AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1252620

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1252620 MtrunA17_Chr8g0368861 97.500 120 3 0 3 122 1 120 3.12e-80 231
Msa1252620 MtrunA17_Chr8g0368831 95.082 122 6 0 1 122 7 128 6.89e-80 230
Msa1252620 MtrunA17_Chr7g0240471 51.515 99 46 2 25 122 20 117 6.73e-27 96.3
Msa1252620 MtrunA17_Chr7g0240451 51.579 95 44 2 29 122 24 117 2.08e-25 92.4
Msa1252620 MtrunA17_Chr7g0240441 57.407 54 22 1 65 118 38 90 9.74e-15 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1252620 AT2G37870.1 70.796 113 30 1 10 122 6 115 2.37e-50 155
Msa1252620 AT5G05960.1 45.902 122 58 3 3 122 1 116 8.98e-29 101
Msa1252620 AT3G53980.2 46.809 94 49 1 29 122 22 114 1.59e-27 98.2
Msa1252620 AT3G53980.1 46.809 94 49 1 29 122 22 114 1.59e-27 98.2

Find 34 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATAAATCAAATTTAAATAT+TGG 0.169390 8_2:+49603294 Msa1252620:three_prime_UTR
GGCATCAAGTGTGTTAATTT+TGG 0.227059 8_2:+49602502 Msa1252620:CDS
ATAAATCAAATTTAAATATT+GGG 0.278134 8_2:+49603295 Msa1252620:three_prime_UTR
AGCTAGTCTAAGTCCATGTT+TGG 0.350440 8_2:+49602574 Msa1252620:CDS
TTCCTAATGTTGCATCTCTT+AGG 0.378053 8_2:-49602749 None:intergenic
TGGGTGCTGTACGTAATGTT+AGG 0.392658 8_2:+49602594 Msa1252620:CDS
AACAATGATGATGGAATTCA+AGG 0.409270 8_2:+49602442 Msa1252620:exon
GAATGTGGAAGGACACCAAT+TGG 0.434211 8_2:+49602542 Msa1252620:CDS
AATTAAATCATAATAGAAGT+TGG 0.445956 8_2:-49603194 None:intergenic
AGAACAGAACAAAGACATCT+TGG 0.469439 8_2:-49602671 None:intergenic
CTTCCACATTTCTTGCCAGC+AGG 0.471841 8_2:-49602776 None:intergenic
CCAACTCTAGCACAACAAAC+TGG 0.478057 8_2:-49602629 None:intergenic
CTAGCTGCTGCTGACCCAAT+TGG 0.492373 8_2:-49602557 None:intergenic
TTCCTAAGAGATGCAACATT+AGG 0.493031 8_2:+49602747 Msa1252620:CDS
GGGTGCTGTACGTAATGTTA+GGG 0.506383 8_2:+49602595 Msa1252620:CDS
CCAGTTTGTTGTGCTAGAGT+TGG 0.508251 8_2:+49602629 Msa1252620:CDS
TTTCTCAGTGTATTGTTGCA+TGG 0.516915 8_2:+49603114 Msa1252620:three_prime_UTR
AATGTGGAAGGACACCAATT+GGG 0.523864 8_2:+49602543 Msa1252620:CDS
AACATTAGGAACCGACCTGC+TGG 0.528203 8_2:+49602761 Msa1252620:CDS
GCTAGTCTAAGTCCATGTTT+GGG 0.544347 8_2:+49602575 Msa1252620:CDS
AGTGAGGCAGCTGGAGAATG+TGG 0.550647 8_2:+49602527 Msa1252620:CDS
AATGAAGTTATCGACTCAAG+TGG 0.551906 8_2:+49603241 Msa1252620:three_prime_UTR
CACATTTCTTGCCAGCAGGT+CGG 0.552674 8_2:-49602772 None:intergenic
ATGTGGCACATTGAATTACA+AGG 0.560934 8_2:-49602395 None:intergenic
CGACCTGCTGGCAAGAAATG+TGG 0.566135 8_2:+49602773 Msa1252620:CDS
ATCACTGACTAGTTTGTATG+TGG 0.579955 8_2:-49602412 None:intergenic
GGAACAGTGATAGCAATAGC+AGG 0.582273 8_2:-49602728 None:intergenic
CACTTCCTTGAAACCAAAGC+AGG 0.584628 8_2:+49602980 Msa1252620:exon
GCTAAATAAATTCTGTAACA+TGG 0.587936 8_2:+49603044 Msa1252620:three_prime_UTR
TTACGTACAGCACCCAAACA+TGG 0.602239 8_2:-49602587 None:intergenic
AGGCAGCTGGAGAATGTGGA+AGG 0.611703 8_2:+49602531 Msa1252620:CDS
AAAACATCACCACTGTTGCA+AGG 0.620969 8_2:-49602475 None:intergenic
TAGAACTTTCCTTGCAACAG+TGG 0.624318 8_2:+49602466 Msa1252620:CDS
ACTCTAGCACAACAAACTGG+TGG 0.633479 8_2:-49602626 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTATTTATTTTATTTACA+GGG + chr8_2:49602953-49602972 Msa1252620:intron 10.0%
!!! CTTTATTTATTTTATTTACA+GGG + chr8_2:49602953-49602972 Msa1252620:intron 10.0%
!! ATTAATATCTACTAAGTTTA+TGG + chr8_2:49602840-49602859 Msa1252620:intron 15.0%
!! AATAAAATAAATAAAGGACA+AGG - chr8_2:49602949-49602968 None:intergenic 15.0%
!! CCTGTAAATAAAATAAATAA+AGG - chr8_2:49602955-49602974 None:intergenic 15.0%
!!! CCTTTATTTATTTTATTTAC+AGG + chr8_2:49602952-49602971 Msa1252620:intron 15.0%
!! AATTAAATCATAATAGAAGT+TGG - chr8_2:49603197-49603216 None:intergenic 15.0%
!! ATTAATATCTACTAAGTTTA+TGG + chr8_2:49602840-49602859 Msa1252620:intron 15.0%
!! AATAAAATAAATAAAGGACA+AGG - chr8_2:49602949-49602968 None:intergenic 15.0%
!! CCTGTAAATAAAATAAATAA+AGG - chr8_2:49602955-49602974 None:intergenic 15.0%
!!! CCTTTATTTATTTTATTTAC+AGG + chr8_2:49602952-49602971 Msa1252620:intron 15.0%
!! AATTAAATCATAATAGAAGT+TGG - chr8_2:49603197-49603216 None:intergenic 15.0%
!!! ATTTTCAAAAACAATGATGA+TGG + chr8_2:49602433-49602452 Msa1252620:exon 20.0%
!!! ATTTTCAAAAACAATGATGA+TGG + chr8_2:49602433-49602452 Msa1252620:exon 20.0%
! GCTAAATAAATTCTGTAACA+TGG + chr8_2:49603044-49603063 Msa1252620:three_prime_UTR 25.0%
! GCTAAATAAATTCTGTAACA+TGG + chr8_2:49603044-49603063 Msa1252620:three_prime_UTR 25.0%
!! AACAATGATGATGGAATTCA+AGG + chr8_2:49602442-49602461 Msa1252620:exon 30.0%
!! TGTGTTAATTTTGGAAAGTG+AGG + chr8_2:49602511-49602530 Msa1252620:CDS 30.0%
!!! ATCTTAGCTTGTTTTGCAAT+AGG - chr8_2:49602704-49602723 None:intergenic 30.0%
! CGTATATTATTTTCCTGCTT+TGG - chr8_2:49602996-49603015 None:intergenic 30.0%
!! AACAATGATGATGGAATTCA+AGG + chr8_2:49602442-49602461 Msa1252620:exon 30.0%
!! TGTGTTAATTTTGGAAAGTG+AGG + chr8_2:49602511-49602530 Msa1252620:CDS 30.0%
!!! ATCTTAGCTTGTTTTGCAAT+AGG - chr8_2:49602704-49602723 None:intergenic 30.0%
! CGTATATTATTTTCCTGCTT+TGG - chr8_2:49602996-49603015 None:intergenic 30.0%
!! ATCACTGACTAGTTTGTATG+TGG - chr8_2:49602415-49602434 None:intergenic 35.0%
!! AACAGTGGTGATGTTTTTGT+TGG + chr8_2:49602481-49602500 Msa1252620:CDS 35.0%
! GGCATCAAGTGTGTTAATTT+TGG + chr8_2:49602502-49602521 Msa1252620:CDS 35.0%
AGAACAGAACAAAGACATCT+TGG - chr8_2:49602674-49602693 None:intergenic 35.0%
TTCCTAAGAGATGCAACATT+AGG + chr8_2:49602747-49602766 Msa1252620:CDS 35.0%
TTCCTAATGTTGCATCTCTT+AGG - chr8_2:49602752-49602771 None:intergenic 35.0%
!! ATTTTCCTGCTTTGGTTTCA+AGG - chr8_2:49602988-49603007 None:intergenic 35.0%
! GTAACATGGCATTTTCTACT+TGG + chr8_2:49603058-49603077 Msa1252620:three_prime_UTR 35.0%
TTTCTCAGTGTATTGTTGCA+TGG + chr8_2:49603114-49603133 Msa1252620:three_prime_UTR 35.0%
!! AATGAAGTTATCGACTCAAG+TGG + chr8_2:49603241-49603260 Msa1252620:three_prime_UTR 35.0%
!! ATCACTGACTAGTTTGTATG+TGG - chr8_2:49602415-49602434 None:intergenic 35.0%
!! AACAGTGGTGATGTTTTTGT+TGG + chr8_2:49602481-49602500 Msa1252620:CDS 35.0%
! GGCATCAAGTGTGTTAATTT+TGG + chr8_2:49602502-49602521 Msa1252620:CDS 35.0%
AGAACAGAACAAAGACATCT+TGG - chr8_2:49602674-49602693 None:intergenic 35.0%
TTCCTAAGAGATGCAACATT+AGG + chr8_2:49602747-49602766 Msa1252620:CDS 35.0%
TTCCTAATGTTGCATCTCTT+AGG - chr8_2:49602752-49602771 None:intergenic 35.0%
!! ATTTTCCTGCTTTGGTTTCA+AGG - chr8_2:49602988-49603007 None:intergenic 35.0%
! GTAACATGGCATTTTCTACT+TGG + chr8_2:49603058-49603077 Msa1252620:three_prime_UTR 35.0%
TTTCTCAGTGTATTGTTGCA+TGG + chr8_2:49603114-49603133 Msa1252620:three_prime_UTR 35.0%
!! AATGAAGTTATCGACTCAAG+TGG + chr8_2:49603241-49603260 Msa1252620:three_prime_UTR 35.0%
TAGAACTTTCCTTGCAACAG+TGG + chr8_2:49602466-49602485 Msa1252620:CDS 40.0%
AAAACATCACCACTGTTGCA+AGG - chr8_2:49602478-49602497 None:intergenic 40.0%
AATGTGGAAGGACACCAATT+GGG + chr8_2:49602543-49602562 Msa1252620:CDS 40.0%
! AGCTAGTCTAAGTCCATGTT+TGG + chr8_2:49602574-49602593 Msa1252620:CDS 40.0%
! GCTAGTCTAAGTCCATGTTT+GGG + chr8_2:49602575-49602594 Msa1252620:CDS 40.0%
TAGAACTTTCCTTGCAACAG+TGG + chr8_2:49602466-49602485 Msa1252620:CDS 40.0%
AAAACATCACCACTGTTGCA+AGG - chr8_2:49602478-49602497 None:intergenic 40.0%
AATGTGGAAGGACACCAATT+GGG + chr8_2:49602543-49602562 Msa1252620:CDS 40.0%
! AGCTAGTCTAAGTCCATGTT+TGG + chr8_2:49602574-49602593 Msa1252620:CDS 40.0%
! GCTAGTCTAAGTCCATGTTT+GGG + chr8_2:49602575-49602594 Msa1252620:CDS 40.0%
!! ATTTTGGAAAGTGAGGCAGC+TGG + chr8_2:49602518-49602537 Msa1252620:CDS 45.0%
GAATGTGGAAGGACACCAAT+TGG + chr8_2:49602542-49602561 Msa1252620:CDS 45.0%
TTACGTACAGCACCCAAACA+TGG - chr8_2:49602590-49602609 None:intergenic 45.0%
! TGGGTGCTGTACGTAATGTT+AGG + chr8_2:49602594-49602613 Msa1252620:CDS 45.0%
! GGGTGCTGTACGTAATGTTA+GGG + chr8_2:49602595-49602614 Msa1252620:CDS 45.0%
ACTCTAGCACAACAAACTGG+TGG - chr8_2:49602629-49602648 None:intergenic 45.0%
CCAACTCTAGCACAACAAAC+TGG - chr8_2:49602632-49602651 None:intergenic 45.0%
!! CCAGTTTGTTGTGCTAGAGT+TGG + chr8_2:49602629-49602648 Msa1252620:CDS 45.0%
GGAACAGTGATAGCAATAGC+AGG - chr8_2:49602731-49602750 None:intergenic 45.0%
CACTTCCTTGAAACCAAAGC+AGG + chr8_2:49602980-49602999 Msa1252620:exon 45.0%
!! ATTTTGGAAAGTGAGGCAGC+TGG + chr8_2:49602518-49602537 Msa1252620:CDS 45.0%
GAATGTGGAAGGACACCAAT+TGG + chr8_2:49602542-49602561 Msa1252620:CDS 45.0%
TTACGTACAGCACCCAAACA+TGG - chr8_2:49602590-49602609 None:intergenic 45.0%
! TGGGTGCTGTACGTAATGTT+AGG + chr8_2:49602594-49602613 Msa1252620:CDS 45.0%
! GGGTGCTGTACGTAATGTTA+GGG + chr8_2:49602595-49602614 Msa1252620:CDS 45.0%
ACTCTAGCACAACAAACTGG+TGG - chr8_2:49602629-49602648 None:intergenic 45.0%
CCAACTCTAGCACAACAAAC+TGG - chr8_2:49602632-49602651 None:intergenic 45.0%
!! CCAGTTTGTTGTGCTAGAGT+TGG + chr8_2:49602629-49602648 Msa1252620:CDS 45.0%
GGAACAGTGATAGCAATAGC+AGG - chr8_2:49602731-49602750 None:intergenic 45.0%
CACTTCCTTGAAACCAAAGC+AGG + chr8_2:49602980-49602999 Msa1252620:exon 45.0%
!! AATAAATCAAATTTAAATAT+TGG + chr8_2:49603294-49603313 Msa1252620:three_prime_UTR 5.0%
!! ATAAATCAAATTTAAATATT+GGG + chr8_2:49603295-49603314 Msa1252620:three_prime_UTR 5.0%
!! AATAAATCAAATTTAAATAT+TGG + chr8_2:49603294-49603313 Msa1252620:three_prime_UTR 5.0%
!! ATAAATCAAATTTAAATATT+GGG + chr8_2:49603295-49603314 Msa1252620:three_prime_UTR 5.0%
AACATTAGGAACCGACCTGC+TGG + chr8_2:49602761-49602780 Msa1252620:CDS 50.0%
CACATTTCTTGCCAGCAGGT+CGG - chr8_2:49602775-49602794 None:intergenic 50.0%
CTTCCACATTTCTTGCCAGC+AGG - chr8_2:49602779-49602798 None:intergenic 50.0%
AACATTAGGAACCGACCTGC+TGG + chr8_2:49602761-49602780 Msa1252620:CDS 50.0%
CACATTTCTTGCCAGCAGGT+CGG - chr8_2:49602775-49602794 None:intergenic 50.0%
CTTCCACATTTCTTGCCAGC+AGG - chr8_2:49602779-49602798 None:intergenic 50.0%
AGTGAGGCAGCTGGAGAATG+TGG + chr8_2:49602527-49602546 Msa1252620:CDS 55.0%
AGGCAGCTGGAGAATGTGGA+AGG + chr8_2:49602531-49602550 Msa1252620:CDS 55.0%
CTAGCTGCTGCTGACCCAAT+TGG - chr8_2:49602560-49602579 None:intergenic 55.0%
CGACCTGCTGGCAAGAAATG+TGG + chr8_2:49602773-49602792 Msa1252620:CDS 55.0%
AGTGAGGCAGCTGGAGAATG+TGG + chr8_2:49602527-49602546 Msa1252620:CDS 55.0%
AGGCAGCTGGAGAATGTGGA+AGG + chr8_2:49602531-49602550 Msa1252620:CDS 55.0%
CTAGCTGCTGCTGACCCAAT+TGG - chr8_2:49602560-49602579 None:intergenic 55.0%
CGACCTGCTGGCAAGAAATG+TGG + chr8_2:49602773-49602792 Msa1252620:CDS 55.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 49602396 49603334 49602396 ID=Msa1252620;Name=Msa1252620
chr8_2 mRNA 49602396 49603334 49602396 ID=Msa1252620-mRNA-1;Parent=Msa1252620;Name=Msa1252620-mRNA-1;_AED=0.00;_eAED=0.00;_QI=50|1|1|1|0|0.5|2|344|122
chr8_2 exon 49602396 49602797 49602396 ID=Msa1252620-mRNA-1:exon:15061;Parent=Msa1252620-mRNA-1
chr8_2 exon 49602974 49603334 49602974 ID=Msa1252620-mRNA-1:exon:15062;Parent=Msa1252620-mRNA-1
chr8_2 five_prime_UTR 49602396 49602445 49602396 ID=Msa1252620-mRNA-1:five_prime_utr;Parent=Msa1252620-mRNA-1
chr8_2 CDS 49602446 49602797 49602446 ID=Msa1252620-mRNA-1:cds;Parent=Msa1252620-mRNA-1
chr8_2 CDS 49602974 49602990 49602974 ID=Msa1252620-mRNA-1:cds;Parent=Msa1252620-mRNA-1
chr8_2 three_prime_UTR 49602991 49603334 49602991 ID=Msa1252620-mRNA-1:three_prime_utr;Parent=Msa1252620-mRNA-1
Gene Sequence

>Msa1252620

ATGATGATGGAATTCAAGGTTAGAACTTTCCTTGCAACAGTGGTGATGTTTTTGTTGGCATCAAGTGTGTTAATTTTGGAAAGTGAGGCAGCTGGAGAATGTGGAAGGACACCAATTGGGTCAGCAGCAGCTAGTCTAAGTCCATGTTTGGGTGCTGTACGTAATGTTAGGGCAAAAGTTCCACCAGTTTGTTGTGCTAGAGTTGGTGCTTTGATTAGAACTTCTCCAAGATGTCTTTGTTCTGTTCTTTTGTCACCTATTGCAAAACAAGCTAAGATTAATCCTGCTATTGCTATCACTGTTCCTAAGAGATGCAACATTAGGAACCGACCTGCTGGCAAGAAATGTGGAAGGTACACACTTCCTTGA
Protein sequence

>Msa1252620

MMMEFKVRTFLATVVMFLLASSVLILESEAAGECGRTPIGSAAASLSPCLGAVRNVRAKVPPVCCARVGALIRTSPRCLCSVLLSPIAKQAKINPAIAITVPKRCNIRNRPAGKKCGRYTLP*