AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0437710


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0437710 MtrunA17_Chr3g0115121 98.795 166 2 0 1 166 1 166 1.36e-119 334
Msa0437710 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
Msa0437710 AT5G14320.1 70.513 156 41 2 1 153 1 154 1.48e-76 226
Msa0437710 AT5G14320.2 62.069 116 39 2 1 113 1 114 3.02e-44 142
Msa0437710 AT1G77750.1 48.387 124 64 0 42 165 27 150 1.72e-37 126

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_3:+1657374 None:intergenic
AATTCAATTCTCTTGTTGTT+TGG 0.264258 3_3:+1657744 None:intergenic
CAGAGGAATAAGGCATATTC+AGG 0.285946 3_3:-1657421 Msa0437710:CDS
AATTGTGTTACCTTTGACTT+TGG 0.293488 3_3:+1657873 None:intergenic
ATCAAGTAACTAAATTAAAA+AGG 0.325206 3_3:+1657299 None:intergenic
GGTAAGAAGGTTACTGTTGC+TGG 0.360552 3_3:-1657348 Msa0437710:CDS
GACTTTGGAGTGTTGAGAAC+TGG 0.363379 3_3:+1657888 None:intergenic
TTCAGTGTTACAGAGGAATA+AGG 0.379843 3_3:-1657431 Msa0437710:CDS
AAGAAGAGCTTATTAGTCTC+AGG 0.387619 3_3:-1657626 Msa0437710:CDS
ATACATGACTGAAGGAGATT+TGG 0.390225 3_3:-1657589 Msa0437710:intron
GGAGAAGTGACCATGGCCTT+TGG 0.397280 3_3:+1657926 None:intergenic
GGGAGATAATGATAAGGATA+TGG 0.401243 3_3:-1658036 Msa0437710:five_prime_UTR
GATTCTAACTGATATCAGTA+TGG 0.462554 3_3:-1657676 Msa0437710:CDS
TTGCAGTACATTCATGGAGT+TGG 0.465952 3_3:-1657717 Msa0437710:CDS
TTGAGCTGACAAATGCTAAG+AGG 0.469959 3_3:+1657118 None:intergenic
TTAATGCACTTAATATAAAG+AGG 0.487114 3_3:-1657464 Msa0437710:CDS
AACTGGGAAAGAAACTCGAT+TGG 0.508056 3_3:+1657905 None:intergenic
GAATAACTGCAGGACATTGA+AGG 0.525777 3_3:-1657370 Msa0437710:CDS
CAGGACATTGAAGGGTAAGA+AGG 0.533951 3_3:-1657361 Msa0437710:CDS
ATTGTGTGCGTTCGTGTTGG+TGG 0.534997 3_3:-1657777 Msa0437710:CDS
AAGGAGAAAACACCAACTCT+CGG 0.539577 3_3:-1658057 None:intergenic
AGGAGAAAACACCAACTCTC+GGG 0.541747 3_3:-1658056 None:intergenic
ATATTATGTGAACTACTGCT+TGG 0.543434 3_3:-1657173 Msa0437710:three_prime_UTR
AATAACTGCAGGACATTGAA+GGG 0.550619 3_3:-1657369 Msa0437710:CDS
ATTGAGAGTGAAGGTGCCAC+AGG 0.552065 3_3:+1657954 None:intergenic
ACTTTGGAGTGTTGAGAACT+GGG 0.555353 3_3:+1657889 None:intergenic
TATCATTATCTCCCGAGAGT+TGG 0.556639 3_3:+1658045 None:intergenic
TAATGATAAGGATATGGCTA+TGG 0.563231 3_3:-1658030 Msa0437710:five_prime_UTR
AACATTGTGTGCGTTCGTGT+TGG 0.564683 3_3:-1657780 Msa0437710:CDS
TGATTGAATTGTAGGTTCAG+AGG 0.566135 3_3:-1657806 Msa0437710:intron
TCAATCATCTCCAAAGGCCA+TGG 0.572793 3_3:-1657936 Msa0437710:CDS
GTGCGTTCGTGTTGGTGGTG+TGG 0.576835 3_3:-1657772 Msa0437710:CDS
TTGGTACGCTGTCCTCTACA+AGG 0.578588 3_3:+1657393 None:intergenic
ACTCTCGGGAGATAATGATA+AGG 0.580530 3_3:-1658042 Msa0437710:five_prime_UTR
AGAGGAATAAGGCATATTCA+GGG 0.580912 3_3:-1657420 Msa0437710:CDS
TCTCAACACTCCAAAGTCAA+AGG 0.589008 3_3:-1657883 Msa0437710:intron
GTTAACAAATACATGACTGA+AGG 0.596392 3_3:-1657597 Msa0437710:CDS
TATGGAGAATAAAGTTACAA+AGG 0.597785 3_3:-1657658 Msa0437710:CDS
AAAGAAATTCAGTGTTACAG+AGG 0.605461 3_3:-1657438 Msa0437710:CDS
TCACTCTCAATCATCTCCAA+AGG 0.619107 3_3:-1657942 Msa0437710:CDS
ATTCAGGGACTTCCTTGTAG+AGG 0.621863 3_3:-1657405 Msa0437710:CDS
AGTACATTCATGGAGTTGGA+AGG 0.622828 3_3:-1657713 Msa0437710:CDS
AGCGTACCAAGAATAACTGC+AGG 0.623820 3_3:-1657380 Msa0437710:CDS
AGAAGAGCTTATTAGTCTCA+GGG 0.625713 3_3:-1657625 Msa0437710:CDS
CTCGATTGGAGAAGTGACCA+TGG 0.660409 3_3:+1657919 None:intergenic
TTGGAGATGATTGAGAGTGA+AGG 0.661623 3_3:+1657945 None:intergenic
ACAAACACTCTCAATGCCTG+TGG 0.676701 3_3:-1657970 Msa0437710:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTGTTTTGTAATTGTAA+TGG - chr3_3:1657652-1657671 Msa0437710:CDS 15.0%
!! ATCAAGTAACTAAATTAAAA+AGG + chr3_3:1657873-1657892 None:intergenic 15.0%
!!! ATTGAGAAAAAAAAATGTTT+TGG - chr3_3:1657900-1657919 Msa0437710:CDS 15.0%
!!! ATTTTGTTTTGTAATTGTAA+TGG - chr3_3:1657652-1657671 Msa0437710:CDS 15.0%
!! ATCAAGTAACTAAATTAAAA+AGG + chr3_3:1657873-1657892 None:intergenic 15.0%
!!! ATTGAGAAAAAAAAATGTTT+TGG - chr3_3:1657900-1657919 Msa0437710:CDS 15.0%
!! TTAATGCACTTAATATAAAG+AGG - chr3_3:1657705-1657724 Msa0437710:CDS 20.0%
!! TTAATGCACTTAATATAAAG+AGG - chr3_3:1657705-1657724 Msa0437710:CDS 20.0%
!!! AATTCAATTCTCTTGTTGTT+TGG + chr3_3:1657428-1657447 None:intergenic 25.0%
! TATGGAGAATAAAGTTACAA+AGG - chr3_3:1657511-1657530 Msa0437710:intron 25.0%
!!! TGCGATTGTTTTTGTTAAAT+TGG - chr3_3:1657927-1657946 Msa0437710:CDS 25.0%
!!! AATTCAATTCTCTTGTTGTT+TGG + chr3_3:1657428-1657447 None:intergenic 25.0%
! TATGGAGAATAAAGTTACAA+AGG - chr3_3:1657511-1657530 Msa0437710:intron 25.0%
!!! TGCGATTGTTTTTGTTAAAT+TGG - chr3_3:1657927-1657946 Msa0437710:CDS 25.0%
TAATGATAAGGATATGGCTA+TGG - chr3_3:1657139-1657158 Msa0437710:three_prime_UTR 30.0%
! AATTGTGTTACCTTTGACTT+TGG + chr3_3:1657299-1657318 None:intergenic 30.0%
AAGTCAAAGGTAACACAATT+AGG - chr3_3:1657299-1657318 Msa0437710:three_prime_UTR 30.0%
AGTCAAAGGTAACACAATTA+GGG - chr3_3:1657300-1657319 Msa0437710:three_prime_UTR 30.0%
ATCAGAATCAGAATGGAATT+TGG + chr3_3:1657347-1657366 None:intergenic 30.0%
CAATTCAATCAGAATCAGAA+TGG + chr3_3:1657354-1657373 None:intergenic 30.0%
TCTGATTCTGATTGAATTGT+AGG - chr3_3:1657355-1657374 Msa0437710:CDS 30.0%
GATTCTAACTGATATCAGTA+TGG - chr3_3:1657493-1657512 Msa0437710:intron 30.0%
GTTAACAAATACATGACTGA+AGG - chr3_3:1657572-1657591 Msa0437710:intron 30.0%
TTGTTTGTGAATTTCAGAGA+AGG - chr3_3:1657681-1657700 Msa0437710:CDS 30.0%
AAAGAAATTCAGTGTTACAG+AGG - chr3_3:1657731-1657750 Msa0437710:CDS 30.0%
ATATTATGTGAACTACTGCT+TGG - chr3_3:1657996-1658015 Msa0437710:exon 30.0%
TAATGATAAGGATATGGCTA+TGG - chr3_3:1657139-1657158 Msa0437710:three_prime_UTR 30.0%
! AATTGTGTTACCTTTGACTT+TGG + chr3_3:1657299-1657318 None:intergenic 30.0%
AAGTCAAAGGTAACACAATT+AGG - chr3_3:1657299-1657318 Msa0437710:three_prime_UTR 30.0%
AGTCAAAGGTAACACAATTA+GGG - chr3_3:1657300-1657319 Msa0437710:three_prime_UTR 30.0%
ATCAGAATCAGAATGGAATT+TGG + chr3_3:1657347-1657366 None:intergenic 30.0%
CAATTCAATCAGAATCAGAA+TGG + chr3_3:1657354-1657373 None:intergenic 30.0%
TCTGATTCTGATTGAATTGT+AGG - chr3_3:1657355-1657374 Msa0437710:CDS 30.0%
GATTCTAACTGATATCAGTA+TGG - chr3_3:1657493-1657512 Msa0437710:intron 30.0%
GTTAACAAATACATGACTGA+AGG - chr3_3:1657572-1657591 Msa0437710:intron 30.0%
TTGTTTGTGAATTTCAGAGA+AGG - chr3_3:1657681-1657700 Msa0437710:CDS 30.0%
AAAGAAATTCAGTGTTACAG+AGG - chr3_3:1657731-1657750 Msa0437710:CDS 30.0%
ATATTATGTGAACTACTGCT+TGG - chr3_3:1657996-1658015 Msa0437710:exon 30.0%
GGGAGATAATGATAAGGATA+TGG - chr3_3:1657133-1657152 Msa0437710:three_prime_UTR 35.0%
TCGCTGTTGAACAGAAAAAA+TGG - chr3_3:1657175-1657194 Msa0437710:three_prime_UTR 35.0%
TGATTGAATTGTAGGTTCAG+AGG - chr3_3:1657363-1657382 Msa0437710:CDS 35.0%
! TTTTCGTTGCAGTACATTCA+TGG - chr3_3:1657446-1657465 Msa0437710:CDS 35.0%
! AAGAAGAGCTTATTAGTCTC+AGG - chr3_3:1657543-1657562 Msa0437710:intron 35.0%
! AGAAGAGCTTATTAGTCTCA+GGG - chr3_3:1657544-1657563 Msa0437710:intron 35.0%
ATACATGACTGAAGGAGATT+TGG - chr3_3:1657580-1657599 Msa0437710:intron 35.0%
TTCAGTGTTACAGAGGAATA+AGG - chr3_3:1657738-1657757 Msa0437710:CDS 35.0%
AGAGGAATAAGGCATATTCA+GGG - chr3_3:1657749-1657768 Msa0437710:CDS 35.0%
AATAACTGCAGGACATTGAA+GGG - chr3_3:1657800-1657819 Msa0437710:intron 35.0%
GGGAGATAATGATAAGGATA+TGG - chr3_3:1657133-1657152 Msa0437710:three_prime_UTR 35.0%
TCGCTGTTGAACAGAAAAAA+TGG - chr3_3:1657175-1657194 Msa0437710:three_prime_UTR 35.0%
TGATTGAATTGTAGGTTCAG+AGG - chr3_3:1657363-1657382 Msa0437710:CDS 35.0%
! TTTTCGTTGCAGTACATTCA+TGG - chr3_3:1657446-1657465 Msa0437710:CDS 35.0%
! AAGAAGAGCTTATTAGTCTC+AGG - chr3_3:1657543-1657562 Msa0437710:intron 35.0%
! AGAAGAGCTTATTAGTCTCA+GGG - chr3_3:1657544-1657563 Msa0437710:intron 35.0%
ATACATGACTGAAGGAGATT+TGG - chr3_3:1657580-1657599 Msa0437710:intron 35.0%
TTCAGTGTTACAGAGGAATA+AGG - chr3_3:1657738-1657757 Msa0437710:CDS 35.0%
AGAGGAATAAGGCATATTCA+GGG - chr3_3:1657749-1657768 Msa0437710:CDS 35.0%
AATAACTGCAGGACATTGAA+GGG - chr3_3:1657800-1657819 Msa0437710:intron 35.0%
ACTCTCGGGAGATAATGATA+AGG - chr3_3:1657127-1657146 Msa0437710:three_prime_UTR 40.0%
TTGGAGATGATTGAGAGTGA+AGG + chr3_3:1657227-1657246 None:intergenic 40.0%
TCACTCTCAATCATCTCCAA+AGG - chr3_3:1657227-1657246 Msa0437710:three_prime_UTR 40.0%
AACTGGGAAAGAAACTCGAT+TGG + chr3_3:1657267-1657286 None:intergenic 40.0%
!! ACTTTGGAGTGTTGAGAACT+GGG + chr3_3:1657283-1657302 None:intergenic 40.0%
TCTCAACACTCCAAAGTCAA+AGG - chr3_3:1657286-1657305 Msa0437710:three_prime_UTR 40.0%
TTGCAGTACATTCATGGAGT+TGG - chr3_3:1657452-1657471 Msa0437710:CDS 40.0%
AGTACATTCATGGAGTTGGA+AGG - chr3_3:1657456-1657475 Msa0437710:CDS 40.0%
CAGAGGAATAAGGCATATTC+AGG - chr3_3:1657748-1657767 Msa0437710:CDS 40.0%
CAATGTCCTGCAGTTATTCT+TGG + chr3_3:1657798-1657817 None:intergenic 40.0%
GAATAACTGCAGGACATTGA+AGG - chr3_3:1657799-1657818 Msa0437710:intron 40.0%
ACTCTCGGGAGATAATGATA+AGG - chr3_3:1657127-1657146 Msa0437710:three_prime_UTR 40.0%
TTGGAGATGATTGAGAGTGA+AGG + chr3_3:1657227-1657246 None:intergenic 40.0%
TCACTCTCAATCATCTCCAA+AGG - chr3_3:1657227-1657246 Msa0437710:three_prime_UTR 40.0%
AACTGGGAAAGAAACTCGAT+TGG + chr3_3:1657267-1657286 None:intergenic 40.0%
!! ACTTTGGAGTGTTGAGAACT+GGG + chr3_3:1657283-1657302 None:intergenic 40.0%
TCTCAACACTCCAAAGTCAA+AGG - chr3_3:1657286-1657305 Msa0437710:three_prime_UTR 40.0%
TTGCAGTACATTCATGGAGT+TGG - chr3_3:1657452-1657471 Msa0437710:CDS 40.0%
AGTACATTCATGGAGTTGGA+AGG - chr3_3:1657456-1657475 Msa0437710:CDS 40.0%
CAGAGGAATAAGGCATATTC+AGG - chr3_3:1657748-1657767 Msa0437710:CDS 40.0%
CAATGTCCTGCAGTTATTCT+TGG + chr3_3:1657798-1657817 None:intergenic 40.0%
GAATAACTGCAGGACATTGA+AGG - chr3_3:1657799-1657818 Msa0437710:intron 40.0%
ACAAACACTCTCAATGCCTG+TGG - chr3_3:1657199-1657218 Msa0437710:three_prime_UTR 45.0%
TCAATCATCTCCAAAGGCCA+TGG - chr3_3:1657233-1657252 Msa0437710:three_prime_UTR 45.0%
!! GACTTTGGAGTGTTGAGAAC+TGG + chr3_3:1657284-1657303 None:intergenic 45.0%
AACATTGTGTGCGTTCGTGT+TGG - chr3_3:1657389-1657408 Msa0437710:CDS 45.0%
ATTCAGGGACTTCCTTGTAG+AGG - chr3_3:1657764-1657783 Msa0437710:CDS 45.0%
AGCGTACCAAGAATAACTGC+AGG - chr3_3:1657789-1657808 Msa0437710:CDS 45.0%
CAGGACATTGAAGGGTAAGA+AGG - chr3_3:1657808-1657827 Msa0437710:intron 45.0%
GGTAAGAAGGTTACTGTTGC+TGG - chr3_3:1657821-1657840 Msa0437710:intron 45.0%
ACAAACACTCTCAATGCCTG+TGG - chr3_3:1657199-1657218 Msa0437710:three_prime_UTR 45.0%
TCAATCATCTCCAAAGGCCA+TGG - chr3_3:1657233-1657252 Msa0437710:three_prime_UTR 45.0%
!! GACTTTGGAGTGTTGAGAAC+TGG + chr3_3:1657284-1657303 None:intergenic 45.0%
AACATTGTGTGCGTTCGTGT+TGG - chr3_3:1657389-1657408 Msa0437710:CDS 45.0%
ATTCAGGGACTTCCTTGTAG+AGG - chr3_3:1657764-1657783 Msa0437710:CDS 45.0%
AGCGTACCAAGAATAACTGC+AGG - chr3_3:1657789-1657808 Msa0437710:CDS 45.0%
CAGGACATTGAAGGGTAAGA+AGG - chr3_3:1657808-1657827 Msa0437710:intron 45.0%
GGTAAGAAGGTTACTGTTGC+TGG - chr3_3:1657821-1657840 Msa0437710:intron 45.0%
!! ATTGAGAGTGAAGGTGCCAC+AGG + chr3_3:1657218-1657237 None:intergenic 50.0%
CTCGATTGGAGAAGTGACCA+TGG + chr3_3:1657253-1657272 None:intergenic 50.0%
ATTGTGTGCGTTCGTGTTGG+TGG - chr3_3:1657392-1657411 Msa0437710:CDS 50.0%
TTGGTACGCTGTCCTCTACA+AGG + chr3_3:1657779-1657798 None:intergenic 50.0%
!! ATTGAGAGTGAAGGTGCCAC+AGG + chr3_3:1657218-1657237 None:intergenic 50.0%
CTCGATTGGAGAAGTGACCA+TGG + chr3_3:1657253-1657272 None:intergenic 50.0%
ATTGTGTGCGTTCGTGTTGG+TGG - chr3_3:1657392-1657411 Msa0437710:CDS 50.0%
TTGGTACGCTGTCCTCTACA+AGG + chr3_3:1657779-1657798 None:intergenic 50.0%
GGAGAAGTGACCATGGCCTT+TGG + chr3_3:1657246-1657265 None:intergenic 55.0%
GGAGAAGTGACCATGGCCTT+TGG + chr3_3:1657246-1657265 None:intergenic 55.0%
!! GTGCGTTCGTGTTGGTGGTG+TGG - chr3_3:1657397-1657416 Msa0437710:CDS 60.0%
!! GTGCGTTCGTGTTGGTGGTG+TGG - chr3_3:1657397-1657416 Msa0437710:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 1657126 1658065 1657126 ID=Msa0437710;Name=Msa0437710
chr3_3 mRNA 1657126 1658065 1657126 ID=Msa0437710-mRNA-1;Parent=Msa0437710;Name=Msa0437710-mRNA-1;_AED=0.09;_eAED=0.09;_QI=68|1|1|1|1|1|3|206|166
chr3_3 exon 1657126 1657493 1657126 ID=Msa0437710-mRNA-1:exon:234;Parent=Msa0437710-mRNA-1
chr3_3 exon 1657590 1657814 1657590 ID=Msa0437710-mRNA-1:exon:233;Parent=Msa0437710-mRNA-1
chr3_3 exon 1657884 1658065 1657884 ID=Msa0437710-mRNA-1:exon:232;Parent=Msa0437710-mRNA-1
chr3_3 five_prime_UTR 1657998 1658065 1657998 ID=Msa0437710-mRNA-1:five_prime_utr;Parent=Msa0437710-mRNA-1
chr3_3 CDS 1657884 1657997 1657884 ID=Msa0437710-mRNA-1:cds;Parent=Msa0437710-mRNA-1
chr3_3 CDS 1657590 1657814 1657590 ID=Msa0437710-mRNA-1:cds;Parent=Msa0437710-mRNA-1
chr3_3 CDS 1657332 1657493 1657332 ID=Msa0437710-mRNA-1:cds;Parent=Msa0437710-mRNA-1
chr3_3 three_prime_UTR 1657126 1657331 1657126 ID=Msa0437710-mRNA-1:three_prime_utr;Parent=Msa0437710-mRNA-1
Gene Sequence

>Msa0437710

ATGGTACAAACACTCTCAATGCCTGTGGCACCTTCACTCTCAATCATCTCCAAAGGCCATGGTCACTTCTCCAATCGAGTTTCTTTCCCAGTTCTCAACACTCCAAAGTCAAAGGTTCAGAGGCTAAACATTGTGTGCGTTCGTGTTGGTGGTGTGGAAATTCCAAACAACAAGAGAATTGAATTTTCGTTGCAGTACATTCATGGAGTTGGAAGGAACAGAGCTAGACAGATTCTAACTGATATCAGTATGGAGAATAAAGTTACAAAGGAATTGAGTGAAGAAGAGCTTATTAGTCTCAGGGATGAAGTTAACAAATACATGACTGAAGGAGATTTGAGAAGGTTTAATGCACTTAATATAAAGAGGTTGAAAGAAATTCAGTGTTACAGAGGAATAAGGCATATTCAGGGACTTCCTTGTAGAGGACAGCGTACCAAGAATAACTGCAGGACATTGAAGGGTAAGAAGGTTACTGTTGCTGGAAAGAAGAAAAAGTAA

Protein sequence

>Msa0437710

MVQTLSMPVAPSLSIISKGHGHFSNRVSFPVLNTPKSKVQRLNIVCVRVGGVEIPNNKRIEFSLQYIHGVGRNRARQILTDISMENKVTKELSEEELISLRDEVNKYMTEGDLRRFNALNIKRLKEIQCYRGIRHIQGLPCRGQRTKNNCRTLKGKKVTVAGKKKK*