AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0627180

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0627180 MtrunA17_Chr4g0003291 67.273 220 29 4 1 182 1 215 6.42e-82 246
Msa0627180 MtrunA17_Chr4g0063941 62.136 103 35 3 2 102 37 137 1.56e-31 116
Msa0627180 MtrunA17_Chr6g0476191 50.980 102 42 3 2 96 36 136 4.97e-25 95.5
Msa0627180 MtrunA17_Chr6g0476211 48.571 105 46 3 2 99 36 139 1.32e-24 93.2
Msa0627180 MtrunA17_Chr6g0476221 50.980 102 42 3 2 96 36 136 1.47e-24 94.4
Msa0627180 MtrunA17_Chr4g0063971 64.384 73 24 2 2 74 37 107 1.64e-24 97.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0627180 AT1G15340.1 61.111 90 32 3 3 91 22 109 2.96e-28 108
Msa0627180 AT3G15790.1 56.667 90 37 2 3 91 22 110 7.36e-26 100
Msa0627180 AT3G15790.3 56.667 90 37 2 3 91 22 110 7.36e-26 100
Msa0627180 AT3G15790.2 56.667 90 37 2 3 91 22 110 7.36e-26 100

Find 50 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTACTTCCTCAATTGTCTTT+TGG 0.222954 4_3:+7215888 None:intergenic
AAAACGATCTCAGGCTTTCT+TGG 0.259149 4_3:+7215940 None:intergenic
TTCCTCAGCATTGGCATCAC+TGG 0.334487 4_3:+7215618 None:intergenic
CTGACATATCAGAGTTTGAT+TGG 0.338629 4_3:-7215843 Msa0627180:CDS
AAGTACCTGAATCAACATTC+TGG 0.339044 4_3:-7215871 Msa0627180:CDS
GATTCCCAGAATGTTGATTC+AGG 0.339175 4_3:+7215866 None:intergenic
CAAGGCGATCAACAAGGATT+AGG 0.339385 4_3:-7215804 Msa0627180:CDS
TGCGGGTAGTGGGGTTGTTT+TGG 0.343609 4_3:+7215774 None:intergenic
GGCTCAGCTTGTGCGGGTAG+TGG 0.359634 4_3:+7215763 None:intergenic
TCAGAGTTTGATTGGGGAAC+CGG 0.377737 4_3:-7215835 Msa0627180:CDS
GCTCAGCTTGTGCGGGTAGT+GGG 0.392438 4_3:+7215764 None:intergenic
TGTCGCTGAAGTTCCGCAAT+TGG 0.398489 4_3:-7215385 Msa0627180:CDS
AAGGCGATCAACAAGGATTA+GGG 0.431961 4_3:-7215803 Msa0627180:CDS
TTTAGATGAGGCCAAGGAAA+AGG 0.437553 4_3:-7215671 Msa0627180:CDS
TGACATATCAGAGTTTGATT+GGG 0.437668 4_3:-7215842 Msa0627180:CDS
CTAATCCTTGTTGATCGCCT+TGG 0.440946 4_3:+7215805 None:intergenic
AAACGTAGTCGGAAATCATC+TGG 0.461272 4_3:-7215733 Msa0627180:CDS
GAACCTATCTCTTCTCCAGT+TGG 0.465821 4_3:+7215910 None:intergenic
TTGCTTAATTTCCTCAGCAT+TGG 0.472724 4_3:+7215609 None:intergenic
CAATCAAACTCTGATATGTC+AGG 0.483410 4_3:+7215844 None:intergenic
ACGTTGATGGCAGAACCAAC+AGG 0.490032 4_3:-7215342 Msa0627180:CDS
TCCTCAGCATTGGCATCACT+GGG 0.492506 4_3:+7215619 None:intergenic
TTCGAAGGCTCAGCTTGTGC+GGG 0.494527 4_3:+7215757 None:intergenic
AGTACCTGAATCAACATTCT+GGG 0.500963 4_3:-7215870 Msa0627180:CDS
CTTCGAAGGCTCAGCTTGTG+CGG 0.503235 4_3:+7215756 None:intergenic
GGAGCAATGAAAACGATCTC+AGG 0.509160 4_3:+7215931 None:intergenic
TCAAGTGGAAGACACGTTGA+TGG 0.510828 4_3:-7215355 Msa0627180:CDS
AGACACTTCTATGACTGAAC+TGG 0.511273 4_3:-7215442 Msa0627180:CDS
GAAATCATCTGGTTCAAAGA+AGG 0.513211 4_3:-7215722 Msa0627180:CDS
TTAGATGAGGCCAAGGAAAA+GGG 0.513798 4_3:-7215670 Msa0627180:CDS
GCTCCAACTGGAGAAGAGAT+AGG 0.514124 4_3:-7215913 Msa0627180:CDS
TTCCGACTACGTTTCTTCGA+AGG 0.515566 4_3:+7215742 None:intergenic
CAGTTCTTCACTAAGAAGAA+AGG 0.540054 4_3:-7215967 Msa0627180:CDS
TGATCGCCTTGGCATCTCGC+CGG 0.540439 4_3:+7215816 None:intergenic
GGGGAACCGGCGAGATGCCA+AGG 0.542959 4_3:-7215822 Msa0627180:CDS
CTCAGCTTGTGCGGGTAGTG+GGG 0.553139 4_3:+7215765 None:intergenic
ATCAACGTGTCTTCCACTTG+AGG 0.566400 4_3:+7215357 None:intergenic
ATCTCCTTTAGATGAGGCCA+AGG 0.569072 4_3:-7215677 Msa0627180:CDS
GCATCTGGAAAAGGCTCAAG+TGG 0.573495 4_3:-7215466 Msa0627180:intron
GACATATCAGAGTTTGATTG+GGG 0.603872 4_3:-7215841 Msa0627180:CDS
GGAAATTAAGCAAAGTAATG+CGG 0.612687 4_3:-7215599 Msa0627180:CDS
AACTGAATCTCCTTTAGATG+AGG 0.620219 4_3:-7215683 Msa0627180:CDS
GCAATTGGAAAATCCTCAAG+TGG 0.631644 4_3:-7215370 Msa0627180:CDS
ATTAAGCAAAGTAATGCGGA+AGG 0.636526 4_3:-7215595 Msa0627180:CDS
AGATGCCAAGGCGATCAACA+AGG 0.640387 4_3:-7215810 Msa0627180:CDS
CGTTGATGGCAGAACCAACA+GGG 0.660262 4_3:-7215341 Msa0627180:CDS
AGCCTTCGAAGAAACGTAGT+CGG 0.661202 4_3:-7215744 Msa0627180:CDS
TAGGTTCCAAAAGACAATTG+AGG 0.662321 4_3:-7215894 Msa0627180:CDS
TGGTTCAAAGAAGGATGACA+AGG 0.662397 4_3:-7215713 Msa0627180:CDS
TCCCAGTGATGCCAATGCTG+AGG 0.700115 4_3:-7215620 Msa0627180:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TGACATATCAGAGTTTGATT+GGG - chr4_3:7215460-7215479 Msa0627180:intron 30.0%
GGAAATTAAGCAAAGTAATG+CGG - chr4_3:7215703-7215722 Msa0627180:CDS 30.0%
CAGTTCTTCACTAAGAAGAA+AGG - chr4_3:7215335-7215354 Msa0627180:CDS 35.0%
TAGGTTCCAAAAGACAATTG+AGG - chr4_3:7215408-7215427 Msa0627180:CDS 35.0%
! GTACTTCCTCAATTGTCTTT+TGG + chr4_3:7215417-7215436 None:intergenic 35.0%
AAGTACCTGAATCAACATTC+TGG - chr4_3:7215431-7215450 Msa0627180:CDS 35.0%
AGTACCTGAATCAACATTCT+GGG - chr4_3:7215432-7215451 Msa0627180:CDS 35.0%
CAATCAAACTCTGATATGTC+AGG + chr4_3:7215461-7215480 None:intergenic 35.0%
CTGACATATCAGAGTTTGAT+TGG - chr4_3:7215459-7215478 Msa0627180:intron 35.0%
GACATATCAGAGTTTGATTG+GGG - chr4_3:7215461-7215480 Msa0627180:intron 35.0%
! GAAATCATCTGGTTCAAAGA+AGG - chr4_3:7215580-7215599 Msa0627180:intron 35.0%
AACTGAATCTCCTTTAGATG+AGG - chr4_3:7215619-7215638 Msa0627180:CDS 35.0%
TTGCTTAATTTCCTCAGCAT+TGG + chr4_3:7215696-7215715 None:intergenic 35.0%
ATTAAGCAAAGTAATGCGGA+AGG - chr4_3:7215707-7215726 Msa0627180:CDS 35.0%
TGCACAAAAATTCGTATTGC+CGG + chr4_3:7215785-7215804 None:intergenic 35.0%
! ACTTGAGGATTTTCCAATTG+CGG + chr4_3:7215933-7215952 None:intergenic 35.0%
AAAACGATCTCAGGCTTTCT+TGG + chr4_3:7215365-7215384 None:intergenic 40.0%
! ATCGTTTTCATTGCTCCAAC+TGG - chr4_3:7215377-7215396 Msa0627180:CDS 40.0%
!! GATTCCCAGAATGTTGATTC+AGG + chr4_3:7215439-7215458 None:intergenic 40.0%
AAGGCGATCAACAAGGATTA+GGG - chr4_3:7215499-7215518 Msa0627180:intron 40.0%
AAACGTAGTCGGAAATCATC+TGG - chr4_3:7215569-7215588 Msa0627180:intron 40.0%
TGGTTCAAAGAAGGATGACA+AGG - chr4_3:7215589-7215608 Msa0627180:CDS 40.0%
! TTTTCCTTGGCCTCATCTAA+AGG + chr4_3:7215632-7215651 None:intergenic 40.0%
TTTAGATGAGGCCAAGGAAA+AGG - chr4_3:7215631-7215650 Msa0627180:CDS 40.0%
TTAGATGAGGCCAAGGAAAA+GGG - chr4_3:7215632-7215651 Msa0627180:CDS 40.0%
! AGAAGAGTTACCCTTTTCCT+TGG + chr4_3:7215645-7215664 None:intergenic 40.0%
GAAAAAACCGCATCTGGAAA+AGG - chr4_3:7215827-7215846 Msa0627180:CDS 40.0%
AGACACTTCTATGACTGAAC+TGG - chr4_3:7215860-7215879 Msa0627180:CDS 40.0%
GCAATTGGAAAATCCTCAAG+TGG - chr4_3:7215932-7215951 Msa0627180:CDS 40.0%
GGAGCAATGAAAACGATCTC+AGG + chr4_3:7215374-7215393 None:intergenic 45.0%
GAACCTATCTCTTCTCCAGT+TGG + chr4_3:7215395-7215414 None:intergenic 45.0%
TCAGAGTTTGATTGGGGAAC+CGG - chr4_3:7215467-7215486 Msa0627180:intron 45.0%
CTAATCCTTGTTGATCGCCT+TGG + chr4_3:7215500-7215519 None:intergenic 45.0%
CAAGGCGATCAACAAGGATT+AGG - chr4_3:7215498-7215517 Msa0627180:intron 45.0%
AGCCTTCGAAGAAACGTAGT+CGG - chr4_3:7215558-7215577 Msa0627180:intron 45.0%
TTCCGACTACGTTTCTTCGA+AGG + chr4_3:7215563-7215582 None:intergenic 45.0%
ATCTCCTTTAGATGAGGCCA+AGG - chr4_3:7215625-7215644 Msa0627180:CDS 45.0%
ATCGACGTGTCTTCGACTTA+AGG + chr4_3:7215755-7215774 None:intergenic 45.0%
TTAAGTCGAAGACACGTCGA+TGG - chr4_3:7215754-7215773 Msa0627180:CDS 45.0%
!!! TCCAGATGCGGTTTTTTCAG+CGG + chr4_3:7215825-7215844 None:intergenic 45.0%
! ACTTGAGCCTTTTCCAGATG+CGG + chr4_3:7215837-7215856 None:intergenic 45.0%
ATCAACGTGTCTTCCACTTG+AGG + chr4_3:7215948-7215967 None:intergenic 45.0%
TCAAGTGGAAGACACGTTGA+TGG - chr4_3:7215947-7215966 Msa0627180:CDS 45.0%
GCTCCAACTGGAGAAGAGAT+AGG - chr4_3:7215389-7215408 Msa0627180:CDS 50.0%
AGATGCCAAGGCGATCAACA+AGG - chr4_3:7215492-7215511 Msa0627180:intron 50.0%
!! TCCTCAGCATTGGCATCACT+GGG + chr4_3:7215686-7215705 None:intergenic 50.0%
!! TTCCTCAGCATTGGCATCAC+TGG + chr4_3:7215687-7215706 None:intergenic 50.0%
GCATCTGGAAAAGGCTCAAG+TGG - chr4_3:7215836-7215855 Msa0627180:CDS 50.0%
TGTCGCTGAAGTTCCGCAAT+TGG - chr4_3:7215917-7215936 Msa0627180:CDS 50.0%
!! ACGTTGATGGCAGAACCAAC+AGG - chr4_3:7215960-7215979 Msa0627180:CDS 50.0%
!! CGTTGATGGCAGAACCAACA+GGG - chr4_3:7215961-7215980 Msa0627180:CDS 50.0%
!!! TGCGGGTAGTGGGGTTGTTT+TGG + chr4_3:7215531-7215550 None:intergenic 55.0%
TTCGAAGGCTCAGCTTGTGC+GGG + chr4_3:7215548-7215567 None:intergenic 55.0%
CTTCGAAGGCTCAGCTTGTG+CGG + chr4_3:7215549-7215568 None:intergenic 55.0%
TCCCAGTGATGCCAATGCTG+AGG - chr4_3:7215682-7215701 Msa0627180:CDS 55.0%
AGACACGTCGATGGCAGAAC+CGG - chr4_3:7215763-7215782 Msa0627180:CDS 55.0%
GCCGCTGAAAAAACCGCATC+TGG - chr4_3:7215821-7215840 Msa0627180:CDS 55.0%
TGATCGCCTTGGCATCTCGC+CGG + chr4_3:7215489-7215508 None:intergenic 60.0%
CTCAGCTTGTGCGGGTAGTG+GGG + chr4_3:7215540-7215559 None:intergenic 60.0%
GCTCAGCTTGTGCGGGTAGT+GGG + chr4_3:7215541-7215560 None:intergenic 60.0%
GGCTCAGCTTGTGCGGGTAG+TGG + chr4_3:7215542-7215561 None:intergenic 65.0%
GGGGAACCGGCGAGATGCCA+AGG - chr4_3:7215480-7215499 Msa0627180:intron 70.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 7215332 7215992 7215332 ID=Msa0627180;Name=Msa0627180
chr4_3 mRNA 7215332 7215992 7215332 ID=Msa0627180-mRNA-1;Parent=Msa0627180;Name=Msa0627180-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|0|0|1|1|1|2|0|182
chr4_3 exon 7215588 7215992 7215588 ID=Msa0627180-mRNA-1:exon:2141;Parent=Msa0627180-mRNA-1
chr4_3 exon 7215332 7215475 7215332 ID=Msa0627180-mRNA-1:exon:2140;Parent=Msa0627180-mRNA-1
chr4_3 CDS 7215588 7215992 7215588 ID=Msa0627180-mRNA-1:cds;Parent=Msa0627180-mRNA-1
chr4_3 CDS 7215332 7215475 7215332 ID=Msa0627180-mRNA-1:cds;Parent=Msa0627180-mRNA-1
Gene Sequence

>Msa0627180

ATGCAGTTCTTCACTAAGAAGAAAGGAACACCAAGAAAGCCTGAGATCGTTTTCATTGCTCCAACTGGAGAAGAGATAGGTTCCAAAAGACAATTGAGGAAGTACCTGAATCAACATTCTGGGAATCCTGACATATCAGAGTTTGATTGGGGAACCGGCGAGATGCCAAGGCGATCAACAAGGATTAGGGAGACTGCCAAAACAACCCCACTACCCGCACAAGCTGAGCCTTCGAAGAAACGTAGTCGGAAATCATCTGGTTCAAAGAAGGATGACAAGGAAGCTGAAACTGAATCTCCTTTAGATGAGGCCAAGGAAAAGGGTAACTCTTCTGAAGTACTGAAAGCTGATCCCAGTGATGCCAATGCTGAGGAAATTAAGCAAAGTAATGCGGAAGGTGAAATTGCTCAAGTGGAAGACACTTCTATGACTGAACTGGTGAAACAACTTTCTGATGAAACTTTGAATGCAGTTGTCGCTGAAGTTCCGCAATTGGAAAATCCTCAAGTGGAAGACACGTTGATGGCAGAACCAACAGGGAAACTTTGA
Protein sequence

>Msa0627180

MQFFTKKKGTPRKPEIVFIAPTGEEIGSKRQLRKYLNQHSGNPDISEFDWGTGEMPRRSTRIRETAKTTPLPAQAEPSKKRSRKSSGSKKDDKEAETESPLDEAKEKGNSSEVLKADPSDANAEEIKQSNAEGEIAQVEDTSMTELVKQLSDETLNAVVAEVPQLENPQVEDTLMAEPTGKL*