AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0825960


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0825960 MtrunA17_Chr5g0448271 92.373 118 9 0 1 118 1 118 2.33e-68 201
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0825960 AT4G13500.1 79.487 78 16 0 41 118 48 125 5.35e-41 132
Msa0825960 AT2G05310.1 78.205 78 17 0 41 118 48 125 6.30e-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 5_3:+66050444 Msa0825960:CDS
ATCAAAGTTTGTGCTCAATT+AGG 0.317774 5_3:+66050085 Msa0825960:CDS
TTTGTTATTACATACTGTTC+TGG 0.320587 5_3:-66050300 None:intergenic
AGAAGTGCTTACAATAAAAT+TGG 0.324738 5_3:-66050587 None:intergenic
TGTGACCTCATCTATCTAAT+TGG 0.325517 5_3:-66050525 None:intergenic
TGAGAAAGTGAAGATGATTT+AGG 0.339562 5_3:-66050028 None:intergenic
ATACCAAATAAGATAATATA+AGG 0.355873 5_3:-66050447 None:intergenic
TACTCGTCCTCTACCGGAAC+TGG 0.385067 5_3:-66050723 None:intergenic
TAAGGAAGTGGCGTCATCAT+TGG 0.409790 5_3:-66050429 None:intergenic
TCACAAATATCCTATCGGTT+TGG 0.435373 5_3:-66049869 None:intergenic
ACACATTACAAGGAAGTGTT+TGG 0.437192 5_3:-66050555 None:intergenic
GCATGTATCATATCCAGTTC+CGG 0.470278 5_3:+66050710 Msa0825960:three_prime_UTR
TTACAAGGAAGTGTTTGGTT+TGG 0.478552 5_3:-66050550 None:intergenic
CAAAACATATACATATCGTT+TGG 0.483836 5_3:+66050796 Msa0825960:three_prime_UTR
AGAAGATAGAAGAGTAACTT+TGG 0.487391 5_3:-66049978 None:intergenic
TACAGATATTGGCAGTCAGC+AGG 0.491895 5_3:+66050387 Msa0825960:intron
GCAATGGCTAAGATTACAAA+AGG 0.495139 5_3:-66050477 None:intergenic
AAATTGTTTATAAATGTGAC+TGG 0.504320 5_3:-66050760 None:intergenic
GATAACAAGTGATGAAATGA+TGG 0.507285 5_3:+66049894 Msa0825960:five_prime_UTR
ATCTATCACAAATATCCTAT+CGG 0.526902 5_3:-66049874 None:intergenic
AAGAGTAACTTTGGCTATGG+TGG 0.537510 5_3:-66049969 None:intergenic
TAGAAGAGTAACTTTGGCTA+TGG 0.540044 5_3:-66049972 None:intergenic
ATCATATCCAGTTCCGGTAG+AGG 0.545395 5_3:+66050716 Msa0825960:three_prime_UTR
AGCACAAACTTTGATACCAA+GGG 0.547969 5_3:-66050077 None:intergenic
TATTCTTACTCGTCCTCTAC+CGG 0.549007 5_3:-66050729 None:intergenic
AATAAGATAATATAAGGAAG+TGG 0.555321 5_3:-66050441 None:intergenic
GAACTGGATATGATACATGC+TGG 0.561899 5_3:-66050707 None:intergenic
CGAGATGAAGAAACCAAGAA+AGG 0.593391 5_3:+66050243 Msa0825960:CDS
CCAACCATTTACAAAAGCAA+TGG 0.600902 5_3:-66050493 None:intergenic
CAGTCAGCAGGAGAGAGAGA+AGG 0.609827 5_3:+66050399 Msa0825960:CDS
AGTACAAAATCCAAACCGAT+AGG 0.615725 5_3:+66049859 Msa0825960:five_prime_UTR
GAGCACAAACTTTGATACCA+AGG 0.618661 5_3:-66050078 None:intergenic
AGGTACCAATTAGATAGATG+AGG 0.649220 5_3:+66050520 Msa0825960:exon
GTGAGAATGAACACATTACA+AGG 0.650557 5_3:-66050565 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTTATACTATATGATTAATA+TGG + chr5_3:66050190-66050209 Msa0825960:intron 15.0%
!! ATACCAAATAAGATAATATA+AGG - chr5_3:66050450-66050469 None:intergenic 15.0%
!! GTTATACTATATGATTAATA+TGG + chr5_3:66050190-66050209 Msa0825960:intron 15.0%
!! ATACCAAATAAGATAATATA+AGG - chr5_3:66050450-66050469 None:intergenic 15.0%
!! CAATTCAATTCAACAAAAAA+TGG + chr5_3:66049946-66049965 Msa0825960:exon 20.0%
!! TGTTGGTATATATTTGTATT+AGG + chr5_3:66050216-66050235 Msa0825960:intron 20.0%
!! AATAAGATAATATAAGGAAG+TGG - chr5_3:66050444-66050463 None:intergenic 20.0%
!! CTTCCTTATATTATCTTATT+TGG + chr5_3:66050444-66050463 Msa0825960:CDS 20.0%
!!! TTACTTTTTCACATATGTAA+CGG + chr5_3:66050655-66050674 Msa0825960:three_prime_UTR 20.0%
!! AAATTGTTTATAAATGTGAC+TGG - chr5_3:66050763-66050782 None:intergenic 20.0%
!! CAATTCAATTCAACAAAAAA+TGG + chr5_3:66049946-66049965 Msa0825960:exon 20.0%
!! TGTTGGTATATATTTGTATT+AGG + chr5_3:66050216-66050235 Msa0825960:intron 20.0%
!! AATAAGATAATATAAGGAAG+TGG - chr5_3:66050444-66050463 None:intergenic 20.0%
!! CTTCCTTATATTATCTTATT+TGG + chr5_3:66050444-66050463 Msa0825960:CDS 20.0%
!!! TTACTTTTTCACATATGTAA+CGG + chr5_3:66050655-66050674 Msa0825960:three_prime_UTR 20.0%
!! AAATTGTTTATAAATGTGAC+TGG - chr5_3:66050763-66050782 None:intergenic 20.0%
! ATCTATCACAAATATCCTAT+CGG - chr5_3:66049877-66049896 None:intergenic 25.0%
!!! AAATGAAGTTTTGAAGGTAA+GGG - chr5_3:66050005-66050024 None:intergenic 25.0%
! TATGATTAATATGGTTGTGT+TGG + chr5_3:66050199-66050218 Msa0825960:intron 25.0%
! TGGTATATATTTGTATTAGG+TGG + chr5_3:66050219-66050238 Msa0825960:intron 25.0%
!!! TTTCTTTTTTTCTCCTTTCT+TGG - chr5_3:66050259-66050278 None:intergenic 25.0%
!!! TTTGTTATTACATACTGTTC+TGG - chr5_3:66050303-66050322 None:intergenic 25.0%
! CACTTTGATTAGTAAAAACA+TGG - chr5_3:66050351-66050370 None:intergenic 25.0%
!! TTTTGTGATACTACAGATAT+TGG + chr5_3:66050376-66050395 Msa0825960:intron 25.0%
!! TTTTGTAAATGGTTGGATTA+AGG + chr5_3:66050500-66050519 Msa0825960:CDS 25.0%
!!! AGAAGTGCTTACAATAAAAT+TGG - chr5_3:66050590-66050609 None:intergenic 25.0%
! CAAAACATATACATATCGTT+TGG + chr5_3:66050796-66050815 Msa0825960:three_prime_UTR 25.0%
! ATCTATCACAAATATCCTAT+CGG - chr5_3:66049877-66049896 None:intergenic 25.0%
!!! AAATGAAGTTTTGAAGGTAA+GGG - chr5_3:66050005-66050024 None:intergenic 25.0%
! TATGATTAATATGGTTGTGT+TGG + chr5_3:66050199-66050218 Msa0825960:intron 25.0%
! TGGTATATATTTGTATTAGG+TGG + chr5_3:66050219-66050238 Msa0825960:intron 25.0%
!!! TTTCTTTTTTTCTCCTTTCT+TGG - chr5_3:66050259-66050278 None:intergenic 25.0%
!!! TTTGTTATTACATACTGTTC+TGG - chr5_3:66050303-66050322 None:intergenic 25.0%
! CACTTTGATTAGTAAAAACA+TGG - chr5_3:66050351-66050370 None:intergenic 25.0%
!! TTTTGTGATACTACAGATAT+TGG + chr5_3:66050376-66050395 Msa0825960:intron 25.0%
!! TTTTGTAAATGGTTGGATTA+AGG + chr5_3:66050500-66050519 Msa0825960:CDS 25.0%
!!! AGAAGTGCTTACAATAAAAT+TGG - chr5_3:66050590-66050609 None:intergenic 25.0%
! CAAAACATATACATATCGTT+TGG + chr5_3:66050796-66050815 Msa0825960:three_prime_UTR 25.0%
GATAACAAGTGATGAAATGA+TGG + chr5_3:66049894-66049913 Msa0825960:five_prime_UTR 30.0%
AGAAGATAGAAGAGTAACTT+TGG - chr5_3:66049981-66050000 None:intergenic 30.0%
!!! AATGAAGTTTTGAAGGTAAG+GGG - chr5_3:66050004-66050023 None:intergenic 30.0%
!!! GAAATGAAGTTTTGAAGGTA+AGG - chr5_3:66050006-66050025 None:intergenic 30.0%
!! AGGAAGAAATGAAGTTTTGA+AGG - chr5_3:66050011-66050030 None:intergenic 30.0%
TGAGAAAGTGAAGATGATTT+AGG - chr5_3:66050031-66050050 None:intergenic 30.0%
! ATACCAAGGGAAGTAATTTT+TGG - chr5_3:66050067-66050086 None:intergenic 30.0%
ATCAAAGTTTGTGCTCAATT+AGG + chr5_3:66050085-66050104 Msa0825960:CDS 30.0%
!! TTAGCCATTGCTTTTGTAAA+TGG + chr5_3:66050489-66050508 Msa0825960:CDS 30.0%
GATAACAAGTGATGAAATGA+TGG + chr5_3:66049894-66049913 Msa0825960:five_prime_UTR 30.0%
AGAAGATAGAAGAGTAACTT+TGG - chr5_3:66049981-66050000 None:intergenic 30.0%
!!! AATGAAGTTTTGAAGGTAAG+GGG - chr5_3:66050004-66050023 None:intergenic 30.0%
!!! GAAATGAAGTTTTGAAGGTA+AGG - chr5_3:66050006-66050025 None:intergenic 30.0%
!! AGGAAGAAATGAAGTTTTGA+AGG - chr5_3:66050011-66050030 None:intergenic 30.0%
TGAGAAAGTGAAGATGATTT+AGG - chr5_3:66050031-66050050 None:intergenic 30.0%
! ATACCAAGGGAAGTAATTTT+TGG - chr5_3:66050067-66050086 None:intergenic 30.0%
ATCAAAGTTTGTGCTCAATT+AGG + chr5_3:66050085-66050104 Msa0825960:CDS 30.0%
!! TTAGCCATTGCTTTTGTAAA+TGG + chr5_3:66050489-66050508 Msa0825960:CDS 30.0%
AGTACAAAATCCAAACCGAT+AGG + chr5_3:66049859-66049878 Msa0825960:five_prime_UTR 35.0%
! TCACAAATATCCTATCGGTT+TGG - chr5_3:66049872-66049891 None:intergenic 35.0%
TAGAAGAGTAACTTTGGCTA+TGG - chr5_3:66049975-66049994 None:intergenic 35.0%
!! AGTAATTTTTGGAGAGGCAA+TGG - chr5_3:66050056-66050075 None:intergenic 35.0%
!! AAGGGAAGTAATTTTTGGAG+AGG - chr5_3:66050062-66050081 None:intergenic 35.0%
TCTCCAAAAATTACTTCCCT+TGG + chr5_3:66050061-66050080 Msa0825960:CDS 35.0%
AGCACAAACTTTGATACCAA+GGG - chr5_3:66050080-66050099 None:intergenic 35.0%
GCAATGGCTAAGATTACAAA+AGG - chr5_3:66050480-66050499 None:intergenic 35.0%
CCAACCATTTACAAAAGCAA+TGG - chr5_3:66050496-66050515 None:intergenic 35.0%
!! CCATTGCTTTTGTAAATGGT+TGG + chr5_3:66050493-66050512 Msa0825960:CDS 35.0%
AGGTACCAATTAGATAGATG+AGG + chr5_3:66050520-66050539 Msa0825960:exon 35.0%
TGTGACCTCATCTATCTAAT+TGG - chr5_3:66050528-66050547 None:intergenic 35.0%
!! TTACAAGGAAGTGTTTGGTT+TGG - chr5_3:66050553-66050572 None:intergenic 35.0%
!! ACACATTACAAGGAAGTGTT+TGG - chr5_3:66050558-66050577 None:intergenic 35.0%
GTGAGAATGAACACATTACA+AGG - chr5_3:66050568-66050587 None:intergenic 35.0%
AGTACAAAATCCAAACCGAT+AGG + chr5_3:66049859-66049878 Msa0825960:five_prime_UTR 35.0%
! TCACAAATATCCTATCGGTT+TGG - chr5_3:66049872-66049891 None:intergenic 35.0%
TAGAAGAGTAACTTTGGCTA+TGG - chr5_3:66049975-66049994 None:intergenic 35.0%
!! AGTAATTTTTGGAGAGGCAA+TGG - chr5_3:66050056-66050075 None:intergenic 35.0%
!! AAGGGAAGTAATTTTTGGAG+AGG - chr5_3:66050062-66050081 None:intergenic 35.0%
TCTCCAAAAATTACTTCCCT+TGG + chr5_3:66050061-66050080 Msa0825960:CDS 35.0%
AGCACAAACTTTGATACCAA+GGG - chr5_3:66050080-66050099 None:intergenic 35.0%
GCAATGGCTAAGATTACAAA+AGG - chr5_3:66050480-66050499 None:intergenic 35.0%
CCAACCATTTACAAAAGCAA+TGG - chr5_3:66050496-66050515 None:intergenic 35.0%
!! CCATTGCTTTTGTAAATGGT+TGG + chr5_3:66050493-66050512 Msa0825960:CDS 35.0%
AGGTACCAATTAGATAGATG+AGG + chr5_3:66050520-66050539 Msa0825960:exon 35.0%
TGTGACCTCATCTATCTAAT+TGG - chr5_3:66050528-66050547 None:intergenic 35.0%
!! TTACAAGGAAGTGTTTGGTT+TGG - chr5_3:66050553-66050572 None:intergenic 35.0%
!! ACACATTACAAGGAAGTGTT+TGG - chr5_3:66050558-66050577 None:intergenic 35.0%
GTGAGAATGAACACATTACA+AGG - chr5_3:66050568-66050587 None:intergenic 35.0%
!! TGGATTTTGTACTGATCACC+TGG - chr5_3:66049852-66049871 None:intergenic 40.0%
AAGAGTAACTTTGGCTATGG+TGG - chr5_3:66049972-66049991 None:intergenic 40.0%
GAGCACAAACTTTGATACCA+AGG - chr5_3:66050081-66050100 None:intergenic 40.0%
CGAGATGAAGAAACCAAGAA+AGG + chr5_3:66050243-66050262 Msa0825960:CDS 40.0%
GAACTGGATATGATACATGC+TGG - chr5_3:66050710-66050729 None:intergenic 40.0%
GCATGTATCATATCCAGTTC+CGG + chr5_3:66050710-66050729 Msa0825960:three_prime_UTR 40.0%
TATTCTTACTCGTCCTCTAC+CGG - chr5_3:66050732-66050751 None:intergenic 40.0%
!! TGGATTTTGTACTGATCACC+TGG - chr5_3:66049852-66049871 None:intergenic 40.0%
AAGAGTAACTTTGGCTATGG+TGG - chr5_3:66049972-66049991 None:intergenic 40.0%
GAGCACAAACTTTGATACCA+AGG - chr5_3:66050081-66050100 None:intergenic 40.0%
CGAGATGAAGAAACCAAGAA+AGG + chr5_3:66050243-66050262 Msa0825960:CDS 40.0%
GAACTGGATATGATACATGC+TGG - chr5_3:66050710-66050729 None:intergenic 40.0%
GCATGTATCATATCCAGTTC+CGG + chr5_3:66050710-66050729 Msa0825960:three_prime_UTR 40.0%
TATTCTTACTCGTCCTCTAC+CGG - chr5_3:66050732-66050751 None:intergenic 40.0%
TACAGATATTGGCAGTCAGC+AGG + chr5_3:66050387-66050406 Msa0825960:intron 45.0%
TAAGGAAGTGGCGTCATCAT+TGG - chr5_3:66050432-66050451 None:intergenic 45.0%
ATCATATCCAGTTCCGGTAG+AGG + chr5_3:66050716-66050735 Msa0825960:three_prime_UTR 45.0%
TACAGATATTGGCAGTCAGC+AGG + chr5_3:66050387-66050406 Msa0825960:intron 45.0%
TAAGGAAGTGGCGTCATCAT+TGG - chr5_3:66050432-66050451 None:intergenic 45.0%
ATCATATCCAGTTCCGGTAG+AGG + chr5_3:66050716-66050735 Msa0825960:three_prime_UTR 45.0%
CAGTCAGCAGGAGAGAGAGA+AGG + chr5_3:66050399-66050418 Msa0825960:CDS 55.0%
TACTCGTCCTCTACCGGAAC+TGG - chr5_3:66050726-66050745 None:intergenic 55.0%
CAGTCAGCAGGAGAGAGAGA+AGG + chr5_3:66050399-66050418 Msa0825960:CDS 55.0%
TACTCGTCCTCTACCGGAAC+TGG - chr5_3:66050726-66050745 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 66049848 66050856 66049848 ID=Msa0825960;Name=Msa0825960
chr5_3 mRNA 66049848 66050856 66049848 ID=Msa0825960-mRNA-1;Parent=Msa0825960;Name=Msa0825960-mRNA-1;_AED=0.05;_eAED=0.05;_QI=117|1|1|1|1|1|3|320|118
chr5_3 exon 66049848 66050106 66049848 ID=Msa0825960-mRNA-1:exon:20699;Parent=Msa0825960-mRNA-1
chr5_3 exon 66050238 66050307 66050238 ID=Msa0825960-mRNA-1:exon:20700;Parent=Msa0825960-mRNA-1
chr5_3 exon 66050392 66050856 66050392 ID=Msa0825960-mRNA-1:exon:20701;Parent=Msa0825960-mRNA-1
chr5_3 five_prime_UTR 66049848 66049964 66049848 ID=Msa0825960-mRNA-1:five_prime_utr;Parent=Msa0825960-mRNA-1
chr5_3 CDS 66049965 66050106 66049965 ID=Msa0825960-mRNA-1:cds;Parent=Msa0825960-mRNA-1
chr5_3 CDS 66050238 66050307 66050238 ID=Msa0825960-mRNA-1:cds;Parent=Msa0825960-mRNA-1
chr5_3 CDS 66050392 66050536 66050392 ID=Msa0825960-mRNA-1:cds;Parent=Msa0825960-mRNA-1
chr5_3 three_prime_UTR 66050537 66050856 66050537 ID=Msa0825960-mRNA-1:three_prime_utr;Parent=Msa0825960-mRNA-1
Gene Sequence

>Msa0825960

ATGGCCACCATAGCCAAAGTTACTCTTCTATCTTCTCCCCTTACCTTCAAAACTTCATTTCTTCCTAAATCATCTTCACTTTCTCACACCATTGCCTCTCCAAAAATTACTTCCCTTGGTATCAAAGTTTGTGCTCAATTAGGTGGTCGAGATGAAGAAACCAAGAAAGGAGAAAAAAAGAAATTTATAACTAGAGAACAAGAACCAGAACAATATTGGCAGTCAGCAGGAGAGAGAGAAGGAGAGAATCCAATGATGACGCCACTTCCTTATATTATCTTATTTGGTATGTCAACTCCTTTTGTAATCTTAGCCATTGCTTTTGTAAATGGTTGGATTAAGGTACCAATTAGATAG

Protein sequence

>Msa0825960

MATIAKVTLLSSPLTFKTSFLPKSSSLSHTIASPKITSLGIKVCAQLGGRDEETKKGEKKKFITREQEPEQYWQSAGEREGENPMMTPLPYIILFGMSTPFVILAIAFVNGWIKVPIR*