AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0431770


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 34 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGATGAAGATTAGAATTT+TGG 0.109540 3_2:-83836509 Msa0431770:CDS
TGAAAACAGTTATGTAAATT+AGG 0.157177 3_2:-83836190 Msa0431770:three_prime_UTR
CTGCCCTTCAATGTAGAAAT+TGG 0.270693 3_2:-83836310 Msa0431770:three_prime_UTR
AATTGGAATGGTATTGGTTC+AGG 0.291222 3_2:-83836293 Msa0431770:three_prime_UTR
ACGTGTTGAGTTGGAGAAAT+TGG 0.294808 3_2:-83836118 Msa0431770:three_prime_UTR
GGTATGGTGGACCCGACTTT+TGG 0.330122 3_2:+83837612 Msa0431760:CDS
CTTATTACAAAGGGTACTAT+TGG 0.350761 3_2:+83836213 Msa0431760:intron
GAAAACAGTTATGTAAATTA+GGG 0.381718 3_2:-83836189 Msa0431770:three_prime_UTR
GGGGTAGTCTAGTCCGATTT+TGG 0.382667 3_2:-83836272 Msa0431770:three_prime_UTR
TATGTAAATTAGGGACAGTT+AGG 0.401801 3_2:-83836180 Msa0431770:three_prime_UTR
TGTAGAAATTGGAATGGTAT+TGG 0.402557 3_2:-83836299 Msa0431770:three_prime_UTR
CATTCCAATTTCTACATTGA+AGG 0.413708 3_2:+83836306 Msa0431760:intron
GAAGAGGCACTTTGCAGCAT+TGG 0.436208 3_2:-83836592 Msa0431770:CDS
TGAGAGTAGACGTGTTGAGT+TGG 0.455451 3_2:-83836127 Msa0431770:three_prime_UTR
CCTGCAAAATAAAATTAAAG+AGG 0.458104 3_2:-83836533 Msa0431770:CDS
TCGTAGTGCATCAGATTCAT+TGG 0.462951 3_2:-83837586 Msa0431770:intron
AATATAACAAAACAACATAC+TGG 0.473274 3_2:+83836149 Msa0431760:intron
GAATCTGATGCACTACGAAC+CGG 0.490977 3_2:+83837591 Msa0431760:CDS
ATTCCAATTTCTACATTGAA+GGG 0.506385 3_2:+83836307 Msa0431760:intron
TTGTTTGTAGATTGATGAAG+AGG 0.507802 3_2:-83836608 Msa0431770:intron
TTGTAGAAAGAATGTAAGAG+AGG 0.519392 3_2:-83836436 Msa0431770:three_prime_UTR
CAACCACCATGCCAAAAGTC+GGG 0.525855 3_2:-83837623 None:intergenic
TGTAGAAAGAATGTAAGAGA+GGG 0.528156 3_2:-83836435 Msa0431770:three_prime_UTR
TTGGAATGGTATTGGTTCAG+GGG 0.528878 3_2:-83836291 Msa0431770:three_prime_UTR
ATTGGAATGGTATTGGTTCA+GGG 0.529334 3_2:-83836292 Msa0431770:three_prime_UTR
AAAAGTCGGGTCCACCATAC+CGG 0.539112 3_2:-83837610 Msa0431770:CDS
TGATGCACTACGAACCGGTA+TGG 0.542602 3_2:+83837596 Msa0431760:CDS
TGCTTATAATAATGATCAGA+GGG 0.555542 3_2:+83836071 Msa0431760:intron
AGAGAGGGAATATAAAGTGA+AGG 0.574810 3_2:-83836420 Msa0431770:three_prime_UTR
TTGCTTATAATAATGATCAG+AGG 0.578065 3_2:+83836070 Msa0431760:intron
CTTCAATGTAGAAATTGGAA+TGG 0.580371 3_2:-83836305 Msa0431770:three_prime_UTR
GCAACCACCATGCCAAAAGT+CGG 0.583837 3_2:-83837624 None:intergenic
TGCACTACGAACCGGTATGG+TGG 0.597923 3_2:+83837599 Msa0431760:CDS
AAGAGACAGAGACAATGAGA+AGG 0.632149 3_2:-83836485 Msa0431770:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAAAAAAGAATTTGTTATA+TGG - chr3_2:83836334-83836353 Msa0431770:three_prime_UTR 10.0%
!!! AACTAAATTTTTTTTTTCTT+TGG - chr3_2:83836545-83836564 Msa0431770:CDS 10.0%
!!! TAAAAAAAGAATTTGTTATA+TGG - chr3_2:83836334-83836353 Msa0431770:three_prime_UTR 10.0%
!!! AACTAAATTTTTTTTTTCTT+TGG - chr3_2:83836545-83836564 Msa0431770:CDS 10.0%
!!! TATAAGATTAGATCTAATTT+TGG - chr3_2:83836172-83836191 Msa0431770:three_prime_UTR 15.0%
!!! CATATATATCAGAATTTTTA+TGG - chr3_2:83836257-83836276 Msa0431770:three_prime_UTR 15.0%
!!! AATTTGAATTTTGATAAAAG+TGG - chr3_2:83837268-83837287 Msa0431770:intron 15.0%
!!! ATTTGAATTTTGATAAAAGT+GGG - chr3_2:83837269-83837288 Msa0431770:intron 15.0%
!!! TATAAGATTAGATCTAATTT+TGG - chr3_2:83836172-83836191 Msa0431770:three_prime_UTR 15.0%
!!! CATATATATCAGAATTTTTA+TGG - chr3_2:83836257-83836276 Msa0431770:three_prime_UTR 15.0%
!!! AATTTGAATTTTGATAAAAG+TGG - chr3_2:83837268-83837287 Msa0431770:intron 15.0%
!!! ATTTGAATTTTGATAAAAGT+GGG - chr3_2:83837269-83837288 Msa0431770:intron 15.0%
!! AAGAAAGTAACATAGTTAAT+AGG - chr3_2:83836518-83836537 Msa0431770:CDS 20.0%
!!! TTGTCAATCACAAATTATTT+TGG - chr3_2:83836682-83836701 Msa0431770:intron 20.0%
!!! TGTCAATCACAAATTATTTT+GGG - chr3_2:83836683-83836702 Msa0431770:intron 20.0%
!!! GAATATTCAATCTTGAATTT+TGG - chr3_2:83836723-83836742 Msa0431770:intron 20.0%
!!! AACTACAGATCTAATTTTTT+TGG + chr3_2:83836825-83836844 Msa0431760:intron 20.0%
!!! ATGTATTATAGCAATTTTTC+AGG - chr3_2:83836901-83836920 Msa0431770:intron 20.0%
!!! TGTATTATAGCAATTTTTCA+GGG - chr3_2:83836902-83836921 Msa0431770:intron 20.0%
!! TGAAAACAGTTATGTAAATT+AGG - chr3_2:83837456-83837475 Msa0431770:intron 20.0%
!! GAAAACAGTTATGTAAATTA+GGG - chr3_2:83837457-83837476 Msa0431770:intron 20.0%
!! AATATAACAAAACAACATAC+TGG + chr3_2:83837500-83837519 Msa0431760:intron 20.0%
!!! TAAGCAAATTTCTACTTTTT+AGG - chr3_2:83837592-83837611 Msa0431770:CDS 20.0%
!! AAGAAAGTAACATAGTTAAT+AGG - chr3_2:83836518-83836537 Msa0431770:CDS 20.0%
!!! TTGTCAATCACAAATTATTT+TGG - chr3_2:83836682-83836701 Msa0431770:intron 20.0%
!!! TGTCAATCACAAATTATTTT+GGG - chr3_2:83836683-83836702 Msa0431770:intron 20.0%
!!! GAATATTCAATCTTGAATTT+TGG - chr3_2:83836723-83836742 Msa0431770:intron 20.0%
!!! AACTACAGATCTAATTTTTT+TGG + chr3_2:83836825-83836844 Msa0431760:intron 20.0%
!!! ATGTATTATAGCAATTTTTC+AGG - chr3_2:83836901-83836920 Msa0431770:intron 20.0%
!!! TGTATTATAGCAATTTTTCA+GGG - chr3_2:83836902-83836921 Msa0431770:intron 20.0%
!! TGAAAACAGTTATGTAAATT+AGG - chr3_2:83837456-83837475 Msa0431770:intron 20.0%
!! GAAAACAGTTATGTAAATTA+GGG - chr3_2:83837457-83837476 Msa0431770:intron 20.0%
!! AATATAACAAAACAACATAC+TGG + chr3_2:83837500-83837519 Msa0431760:intron 20.0%
!!! TAAGCAAATTTCTACTTTTT+AGG - chr3_2:83837592-83837611 Msa0431770:CDS 20.0%
! GATGAAAATATAGTTGTGTA+AGG - chr3_2:83836492-83836511 Msa0431770:CDS 25.0%
!!! CCTCTTTAATTTTATTTTGC+AGG + chr3_2:83837116-83837135 Msa0431760:intron 25.0%
! CCTGCAAAATAAAATTAAAG+AGG - chr3_2:83837113-83837132 Msa0431770:intron 25.0%
!! GAAGATGAAGATTAGAATTT+TGG - chr3_2:83837137-83837156 Msa0431770:intron 25.0%
! ATTCCAATTTCTACATTGAA+GGG + chr3_2:83837342-83837361 Msa0431760:intron 25.0%
!! CTGTTTTCACTTATTACAAA+GGG + chr3_2:83837445-83837464 Msa0431760:intron 25.0%
!! ACTGTTTTCACTTATTACAA+AGG + chr3_2:83837446-83837465 Msa0431760:intron 25.0%
! TGCTTATAATAATGATCAGA+GGG + chr3_2:83837578-83837597 Msa0431760:CDS 25.0%
! TTGCTTATAATAATGATCAG+AGG + chr3_2:83837579-83837598 Msa0431760:CDS 25.0%
! GATGAAAATATAGTTGTGTA+AGG - chr3_2:83836492-83836511 Msa0431770:CDS 25.0%
!!! CCTCTTTAATTTTATTTTGC+AGG + chr3_2:83837116-83837135 Msa0431760:intron 25.0%
! CCTGCAAAATAAAATTAAAG+AGG - chr3_2:83837113-83837132 Msa0431770:intron 25.0%
!! GAAGATGAAGATTAGAATTT+TGG - chr3_2:83837137-83837156 Msa0431770:intron 25.0%
! ATTCCAATTTCTACATTGAA+GGG + chr3_2:83837342-83837361 Msa0431760:intron 25.0%
!! CTGTTTTCACTTATTACAAA+GGG + chr3_2:83837445-83837464 Msa0431760:intron 25.0%
!! ACTGTTTTCACTTATTACAA+AGG + chr3_2:83837446-83837465 Msa0431760:intron 25.0%
! TGCTTATAATAATGATCAGA+GGG + chr3_2:83837578-83837597 Msa0431760:CDS 25.0%
! TTGCTTATAATAATGATCAG+AGG + chr3_2:83837579-83837598 Msa0431760:CDS 25.0%
!!! ACAGATCTAATTTTTTTGGC+AGG + chr3_2:83836821-83836840 Msa0431760:intron 30.0%
TTGTTTGTAGATTGATGAAG+AGG - chr3_2:83837038-83837057 Msa0431770:intron 30.0%
TTGTAGAAAGAATGTAAGAG+AGG - chr3_2:83837210-83837229 Msa0431770:intron 30.0%
TGTAGAAAGAATGTAAGAGA+GGG - chr3_2:83837211-83837230 Msa0431770:intron 30.0%
CATTCCAATTTCTACATTGA+AGG + chr3_2:83837343-83837362 Msa0431760:intron 30.0%
CTTCAATGTAGAAATTGGAA+TGG - chr3_2:83837341-83837360 Msa0431770:intron 30.0%
TGTAGAAATTGGAATGGTAT+TGG - chr3_2:83837347-83837366 Msa0431770:intron 30.0%
! GTGAGCTTTTTAACCAAAAT+CGG + chr3_2:83837390-83837409 Msa0431760:intron 30.0%
!! CTTATTACAAAGGGTACTAT+TGG + chr3_2:83837436-83837455 Msa0431760:intron 30.0%
TATGTAAATTAGGGACAGTT+AGG - chr3_2:83837466-83837485 Msa0431770:intron 30.0%
!!! ACAGATCTAATTTTTTTGGC+AGG + chr3_2:83836821-83836840 Msa0431760:intron 30.0%
TTGTTTGTAGATTGATGAAG+AGG - chr3_2:83837038-83837057 Msa0431770:intron 30.0%
TTGTAGAAAGAATGTAAGAG+AGG - chr3_2:83837210-83837229 Msa0431770:intron 30.0%
TGTAGAAAGAATGTAAGAGA+GGG - chr3_2:83837211-83837230 Msa0431770:intron 30.0%
CATTCCAATTTCTACATTGA+AGG + chr3_2:83837343-83837362 Msa0431760:intron 30.0%
CTTCAATGTAGAAATTGGAA+TGG - chr3_2:83837341-83837360 Msa0431770:intron 30.0%
TGTAGAAATTGGAATGGTAT+TGG - chr3_2:83837347-83837366 Msa0431770:intron 30.0%
! GTGAGCTTTTTAACCAAAAT+CGG + chr3_2:83837390-83837409 Msa0431760:intron 30.0%
!! CTTATTACAAAGGGTACTAT+TGG + chr3_2:83837436-83837455 Msa0431760:intron 30.0%
TATGTAAATTAGGGACAGTT+AGG - chr3_2:83837466-83837485 Msa0431770:intron 30.0%
TAAGTCTTCATGTCATGATG+AGG - chr3_2:83836087-83836106 Msa0431770:three_prime_UTR 35.0%
! TGTTTCAAGTATGACAGTAG+TGG + chr3_2:83836130-83836149 Msa0431760:intron 35.0%
!!! GGATCTGTCATTTTTGTTGT+TGG - chr3_2:83836355-83836374 Msa0431770:three_prime_UTR 35.0%
AGAGAGGGAATATAAAGTGA+AGG - chr3_2:83837226-83837245 Msa0431770:intron 35.0%
!! AATTGGAATGGTATTGGTTC+AGG - chr3_2:83837353-83837372 Msa0431770:intron 35.0%
!! ATTGGAATGGTATTGGTTCA+GGG - chr3_2:83837354-83837373 Msa0431770:intron 35.0%
TAAGTCTTCATGTCATGATG+AGG - chr3_2:83836087-83836106 Msa0431770:three_prime_UTR 35.0%
! TGTTTCAAGTATGACAGTAG+TGG + chr3_2:83836130-83836149 Msa0431760:intron 35.0%
!!! GGATCTGTCATTTTTGTTGT+TGG - chr3_2:83836355-83836374 Msa0431770:three_prime_UTR 35.0%
AGAGAGGGAATATAAAGTGA+AGG - chr3_2:83837226-83837245 Msa0431770:intron 35.0%
!! AATTGGAATGGTATTGGTTC+AGG - chr3_2:83837353-83837372 Msa0431770:intron 35.0%
!! ATTGGAATGGTATTGGTTCA+GGG - chr3_2:83837354-83837373 Msa0431770:intron 35.0%
TCGTAGTGCATCAGATTCAT+TGG - chr3_2:83836060-83836079 Msa0431770:three_prime_UTR 40.0%
AGTGCATCAGATTCATTGGT+TGG - chr3_2:83836064-83836083 Msa0431770:three_prime_UTR 40.0%
AAGAGACAGAGACAATGAGA+AGG - chr3_2:83837161-83837180 Msa0431770:intron 40.0%
CTGCCCTTCAATGTAGAAAT+TGG - chr3_2:83837336-83837355 Msa0431770:intron 40.0%
!! TTGGAATGGTATTGGTTCAG+GGG - chr3_2:83837355-83837374 Msa0431770:intron 40.0%
!! ACGTGTTGAGTTGGAGAAAT+TGG - chr3_2:83837528-83837547 Msa0431770:intron 40.0%
TCGTAGTGCATCAGATTCAT+TGG - chr3_2:83836060-83836079 Msa0431770:three_prime_UTR 40.0%
AGTGCATCAGATTCATTGGT+TGG - chr3_2:83836064-83836083 Msa0431770:three_prime_UTR 40.0%
AAGAGACAGAGACAATGAGA+AGG - chr3_2:83837161-83837180 Msa0431770:intron 40.0%
CTGCCCTTCAATGTAGAAAT+TGG - chr3_2:83837336-83837355 Msa0431770:intron 40.0%
!! TTGGAATGGTATTGGTTCAG+GGG - chr3_2:83837355-83837374 Msa0431770:intron 40.0%
!! ACGTGTTGAGTTGGAGAAAT+TGG - chr3_2:83837528-83837547 Msa0431770:intron 40.0%
GAATCTGATGCACTACGAAC+CGG + chr3_2:83836058-83836077 Msa0431760:intron 45.0%
TGAGAGTAGACGTGTTGAGT+TGG - chr3_2:83837519-83837538 Msa0431770:intron 45.0%
GAATCTGATGCACTACGAAC+CGG + chr3_2:83836058-83836077 Msa0431760:intron 45.0%
TGAGAGTAGACGTGTTGAGT+TGG - chr3_2:83837519-83837538 Msa0431770:intron 45.0%
AAAAGTCGGGTCCACCATAC+CGG - chr3_2:83836036-83836055 Msa0431770:three_prime_UTR 50.0%
TGATGCACTACGAACCGGTA+TGG + chr3_2:83836053-83836072 Msa0431760:intron 50.0%
!! GAAGAGGCACTTTGCAGCAT+TGG - chr3_2:83837054-83837073 Msa0431770:intron 50.0%
! GGGGTAGTCTAGTCCGATTT+TGG - chr3_2:83837374-83837393 Msa0431770:intron 50.0%
AAAAGTCGGGTCCACCATAC+CGG - chr3_2:83836036-83836055 Msa0431770:three_prime_UTR 50.0%
TGATGCACTACGAACCGGTA+TGG + chr3_2:83836053-83836072 Msa0431760:intron 50.0%
!! GAAGAGGCACTTTGCAGCAT+TGG - chr3_2:83837054-83837073 Msa0431770:intron 50.0%
! GGGGTAGTCTAGTCCGATTT+TGG - chr3_2:83837374-83837393 Msa0431770:intron 50.0%
!!! GGTATGGTGGACCCGACTTT+TGG + chr3_2:83836037-83836056 Msa0431760:intron 55.0%
TGCACTACGAACCGGTATGG+TGG + chr3_2:83836050-83836069 Msa0431760:intron 55.0%
!!! GGTATGGTGGACCCGACTTT+TGG + chr3_2:83836037-83836056 Msa0431760:intron 55.0%
TGCACTACGAACCGGTATGG+TGG + chr3_2:83836050-83836069 Msa0431760:intron 55.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 83836031 83837637 83836031 ID=Msa0431770;Name=Msa0431770
chr3_2 mRNA 83836031 83837637 83836031 ID=Msa0431770-mRNA-1;Parent=Msa0431770;Name=Msa0431770-mRNA-1;_AED=0.20;_eAED=0.27;_QI=0|0|0.5|1|0|0.5|2|446|64
chr3_2 exon 83836031 83836620 83836031 ID=Msa0431770-mRNA-1:exon:23590;Parent=Msa0431770-mRNA-1
chr3_2 exon 83837587 83837637 83837587 ID=Msa0431770-mRNA-1:exon:23589;Parent=Msa0431770-mRNA-1
chr3_2 CDS 83837587 83837637 83837587 ID=Msa0431770-mRNA-1:cds;Parent=Msa0431770-mRNA-1
chr3_2 CDS 83836477 83836620 83836477 ID=Msa0431770-mRNA-1:cds;Parent=Msa0431770-mRNA-1
chr3_2 three_prime_UTR 83836031 83836476 83836031 ID=Msa0431770-mRNA-1:three_prime_utr;Parent=Msa0431770-mRNA-1
Gene Sequence

>Msa0431770

ATGCCAAAAGTCGGGTCCACCATACCGGTTCGTAGTGCATCAGATTCATTGATTGATGAAGAGGCACTTTGCAGCATTGGACTACTTGTTTTGATGAGTAAAGAAGTTTCACGTTTCCTGCAAAATAAAATTAAAGAGGAGAAGATGAAGATTAGAATTTTGGAAAGAGACAGAGACAATGAGAAGGAGAGATGA

Protein sequence

>Msa0431770

MPKVGSTIPVRSASDSLIDEEALCSIGLLVLMSKEVSRFLQNKIKEEKMKIRILERDRDNEKER*