AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0745010


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0745010 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
Msa0745010 AT4G13500.1 79.487 78 16 0 41 118 48 125 4.39e-41 132
Msa0745010 AT2G05310.1 78.205 78 17 0 41 118 48 125 5.46e-41 132

Find 35 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 5_1:-66156664 Msa0745010:CDS
ATCAAAGTTTGTGCTCAATT+AGG 0.317774 5_1:-66157023 Msa0745010:intron
TTTGTTATTACATACTGTTC+TGG 0.320587 5_1:+66156808 None:intergenic
AGAAGTGCTTACAATAAAAT+TGG 0.324738 5_1:+66156521 None:intergenic
TGTGACCTCATCTATCTAAT+TGG 0.325517 5_1:+66156583 None:intergenic
TGAGAAAGTGAAGATGATTT+AGG 0.339562 5_1:+66157080 None:intergenic
ATACCAAATAAGATAATATA+AGG 0.355873 5_1:+66156661 None:intergenic
TACTCGTCCTCTACCGGAAC+TGG 0.385067 5_1:+66156385 None:intergenic
TAAGGAAGTGGCGTCATCAT+TGG 0.409790 5_1:+66156679 None:intergenic
TCACAAATATCCTATCGGTT+TGG 0.435373 5_1:+66157239 None:intergenic
ACACATTACAAGGAAGTGTT+TGG 0.437192 5_1:+66156553 None:intergenic
GCATGTATCATATCCAGTTC+CGG 0.470278 5_1:-66156398 Msa0745010:three_prime_UTR
TTACAAGGAAGTGTTTGGTT+TGG 0.478552 5_1:+66156558 None:intergenic
AGAAGATAGAAGAGTTACTT+TGG 0.480230 5_1:+66157130 None:intergenic
CAAAACATATACATATCGTT+TGG 0.483836 5_1:-66156312 Msa0745010:three_prime_UTR
TACAGATATTGGCAGTCAGC+AGG 0.491895 5_1:-66156721 Msa0745010:intron
GCAATGGCTAAGATTACAAA+AGG 0.495139 5_1:+66156631 None:intergenic
AAATTGTTTATAAATGTGAC+TGG 0.504320 5_1:+66156348 None:intergenic
GATAACAAGTGATGAAATGA+TGG 0.507285 5_1:-66157214 Msa0745010:five_prime_UTR
TAGAAGAGTTACTTTGGCTA+TGG 0.509481 5_1:+66157136 None:intergenic
AAGAGTTACTTTGGCTATGG+TGG 0.517669 5_1:+66157139 None:intergenic
ATCTATCACAAATATCCTAT+CGG 0.526902 5_1:+66157234 None:intergenic
ATCATATCCAGTTCCGGTAG+AGG 0.545395 5_1:-66156392 Msa0745010:three_prime_UTR
AGCACAAACTTTGATACCAA+GGG 0.547969 5_1:+66157031 None:intergenic
TATTCTTACTCGTCCTCTAC+CGG 0.549007 5_1:+66156379 None:intergenic
AATAAGATAATATAAGGAAG+TGG 0.555321 5_1:+66156667 None:intergenic
TTACTTGTTCACATATGTAA+CGG 0.557335 5_1:-66156453 Msa0745010:three_prime_UTR
GAACTGGATATGATACATGC+TGG 0.561899 5_1:+66156401 None:intergenic
CGAGATGAAGAAACCAAGAA+AGG 0.593391 5_1:-66156865 Msa0745010:CDS
CCAACCATTTACAAAAGCAA+TGG 0.600902 5_1:+66156615 None:intergenic
CAGTCAGCAGGAGAGAGAGA+AGG 0.609827 5_1:-66156709 Msa0745010:CDS
AGTACAAAATCCAAACCGAT+AGG 0.615725 5_1:-66157249 Msa0745010:five_prime_UTR
GAGCACAAACTTTGATACCA+AGG 0.618661 5_1:+66157030 None:intergenic
AGGTACCAATTAGATAGATG+AGG 0.649220 5_1:-66156588 Msa0745010:exon
GTGAGAATGAACACATTACA+AGG 0.650557 5_1:+66156543 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTATACTATATGATTAATA+TGG - chr5_1:66156616-66156635 Msa0745010:CDS 15.0%
!! ATACCAAATAAGATAATATA+AGG + chr5_1:66156876-66156895 None:intergenic 15.0%
!! GTTATACTATATGATTAATA+TGG - chr5_1:66156616-66156635 Msa0745010:CDS 15.0%
!! ATACCAAATAAGATAATATA+AGG + chr5_1:66156876-66156895 None:intergenic 15.0%
!! CAATTCAATTCAACAAAAAA+TGG - chr5_1:66156372-66156391 Msa0745010:three_prime_UTR 20.0%
!! TGTTGGTATATATTTGTATT+AGG - chr5_1:66156642-66156661 Msa0745010:CDS 20.0%
!! AATAAGATAATATAAGGAAG+TGG + chr5_1:66156870-66156889 None:intergenic 20.0%
!! CTTCCTTATATTATCTTATT+TGG - chr5_1:66156870-66156889 Msa0745010:CDS 20.0%
!! AAATTGTTTATAAATGTGAC+TGG + chr5_1:66157189-66157208 None:intergenic 20.0%
!! CAATTCAATTCAACAAAAAA+TGG - chr5_1:66156372-66156391 Msa0745010:three_prime_UTR 20.0%
!! TGTTGGTATATATTTGTATT+AGG - chr5_1:66156642-66156661 Msa0745010:CDS 20.0%
!! AATAAGATAATATAAGGAAG+TGG + chr5_1:66156870-66156889 None:intergenic 20.0%
!! CTTCCTTATATTATCTTATT+TGG - chr5_1:66156870-66156889 Msa0745010:CDS 20.0%
!! AAATTGTTTATAAATGTGAC+TGG + chr5_1:66157189-66157208 None:intergenic 20.0%
! ATCTATCACAAATATCCTAT+CGG + chr5_1:66156303-66156322 None:intergenic 25.0%
!!! AAATGAAGTTTTGAAGGTAA+GGG + chr5_1:66156431-66156450 None:intergenic 25.0%
! TATGATTAATATGGTTGTGT+TGG - chr5_1:66156625-66156644 Msa0745010:CDS 25.0%
! TGGTATATATTTGTATTAGG+TGG - chr5_1:66156645-66156664 Msa0745010:CDS 25.0%
!!! TTTCTTTTTTTCTCCTTTCT+TGG + chr5_1:66156685-66156704 None:intergenic 25.0%
!!! TTTGTTATTACATACTGTTC+TGG + chr5_1:66156729-66156748 None:intergenic 25.0%
! CACTTTGATTAGTAAAAACA+TGG + chr5_1:66156777-66156796 None:intergenic 25.0%
!! TTTTGTGATACTACAGATAT+TGG - chr5_1:66156802-66156821 Msa0745010:intron 25.0%
!! TTTTGTAAATGGTTGGATTA+AGG - chr5_1:66156926-66156945 Msa0745010:intron 25.0%
!!! AGAAGTGCTTACAATAAAAT+TGG + chr5_1:66157016-66157035 None:intergenic 25.0%
! TTACTTGTTCACATATGTAA+CGG - chr5_1:66157081-66157100 Msa0745010:CDS 25.0%
! CAAAACATATACATATCGTT+TGG - chr5_1:66157222-66157241 Msa0745010:five_prime_UTR 25.0%
! ATCTATCACAAATATCCTAT+CGG + chr5_1:66156303-66156322 None:intergenic 25.0%
!!! AAATGAAGTTTTGAAGGTAA+GGG + chr5_1:66156431-66156450 None:intergenic 25.0%
! TATGATTAATATGGTTGTGT+TGG - chr5_1:66156625-66156644 Msa0745010:CDS 25.0%
! TGGTATATATTTGTATTAGG+TGG - chr5_1:66156645-66156664 Msa0745010:CDS 25.0%
!!! TTTCTTTTTTTCTCCTTTCT+TGG + chr5_1:66156685-66156704 None:intergenic 25.0%
!!! TTTGTTATTACATACTGTTC+TGG + chr5_1:66156729-66156748 None:intergenic 25.0%
! CACTTTGATTAGTAAAAACA+TGG + chr5_1:66156777-66156796 None:intergenic 25.0%
!! TTTTGTGATACTACAGATAT+TGG - chr5_1:66156802-66156821 Msa0745010:intron 25.0%
!! TTTTGTAAATGGTTGGATTA+AGG - chr5_1:66156926-66156945 Msa0745010:intron 25.0%
!!! AGAAGTGCTTACAATAAAAT+TGG + chr5_1:66157016-66157035 None:intergenic 25.0%
! TTACTTGTTCACATATGTAA+CGG - chr5_1:66157081-66157100 Msa0745010:CDS 25.0%
! CAAAACATATACATATCGTT+TGG - chr5_1:66157222-66157241 Msa0745010:five_prime_UTR 25.0%
GATAACAAGTGATGAAATGA+TGG - chr5_1:66156320-66156339 Msa0745010:three_prime_UTR 30.0%
AGAAGATAGAAGAGTTACTT+TGG + chr5_1:66156407-66156426 None:intergenic 30.0%
!!! AATGAAGTTTTGAAGGTAAG+GGG + chr5_1:66156430-66156449 None:intergenic 30.0%
!!! GAAATGAAGTTTTGAAGGTA+AGG + chr5_1:66156432-66156451 None:intergenic 30.0%
!! AGGAAGAAATGAAGTTTTGA+AGG + chr5_1:66156437-66156456 None:intergenic 30.0%
TGAGAAAGTGAAGATGATTT+AGG + chr5_1:66156457-66156476 None:intergenic 30.0%
ATCAAAGTTTGTGCTCAATT+AGG - chr5_1:66156511-66156530 Msa0745010:three_prime_UTR 30.0%
!! TTAGCCATTGCTTTTGTAAA+TGG - chr5_1:66156915-66156934 Msa0745010:intron 30.0%
GATAACAAGTGATGAAATGA+TGG - chr5_1:66156320-66156339 Msa0745010:three_prime_UTR 30.0%
AGAAGATAGAAGAGTTACTT+TGG + chr5_1:66156407-66156426 None:intergenic 30.0%
!!! AATGAAGTTTTGAAGGTAAG+GGG + chr5_1:66156430-66156449 None:intergenic 30.0%
!!! GAAATGAAGTTTTGAAGGTA+AGG + chr5_1:66156432-66156451 None:intergenic 30.0%
!! AGGAAGAAATGAAGTTTTGA+AGG + chr5_1:66156437-66156456 None:intergenic 30.0%
TGAGAAAGTGAAGATGATTT+AGG + chr5_1:66156457-66156476 None:intergenic 30.0%
ATCAAAGTTTGTGCTCAATT+AGG - chr5_1:66156511-66156530 Msa0745010:three_prime_UTR 30.0%
!! TTAGCCATTGCTTTTGTAAA+TGG - chr5_1:66156915-66156934 Msa0745010:intron 30.0%
AGTACAAAATCCAAACCGAT+AGG - chr5_1:66156285-66156304 Msa0745010:three_prime_UTR 35.0%
! TCACAAATATCCTATCGGTT+TGG + chr5_1:66156298-66156317 None:intergenic 35.0%
! TAGAAGAGTTACTTTGGCTA+TGG + chr5_1:66156401-66156420 None:intergenic 35.0%
! ATACCAAGGGAAGTAGTTTT+TGG + chr5_1:66156493-66156512 None:intergenic 35.0%
AGCACAAACTTTGATACCAA+GGG + chr5_1:66156506-66156525 None:intergenic 35.0%
GCAATGGCTAAGATTACAAA+AGG + chr5_1:66156906-66156925 None:intergenic 35.0%
CCAACCATTTACAAAAGCAA+TGG + chr5_1:66156922-66156941 None:intergenic 35.0%
!! CCATTGCTTTTGTAAATGGT+TGG - chr5_1:66156919-66156938 Msa0745010:intron 35.0%
AGGTACCAATTAGATAGATG+AGG - chr5_1:66156946-66156965 Msa0745010:intron 35.0%
TGTGACCTCATCTATCTAAT+TGG + chr5_1:66156954-66156973 None:intergenic 35.0%
!! TTACAAGGAAGTGTTTGGTT+TGG + chr5_1:66156979-66156998 None:intergenic 35.0%
!! ACACATTACAAGGAAGTGTT+TGG + chr5_1:66156984-66157003 None:intergenic 35.0%
GTGAGAATGAACACATTACA+AGG + chr5_1:66156994-66157013 None:intergenic 35.0%
AGTACAAAATCCAAACCGAT+AGG - chr5_1:66156285-66156304 Msa0745010:three_prime_UTR 35.0%
! TCACAAATATCCTATCGGTT+TGG + chr5_1:66156298-66156317 None:intergenic 35.0%
! TAGAAGAGTTACTTTGGCTA+TGG + chr5_1:66156401-66156420 None:intergenic 35.0%
! ATACCAAGGGAAGTAGTTTT+TGG + chr5_1:66156493-66156512 None:intergenic 35.0%
AGCACAAACTTTGATACCAA+GGG + chr5_1:66156506-66156525 None:intergenic 35.0%
GCAATGGCTAAGATTACAAA+AGG + chr5_1:66156906-66156925 None:intergenic 35.0%
CCAACCATTTACAAAAGCAA+TGG + chr5_1:66156922-66156941 None:intergenic 35.0%
!! CCATTGCTTTTGTAAATGGT+TGG - chr5_1:66156919-66156938 Msa0745010:intron 35.0%
AGGTACCAATTAGATAGATG+AGG - chr5_1:66156946-66156965 Msa0745010:intron 35.0%
TGTGACCTCATCTATCTAAT+TGG + chr5_1:66156954-66156973 None:intergenic 35.0%
!! TTACAAGGAAGTGTTTGGTT+TGG + chr5_1:66156979-66156998 None:intergenic 35.0%
!! ACACATTACAAGGAAGTGTT+TGG + chr5_1:66156984-66157003 None:intergenic 35.0%
GTGAGAATGAACACATTACA+AGG + chr5_1:66156994-66157013 None:intergenic 35.0%
!! TGGATTTTGTACTGATCACC+TGG + chr5_1:66156278-66156297 None:intergenic 40.0%
! AAGAGTTACTTTGGCTATGG+TGG + chr5_1:66156398-66156417 None:intergenic 40.0%
!! AGTAGTTTTTGGAGAGGCAA+TGG + chr5_1:66156482-66156501 None:intergenic 40.0%
!! AAGGGAAGTAGTTTTTGGAG+AGG + chr5_1:66156488-66156507 None:intergenic 40.0%
TCTCCAAAAACTACTTCCCT+TGG - chr5_1:66156487-66156506 Msa0745010:three_prime_UTR 40.0%
GAGCACAAACTTTGATACCA+AGG + chr5_1:66156507-66156526 None:intergenic 40.0%
CGAGATGAAGAAACCAAGAA+AGG - chr5_1:66156669-66156688 Msa0745010:CDS 40.0%
GAACTGGATATGATACATGC+TGG + chr5_1:66157136-66157155 None:intergenic 40.0%
GCATGTATCATATCCAGTTC+CGG - chr5_1:66157136-66157155 Msa0745010:CDS 40.0%
TATTCTTACTCGTCCTCTAC+CGG + chr5_1:66157158-66157177 None:intergenic 40.0%
!! TGGATTTTGTACTGATCACC+TGG + chr5_1:66156278-66156297 None:intergenic 40.0%
! AAGAGTTACTTTGGCTATGG+TGG + chr5_1:66156398-66156417 None:intergenic 40.0%
!! AGTAGTTTTTGGAGAGGCAA+TGG + chr5_1:66156482-66156501 None:intergenic 40.0%
!! AAGGGAAGTAGTTTTTGGAG+AGG + chr5_1:66156488-66156507 None:intergenic 40.0%
TCTCCAAAAACTACTTCCCT+TGG - chr5_1:66156487-66156506 Msa0745010:three_prime_UTR 40.0%
GAGCACAAACTTTGATACCA+AGG + chr5_1:66156507-66156526 None:intergenic 40.0%
CGAGATGAAGAAACCAAGAA+AGG - chr5_1:66156669-66156688 Msa0745010:CDS 40.0%
GAACTGGATATGATACATGC+TGG + chr5_1:66157136-66157155 None:intergenic 40.0%
GCATGTATCATATCCAGTTC+CGG - chr5_1:66157136-66157155 Msa0745010:CDS 40.0%
TATTCTTACTCGTCCTCTAC+CGG + chr5_1:66157158-66157177 None:intergenic 40.0%
TACAGATATTGGCAGTCAGC+AGG - chr5_1:66156813-66156832 Msa0745010:intron 45.0%
TAAGGAAGTGGCGTCATCAT+TGG + chr5_1:66156858-66156877 None:intergenic 45.0%
ATCATATCCAGTTCCGGTAG+AGG - chr5_1:66157142-66157161 Msa0745010:CDS 45.0%
TACAGATATTGGCAGTCAGC+AGG - chr5_1:66156813-66156832 Msa0745010:intron 45.0%
TAAGGAAGTGGCGTCATCAT+TGG + chr5_1:66156858-66156877 None:intergenic 45.0%
ATCATATCCAGTTCCGGTAG+AGG - chr5_1:66157142-66157161 Msa0745010:CDS 45.0%
CAGTCAGCAGGAGAGAGAGA+AGG - chr5_1:66156825-66156844 Msa0745010:CDS 55.0%
TACTCGTCCTCTACCGGAAC+TGG + chr5_1:66157152-66157171 None:intergenic 55.0%
CAGTCAGCAGGAGAGAGAGA+AGG - chr5_1:66156825-66156844 Msa0745010:CDS 55.0%
TACTCGTCCTCTACCGGAAC+TGG + chr5_1:66157152-66157171 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 66156274 66157282 66156274 ID=Msa0745010;Name=Msa0745010
chr5_1 mRNA 66156274 66157282 66156274 ID=Msa0745010-mRNA-1;Parent=Msa0745010;Name=Msa0745010-mRNA-1;_AED=0.05;_eAED=0.05;_QI=117|1|1|1|1|1|3|320|118
chr5_1 exon 66156274 66156738 66156274 ID=Msa0745010-mRNA-1:exon:19680;Parent=Msa0745010-mRNA-1
chr5_1 exon 66156823 66156892 66156823 ID=Msa0745010-mRNA-1:exon:19679;Parent=Msa0745010-mRNA-1
chr5_1 exon 66157024 66157282 66157024 ID=Msa0745010-mRNA-1:exon:19678;Parent=Msa0745010-mRNA-1
chr5_1 five_prime_UTR 66157166 66157282 66157166 ID=Msa0745010-mRNA-1:five_prime_utr;Parent=Msa0745010-mRNA-1
chr5_1 CDS 66157024 66157165 66157024 ID=Msa0745010-mRNA-1:cds;Parent=Msa0745010-mRNA-1
chr5_1 CDS 66156823 66156892 66156823 ID=Msa0745010-mRNA-1:cds;Parent=Msa0745010-mRNA-1
chr5_1 CDS 66156594 66156738 66156594 ID=Msa0745010-mRNA-1:cds;Parent=Msa0745010-mRNA-1
chr5_1 three_prime_UTR 66156274 66156593 66156274 ID=Msa0745010-mRNA-1:three_prime_utr;Parent=Msa0745010-mRNA-1
Gene Sequence

>Msa0745010

ATGGCCACCATAGCCAAAGTAACTCTTCTATCTTCTCCCCTTACCTTCAAAACTTCATTTCTTCCTAAATCATCTTCACTTTCTCACACCATTGCCTCTCCAAAAACTACTTCCCTTGGTATCAAAGTTTGTGCTCAATTAGGTGGTCGAGATGAAGAAACCAAGAAAGGAGAAAAAAAGAAATTTATAACTAGAGAACAAGAACCAGAACAATATTGGCAGTCAGCAGGAGAGAGAGAAGGAGAGAATCCAATGATGACGCCACTTCCTTATATTATCTTATTTGGTATGTCAACTCCTTTTGTAATCTTAGCCATTGCTTTTGTAAATGGTTGGATTAAGGTACCAATTAGATAG

Protein sequence

>Msa0745010

MATIAKVTLLSSPLTFKTSFLPKSSSLSHTIASPKTTSLGIKVCAQLGGRDEETKKGEKKKFITREQEPEQYWQSAGEREGENPMMTPLPYIILFGMSTPFVILAIAFVNGWIKVPIR*