AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1004420


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 32 sgRNAs with CRISPR-Local

Find 107 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGATGAAGATTAGAATTT+TGG 0.109540 7_1:-1904880 Msa1004420:CDS
TGAAAACAGTTATGTAATTT+AGG 0.115982 7_1:-1904561 Msa1004420:three_prime_UTR
CTGCCCTTCAATGTAGAAAT+TGG 0.270693 7_1:-1904681 Msa1004420:three_prime_UTR
AATTGGAATGGTATTGGTTC+AGG 0.291222 7_1:-1904664 Msa1004420:three_prime_UTR
GAAAACAGTTATGTAATTTA+GGG 0.292923 7_1:-1904560 Msa1004420:three_prime_UTR
GGTATGGTGGACCCGACTTT+TGG 0.330122 7_1:+1905983 Msa1004410:intron
CTTATTACAAAGGGTACTAT+TGG 0.350761 7_1:+1904584 Msa1004410:intron
TATGTAATTTAGGGACAGTT+AGG 0.372784 7_1:-1904551 Msa1004420:three_prime_UTR
GGGGTAGTCTAGTCCGATTT+TGG 0.382667 7_1:-1904643 Msa1004420:three_prime_UTR
GCATTATGATGTGATTTGAT+TGG 0.390722 7_1:+1904461 Msa1004410:intron
TGTAGAAATTGGAATGGTAT+TGG 0.402557 7_1:-1904670 Msa1004420:three_prime_UTR
CATTCCAATTTCTACATTGA+AGG 0.413708 7_1:+1904677 Msa1004410:intron
GAAGAGGCACTTTGCAGCAT+TGG 0.436208 7_1:-1904963 Msa1004420:CDS
CCTGCAAAATAAAATTAAAG+AGG 0.458104 7_1:-1904904 Msa1004420:CDS
TCGTAGTGCATCAGATTCAT+TGG 0.462951 7_1:-1905957 Msa1004420:intron
TATGATGTGATTTGATTGGA+TGG 0.468882 7_1:+1904465 Msa1004410:intron
AATATAACAAAACAACATAC+TGG 0.473274 7_1:+1904520 Msa1004410:intron
GAATCTGATGCACTACGAAC+CGG 0.490977 7_1:+1905962 Msa1004410:CDS
ATTCCAATTTCTACATTGAA+GGG 0.506385 7_1:+1904678 Msa1004410:intron
TTGTTTGTAGATTGATGAAG+AGG 0.507802 7_1:-1904979 Msa1004420:intron
CAACCACCATGCCAAAAGTC+GGG 0.525855 7_1:-1905994 None:intergenic
TTGGAATGGTATTGGTTCAG+GGG 0.528878 7_1:-1904662 Msa1004420:three_prime_UTR
ATTGGAATGGTATTGGTTCA+GGG 0.529334 7_1:-1904663 Msa1004420:three_prime_UTR
AGAGAGAGAATATAAAGTGA+AGG 0.530243 7_1:-1904791 Msa1004420:three_prime_UTR
AAAAGTCGGGTCCACCATAC+CGG 0.539112 7_1:-1905981 Msa1004420:CDS
TGATGCACTACGAACCGGTA+TGG 0.542602 7_1:+1905967 Msa1004410:intron
AGGATTTAAGTTGTTTACAT+TGG 0.555863 7_1:+1904366 Msa1004410:intron
CTTCAATGTAGAAATTGGAA+TGG 0.580371 7_1:-1904676 Msa1004420:three_prime_UTR
GCAACCACCATGCCAAAAGT+CGG 0.583837 7_1:-1905995 None:intergenic
TGCACTACGAACCGGTATGG+TGG 0.597923 7_1:+1905970 Msa1004410:intron
AAGAGACAGAGACAATGAGA+AGG 0.632149 7_1:-1904856 Msa1004420:CDS
ATGCATCAAATCATGATGTG+TGG 0.675789 7_1:+1904410 Msa1004410:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TAAAAAAAGAATTTGTTATA+TGG - chr7_1:1904670-1904689 Msa1004420:three_prime_UTR 10.0%
!!! AACTAAATTTTTTTTTTCTT+TGG - chr7_1:1904881-1904900 Msa1004420:CDS 10.0%
!!! TAAAAAAAGAATTTGTTATA+TGG - chr7_1:1904670-1904689 Msa1004420:three_prime_UTR 10.0%
!!! AACTAAATTTTTTTTTTCTT+TGG - chr7_1:1904881-1904900 Msa1004420:CDS 10.0%
!!! TATAAGATTAGATCTAATTT+TGG - chr7_1:1904508-1904527 Msa1004420:three_prime_UTR 15.0%
!!! CATATATATCAGAATTTTTA+TGG - chr7_1:1904593-1904612 Msa1004420:three_prime_UTR 15.0%
!!! ATTTTGAATTTTGATAAAAG+TGG - chr7_1:1905604-1905623 Msa1004420:intron 15.0%
!!! TTTTGAATTTTGATAAAAGT+GGG - chr7_1:1905605-1905624 Msa1004420:intron 15.0%
!!! TATAAGATTAGATCTAATTT+TGG - chr7_1:1904508-1904527 Msa1004420:three_prime_UTR 15.0%
!!! CATATATATCAGAATTTTTA+TGG - chr7_1:1904593-1904612 Msa1004420:three_prime_UTR 15.0%
!!! ATTTTGAATTTTGATAAAAG+TGG - chr7_1:1905604-1905623 Msa1004420:intron 15.0%
!!! TTTTGAATTTTGATAAAAGT+GGG - chr7_1:1905605-1905624 Msa1004420:intron 15.0%
!! AAGAAAGTAACATAGTTAAT+AGG - chr7_1:1904854-1904873 Msa1004420:CDS 20.0%
!!! TTGTCAATCACAAATTATTT+TGG - chr7_1:1905018-1905037 Msa1004420:intron 20.0%
!!! TGTCAATCACAAATTATTTT+GGG - chr7_1:1905019-1905038 Msa1004420:intron 20.0%
!!! GAATATTCAATCTTGAATTT+TGG - chr7_1:1905059-1905078 Msa1004420:intron 20.0%
!!! AACTACAGATCTAATTTTTT+TGG + chr7_1:1905161-1905180 Msa1004410:intron 20.0%
!!! ATGTATTATAGCAATTTTTC+AGG - chr7_1:1905237-1905256 Msa1004420:intron 20.0%
!!! TGTATTATAGCAATTTTTCA+GGG - chr7_1:1905238-1905257 Msa1004420:intron 20.0%
!! TGAAAACAGTTATGTAATTT+AGG - chr7_1:1905792-1905811 Msa1004420:intron 20.0%
!! GAAAACAGTTATGTAATTTA+GGG - chr7_1:1905793-1905812 Msa1004420:intron 20.0%
!! AATATAACAAAACAACATAC+TGG + chr7_1:1905836-1905855 Msa1004410:intron 20.0%
!!! CATCATAATGCTATTTTTAT+TGG - chr7_1:1905904-1905923 Msa1004420:intron 20.0%
!! AAGAAAGTAACATAGTTAAT+AGG - chr7_1:1904854-1904873 Msa1004420:CDS 20.0%
!!! TTGTCAATCACAAATTATTT+TGG - chr7_1:1905018-1905037 Msa1004420:intron 20.0%
!!! TGTCAATCACAAATTATTTT+GGG - chr7_1:1905019-1905038 Msa1004420:intron 20.0%
!!! GAATATTCAATCTTGAATTT+TGG - chr7_1:1905059-1905078 Msa1004420:intron 20.0%
!!! AACTACAGATCTAATTTTTT+TGG + chr7_1:1905161-1905180 Msa1004410:intron 20.0%
!!! ATGTATTATAGCAATTTTTC+AGG - chr7_1:1905237-1905256 Msa1004420:intron 20.0%
!!! TGTATTATAGCAATTTTTCA+GGG - chr7_1:1905238-1905257 Msa1004420:intron 20.0%
!! TGAAAACAGTTATGTAATTT+AGG - chr7_1:1905792-1905811 Msa1004420:intron 20.0%
!! GAAAACAGTTATGTAATTTA+GGG - chr7_1:1905793-1905812 Msa1004420:intron 20.0%
!! AATATAACAAAACAACATAC+TGG + chr7_1:1905836-1905855 Msa1004410:intron 20.0%
!!! CATCATAATGCTATTTTTAT+TGG - chr7_1:1905904-1905923 Msa1004420:intron 20.0%
! GATGAAAATATAGTTGTGTA+AGG - chr7_1:1904828-1904847 Msa1004420:three_prime_UTR 25.0%
!!! CCTCTTTAATTTTATTTTGC+AGG + chr7_1:1905452-1905471 Msa1004410:intron 25.0%
! CCTGCAAAATAAAATTAAAG+AGG - chr7_1:1905449-1905468 Msa1004420:intron 25.0%
!! GAAGATGAAGATTAGAATTT+TGG - chr7_1:1905473-1905492 Msa1004420:intron 25.0%
! ATTCCAATTTCTACATTGAA+GGG + chr7_1:1905678-1905697 Msa1004410:intron 25.0%
!! CTGTTTTCACTTATTACAAA+GGG + chr7_1:1905781-1905800 Msa1004410:intron 25.0%
!! ACTGTTTTCACTTATTACAA+AGG + chr7_1:1905782-1905801 Msa1004410:intron 25.0%
! GATGAAAATATAGTTGTGTA+AGG - chr7_1:1904828-1904847 Msa1004420:three_prime_UTR 25.0%
!!! CCTCTTTAATTTTATTTTGC+AGG + chr7_1:1905452-1905471 Msa1004410:intron 25.0%
! CCTGCAAAATAAAATTAAAG+AGG - chr7_1:1905449-1905468 Msa1004420:intron 25.0%
!! GAAGATGAAGATTAGAATTT+TGG - chr7_1:1905473-1905492 Msa1004420:intron 25.0%
! ATTCCAATTTCTACATTGAA+GGG + chr7_1:1905678-1905697 Msa1004410:intron 25.0%
!! CTGTTTTCACTTATTACAAA+GGG + chr7_1:1905781-1905800 Msa1004410:intron 25.0%
!! ACTGTTTTCACTTATTACAA+AGG + chr7_1:1905782-1905801 Msa1004410:intron 25.0%
!!! ACAGATCTAATTTTTTTGGC+AGG + chr7_1:1905157-1905176 Msa1004410:intron 30.0%
TTGTTTGTAGATTGATGAAG+AGG - chr7_1:1905374-1905393 Msa1004420:intron 30.0%
AGAGAGAGAATATAAAGTGA+AGG - chr7_1:1905562-1905581 Msa1004420:intron 30.0%
CATTCCAATTTCTACATTGA+AGG + chr7_1:1905679-1905698 Msa1004410:intron 30.0%
CTTCAATGTAGAAATTGGAA+TGG - chr7_1:1905677-1905696 Msa1004420:intron 30.0%
TGTAGAAATTGGAATGGTAT+TGG - chr7_1:1905683-1905702 Msa1004420:intron 30.0%
! GTGAGCTTTTTAACCAAAAT+CGG + chr7_1:1905726-1905745 Msa1004410:intron 30.0%
!! CTTATTACAAAGGGTACTAT+TGG + chr7_1:1905772-1905791 Msa1004410:intron 30.0%
TATGTAATTTAGGGACAGTT+AGG - chr7_1:1905802-1905821 Msa1004420:intron 30.0%
TATGATGTGATTTGATTGGA+TGG + chr7_1:1905891-1905910 Msa1004410:intron 30.0%
GCATTATGATGTGATTTGAT+TGG + chr7_1:1905895-1905914 Msa1004410:intron 30.0%
!!! ACAGATCTAATTTTTTTGGC+AGG + chr7_1:1905157-1905176 Msa1004410:intron 30.0%
TTGTTTGTAGATTGATGAAG+AGG - chr7_1:1905374-1905393 Msa1004420:intron 30.0%
AGAGAGAGAATATAAAGTGA+AGG - chr7_1:1905562-1905581 Msa1004420:intron 30.0%
CATTCCAATTTCTACATTGA+AGG + chr7_1:1905679-1905698 Msa1004410:intron 30.0%
CTTCAATGTAGAAATTGGAA+TGG - chr7_1:1905677-1905696 Msa1004420:intron 30.0%
TGTAGAAATTGGAATGGTAT+TGG - chr7_1:1905683-1905702 Msa1004420:intron 30.0%
! GTGAGCTTTTTAACCAAAAT+CGG + chr7_1:1905726-1905745 Msa1004410:intron 30.0%
!! CTTATTACAAAGGGTACTAT+TGG + chr7_1:1905772-1905791 Msa1004410:intron 30.0%
TATGTAATTTAGGGACAGTT+AGG - chr7_1:1905802-1905821 Msa1004420:intron 30.0%
TATGATGTGATTTGATTGGA+TGG + chr7_1:1905891-1905910 Msa1004410:intron 30.0%
GCATTATGATGTGATTTGAT+TGG + chr7_1:1905895-1905914 Msa1004410:intron 30.0%
TAAGTCTTCATGTCATGATG+AGG - chr7_1:1904423-1904442 Msa1004420:three_prime_UTR 35.0%
! TGTTTCAAGTATGACAGTAG+TGG + chr7_1:1904466-1904485 Msa1004410:intron 35.0%
!!! GGATCTGTCATTTTTGTTGT+TGG - chr7_1:1904691-1904710 Msa1004420:three_prime_UTR 35.0%
!! AATTGGAATGGTATTGGTTC+AGG - chr7_1:1905689-1905708 Msa1004420:intron 35.0%
!! ATTGGAATGGTATTGGTTCA+GGG - chr7_1:1905690-1905709 Msa1004420:intron 35.0%
ATGCATCAAATCATGATGTG+TGG + chr7_1:1905946-1905965 Msa1004410:CDS 35.0%
TAAGTCTTCATGTCATGATG+AGG - chr7_1:1904423-1904442 Msa1004420:three_prime_UTR 35.0%
! TGTTTCAAGTATGACAGTAG+TGG + chr7_1:1904466-1904485 Msa1004410:intron 35.0%
!!! GGATCTGTCATTTTTGTTGT+TGG - chr7_1:1904691-1904710 Msa1004420:three_prime_UTR 35.0%
!! AATTGGAATGGTATTGGTTC+AGG - chr7_1:1905689-1905708 Msa1004420:intron 35.0%
!! ATTGGAATGGTATTGGTTCA+GGG - chr7_1:1905690-1905709 Msa1004420:intron 35.0%
ATGCATCAAATCATGATGTG+TGG + chr7_1:1905946-1905965 Msa1004410:CDS 35.0%
TCGTAGTGCATCAGATTCAT+TGG - chr7_1:1904396-1904415 Msa1004420:three_prime_UTR 40.0%
AGTGCATCAGATTCATTGGT+TGG - chr7_1:1904400-1904419 Msa1004420:three_prime_UTR 40.0%
AAGAGACAGAGACAATGAGA+AGG - chr7_1:1905497-1905516 Msa1004420:intron 40.0%
CTGCCCTTCAATGTAGAAAT+TGG - chr7_1:1905672-1905691 Msa1004420:intron 40.0%
!! TTGGAATGGTATTGGTTCAG+GGG - chr7_1:1905691-1905710 Msa1004420:intron 40.0%
TCGTAGTGCATCAGATTCAT+TGG - chr7_1:1904396-1904415 Msa1004420:three_prime_UTR 40.0%
AGTGCATCAGATTCATTGGT+TGG - chr7_1:1904400-1904419 Msa1004420:three_prime_UTR 40.0%
AAGAGACAGAGACAATGAGA+AGG - chr7_1:1905497-1905516 Msa1004420:intron 40.0%
CTGCCCTTCAATGTAGAAAT+TGG - chr7_1:1905672-1905691 Msa1004420:intron 40.0%
!! TTGGAATGGTATTGGTTCAG+GGG - chr7_1:1905691-1905710 Msa1004420:intron 40.0%
GAATCTGATGCACTACGAAC+CGG + chr7_1:1904394-1904413 Msa1004410:intron 45.0%
GAATCTGATGCACTACGAAC+CGG + chr7_1:1904394-1904413 Msa1004410:intron 45.0%
AAAAGTCGGGTCCACCATAC+CGG - chr7_1:1904372-1904391 Msa1004420:three_prime_UTR 50.0%
TGATGCACTACGAACCGGTA+TGG + chr7_1:1904389-1904408 Msa1004410:intron 50.0%
!! GAAGAGGCACTTTGCAGCAT+TGG - chr7_1:1905390-1905409 Msa1004420:intron 50.0%
! GGGGTAGTCTAGTCCGATTT+TGG - chr7_1:1905710-1905729 Msa1004420:intron 50.0%
AAAAGTCGGGTCCACCATAC+CGG - chr7_1:1904372-1904391 Msa1004420:three_prime_UTR 50.0%
TGATGCACTACGAACCGGTA+TGG + chr7_1:1904389-1904408 Msa1004410:intron 50.0%
!! GAAGAGGCACTTTGCAGCAT+TGG - chr7_1:1905390-1905409 Msa1004420:intron 50.0%
! GGGGTAGTCTAGTCCGATTT+TGG - chr7_1:1905710-1905729 Msa1004420:intron 50.0%
!!! GGTATGGTGGACCCGACTTT+TGG + chr7_1:1904373-1904392 Msa1004410:intron 55.0%
TGCACTACGAACCGGTATGG+TGG + chr7_1:1904386-1904405 Msa1004410:intron 55.0%
!!! GGTATGGTGGACCCGACTTT+TGG + chr7_1:1904373-1904392 Msa1004410:intron 55.0%
TGCACTACGAACCGGTATGG+TGG + chr7_1:1904386-1904405 Msa1004410:intron 55.0%
! GGTGGACCCGACTTTTGGCA+TGG + chr7_1:1904368-1904387 Msa1004410:intron 60.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 1904367 1906008 1904367 ID=Msa1004420;Name=Msa1004420
chr7_1 mRNA 1904367 1906008 1904367 ID=Msa1004420-mRNA-1;Parent=Msa1004420;Name=Msa1004420-mRNA-1;_AED=0.20;_eAED=0.26;_QI=0|0|0.5|1|0|0|2|481|64
chr7_1 exon 1904367 1904991 1904367 ID=Msa1004420-mRNA-1:exon:768;Parent=Msa1004420-mRNA-1
chr7_1 exon 1905958 1906008 1905958 ID=Msa1004420-mRNA-1:exon:767;Parent=Msa1004420-mRNA-1
chr7_1 CDS 1905958 1906008 1905958 ID=Msa1004420-mRNA-1:cds;Parent=Msa1004420-mRNA-1
chr7_1 CDS 1904848 1904991 1904848 ID=Msa1004420-mRNA-1:cds;Parent=Msa1004420-mRNA-1
chr7_1 three_prime_UTR 1904367 1904847 1904367 ID=Msa1004420-mRNA-1:three_prime_utr;Parent=Msa1004420-mRNA-1
Gene Sequence

>Msa1004420

ATGCCAAAAGTCGGGTCCACCATACCGGTTCGTAGTGCATCAGATTCATTGATTGATGAAGAGGCACTTTGCAGCATTGGACTACTTGTTTTGATGAGTAAAGAAGTTTCACGTTTCCTGCAAAATAAAATTAAAGAGGAGAAGATGAAGATTAGAATTTTGGAAAGAGACAGAGACAATGAGAAGGAGAGATGA

Protein sequence

>Msa1004420

MPKVGSTIPVRSASDSLIDEEALCSIGLLVLMSKEVSRFLQNKIKEEKMKIRILERDRDNEKER*