AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1269730


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1269730 MtrunA17_Chr5g0448271 92.373 118 9 0 1 118 1 118 1.01e-68 202
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1269730 AT4G13500.1 79.487 78 16 0 41 118 48 125 4.39e-41 132
Msa1269730 AT2G05310.1 78.205 78 17 0 41 118 48 125 5.46e-41 132

Find 34 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCCTTATATTATCTTATT+TGG 0.144829 8_3:+2894710 Msa1269730:CDS
ATCAAAGTTTGTGCTCAATT+AGG 0.317774 8_3:+2894350 Msa1269730:CDS
TTTGTTATTACATACTGTTC+TGG 0.320587 8_3:-2894566 None:intergenic
AGAAGTGCTTACAATAAAAT+TGG 0.324738 8_3:-2894853 None:intergenic
TGTGACCTCATCTATCTAAT+TGG 0.325517 8_3:-2894791 None:intergenic
TGAGAAAGTGAAGATGATTT+AGG 0.339562 8_3:-2894293 None:intergenic
ATACCAAATAAGATAATATA+AGG 0.355873 8_3:-2894713 None:intergenic
TACTCGTCCTCTACCGGAAC+TGG 0.385067 8_3:-2894989 None:intergenic
TAAGGAAGTGGCGTCATCAT+TGG 0.409790 8_3:-2894695 None:intergenic
TCACAAATATCCTATCGGTT+TGG 0.435373 8_3:-2894134 None:intergenic
ACACATTACAAGGAAGTGTT+TGG 0.437192 8_3:-2894821 None:intergenic
GCATGTATCATATCCAGTTC+CGG 0.470278 8_3:+2894976 Msa1269730:three_prime_UTR
TTACAAGGAAGTGTTTGGTT+TGG 0.478552 8_3:-2894816 None:intergenic
AGAAGATAGAAGAGTTACTT+TGG 0.480230 8_3:-2894243 None:intergenic
CAAAACATATACATATCGTT+TGG 0.483836 8_3:+2895062 Msa1269730:three_prime_UTR
TACAGATATTGGCAGTCAGC+AGG 0.491895 8_3:+2894653 Msa1269730:intron
GCAATGGCTAAGATTACAAA+AGG 0.495139 8_3:-2894743 None:intergenic
AAATTGTTTATAAATGTGAC+TGG 0.504320 8_3:-2895026 None:intergenic
GATAACAAGTGATGAAATGA+TGG 0.507285 8_3:+2894159 Msa1269730:five_prime_UTR
TAGAAGAGTTACTTTGGCTA+TGG 0.509481 8_3:-2894237 None:intergenic
AAGAGTTACTTTGGCTATGG+TGG 0.517669 8_3:-2894234 None:intergenic
ATCTATCACAAATATCCTAT+CGG 0.526902 8_3:-2894139 None:intergenic
ATCATATCCAGTTCCGGTAG+AGG 0.545395 8_3:+2894982 Msa1269730:three_prime_UTR
AGCACAAACTTTGATACCAA+GGG 0.547969 8_3:-2894342 None:intergenic
TATTCTTACTCGTCCTCTAC+CGG 0.549007 8_3:-2894995 None:intergenic
AATAAGATAATATAAGGAAG+TGG 0.555321 8_3:-2894707 None:intergenic
GAACTGGATATGATACATGC+TGG 0.561899 8_3:-2894973 None:intergenic
CGAGATGAAGAAACCAAGAA+AGG 0.593391 8_3:+2894509 Msa1269730:CDS
CCAACCATTTACAAAAGCAA+TGG 0.600902 8_3:-2894759 None:intergenic
CAGTCAGCAGGAGAGAGAGA+AGG 0.609827 8_3:+2894665 Msa1269730:CDS
AGTACAAAATCCAAACCGAT+AGG 0.615725 8_3:+2894124 Msa1269730:five_prime_UTR
GAGCACAAACTTTGATACCA+AGG 0.618661 8_3:-2894343 None:intergenic
AGGTACCAATTAGATAGATG+AGG 0.649220 8_3:+2894786 Msa1269730:exon
GTGAGAATGAACACATTACA+AGG 0.650557 8_3:-2894831 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTATACTATATGATTAATA+TGG + chr8_3:2894456-2894475 Msa1269730:intron 15.0%
!! ATACCAAATAAGATAATATA+AGG - chr8_3:2894716-2894735 None:intergenic 15.0%
!! GTTATACTATATGATTAATA+TGG + chr8_3:2894456-2894475 Msa1269730:intron 15.0%
!! ATACCAAATAAGATAATATA+AGG - chr8_3:2894716-2894735 None:intergenic 15.0%
!! CAATTCAATTCAACAAAAAA+TGG + chr8_3:2894211-2894230 Msa1269730:exon 20.0%
!! TGTTGGTATATATTTGTATT+AGG + chr8_3:2894482-2894501 Msa1269730:intron 20.0%
!! AATAAGATAATATAAGGAAG+TGG - chr8_3:2894710-2894729 None:intergenic 20.0%
!! CTTCCTTATATTATCTTATT+TGG + chr8_3:2894710-2894729 Msa1269730:CDS 20.0%
!!! TTACTTTTTCACATATGTAA+CGG + chr8_3:2894921-2894940 Msa1269730:three_prime_UTR 20.0%
!! AAATTGTTTATAAATGTGAC+TGG - chr8_3:2895029-2895048 None:intergenic 20.0%
!! CAATTCAATTCAACAAAAAA+TGG + chr8_3:2894211-2894230 Msa1269730:exon 20.0%
!! TGTTGGTATATATTTGTATT+AGG + chr8_3:2894482-2894501 Msa1269730:intron 20.0%
!! AATAAGATAATATAAGGAAG+TGG - chr8_3:2894710-2894729 None:intergenic 20.0%
!! CTTCCTTATATTATCTTATT+TGG + chr8_3:2894710-2894729 Msa1269730:CDS 20.0%
!!! TTACTTTTTCACATATGTAA+CGG + chr8_3:2894921-2894940 Msa1269730:three_prime_UTR 20.0%
!! AAATTGTTTATAAATGTGAC+TGG - chr8_3:2895029-2895048 None:intergenic 20.0%
! ATCTATCACAAATATCCTAT+CGG - chr8_3:2894142-2894161 None:intergenic 25.0%
!!! AAATGAAGTTTTGAAGGTAA+GGG - chr8_3:2894270-2894289 None:intergenic 25.0%
! TATGATTAATATGGTTGTGT+TGG + chr8_3:2894465-2894484 Msa1269730:intron 25.0%
! TGGTATATATTTGTATTAGG+TGG + chr8_3:2894485-2894504 Msa1269730:intron 25.0%
!!! TTTCTTTTTTTCTCCTTTCT+TGG - chr8_3:2894525-2894544 None:intergenic 25.0%
!!! TTTGTTATTACATACTGTTC+TGG - chr8_3:2894569-2894588 None:intergenic 25.0%
! CACTTTGATTAGTAAAAACA+TGG - chr8_3:2894617-2894636 None:intergenic 25.0%
!! TTTTGTGATACTACAGATAT+TGG + chr8_3:2894642-2894661 Msa1269730:intron 25.0%
!! TTTTGTAAATGGTTGGATTA+AGG + chr8_3:2894766-2894785 Msa1269730:CDS 25.0%
!!! AGAAGTGCTTACAATAAAAT+TGG - chr8_3:2894856-2894875 None:intergenic 25.0%
! CAAAACATATACATATCGTT+TGG + chr8_3:2895062-2895081 Msa1269730:three_prime_UTR 25.0%
! ATCTATCACAAATATCCTAT+CGG - chr8_3:2894142-2894161 None:intergenic 25.0%
!!! AAATGAAGTTTTGAAGGTAA+GGG - chr8_3:2894270-2894289 None:intergenic 25.0%
! TATGATTAATATGGTTGTGT+TGG + chr8_3:2894465-2894484 Msa1269730:intron 25.0%
! TGGTATATATTTGTATTAGG+TGG + chr8_3:2894485-2894504 Msa1269730:intron 25.0%
!!! TTTCTTTTTTTCTCCTTTCT+TGG - chr8_3:2894525-2894544 None:intergenic 25.0%
!!! TTTGTTATTACATACTGTTC+TGG - chr8_3:2894569-2894588 None:intergenic 25.0%
! CACTTTGATTAGTAAAAACA+TGG - chr8_3:2894617-2894636 None:intergenic 25.0%
!! TTTTGTGATACTACAGATAT+TGG + chr8_3:2894642-2894661 Msa1269730:intron 25.0%
!! TTTTGTAAATGGTTGGATTA+AGG + chr8_3:2894766-2894785 Msa1269730:CDS 25.0%
!!! AGAAGTGCTTACAATAAAAT+TGG - chr8_3:2894856-2894875 None:intergenic 25.0%
! CAAAACATATACATATCGTT+TGG + chr8_3:2895062-2895081 Msa1269730:three_prime_UTR 25.0%
GATAACAAGTGATGAAATGA+TGG + chr8_3:2894159-2894178 Msa1269730:five_prime_UTR 30.0%
AGAAGATAGAAGAGTTACTT+TGG - chr8_3:2894246-2894265 None:intergenic 30.0%
!!! AATGAAGTTTTGAAGGTAAG+GGG - chr8_3:2894269-2894288 None:intergenic 30.0%
!!! GAAATGAAGTTTTGAAGGTA+AGG - chr8_3:2894271-2894290 None:intergenic 30.0%
!! AGGAAGAAATGAAGTTTTGA+AGG - chr8_3:2894276-2894295 None:intergenic 30.0%
TGAGAAAGTGAAGATGATTT+AGG - chr8_3:2894296-2894315 None:intergenic 30.0%
ATCAAAGTTTGTGCTCAATT+AGG + chr8_3:2894350-2894369 Msa1269730:CDS 30.0%
!! TTAGCCATTGCTTTTGTAAA+TGG + chr8_3:2894755-2894774 Msa1269730:CDS 30.0%
GATAACAAGTGATGAAATGA+TGG + chr8_3:2894159-2894178 Msa1269730:five_prime_UTR 30.0%
AGAAGATAGAAGAGTTACTT+TGG - chr8_3:2894246-2894265 None:intergenic 30.0%
!!! AATGAAGTTTTGAAGGTAAG+GGG - chr8_3:2894269-2894288 None:intergenic 30.0%
!!! GAAATGAAGTTTTGAAGGTA+AGG - chr8_3:2894271-2894290 None:intergenic 30.0%
!! AGGAAGAAATGAAGTTTTGA+AGG - chr8_3:2894276-2894295 None:intergenic 30.0%
TGAGAAAGTGAAGATGATTT+AGG - chr8_3:2894296-2894315 None:intergenic 30.0%
ATCAAAGTTTGTGCTCAATT+AGG + chr8_3:2894350-2894369 Msa1269730:CDS 30.0%
!! TTAGCCATTGCTTTTGTAAA+TGG + chr8_3:2894755-2894774 Msa1269730:CDS 30.0%
AGTACAAAATCCAAACCGAT+AGG + chr8_3:2894124-2894143 Msa1269730:five_prime_UTR 35.0%
! TCACAAATATCCTATCGGTT+TGG - chr8_3:2894137-2894156 None:intergenic 35.0%
! TAGAAGAGTTACTTTGGCTA+TGG - chr8_3:2894240-2894259 None:intergenic 35.0%
! ATACCAAGGGAAGTAGTTTT+TGG - chr8_3:2894332-2894351 None:intergenic 35.0%
AGCACAAACTTTGATACCAA+GGG - chr8_3:2894345-2894364 None:intergenic 35.0%
GCAATGGCTAAGATTACAAA+AGG - chr8_3:2894746-2894765 None:intergenic 35.0%
CCAACCATTTACAAAAGCAA+TGG - chr8_3:2894762-2894781 None:intergenic 35.0%
!! CCATTGCTTTTGTAAATGGT+TGG + chr8_3:2894759-2894778 Msa1269730:CDS 35.0%
AGGTACCAATTAGATAGATG+AGG + chr8_3:2894786-2894805 Msa1269730:exon 35.0%
TGTGACCTCATCTATCTAAT+TGG - chr8_3:2894794-2894813 None:intergenic 35.0%
!! TTACAAGGAAGTGTTTGGTT+TGG - chr8_3:2894819-2894838 None:intergenic 35.0%
!! ACACATTACAAGGAAGTGTT+TGG - chr8_3:2894824-2894843 None:intergenic 35.0%
GTGAGAATGAACACATTACA+AGG - chr8_3:2894834-2894853 None:intergenic 35.0%
AGTACAAAATCCAAACCGAT+AGG + chr8_3:2894124-2894143 Msa1269730:five_prime_UTR 35.0%
! TCACAAATATCCTATCGGTT+TGG - chr8_3:2894137-2894156 None:intergenic 35.0%
! TAGAAGAGTTACTTTGGCTA+TGG - chr8_3:2894240-2894259 None:intergenic 35.0%
! ATACCAAGGGAAGTAGTTTT+TGG - chr8_3:2894332-2894351 None:intergenic 35.0%
AGCACAAACTTTGATACCAA+GGG - chr8_3:2894345-2894364 None:intergenic 35.0%
GCAATGGCTAAGATTACAAA+AGG - chr8_3:2894746-2894765 None:intergenic 35.0%
CCAACCATTTACAAAAGCAA+TGG - chr8_3:2894762-2894781 None:intergenic 35.0%
!! CCATTGCTTTTGTAAATGGT+TGG + chr8_3:2894759-2894778 Msa1269730:CDS 35.0%
AGGTACCAATTAGATAGATG+AGG + chr8_3:2894786-2894805 Msa1269730:exon 35.0%
TGTGACCTCATCTATCTAAT+TGG - chr8_3:2894794-2894813 None:intergenic 35.0%
!! TTACAAGGAAGTGTTTGGTT+TGG - chr8_3:2894819-2894838 None:intergenic 35.0%
!! ACACATTACAAGGAAGTGTT+TGG - chr8_3:2894824-2894843 None:intergenic 35.0%
GTGAGAATGAACACATTACA+AGG - chr8_3:2894834-2894853 None:intergenic 35.0%
!! TGGATTTTGTACTGATCACC+TGG - chr8_3:2894117-2894136 None:intergenic 40.0%
! AAGAGTTACTTTGGCTATGG+TGG - chr8_3:2894237-2894256 None:intergenic 40.0%
!! AGTAGTTTTTGGAGAGGCAA+TGG - chr8_3:2894321-2894340 None:intergenic 40.0%
!! AAGGGAAGTAGTTTTTGGAG+AGG - chr8_3:2894327-2894346 None:intergenic 40.0%
TCTCCAAAAACTACTTCCCT+TGG + chr8_3:2894326-2894345 Msa1269730:CDS 40.0%
GAGCACAAACTTTGATACCA+AGG - chr8_3:2894346-2894365 None:intergenic 40.0%
CGAGATGAAGAAACCAAGAA+AGG + chr8_3:2894509-2894528 Msa1269730:CDS 40.0%
GAACTGGATATGATACATGC+TGG - chr8_3:2894976-2894995 None:intergenic 40.0%
GCATGTATCATATCCAGTTC+CGG + chr8_3:2894976-2894995 Msa1269730:three_prime_UTR 40.0%
TATTCTTACTCGTCCTCTAC+CGG - chr8_3:2894998-2895017 None:intergenic 40.0%
!! TGGATTTTGTACTGATCACC+TGG - chr8_3:2894117-2894136 None:intergenic 40.0%
! AAGAGTTACTTTGGCTATGG+TGG - chr8_3:2894237-2894256 None:intergenic 40.0%
!! AGTAGTTTTTGGAGAGGCAA+TGG - chr8_3:2894321-2894340 None:intergenic 40.0%
!! AAGGGAAGTAGTTTTTGGAG+AGG - chr8_3:2894327-2894346 None:intergenic 40.0%
TCTCCAAAAACTACTTCCCT+TGG + chr8_3:2894326-2894345 Msa1269730:CDS 40.0%
GAGCACAAACTTTGATACCA+AGG - chr8_3:2894346-2894365 None:intergenic 40.0%
CGAGATGAAGAAACCAAGAA+AGG + chr8_3:2894509-2894528 Msa1269730:CDS 40.0%
GAACTGGATATGATACATGC+TGG - chr8_3:2894976-2894995 None:intergenic 40.0%
GCATGTATCATATCCAGTTC+CGG + chr8_3:2894976-2894995 Msa1269730:three_prime_UTR 40.0%
TATTCTTACTCGTCCTCTAC+CGG - chr8_3:2894998-2895017 None:intergenic 40.0%
TACAGATATTGGCAGTCAGC+AGG + chr8_3:2894653-2894672 Msa1269730:intron 45.0%
TAAGGAAGTGGCGTCATCAT+TGG - chr8_3:2894698-2894717 None:intergenic 45.0%
ATCATATCCAGTTCCGGTAG+AGG + chr8_3:2894982-2895001 Msa1269730:three_prime_UTR 45.0%
TACAGATATTGGCAGTCAGC+AGG + chr8_3:2894653-2894672 Msa1269730:intron 45.0%
TAAGGAAGTGGCGTCATCAT+TGG - chr8_3:2894698-2894717 None:intergenic 45.0%
ATCATATCCAGTTCCGGTAG+AGG + chr8_3:2894982-2895001 Msa1269730:three_prime_UTR 45.0%
CAGTCAGCAGGAGAGAGAGA+AGG + chr8_3:2894665-2894684 Msa1269730:CDS 55.0%
TACTCGTCCTCTACCGGAAC+TGG - chr8_3:2894992-2895011 None:intergenic 55.0%
CAGTCAGCAGGAGAGAGAGA+AGG + chr8_3:2894665-2894684 Msa1269730:CDS 55.0%
TACTCGTCCTCTACCGGAAC+TGG - chr8_3:2894992-2895011 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 2894113 2895122 2894113 ID=Msa1269730;Name=Msa1269730
chr8_3 mRNA 2894113 2895122 2894113 ID=Msa1269730-mRNA-1;Parent=Msa1269730;Name=Msa1269730-mRNA-1;_AED=0.11;_eAED=0.11;_QI=117|1|1|1|1|1|3|320|118
chr8_3 exon 2894113 2894371 2894113 ID=Msa1269730-mRNA-1:exon:968;Parent=Msa1269730-mRNA-1
chr8_3 exon 2894504 2894573 2894504 ID=Msa1269730-mRNA-1:exon:969;Parent=Msa1269730-mRNA-1
chr8_3 exon 2894658 2895122 2894658 ID=Msa1269730-mRNA-1:exon:970;Parent=Msa1269730-mRNA-1
chr8_3 five_prime_UTR 2894113 2894229 2894113 ID=Msa1269730-mRNA-1:five_prime_utr;Parent=Msa1269730-mRNA-1
chr8_3 CDS 2894230 2894371 2894230 ID=Msa1269730-mRNA-1:cds;Parent=Msa1269730-mRNA-1
chr8_3 CDS 2894504 2894573 2894504 ID=Msa1269730-mRNA-1:cds;Parent=Msa1269730-mRNA-1
chr8_3 CDS 2894658 2894802 2894658 ID=Msa1269730-mRNA-1:cds;Parent=Msa1269730-mRNA-1
chr8_3 three_prime_UTR 2894803 2895122 2894803 ID=Msa1269730-mRNA-1:three_prime_utr;Parent=Msa1269730-mRNA-1
Gene Sequence

>Msa1269730

ATGGCCACCATAGCCAAAGTAACTCTTCTATCTTCTCCCCTTACCTTCAAAACTTCATTTCTTCCTAAATCATCTTCACTTTCTCACACCATTGCCTCTCCAAAAACTACTTCCCTTGGTATCAAAGTTTGTGCTCAATTAGGTGGTCGAGATGAAGAAACCAAGAAAGGAGAAAAAAAGAAATTTATAACTAGAGAACAAGAACCAGAACAATATTGGCAGTCAGCAGGAGAGAGAGAAGGAGAGAATCCAATGATGACGCCACTTCCTTATATTATCTTATTTGGTATGTCAACTCCTTTTGTAATCTTAGCCATTGCTTTTGTAAATGGTTGGATTAAGGTACCAATTAGATAG

Protein sequence

>Msa1269730

MATIAKVTLLSSPLTFKTSFLPKSSSLSHTIASPKTTSLGIKVCAQLGGRDEETKKGEKKKFITREQEPEQYWQSAGEREGENPMMTPLPYIILFGMSTPFVILAIAFVNGWIKVPIR*