AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0774160


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATTTCAGGCGACAGTTTA+AGG 0.122983 5_2:-50019016 None:intergenic
TAATTAATGTATGTGACTTT+TGG 0.258825 5_2:+50019971 Msa0774160:three_prime_UTR
CAGTTATGGAGGTGAAGATT+TGG 0.301937 5_2:+50017505 None:intergenic
CATTGCTGTAAAACGTGTTT+TGG 0.309510 5_2:-50019886 None:intergenic
AGTTATGGAGGTGAAGATTT+GGG 0.363283 5_2:+50017506 None:intergenic
CGGAAACTGAAGCTGCTTCA+TGG 0.407186 5_2:+50017571 Msa0774160:CDS
AGAGTTCAAGATCCGGGTTA+TGG 0.417330 5_2:+50017537 Msa0774160:CDS
AGAAATTACTCGTCTTCATC+AGG 0.431687 5_2:+50018939 Msa0774160:CDS
AAGTTTGAGTAATTTAAAGA+AGG 0.477272 5_2:+50019909 Msa0774160:three_prime_UTR
CGAGATTAGAGTTCAAGATC+CGG 0.501880 5_2:+50017530 Msa0774160:CDS
ATCTTATTTGAAAGATTGAA+AGG 0.529072 5_2:+50019757 Msa0774160:intron
GATCCGGGTTATGGAGGTGA+AGG 0.537187 5_2:+50017546 Msa0774160:CDS
AGGCAATCAATACAACTTAG+TGG 0.556871 5_2:-50020021 None:intergenic
TGAAGAGTGTGTGGGAGAGA+AGG 0.573340 5_2:+50019046 Msa0774160:CDS
TTGCCTCAATTATCACGTGA+AGG 0.577241 5_2:+50020038 Msa0774160:three_prime_UTR
GAGATTAGAGTTCAAGATCC+GGG 0.587082 5_2:+50017531 Msa0774160:CDS
CAACCTTCACGTGATAATTG+AGG 0.587359 5_2:-50020041 None:intergenic
GACCCTTCACCTCCATAACC+CGG 0.593049 5_2:-50017549 None:intergenic
GGGTTATGGAGGTGAAGGGT+CGG 0.593897 5_2:+50017551 Msa0774160:CDS
GAATACAAACAATTGCAGAA+AGG 0.599398 5_2:+50019796 Msa0774160:CDS
GTTCAAGATCCGGGTTATGG+AGG 0.626430 5_2:+50017540 Msa0774160:CDS
ATCCGGGTTATGGAGGTGAA+GGG 0.669658 5_2:+50017547 Msa0774160:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAATACAATTTGTATACAA+TGG + chr5_2:50018151-50018170 Msa0774160:intron 15.0%
!! TTATAGTTATAATTGAGTTT+AGG - chr5_2:50018413-50018432 None:intergenic 15.0%
!!! TTTGAAATTTTGATAAAAGT+GGG - chr5_2:50018478-50018497 None:intergenic 15.0%
!!! ATTTGAAATTTTGATAAAAG+TGG - chr5_2:50018479-50018498 None:intergenic 15.0%
!!! GAAATTCAAACATTTTTTTA+AGG - chr5_2:50019116-50019135 None:intergenic 15.0%
!! AAATAAGATAAATGAGATAA+GGG - chr5_2:50019746-50019765 None:intergenic 15.0%
!!! GTAATTAAGTCTCATTTTTT+AGG + chr5_2:50018033-50018052 Msa0774160:intron 20.0%
!!! AACTACAATATACTTTTACA+AGG + chr5_2:50018100-50018119 Msa0774160:intron 20.0%
!!! ACTACAATATACTTTTACAA+GGG + chr5_2:50018101-50018120 Msa0774160:intron 20.0%
!!! AACTACAATATACTTTTACA+AGG + chr5_2:50018100-50018119 Msa0774160:intron 20.0%
!!! ACTACAATATACTTTTACAA+GGG + chr5_2:50018101-50018120 Msa0774160:intron 20.0%
!!! GTAGTTAAAAATTTGAAACA+GGG - chr5_2:50018303-50018322 None:intergenic 20.0%
!!! TGTAGTTAAAAATTTGAAAC+AGG - chr5_2:50018304-50018323 None:intergenic 20.0%
!!! TTTAACTACACTTTTTTTCA+AGG + chr5_2:50018314-50018333 Msa0774160:intron 20.0%
!!! TTAACTACACTTTTTTTCAA+GGG + chr5_2:50018315-50018334 Msa0774160:intron 20.0%
!!! ATGGTAACAAATTTTCAAAT+GGG + chr5_2:50018342-50018361 Msa0774160:intron 20.0%
!! CAATTATAACTATAACACAA+AGG + chr5_2:50018418-50018437 Msa0774160:intron 20.0%
!! TTGAAATTTGAAGAAATAGA+AGG - chr5_2:50018724-50018743 None:intergenic 20.0%
!!! TACACATTTTTAGAAATAGA+AGG - chr5_2:50018779-50018798 None:intergenic 20.0%
!!! AGTTAAAATCATCTCATTTT+CGG - chr5_2:50018983-50019002 None:intergenic 20.0%
!! GTTATGAAGAAATAAATATG+AGG + chr5_2:50019274-50019293 Msa0774160:intron 20.0%
!! CAAATAAGATAAATGAGATA+AGG - chr5_2:50019747-50019766 None:intergenic 20.0%
!!! ATCTTATTTGAAAGATTGAA+AGG + chr5_2:50019757-50019776 Msa0774160:intron 20.0%
!!! AGAAACTTTTGAGTAATTTA+CGG + chr5_2:50019849-50019868 Msa0774160:exon 20.0%
!! AAGTTTGAGTAATTTAAAGA+AGG + chr5_2:50019909-50019928 Msa0774160:three_prime_UTR 20.0%
!!! TAATTAATGTATGTGACTTT+TGG + chr5_2:50019971-50019990 Msa0774160:three_prime_UTR 20.0%
!!! CATTTTTGGAGGAAAAAATA+GGG + chr5_2:50017903-50017922 Msa0774160:intron 25.0%
!!! ATTTTTGGAGGAAAAAATAG+GGG + chr5_2:50017904-50017923 Msa0774160:intron 25.0%
!!! TCATCATTTTTTTGCACTTT+TGG - chr5_2:50017936-50017955 None:intergenic 25.0%
!!! AGTTTTGTCAGGTTTTAAAA+GGG + chr5_2:50017966-50017985 Msa0774160:intron 25.0%
!! ATGAGACTTAATTACACTTT+TGG - chr5_2:50018028-50018047 None:intergenic 25.0%
! TATGTCTAGTTACTGATATA+TGG + chr5_2:50018056-50018075 Msa0774160:intron 25.0%
! ATGTCTAGTTACTGATATAT+GGG + chr5_2:50018057-50018076 Msa0774160:intron 25.0%
! TACAATTTGTATACAATGGA+AGG + chr5_2:50018155-50018174 Msa0774160:intron 25.0%
!! GATGGTAACAAATTTTCAAA+TGG + chr5_2:50018341-50018360 Msa0774160:intron 25.0%
! TATAATTGAGTTTAGGAGAA+GGG - chr5_2:50018406-50018425 None:intergenic 25.0%
! TTATAATTGAGTTTAGGAGA+AGG - chr5_2:50018407-50018426 None:intergenic 25.0%
! TAGAAATAGAAGGTAAATGA+TGG - chr5_2:50018769-50018788 None:intergenic 25.0%
! TAGTAATATAGAAGATGAGA+AGG - chr5_2:50018822-50018841 None:intergenic 25.0%
! TTTGTTTGTAGATCAATGAA+GGG - chr5_2:50019211-50019230 None:intergenic 25.0%
! ATCTGTAGATTTAAAAAAGC+AGG - chr5_2:50019363-50019382 None:intergenic 25.0%
!!! ATTTAAAGAAGGCATCTTTT+TGG + chr5_2:50019920-50019939 Msa0774160:three_prime_UTR 25.0%
!!! TTGATTGTGTTTGTTTTGTG+AGG + chr5_2:50017619-50017638 Msa0774160:intron 30.0%
!!! TGTAATGTCATTTTCCAAGT+TGG + chr5_2:50017826-50017845 Msa0774160:intron 30.0%
!! TGTCACAATTTTAAGTGATG+TGG - chr5_2:50017877-50017896 None:intergenic 30.0%
!! GCATTTTTGGAGGAAAAAAT+AGG + chr5_2:50017902-50017921 Msa0774160:intron 30.0%
!! TTTTTGGAGGAAAAAATAGG+GGG + chr5_2:50017905-50017924 Msa0774160:intron 30.0%
TGCAAAAAAATGATGACTGA+AGG + chr5_2:50017940-50017959 Msa0774160:intron 30.0%
!!! CTTTTAAAACCTGACAAAAC+TGG - chr5_2:50017967-50017986 None:intergenic 30.0%
!!! CAGTTTTGTCAGGTTTTAAA+AGG + chr5_2:50017965-50017984 Msa0774160:intron 30.0%
!! GACAGTTATGAAATTTTGGT+AGG - chr5_2:50018281-50018300 None:intergenic 30.0%
!!! ACTTTTTTTCAAGGGTAAGA+TGG + chr5_2:50018323-50018342 Msa0774160:intron 30.0%
TGTAGAAAGAATGTAAGAGA+GGG - chr5_2:50018578-50018597 None:intergenic 30.0%
TTGTAGAAAGAATGTAAGAG+AGG - chr5_2:50018579-50018598 None:intergenic 30.0%
!!! GAGTTTTAGCTAAAATGAGA+AGG - chr5_2:50018628-50018647 None:intergenic 30.0%
! TCTTCAGTTTTTGCAATTTC+AGG - chr5_2:50019032-50019051 None:intergenic 30.0%
! CTTTGTTTGTAGATCAATGA+AGG - chr5_2:50019212-50019231 None:intergenic 30.0%
AAAGAAAAGAGACACAAATG+AGG + chr5_2:50019228-50019247 Msa0774160:intron 30.0%
GAATACAAACAATTGCAGAA+AGG + chr5_2:50019796-50019815 Msa0774160:CDS 30.0%
! TTGTGACACATCAGCATTTT+TGG + chr5_2:50017889-50017908 Msa0774160:intron 35.0%
! CAGGGACAGTTATGAAATTT+TGG - chr5_2:50018285-50018304 None:intergenic 35.0%
!! CCTATGCTTTTTACCATTAC+CGG + chr5_2:50018370-50018389 Msa0774160:intron 35.0%
! TTGATTGTTGTTATTGCTGC+AGG + chr5_2:50018905-50018924 Msa0774160:intron 35.0%
AGAAATTACTCGTCTTCATC+AGG + chr5_2:50018939-50018958 Msa0774160:CDS 35.0%
TGCTCTATAAATGTTGTTGC+AGG + chr5_2:50019164-50019183 Msa0774160:intron 35.0%
GTTGTTGCAGGATAATGTAA+TGG + chr5_2:50019176-50019195 Msa0774160:intron 35.0%
! CATTGCTGTAAAACGTGTTT+TGG - chr5_2:50019889-50019908 None:intergenic 35.0%
!! TGTATGTGACTTTTGGAGAA+TGG + chr5_2:50019978-50019997 Msa0774160:three_prime_UTR 35.0%
AGGCAATCAATACAACTTAG+TGG - chr5_2:50020024-50020043 None:intergenic 35.0%
CGAGATTAGAGTTCAAGATC+CGG + chr5_2:50017530-50017549 Msa0774160:CDS 40.0%
GAGATTAGAGTTCAAGATCC+GGG + chr5_2:50017531-50017550 Msa0774160:CDS 40.0%
! TTTTGTGAGGTTGTTCTTGC+TGG + chr5_2:50017632-50017651 Msa0774160:intron 40.0%
TTTGTGAGGTTGTTCTTGCT+GGG + chr5_2:50017633-50017652 Msa0774160:intron 40.0%
TTATGAGGTATAGGAGCAAG+AGG + chr5_2:50017688-50017707 Msa0774160:intron 40.0%
ATCGTCATTTGGGCATGATT+TGG + chr5_2:50017719-50017738 Msa0774160:intron 40.0%
!! TGACACATCAGCATTTTTGG+AGG + chr5_2:50017892-50017911 Msa0774160:intron 40.0%
!!! TTGTCAGGTTTTAAAAGGGC+AGG + chr5_2:50017970-50017989 Msa0774160:intron 40.0%
! TTTTGCCAAACTCGCGAAAT+TGG - chr5_2:50017997-50018016 None:intergenic 40.0%
CTAGTTACTGATATATGGGC+AGG + chr5_2:50018061-50018080 Msa0774160:intron 40.0%
! CCGGTAATGGTAAAAAGCAT+AGG - chr5_2:50018373-50018392 None:intergenic 40.0%
GGGTATTATAAGTCCGGTAA+TGG - chr5_2:50018386-50018405 None:intergenic 40.0%
!! GGAGAAGGGTATTATAAGTC+CGG - chr5_2:50018392-50018411 None:intergenic 40.0%
CAATTTCAGGCGACAGTTTA+AGG - chr5_2:50019019-50019038 None:intergenic 40.0%
! TGCAAAAACTGAAGAGTGTG+TGG + chr5_2:50019037-50019056 Msa0774160:CDS 40.0%
! GCAAAAACTGAAGAGTGTGT+GGG + chr5_2:50019038-50019057 Msa0774160:CDS 40.0%
TTTATAGAGCAGAGAGACAG+TGG - chr5_2:50019155-50019174 None:intergenic 40.0%
TTGCCTCAATTATCACGTGA+AGG + chr5_2:50020038-50020057 Msa0774160:three_prime_UTR 40.0%
CAACCTTCACGTGATAATTG+AGG - chr5_2:50020044-50020063 None:intergenic 40.0%
AGAGTTCAAGATCCGGGTTA+TGG + chr5_2:50017537-50017556 Msa0774160:CDS 45.0%
TGGGTTTCATGTGTCTTGCT+GGG + chr5_2:50017652-50017671 Msa0774160:intron 45.0%
ATGTGTCTTGCTGGGTTTAC+AGG + chr5_2:50017660-50017679 Msa0774160:intron 45.0%
TGTGTCTTGCTGGGTTTACA+GGG + chr5_2:50017661-50017680 Msa0774160:intron 45.0%
GGTTTACAGGGAGGTTTATG+AGG + chr5_2:50017673-50017692 Msa0774160:intron 45.0%
CAGGGAGGTTTATGAGGTAT+AGG + chr5_2:50017679-50017698 Msa0774160:intron 45.0%
AGGTATAGGAGCAAGAGGAA+AGG + chr5_2:50017693-50017712 Msa0774160:intron 45.0%
GGTATAGGAGCAAGAGGAAA+GGG + chr5_2:50017694-50017713 Msa0774160:intron 45.0%
AGGAAAGGGTGATCGTCATT+TGG + chr5_2:50017708-50017727 Msa0774160:intron 45.0%
GGAAAGGGTGATCGTCATTT+GGG + chr5_2:50017709-50017728 Msa0774160:intron 45.0%
! CTGCCACATAGGTGTTCTTT+TGG + chr5_2:50017851-50017870 Msa0774160:intron 45.0%
TGGCCAAAAGAACACCTATG+TGG - chr5_2:50017857-50017876 None:intergenic 45.0%
TGGAGGAAAAAATAGGGGGT+AGG + chr5_2:50017909-50017928 Msa0774160:intron 45.0%
!! ACTGAAGGACCAGTTTTGTC+AGG + chr5_2:50017955-50017974 Msa0774160:intron 45.0%
ATATATGGGCAGGTTGCTCA+AGG + chr5_2:50018071-50018090 Msa0774160:intron 45.0%
TATATGGGCAGGTTGCTCAA+GGG + chr5_2:50018072-50018091 Msa0774160:intron 45.0%
!! TTTATATGATAAAAAATATT+TGG + chr5_2:50019563-50019582 Msa0774160:intron 5.0%
GTTCAAGATCCGGGTTATGG+AGG + chr5_2:50017540-50017559 Msa0774160:CDS 50.0%
ATCCGGGTTATGGAGGTGAA+GGG + chr5_2:50017547-50017566 Msa0774160:CDS 50.0%
CGGAAACTGAAGCTGCTTCA+TGG + chr5_2:50017571-50017590 Msa0774160:CDS 50.0%
CTGGGTTTCATGTGTCTTGC+TGG + chr5_2:50017651-50017670 Msa0774160:intron 50.0%
CAGGACCAATTTCGCGAGTT+TGG + chr5_2:50017989-50018008 Msa0774160:intron 50.0%
! TGAAGAGTGTGTGGGAGAGA+AGG + chr5_2:50019046-50019065 Msa0774160:CDS 50.0%
TAGAGCAGAGAGACAGTGGT+TGG - chr5_2:50019151-50019170 None:intergenic 50.0%
GATCCGGGTTATGGAGGTGA+AGG + chr5_2:50017546-50017565 Msa0774160:CDS 55.0%
GACCCTTCACCTCCATAACC+CGG - chr5_2:50017552-50017571 None:intergenic 55.0%
GGGTTATGGAGGTGAAGGGT+CGG + chr5_2:50017551-50017570 Msa0774160:CDS 55.0%
GTCTTGCTGGGTTTACAGGG+AGG + chr5_2:50017664-50017683 Msa0774160:intron 55.0%
CCTATGTGGCAGTGCCAACT+TGG - chr5_2:50017843-50017862 None:intergenic 55.0%
! CCAAGTTGGCACTGCCACAT+AGG + chr5_2:50017840-50017859 Msa0774160:intron 55.0%
CGCGAGTTTGGCAAAACACG+AGG + chr5_2:50018001-50018020 Msa0774160:intron 55.0%
TGGGCAGGTTGCTCAAGGGA+AGG + chr5_2:50018076-50018095 Msa0774160:intron 60.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 50017510 50020070 50017510 ID=Msa0774160;Name=Msa0774160
chr5_2 mRNA 50017510 50020070 50017510 ID=Msa0774160-mRNA-1;Parent=Msa0774160;Name=Msa0774160-mRNA-1;_AED=0.39;_eAED=0.39;_QI=0|0.33|0.25|0.75|0|0.5|4|206|115
chr5_2 exon 50017510 50017616 50017510 ID=Msa0774160-mRNA-1:exon:14923;Parent=Msa0774160-mRNA-1
chr5_2 exon 50018927 50019067 50018927 ID=Msa0774160-mRNA-1:exon:14924;Parent=Msa0774160-mRNA-1
chr5_2 exon 50019186 50019191 50019186 ID=Msa0774160-mRNA-1:exon:14925;Parent=Msa0774160-mRNA-1
chr5_2 exon 50019771 50020070 50019771 ID=Msa0774160-mRNA-1:exon:14926;Parent=Msa0774160-mRNA-1
chr5_2 CDS 50017510 50017616 50017510 ID=Msa0774160-mRNA-1:cds;Parent=Msa0774160-mRNA-1
chr5_2 CDS 50018927 50019067 50018927 ID=Msa0774160-mRNA-1:cds;Parent=Msa0774160-mRNA-1
chr5_2 CDS 50019186 50019191 50019186 ID=Msa0774160-mRNA-1:cds;Parent=Msa0774160-mRNA-1
chr5_2 CDS 50019771 50019864 50019771 ID=Msa0774160-mRNA-1:cds;Parent=Msa0774160-mRNA-1
chr5_2 three_prime_UTR 50019865 50020070 50019865 ID=Msa0774160-mRNA-1:three_prime_utr;Parent=Msa0774160-mRNA-1
Gene Sequence

>Msa0774160

ATGGAGGTGAAGATTTGGGTCGAGATTAGAGTTCAAGATCCGGGTTATGGAGGTGAAGGGTCGGAAACTGAAGCTGCTTCATGGTTGAAAGAAAATCTTTGCATCATGTATGAGAGAAAAGAAATTACTCGTCTTCATCAGGTGAAGAAAGATGTACAAACCGAAAATGAGATGATTTTAACTGTTAATTTTGTTTCCTTAAACTGTCGCCTGAAATTGCAAAAACTGAAGAGTGTGTGGGAGAGAAGGATAATATTGAAAGGAAGATTGAAAGATGAAGAATACAAACAATTGCAGAAAGGAAGAGAGAAAGAGATGAAGATGTACATAGAAGAAACTTTTGAGTAA

Protein sequence

>Msa0774160

MEVKIWVEIRVQDPGYGGEGSETEAASWLKENLCIMYERKEITRLHQVKKDVQTENEMILTVNFVSLNCRLKLQKLKSVWERRIILKGRLKDEEYKQLQKGREKEMKMYIEETFE*