AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0870440


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0870440 MtrunA17_Chr6g0451941 98.013 151 3 0 1 151 1 151 2.32e-109 307
Msa0870440 MtrunA17_Chr7g0262351 34.211 114 74 1 25 138 14 126 3.53e-18 75.9
Msa0870440 MtrunA17_Chr8g0364781 35.849 106 66 1 33 136 12 117 2.23e-15 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0870440 AT5G26594.1 32.143 112 76 0 33 144 18 129 2.13e-18 76.6

Find 28 sgRNAs with CRISPR-Local

Find 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACCTCAGGTCCATTGATTA+TGG 0.203630 6_1:-4847368 None:intergenic
CTCTCTAGGGTCAAAGGTTT+TGG 0.224274 6_1:-4848082 None:intergenic
AGCAATGCATTCATTGGATA+TGG 0.328332 6_1:-4847193 None:intergenic
GCTTCTTGAGCACTATTTGC+AGG 0.339727 6_1:-4847286 None:intergenic
CACTATTTGCAGGCTCTGTT+CGG 0.378455 6_1:-4847276 None:intergenic
CATCATATGCTTGAATCAAT+AGG 0.390164 6_1:+4847250 Msa0870440:CDS
TTTGATTTGCCCATAATCAA+TGG 0.409566 6_1:+4847358 Msa0870440:CDS
GATCAAAATGTGCAAATGTT+TGG 0.412226 6_1:+4848034 Msa0870440:CDS
ACCTCAGGTCCATTGATTAT+GGG 0.435172 6_1:-4847367 None:intergenic
TCTACTAGCAATGCATTCAT+TGG 0.442738 6_1:-4847199 None:intergenic
GTGAGGCAGATGCGTGCAAT+GGG 0.459873 6_1:+4847971 Msa0870440:CDS
TGATGAACACAAAACTCTCT+AGG 0.498014 6_1:-4848096 None:intergenic
CATATGATGCTCTAAGCGTC+TGG 0.510351 6_1:-4847236 None:intergenic
ATGAATGCATTGCTAGTAGA+TGG 0.520529 6_1:+4847202 Msa0870440:CDS
GATGAACACAAAACTCTCTA+GGG 0.551234 6_1:-4848095 None:intergenic
ACAAAACTCTCTAGGGTCAA+AGG 0.559403 6_1:-4848088 None:intergenic
AAGTTGCAATCAACAATGGA+TGG 0.566106 6_1:+4847091 None:intergenic
GGGATACAAAGCAAGGTGGT+TGG 0.582991 6_1:+4847992 Msa0870440:CDS
GGTGAGGCAGATGCGTGCAA+TGG 0.598157 6_1:+4847970 Msa0870440:CDS
AACAATGGATGGAGGAACCA+CGG 0.600766 6_1:+4847102 None:intergenic
TGCAATGGGGATACAAAGCA+AGG 0.629234 6_1:+4847985 Msa0870440:CDS
GCCCATAATCAATGGACCTG+AGG 0.632543 6_1:+4847366 Msa0870440:CDS
ACAATGGATGGAGGAACCAC+GGG 0.635016 6_1:+4847103 None:intergenic
GAGGAACCACGGGATATAAG+CGG 0.658571 6_1:+4847113 Msa0870440:CDS
ATATGCATTAGTTTCACATG+CGG 0.660237 6_1:-4848132 None:intergenic
TTGCAATCAACAATGGATGG+AGG 0.668830 6_1:+4847094 None:intergenic
AATGGGGATACAAAGCAAGG+TGG 0.770167 6_1:+4847988 Msa0870440:CDS
TGAGGCAGATGCGTGCAATG+GGG 0.781176 6_1:+4847972 Msa0870440:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATATATAAGTAATTTTGTC+CGG - chr6_1:4847563-4847582 None:intergenic 15.0%
!!! AATATATAAGTAATTTTGTC+CGG - chr6_1:4847563-4847582 None:intergenic 15.0%
!!! AAATAAATTTTTGATACCTC+AGG - chr6_1:4847385-4847404 None:intergenic 20.0%
!!! ATATATAAGTAATTTTGTCC+GGG - chr6_1:4847562-4847581 None:intergenic 20.0%
!! ATTACTTATATATTAACCAC+TGG + chr6_1:4847569-4847588 Msa0870440:intron 20.0%
!! AAAATTGACAACTCATTTAT+GGG - chr6_1:4847870-4847889 None:intergenic 20.0%
!! TAAAATTGACAACTCATTTA+TGG - chr6_1:4847871-4847890 None:intergenic 20.0%
!!! AAATAAATTTTTGATACCTC+AGG - chr6_1:4847385-4847404 None:intergenic 20.0%
!!! ATATATAAGTAATTTTGTCC+GGG - chr6_1:4847562-4847581 None:intergenic 20.0%
!! ATTACTTATATATTAACCAC+TGG + chr6_1:4847569-4847588 Msa0870440:intron 20.0%
!! AAAATTGACAACTCATTTAT+GGG - chr6_1:4847870-4847889 None:intergenic 20.0%
!! TAAAATTGACAACTCATTTA+TGG - chr6_1:4847871-4847890 None:intergenic 20.0%
!! CAACTAGTTAGTTTAAAATG+TGG - chr6_1:4847444-4847463 None:intergenic 25.0%
! CAGTTAATCTCATATTTAGA+CGG + chr6_1:4847490-4847509 Msa0870440:intron 25.0%
! TAAGATGAATTCTTATCAAC+TGG + chr6_1:4847642-4847661 Msa0870440:intron 25.0%
!!! GGATCTATTTTGATCATATA+TGG - chr6_1:4847699-4847718 None:intergenic 25.0%
!!! TTCCTAATTACTTTTGTAGT+TGG + chr6_1:4847949-4847968 Msa0870440:intron 25.0%
!! CAACTAGTTAGTTTAAAATG+TGG - chr6_1:4847444-4847463 None:intergenic 25.0%
! CAGTTAATCTCATATTTAGA+CGG + chr6_1:4847490-4847509 Msa0870440:intron 25.0%
! TAAGATGAATTCTTATCAAC+TGG + chr6_1:4847642-4847661 Msa0870440:intron 25.0%
!!! GGATCTATTTTGATCATATA+TGG - chr6_1:4847699-4847718 None:intergenic 25.0%
!!! TTCCTAATTACTTTTGTAGT+TGG + chr6_1:4847949-4847968 Msa0870440:intron 25.0%
CATCATATGCTTGAATCAAT+AGG + chr6_1:4847250-4847269 Msa0870440:CDS 30.0%
!! TTTGATTTGCCCATAATCAA+TGG + chr6_1:4847358-4847377 Msa0870440:CDS 30.0%
TTAATCTCATATTTAGACGG+TGG + chr6_1:4847493-4847512 Msa0870440:intron 30.0%
TAATCTCATATTTAGACGGT+GGG + chr6_1:4847494-4847513 Msa0870440:intron 30.0%
ACTTATATATTAACCACTGG+CGG + chr6_1:4847572-4847591 Msa0870440:intron 30.0%
ATCCTTTGTCATCAACTTTA+TGG + chr6_1:4847715-4847734 Msa0870440:intron 30.0%
!! TACCATAAAGTTGATGACAA+AGG - chr6_1:4847720-4847739 None:intergenic 30.0%
CACCAACTACAAAAGTAATT+AGG - chr6_1:4847954-4847973 None:intergenic 30.0%
!! AATTACTTTTGTAGTTGGTG+AGG + chr6_1:4847954-4847973 Msa0870440:intron 30.0%
GATCAAAATGTGCAAATGTT+TGG + chr6_1:4848034-4848053 Msa0870440:CDS 30.0%
CATCATATGCTTGAATCAAT+AGG + chr6_1:4847250-4847269 Msa0870440:CDS 30.0%
!! TTTGATTTGCCCATAATCAA+TGG + chr6_1:4847358-4847377 Msa0870440:CDS 30.0%
TTAATCTCATATTTAGACGG+TGG + chr6_1:4847493-4847512 Msa0870440:intron 30.0%
TAATCTCATATTTAGACGGT+GGG + chr6_1:4847494-4847513 Msa0870440:intron 30.0%
ACTTATATATTAACCACTGG+CGG + chr6_1:4847572-4847591 Msa0870440:intron 30.0%
ATCCTTTGTCATCAACTTTA+TGG + chr6_1:4847715-4847734 Msa0870440:intron 30.0%
!! TACCATAAAGTTGATGACAA+AGG - chr6_1:4847720-4847739 None:intergenic 30.0%
CACCAACTACAAAAGTAATT+AGG - chr6_1:4847954-4847973 None:intergenic 30.0%
!! AATTACTTTTGTAGTTGGTG+AGG + chr6_1:4847954-4847973 Msa0870440:intron 30.0%
GATCAAAATGTGCAAATGTT+TGG + chr6_1:4848034-4848053 Msa0870440:CDS 30.0%
!!! ATCCACATTTTTTTCTCCTC+GGG - chr6_1:4847148-4847167 None:intergenic 35.0%
!!! GATCCACATTTTTTTCTCCT+CGG - chr6_1:4847149-4847168 None:intergenic 35.0%
AGCAATGCATTCATTGGATA+TGG - chr6_1:4847196-4847215 None:intergenic 35.0%
TCTACTAGCAATGCATTCAT+TGG - chr6_1:4847202-4847221 None:intergenic 35.0%
ATGAATGCATTGCTAGTAGA+TGG + chr6_1:4847202-4847221 Msa0870440:CDS 35.0%
TCTCACGTATTTCTTTGTTC+TGG - chr6_1:4847532-4847551 None:intergenic 35.0%
!!! TCAACTGGACTCTTTTTTGT+TGG + chr6_1:4847657-4847676 Msa0870440:intron 35.0%
ATTTATGGGCTTGGATTTGA+CGG - chr6_1:4847856-4847875 None:intergenic 35.0%
GATGAACACAAAACTCTCTA+GGG - chr6_1:4848098-4848117 None:intergenic 35.0%
TGATGAACACAAAACTCTCT+AGG - chr6_1:4848099-4848118 None:intergenic 35.0%
!! AGAGTTTTGTGTTCATCACT+GGG + chr6_1:4848101-4848120 Msa0870440:CDS 35.0%
!!! ATCCACATTTTTTTCTCCTC+GGG - chr6_1:4847148-4847167 None:intergenic 35.0%
!!! GATCCACATTTTTTTCTCCT+CGG - chr6_1:4847149-4847168 None:intergenic 35.0%
AGCAATGCATTCATTGGATA+TGG - chr6_1:4847196-4847215 None:intergenic 35.0%
TCTACTAGCAATGCATTCAT+TGG - chr6_1:4847202-4847221 None:intergenic 35.0%
ATGAATGCATTGCTAGTAGA+TGG + chr6_1:4847202-4847221 Msa0870440:CDS 35.0%
TCTCACGTATTTCTTTGTTC+TGG - chr6_1:4847532-4847551 None:intergenic 35.0%
!!! TCAACTGGACTCTTTTTTGT+TGG + chr6_1:4847657-4847676 Msa0870440:intron 35.0%
ATTTATGGGCTTGGATTTGA+CGG - chr6_1:4847856-4847875 None:intergenic 35.0%
GATGAACACAAAACTCTCTA+GGG - chr6_1:4848098-4848117 None:intergenic 35.0%
TGATGAACACAAAACTCTCT+AGG - chr6_1:4848099-4848118 None:intergenic 35.0%
!! AGAGTTTTGTGTTCATCACT+GGG + chr6_1:4848101-4848120 Msa0870440:CDS 35.0%
! GCGATGCAAATTTTGTTGAC+TGG + chr6_1:4847307-4847326 Msa0870440:CDS 40.0%
! ACCTCAGGTCCATTGATTAT+GGG - chr6_1:4847370-4847389 None:intergenic 40.0%
! TACCTCAGGTCCATTGATTA+TGG - chr6_1:4847371-4847390 None:intergenic 40.0%
TATTTAGACGGTGGGTCTTT+CGG + chr6_1:4847502-4847521 Msa0870440:intron 40.0%
! AGTAATTTTGTCCGGGATCT+GGG - chr6_1:4847555-4847574 None:intergenic 40.0%
! AAGTAATTTTGTCCGGGATC+TGG - chr6_1:4847556-4847575 None:intergenic 40.0%
AATCAAACAACCCCACTTGA+TGG + chr6_1:4847800-4847819 Msa0870440:intron 40.0%
!! TCAAGTTGACTCCATCAAGT+GGG - chr6_1:4847814-4847833 None:intergenic 40.0%
TGACAACTCATTTATGGGCT+TGG - chr6_1:4847865-4847884 None:intergenic 40.0%
!! ACAAAACTCTCTAGGGTCAA+AGG - chr6_1:4848091-4848110 None:intergenic 40.0%
!! GAGAGTTTTGTGTTCATCAC+TGG + chr6_1:4848100-4848119 Msa0870440:CDS 40.0%
! GCGATGCAAATTTTGTTGAC+TGG + chr6_1:4847307-4847326 Msa0870440:CDS 40.0%
! ACCTCAGGTCCATTGATTAT+GGG - chr6_1:4847370-4847389 None:intergenic 40.0%
! TACCTCAGGTCCATTGATTA+TGG - chr6_1:4847371-4847390 None:intergenic 40.0%
TATTTAGACGGTGGGTCTTT+CGG + chr6_1:4847502-4847521 Msa0870440:intron 40.0%
! AGTAATTTTGTCCGGGATCT+GGG - chr6_1:4847555-4847574 None:intergenic 40.0%
! AAGTAATTTTGTCCGGGATC+TGG - chr6_1:4847556-4847575 None:intergenic 40.0%
AATCAAACAACCCCACTTGA+TGG + chr6_1:4847800-4847819 Msa0870440:intron 40.0%
!! TCAAGTTGACTCCATCAAGT+GGG - chr6_1:4847814-4847833 None:intergenic 40.0%
TGACAACTCATTTATGGGCT+TGG - chr6_1:4847865-4847884 None:intergenic 40.0%
!! ACAAAACTCTCTAGGGTCAA+AGG - chr6_1:4848091-4848110 None:intergenic 40.0%
!! GAGAGTTTTGTGTTCATCAC+TGG + chr6_1:4848100-4848119 Msa0870440:CDS 40.0%
!! TTTTTGCCGCTTATATCCCG+TGG - chr6_1:4847122-4847141 None:intergenic 45.0%
AGCCCGAGGAGAAAAAAATG+TGG + chr6_1:4847143-4847162 Msa0870440:CDS 45.0%
! CATATGATGCTCTAAGCGTC+TGG - chr6_1:4847239-4847258 None:intergenic 45.0%
CACTATTTGCAGGCTCTGTT+CGG - chr6_1:4847279-4847298 None:intergenic 45.0%
GCTTCTTGAGCACTATTTGC+AGG - chr6_1:4847289-4847308 None:intergenic 45.0%
GGTATCCTCATACTGACGAT+GGG + chr6_1:4847593-4847612 Msa0870440:intron 45.0%
TGAAACCCATCGTCAGTATG+AGG - chr6_1:4847601-4847620 None:intergenic 45.0%
! CAAGTTGACTCCATCAAGTG+GGG - chr6_1:4847813-4847832 None:intergenic 45.0%
!! GTCAAGTTGACTCCATCAAG+TGG - chr6_1:4847815-4847834 None:intergenic 45.0%
TGCAATGGGGATACAAAGCA+AGG + chr6_1:4847985-4848004 Msa0870440:CDS 45.0%
AATGGGGATACAAAGCAAGG+TGG + chr6_1:4847988-4848007 Msa0870440:CDS 45.0%
!!! CTCTCTAGGGTCAAAGGTTT+TGG - chr6_1:4848085-4848104 None:intergenic 45.0%
!! TTTTTGCCGCTTATATCCCG+TGG - chr6_1:4847122-4847141 None:intergenic 45.0%
AGCCCGAGGAGAAAAAAATG+TGG + chr6_1:4847143-4847162 Msa0870440:CDS 45.0%
! CATATGATGCTCTAAGCGTC+TGG - chr6_1:4847239-4847258 None:intergenic 45.0%
CACTATTTGCAGGCTCTGTT+CGG - chr6_1:4847279-4847298 None:intergenic 45.0%
GCTTCTTGAGCACTATTTGC+AGG - chr6_1:4847289-4847308 None:intergenic 45.0%
GGTATCCTCATACTGACGAT+GGG + chr6_1:4847593-4847612 Msa0870440:intron 45.0%
TGAAACCCATCGTCAGTATG+AGG - chr6_1:4847601-4847620 None:intergenic 45.0%
! CAAGTTGACTCCATCAAGTG+GGG - chr6_1:4847813-4847832 None:intergenic 45.0%
!! GTCAAGTTGACTCCATCAAG+TGG - chr6_1:4847815-4847834 None:intergenic 45.0%
TGCAATGGGGATACAAAGCA+AGG + chr6_1:4847985-4848004 Msa0870440:CDS 45.0%
AATGGGGATACAAAGCAAGG+TGG + chr6_1:4847988-4848007 Msa0870440:CDS 45.0%
!!! CTCTCTAGGGTCAAAGGTTT+TGG - chr6_1:4848085-4848104 None:intergenic 45.0%
GAGGAACCACGGGATATAAG+CGG + chr6_1:4847113-4847132 Msa0870440:CDS 50.0%
TAAGCGGCAAAAAAAGCCCG+AGG + chr6_1:4847129-4847148 Msa0870440:CDS 50.0%
GCCCATAATCAATGGACCTG+AGG + chr6_1:4847366-4847385 Msa0870440:CDS 50.0%
AATACGTGAGACCCAGATCC+CGG + chr6_1:4847541-4847560 Msa0870440:intron 50.0%
CGGTATCCTCATACTGACGA+TGG + chr6_1:4847592-4847611 Msa0870440:intron 50.0%
GGGATACAAAGCAAGGTGGT+TGG + chr6_1:4847992-4848011 Msa0870440:CDS 50.0%
GAGGAACCACGGGATATAAG+CGG + chr6_1:4847113-4847132 Msa0870440:CDS 50.0%
TAAGCGGCAAAAAAAGCCCG+AGG + chr6_1:4847129-4847148 Msa0870440:CDS 50.0%
GCCCATAATCAATGGACCTG+AGG + chr6_1:4847366-4847385 Msa0870440:CDS 50.0%
AATACGTGAGACCCAGATCC+CGG + chr6_1:4847541-4847560 Msa0870440:intron 50.0%
CGGTATCCTCATACTGACGA+TGG + chr6_1:4847592-4847611 Msa0870440:intron 50.0%
GGGATACAAAGCAAGGTGGT+TGG + chr6_1:4847992-4848011 Msa0870440:CDS 50.0%
CAGTATGAGGATACCGCCAG+TGG - chr6_1:4847588-4847607 None:intergenic 55.0%
GTGAGGCAGATGCGTGCAAT+GGG + chr6_1:4847971-4847990 Msa0870440:CDS 55.0%
TGAGGCAGATGCGTGCAATG+GGG + chr6_1:4847972-4847991 Msa0870440:CDS 55.0%
CAGTATGAGGATACCGCCAG+TGG - chr6_1:4847588-4847607 None:intergenic 55.0%
GTGAGGCAGATGCGTGCAAT+GGG + chr6_1:4847971-4847990 Msa0870440:CDS 55.0%
TGAGGCAGATGCGTGCAATG+GGG + chr6_1:4847972-4847991 Msa0870440:CDS 55.0%
GGTGAGGCAGATGCGTGCAA+TGG + chr6_1:4847970-4847989 Msa0870440:CDS 60.0%
GGTGAGGCAGATGCGTGCAA+TGG + chr6_1:4847970-4847989 Msa0870440:CDS 60.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 4847106 4848141 4847106 ID=Msa0870440;Name=Msa0870440
chr6_1 mRNA 4847106 4848141 4847106 ID=Msa0870440-mRNA-1;Parent=Msa0870440;Name=Msa0870440-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|151
chr6_1 exon 4847106 4847387 4847106 ID=Msa0870440-mRNA-1:exon:1509;Parent=Msa0870440-mRNA-1
chr6_1 exon 4847968 4848141 4847968 ID=Msa0870440-mRNA-1:exon:1510;Parent=Msa0870440-mRNA-1
chr6_1 CDS 4847106 4847387 4847106 ID=Msa0870440-mRNA-1:cds;Parent=Msa0870440-mRNA-1
chr6_1 CDS 4847968 4848141 4847968 ID=Msa0870440-mRNA-1:cds;Parent=Msa0870440-mRNA-1
Gene Sequence

>Msa0870440

ATGGATGGAGGAACCACGGGATATAAGCGGCAAAAAAAGCCCGAGGAGAAAAAAATGTGGATCAAAAAGCGTGAATTGTATGACACTCCATATCCAATGAATGCATTGCTAGTAGATGGTGTGACTGCAACCAGACGCTTAGAGCATCATATGCTTGAATCAATAGGCATCCGAACAGAGCCTGCAAATAGTGCTCAAGAAGCGATGCAAATTTTGTTGACTGGTGTCAAATTTGACTTCATATTTGTTGATTTTGATTTGCCCATAATCAATGGACCTGAGTTGGTGAGGCAGATGCGTGCAATGGGGATACAAAGCAAGGTGGTTGGTATGTTAACAAACTTCAATGATCAAAATGTGCAAATGTTTGGAGAAGCAAGAGCTAATGCTAGCACTCCAAAACCTTTGACCCTAGAGAGTTTTGTGTTCATCACTGGGATCTTGCGCCGCATGTGA

Protein sequence

>Msa0870440

MDGGTTGYKRQKKPEEKKMWIKKRELYDTPYPMNALLVDGVTATRRLEHHMLESIGIRTEPANSAQEAMQILLTGVKFDFIFVDFDLPIINGPELVRQMRAMGIQSKVVGMLTNFNDQNVQMFGEARANASTPKPLTLESFVFITGILRRM*