGAAGGAAACTCGAT+TGG + chr3_1:67717064-67717083 None:intergenic 45.0%
!! GACTTTGGAGTGTTGAGAAC+TGG + chr3_1:67717081-67717100 None:intergenic 45.0%
AACATTGTGTGCGTTCGTGT+TGG - chr3_1:67717188-67717207 Msa0370180:CDS 45.0%
ATTCAGGGACTTCCTTGTAG+AGG - chr3_1:67717563-67717582 Msa0370180:CDS 45.0%
AGCGTACCAAGAATAACTGC+AGG - chr3_1:67717588-67717607 Msa0370180:CDS 45.0%
CAGGACATTGAAGGGTAAGA+AGG - chr3_1:67717607-67717626 Msa0370180:intron 45.0%
GGTAAGAAGGTTACTGTTGC+TGG - chr3_1:67717620-67717639 Msa0370180:intron 45.0%
ACAAACACTCTCAATGCCTG+TGG - chr3_1:67716996-67717015 Msa0370180:three_prime_UTR 45.0%
CTCGATTGGAGAAGTTAGCA+TGG + chr3_1:67717050-67717069 None:intergenic 45.0%
AACTGGGAAGGAAACTCGAT+TGG + chr3_1:67717064-67717083 None:intergenic 45.0%
!! GACTTTGGAGTGTTGAGAAC+TGG + chr3_1:67717081-67717100 None:intergenic 45.0%
AACATTGTGTGCGTTCGTGT+TGG - chr3_1:67717188-67717207 Msa0370180:CDS 45.0%
ATTCAGGGACTTCCTTGTAG+AGG - chr3_1:67717563-67717582 Msa0370180:CDS 45.0%
AGCGTACCAAGAATAACTGC+AGG - chr3_1:67717588-67717607 Msa0370180:CDS 45.0%
CAGGACATTGAAGGGTAAGA+AGG - chr3_1:67717607-67717626 Msa0370180:intron 45.0%
GGTAAGAAGGTTACTGTTGC+TGG - chr3_1:67717620-67717639 Msa0370180:intron 45.0%
!! ATTGAGAGTGAAGGTGCCAC+AGG + chr3_1:67717015-67717034 None:intergenic 50.0%
GGAGAAGTTAGCATGGCCTT+TGG + chr3_1:67717043-67717062 None:intergenic 50.0%
!! TGGAGTGTTGAGAACTGGGA+AGG + chr3_1:67717076-67717095 None:intergenic 50.0%
ATTGTGTGCGTTCGTGTTGG+TGG - chr3_1:67717191-67717210 Msa0370180:CDS 50.0%
TTGGTACGCTGTCCTCTACA+AGG + chr3_1:67717578-67717597 None:intergenic 50.0%
!! ATTGAGAGTGAAGGTGCCAC+AGG + chr3_1:67717015-67717034 None:intergenic 50.0%
GGAGAAGTTAGCATGGCCTT+TGG + chr3_1:67717043-67717062 None:intergenic 50.0%
!! TGGAGTGTTGAGAACTGGGA+AGG + chr3_1:67717076-67717095 None:intergenic 50.0%
ATTGTGTGCGTTCGTGTTGG+TGG - chr3_1:67717191-67717210 Msa0370180:CDS 50.0%
TTGGTACGCTGTCCTCTACA+AGG + chr3_1:67717578-67717597 None:intergenic 50.0%
!! GTGCGTTCGTGTTGGTGGTG+TGG - chr3_1:67717196-67717215 Msa0370180:CDS 60.0%
!! GTGCGTTCGTGTTGGTGGTG+TGG - chr3_1:67717196-67717215 Msa0370180:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 67716923 67717864 67716923 ID=Msa0370180;Name=Msa0370180
chr3_1 mRNA 67716923 67717864 67716923 ID=Msa0370180-mRNA-1;Parent=Msa0370180;Name=Msa0370180-mRNA-1;_AED=0.06;_eAED=0.06;_QI=68|1|1|1|1|1|3|206|166
chr3_1 exon 67716923 67717290 67716923 ID=Msa0370180-mRNA-1:exon:14049;Parent=Msa0370180-mRNA-1
chr3_1 exon 67717387 67717611 67717387 ID=Msa0370180-mRNA-1:exon:14048;Parent=Msa0370180-mRNA-1
chr3_1 exon 67717683 67717864 67717683 ID=Msa0370180-mRNA-1:exon:14047;Parent=Msa0370180-mRNA-1
chr3_1 five_prime_UTR 67717797 67717864 67717797 ID=Msa0370180-mRNA-1:five_prime_utr;Parent=Msa0370180-mRNA-1
chr3_1 CDS 67717683 67717796 67717683 ID=Msa0370180-mRNA-1:cds;Parent=Msa0370180-mRNA-1
chr3_1 CDS 67717387 67717611 67717387 ID=Msa0370180-mRNA-1:cds;Parent=Msa0370180-mRNA-1
chr3_1 CDS 67717129 67717290 67717129 ID=Msa0370180-mRNA-1:cds;Parent=Msa0370180-mRNA-1
chr3_1 three_prime_UTR 67716923 67717128 67716923 ID=Msa0370180-mRNA-1:three_prime_utr;Parent=Msa0370180-mRNA-1
Gene Sequence

>Msa0370180

ATGGTACAAACACTCTCAATGCCTGTGGCACCTTCACTCTCAATCATCTCCAAAGGCCATGCTAACTTCTCCAATCGAGTTTCCTTCCCAGTTCTCAACACTCCAAAGTCAAAGGTTCAAAGGCTAAACATTGTGTGCGTTCGTGTTGGTGGTGTGGAAATTCCAAACAACAAGAGAATTGAATTTTCGTTGCAGTACATTCATGGAGTTGGAAGGAACAGAGCTAGACAGATTCTAACTGATATCAGTATGGAGAATAAAGTTACAAAGGAATTGAGTGAAGAAGAGCTTATTAGTCTCAGGGATGAAGTTAACAAATACATGACTGAAGGAGATTTGAGAAGGTTTAATGCACTTAATATAAAGAGGTTGAAAGAAATTCAGTGTTACAGAGGAATAAGGCATATTCAGGGACTTCCTTGTAGAGGACAGCGTACCAAGAATAACTGCAGGACATTGAAGGGTAAGAAGGTTACTGTTGCTGGAAAGAAGAAAAAGTAA

Protein sequence

>Msa0370180

MVQTLSMPVAPSLSIISKGHANFSNRVSFPVLNTPKSKVQRLNIVCVRVGGVEIPNNKRIEFSLQYIHGVGRNRARQILTDISMENKVTKELSEEELISLRDEVNKYMTEGDLRRFNALNIKRLKEIQCYRGIRHIQGLPCRGQRTKNNCRTLKGKKVTVAGKKKK*