AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0382590


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0382590 MtrunA17_Chr3g0137861 100.000 80 0 0 1 80 61 140 8.23e-54 163
Msa0382590 MtrunA17_Chr4g0063651 63.750 80 28 1 1 79 53 132 1.09e-31 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0382590 AT3G47650.1 68.750 80 25 0 1 80 57 136 6.51e-37 120

Find 28 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAATGAAGTATGTAATAA+TGG 0.243773 3_1:+85229539 None:intergenic
GTGCCTCCTGTTGGCTTTGC+GGG 0.255239 3_1:-85230066 Msa0382590:intron
TCAGCACAGATGACACTATT+TGG 0.263290 3_1:+85230392 None:intergenic
TGCAATGGAGCTGGATTTAT+CGG 0.322631 3_1:-85229810 Msa0382590:CDS
TCAATGAAGTATGTAATAAT+GGG 0.409734 3_1:+85229540 None:intergenic
TTATTACATACTTCATTGAA+TGG 0.423113 3_1:-85229536 Msa0382590:three_prime_UTR
GGTGCCTCCTGTTGGCTTTG+CGG 0.447694 3_1:-85230067 Msa0382590:CDS
TTGGATCTGTCCCTCCCTAC+TGG 0.458506 3_1:+85229766 None:intergenic
TTCGATGGACTGTTTAAAGC+TGG 0.460757 3_1:-85230088 Msa0382590:CDS
CAGTTCACTTGTAGCCATAG+TGG 0.465843 3_1:-85229651 Msa0382590:three_prime_UTR
TAGGTACCCGCAAAGCCAAC+AGG 0.473779 3_1:+85230060 None:intergenic
CTGAACTTGTTCGCAGTCGT+TGG 0.486092 3_1:+85229747 None:intergenic
TTAAAGCTGGTGCCTCCTGT+TGG 0.514045 3_1:-85230075 Msa0382590:CDS
TGTGGGAATTGCAATGGAGC+TGG 0.521634 3_1:-85229819 Msa0382590:CDS
GGCAGGAAGGAGATGTTATG+TGG 0.530714 3_1:-85229837 Msa0382590:CDS
TGTGCTGATTGTGATGGAAA+TGG 0.538508 3_1:-85230377 Msa0382590:intron
GCAGGAAGGAGATGTTATGT+GGG 0.542628 3_1:-85229836 Msa0382590:CDS
TGCTCTCAATGCAAAGGTAG+CGG 0.551522 3_1:-85230130 Msa0382590:CDS
CTTGAGCACATATGACCAGT+AGG 0.554604 3_1:-85229781 Msa0382590:exon
ATGTTATGTGGGAATTGCAA+TGG 0.609174 3_1:-85229825 Msa0382590:CDS
AATGGAGCTGGATTTATCGG+TGG 0.609254 3_1:-85229807 Msa0382590:CDS
TTGAGCACATATGACCAGTA+GGG 0.613108 3_1:-85229780 Msa0382590:exon
ATTGTCTGCTCTCAATGCAA+AGG 0.622596 3_1:-85230136 Msa0382590:CDS
GTCATCTGTGCTGATTGTGA+TGG 0.623087 3_1:-85230383 Msa0382590:CDS
AGCACATATGACCAGTAGGG+AGG 0.624035 3_1:-85229777 Msa0382590:exon
CACTATCATACTGATGCTCA+AGG 0.627147 3_1:-85229598 Msa0382590:three_prime_UTR
GCACATATGACCAGTAGGGA+GGG 0.642431 3_1:-85229776 Msa0382590:exon
GTACCCGCAAAGCCAACAGG+AGG 0.718423 3_1:+85230063 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAATAAAAAAATGC+AGG - chr3_1:85230326-85230345 Msa0382590:intron 10.0%
!! AAAAAAAAATAAAAAAATGC+AGG - chr3_1:85230326-85230345 Msa0382590:intron 10.0%
!!! TTATATTTTGTGTAATTAAC+AGG - chr3_1:85229785-85229804 Msa0382590:CDS 15.0%
!!! ATAGAATGATTTTACTAATT+AGG + chr3_1:85229910-85229929 None:intergenic 15.0%
!! AAAATTTGCATTTAACAATT+AGG + chr3_1:85229970-85229989 None:intergenic 15.0%
!!! TTATATTTTGTGTAATTAAC+AGG - chr3_1:85229785-85229804 Msa0382590:CDS 15.0%
!!! ATAGAATGATTTTACTAATT+AGG + chr3_1:85229910-85229929 None:intergenic 15.0%
!! AAAATTTGCATTTAACAATT+AGG + chr3_1:85229970-85229989 None:intergenic 15.0%
!!! AGATGACATATGATTTTATA+AGG - chr3_1:85229596-85229615 Msa0382590:three_prime_UTR 20.0%
!! CGATGAACAATAATAATATA+AGG + chr3_1:85230077-85230096 None:intergenic 20.0%
!! TCAATGAAGTATGTAATAAT+GGG + chr3_1:85230411-85230430 None:intergenic 20.0%
!! TTCAATGAAGTATGTAATAA+TGG + chr3_1:85230412-85230431 None:intergenic 20.0%
!! TTATTACATACTTCATTGAA+TGG - chr3_1:85230412-85230431 Msa0382590:CDS 20.0%
!!! AGATGACATATGATTTTATA+AGG - chr3_1:85229596-85229615 Msa0382590:three_prime_UTR 20.0%
!! CGATGAACAATAATAATATA+AGG + chr3_1:85230077-85230096 None:intergenic 20.0%
!! TCAATGAAGTATGTAATAAT+GGG + chr3_1:85230411-85230430 None:intergenic 20.0%
!! TTCAATGAAGTATGTAATAA+TGG + chr3_1:85230412-85230431 None:intergenic 20.0%
!! TTATTACATACTTCATTGAA+TGG - chr3_1:85230412-85230431 Msa0382590:CDS 20.0%
!!! TATTTGGTTTTGTGTTTTGT+TGG + chr3_1:85229543-85229562 None:intergenic 25.0%
! CAAGAGAAAATATACATCTA+CGG - chr3_1:85229749-85229768 Msa0382590:three_prime_UTR 25.0%
! TAATAATATAAGGCACATTG+TGG + chr3_1:85230067-85230086 None:intergenic 25.0%
!!! TTTTTTTTTAGCAACCACTA+TGG + chr3_1:85230314-85230333 None:intergenic 25.0%
!!! TATTTGGTTTTGTGTTTTGT+TGG + chr3_1:85229543-85229562 None:intergenic 25.0%
! CAAGAGAAAATATACATCTA+CGG - chr3_1:85229749-85229768 Msa0382590:three_prime_UTR 25.0%
! TAATAATATAAGGCACATTG+TGG + chr3_1:85230067-85230086 None:intergenic 25.0%
!!! TTTTTTTTTAGCAACCACTA+TGG + chr3_1:85230314-85230333 None:intergenic 25.0%
AACGATTTACATGCTCATAA+CGG + chr3_1:85229675-85229694 None:intergenic 30.0%
TGCTTCTTGTAATGTATTTG+TGG - chr3_1:85229710-85229729 Msa0382590:three_prime_UTR 30.0%
AATGTATTTGTGGTTGTTGA+AGG - chr3_1:85229720-85229739 Msa0382590:three_prime_UTR 30.0%
! AACTCTGTTGATATTTTCGA+TGG - chr3_1:85229845-85229864 Msa0382590:intron 30.0%
AACGATTTACATGCTCATAA+CGG + chr3_1:85229675-85229694 None:intergenic 30.0%
TGCTTCTTGTAATGTATTTG+TGG - chr3_1:85229710-85229729 Msa0382590:three_prime_UTR 30.0%
AATGTATTTGTGGTTGTTGA+AGG - chr3_1:85229720-85229739 Msa0382590:three_prime_UTR 30.0%
! AACTCTGTTGATATTTTCGA+TGG - chr3_1:85229845-85229864 Msa0382590:intron 30.0%
AAGGCTTCATTGTATTCTAG+AGG + chr3_1:85230005-85230024 None:intergenic 35.0%
! AATGAAGCCTTATGATCAGT+AGG - chr3_1:85230014-85230033 Msa0382590:intron 35.0%
! ATGAAGCCTTATGATCAGTA+GGG - chr3_1:85230015-85230034 Msa0382590:intron 35.0%
!!! TTCATCGTTTTTTACTCCAG+AGG - chr3_1:85230090-85230109 Msa0382590:CDS 35.0%
ATGTTATGTGGGAATTGCAA+TGG - chr3_1:85230123-85230142 Msa0382590:CDS 35.0%
! TTGTTGGTTGTCATTTGTAG+CGG + chr3_1:85229527-85229546 None:intergenic 35.0%
AAGGCTTCATTGTATTCTAG+AGG + chr3_1:85230005-85230024 None:intergenic 35.0%
! AATGAAGCCTTATGATCAGT+AGG - chr3_1:85230014-85230033 Msa0382590:intron 35.0%
! ATGAAGCCTTATGATCAGTA+GGG - chr3_1:85230015-85230034 Msa0382590:intron 35.0%
!!! TTCATCGTTTTTTACTCCAG+AGG - chr3_1:85230090-85230109 Msa0382590:CDS 35.0%
ATGTTATGTGGGAATTGCAA+TGG - chr3_1:85230123-85230142 Msa0382590:CDS 35.0%
TCAGCACAGATGACACTATT+TGG + chr3_1:85229559-85229578 None:intergenic 40.0%
!! TGTGCTGATTGTGATGGAAA+TGG - chr3_1:85229571-85229590 Msa0382590:three_prime_UTR 40.0%
ATTGTCTGCTCTCAATGCAA+AGG - chr3_1:85229812-85229831 Msa0382590:CDS 40.0%
!! TTCGATGGACTGTTTAAAGC+TGG - chr3_1:85229860-85229879 Msa0382590:intron 40.0%
TGCAATGGAGCTGGATTTAT+CGG - chr3_1:85230138-85230157 Msa0382590:CDS 40.0%
TTGAGCACATATGACCAGTA+GGG - chr3_1:85230168-85230187 Msa0382590:intron 40.0%
CACTATCATACTGATGCTCA+AGG - chr3_1:85230350-85230369 Msa0382590:intron 40.0%
TCAGCACAGATGACACTATT+TGG + chr3_1:85229559-85229578 None:intergenic 40.0%
!! TGTGCTGATTGTGATGGAAA+TGG - chr3_1:85229571-85229590 Msa0382590:three_prime_UTR 40.0%
ATTGTCTGCTCTCAATGCAA+AGG - chr3_1:85229812-85229831 Msa0382590:CDS 40.0%
!! TTCGATGGACTGTTTAAAGC+TGG - chr3_1:85229860-85229879 Msa0382590:intron 40.0%
TGCAATGGAGCTGGATTTAT+CGG - chr3_1:85230138-85230157 Msa0382590:CDS 40.0%
TTGAGCACATATGACCAGTA+GGG - chr3_1:85230168-85230187 Msa0382590:intron 40.0%
CACTATCATACTGATGCTCA+AGG - chr3_1:85230350-85230369 Msa0382590:intron 40.0%
!! GTCATCTGTGCTGATTGTGA+TGG - chr3_1:85229565-85229584 Msa0382590:three_prime_UTR 45.0%
TGCTCTCAATGCAAAGGTAG+CGG - chr3_1:85229818-85229837 Msa0382590:CDS 45.0%
! AAGCCTTATGATCAGTAGGG+AGG - chr3_1:85230018-85230037 Msa0382590:intron 45.0%
GTTCCTCCCTACTGATCATA+AGG + chr3_1:85230024-85230043 None:intergenic 45.0%
!!! TCGTTTTTTACTCCAGAGGC+AGG - chr3_1:85230094-85230113 Msa0382590:CDS 45.0%
! TTTTTACTCCAGAGGCAGGA+AGG - chr3_1:85230098-85230117 Msa0382590:CDS 45.0%
GCAGGAAGGAGATGTTATGT+GGG - chr3_1:85230112-85230131 Msa0382590:CDS 45.0%
AATGGAGCTGGATTTATCGG+TGG - chr3_1:85230141-85230160 Msa0382590:CDS 45.0%
CTTGAGCACATATGACCAGT+AGG - chr3_1:85230167-85230186 Msa0382590:intron 45.0%
CAGTTCACTTGTAGCCATAG+TGG - chr3_1:85230297-85230316 Msa0382590:intron 45.0%
!! GTCATCTGTGCTGATTGTGA+TGG - chr3_1:85229565-85229584 Msa0382590:three_prime_UTR 45.0%
TGCTCTCAATGCAAAGGTAG+CGG - chr3_1:85229818-85229837 Msa0382590:CDS 45.0%
! AAGCCTTATGATCAGTAGGG+AGG - chr3_1:85230018-85230037 Msa0382590:intron 45.0%
GTTCCTCCCTACTGATCATA+AGG + chr3_1:85230024-85230043 None:intergenic 45.0%
!!! TCGTTTTTTACTCCAGAGGC+AGG - chr3_1:85230094-85230113 Msa0382590:CDS 45.0%
! TTTTTACTCCAGAGGCAGGA+AGG - chr3_1:85230098-85230117 Msa0382590:CDS 45.0%
GCAGGAAGGAGATGTTATGT+GGG - chr3_1:85230112-85230131 Msa0382590:CDS 45.0%
AATGGAGCTGGATTTATCGG+TGG - chr3_1:85230141-85230160 Msa0382590:CDS 45.0%
CTTGAGCACATATGACCAGT+AGG - chr3_1:85230167-85230186 Msa0382590:intron 45.0%
CAGTTCACTTGTAGCCATAG+TGG - chr3_1:85230297-85230316 Msa0382590:intron 45.0%
TTAAAGCTGGTGCCTCCTGT+TGG - chr3_1:85229873-85229892 Msa0382590:intron 50.0%
TAACATCTCCTTCCTGCCTC+TGG + chr3_1:85230109-85230128 None:intergenic 50.0%
GGCAGGAAGGAGATGTTATG+TGG - chr3_1:85230111-85230130 Msa0382590:CDS 50.0%
TGTGGGAATTGCAATGGAGC+TGG - chr3_1:85230129-85230148 Msa0382590:CDS 50.0%
AGCACATATGACCAGTAGGG+AGG - chr3_1:85230171-85230190 Msa0382590:intron 50.0%
GCACATATGACCAGTAGGGA+GGG - chr3_1:85230172-85230191 Msa0382590:intron 50.0%
! CTGAACTTGTTCGCAGTCGT+TGG + chr3_1:85230204-85230223 None:intergenic 50.0%
TTAAAGCTGGTGCCTCCTGT+TGG - chr3_1:85229873-85229892 Msa0382590:intron 50.0%
TAACATCTCCTTCCTGCCTC+TGG + chr3_1:85230109-85230128 None:intergenic 50.0%
GGCAGGAAGGAGATGTTATG+TGG - chr3_1:85230111-85230130 Msa0382590:CDS 50.0%
TGTGGGAATTGCAATGGAGC+TGG - chr3_1:85230129-85230148 Msa0382590:CDS 50.0%
AGCACATATGACCAGTAGGG+AGG - chr3_1:85230171-85230190 Msa0382590:intron 50.0%
GCACATATGACCAGTAGGGA+GGG - chr3_1:85230172-85230191 Msa0382590:intron 50.0%
! CTGAACTTGTTCGCAGTCGT+TGG + chr3_1:85230204-85230223 None:intergenic 50.0%
TAGGTACCCGCAAAGCCAAC+AGG + chr3_1:85229891-85229910 None:intergenic 55.0%
TTGGATCTGTCCCTCCCTAC+TGG + chr3_1:85230185-85230204 None:intergenic 55.0%
TAGGTACCCGCAAAGCCAAC+AGG + chr3_1:85229891-85229910 None:intergenic 55.0%
TTGGATCTGTCCCTCCCTAC+TGG + chr3_1:85230185-85230204 None:intergenic 55.0%
!! GGTGCCTCCTGTTGGCTTTG+CGG - chr3_1:85229881-85229900 Msa0382590:intron 60.0%
!! GTGCCTCCTGTTGGCTTTGC+GGG - chr3_1:85229882-85229901 Msa0382590:intron 60.0%
GTACCCGCAAAGCCAACAGG+AGG + chr3_1:85229888-85229907 None:intergenic 60.0%
!! GGTGCCTCCTGTTGGCTTTG+CGG - chr3_1:85229881-85229900 Msa0382590:intron 60.0%
!! GTGCCTCCTGTTGGCTTTGC+GGG - chr3_1:85229882-85229901 Msa0382590:intron 60.0%
GTACCCGCAAAGCCAACAGG+AGG + chr3_1:85229888-85229907 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 85229526 85230444 85229526 ID=Msa0382590;Name=Msa0382590
chr3_1 mRNA 85229526 85230444 85229526 ID=Msa0382590-mRNA-1;Parent=Msa0382590;Name=Msa0382590-mRNA-1;_AED=0.12;_eAED=0.12;_QI=0|0.5|0.33|1|1|1|3|256|80
chr3_1 exon 85229526 85229860 85229526 ID=Msa0382590-mRNA-1:exon:22338;Parent=Msa0382590-mRNA-1
chr3_1 exon 85230067 85230163 85230067 ID=Msa0382590-mRNA-1:exon:22337;Parent=Msa0382590-mRNA-1
chr3_1 exon 85230378 85230444 85230378 ID=Msa0382590-mRNA-1:exon:22336;Parent=Msa0382590-mRNA-1
chr3_1 CDS 85230378 85230444 85230378 ID=Msa0382590-mRNA-1:cds;Parent=Msa0382590-mRNA-1
chr3_1 CDS 85230067 85230163 85230067 ID=Msa0382590-mRNA-1:cds;Parent=Msa0382590-mRNA-1
chr3_1 CDS 85229782 85229860 85229782 ID=Msa0382590-mRNA-1:cds;Parent=Msa0382590-mRNA-1
chr3_1 three_prime_UTR 85229526 85229781 85229526 ID=Msa0382590-mRNA-1:three_prime_utr;Parent=Msa0382590-mRNA-1
Gene Sequence

>Msa0382590

GCTACAAATGACAACCAACAAAACACAAAACCAAATAGTGTCATCTGTGCTGATTGTGATGGAAATGGAGCTATTGTCTGCTCTCAATGCAAAGGTAGCGGAGTGAACTCTGTTGATATTTTCGATGGACTGTTTAAAGCTGGTGCCTCCTGTTGGCTTTGCGGAGGCAGGAAGGAGATGTTATGTGGGAATTGCAATGGAGCTGGATTTATCGGTGGCTTCTTGAGCACATATGACCAGTAG

Protein sequence

>Msa0382590

ATNDNQQNTKPNSVICADCDGNGAIVCSQCKGSGVNSVDIFDGLFKAGASCWLCGGRKEMLCGNCNGAGFIGGFLSTYDQ*