AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0257250


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0257250 MtrunA17_Chr2g0319211 87.755 98 9 1 6 103 161 255 2.21e-59 182
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0257250 AT5G54660.1 58.750 80 28 3 20 94 107 186 9.91e-26 95.1

Find 23 sgRNAs with CRISPR-Local

Find 148 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTGGTCATTGGTGGGAAAA+TGG 0.259017 2_2:+53017552 Msa0257250:CDS
ATTCAAGTCCATGTTGATAA+AGG 0.284747 2_2:+53017465 Msa0257250:CDS
TAAAATGCCAAAGATCAAAA+AGG 0.291755 2_2:+53017659 Msa0257250:CDS
TTCAAGTCCATGTTGATAAA+GGG 0.436330 2_2:+53017466 Msa0257250:CDS
TTCTTCCAATCTGCATCCTC+TGG 0.460108 2_2:-53017597 None:intergenic
GAGACTCAAAGACAAATGAT+TGG 0.472039 2_2:+53017526 Msa0257250:CDS
AGATGCCAGAGGATGCAGAT+TGG 0.502624 2_2:+53017592 Msa0257250:CDS
GGGAAAATGGATATGTAAGA+AGG 0.521141 2_2:+53017565 Msa0257250:CDS
ATTGGAGGTGTGGTCATTGG+TGG 0.523846 2_2:+53017544 Msa0257250:CDS
ATGATTGGAGGTGTGGTCAT+TGG 0.535519 2_2:+53017541 Msa0257250:CDS
CCACCTTCCCTTTATCAACA+TGG 0.538491 2_2:-53017473 None:intergenic
AAGGGTTCTGATCATGCTCA+AGG 0.575715 2_2:+53017678 Msa0257250:CDS
AAGACAAATGATTGGAGGTG+TGG 0.588863 2_2:+53017534 Msa0257250:CDS
AAAATGGCAATACCTACGAA+GGG 0.594804 2_2:+53016912 None:intergenic
TTGGAGGTGTGGTCATTGGT+GGG 0.595589 2_2:+53017545 Msa0257250:CDS
ACTCAAAGACAAATGATTGG+AGG 0.607196 2_2:+53017529 Msa0257250:CDS
GGGAAGGTGGTGGAAATCAG+TGG 0.621675 2_2:+53017486 Msa0257250:CDS
TGTTGATAAAGGGAAGGTGG+TGG 0.624580 2_2:+53017476 Msa0257250:CDS
CCATGTTGATAAAGGGAAGG+TGG 0.624798 2_2:+53017473 Msa0257250:CDS
TGGTGGAAATCAGTGGACAA+TGG 0.653289 2_2:+53017493 Msa0257250:CDS
AGTCCATGTTGATAAAGGGA+AGG 0.656983 2_2:+53017470 Msa0257250:CDS
AAATGGCAATACCTACGAAG+GGG 0.689196 2_2:+53016913 None:intergenic
AAGAAGGCTTGAGATGCCAG+AGG 0.727204 2_2:+53017581 Msa0257250:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATTCGAAAAATTAAATA+GGG - chr2_2:53017309-53017328 None:intergenic 10.0%
!! TAAAATTCGAAAAATTAAAT+AGG - chr2_2:53017310-53017329 None:intergenic 10.0%
!! AAAATTCGAAAAATTAAATA+GGG - chr2_2:53017309-53017328 None:intergenic 10.0%
!! TAAAATTCGAAAAATTAAAT+AGG - chr2_2:53017310-53017329 None:intergenic 10.0%
!! TAGTCCTTATATATATTTAA+AGG + chr2_2:53017219-53017238 Msa0257250:intron 15.0%
!! AGTCCTTATATATATTTAAA+GGG + chr2_2:53017220-53017239 Msa0257250:intron 15.0%
!! TAGTCCTTATATATATTTAA+AGG + chr2_2:53017219-53017238 Msa0257250:intron 15.0%
!! AGTCCTTATATATATTTAAA+GGG + chr2_2:53017220-53017239 Msa0257250:intron 15.0%
!!! CATTCACATTTTATATGATA+CGG - chr2_2:53017153-53017172 None:intergenic 20.0%
!! TGACCCTTTAAATATATATA+AGG - chr2_2:53017226-53017245 None:intergenic 20.0%
!! GAATTCTAAGCAAAATTATA+GGG - chr2_2:53017345-53017364 None:intergenic 20.0%
!! AGAATTCTAAGCAAAATTAT+AGG - chr2_2:53017346-53017365 None:intergenic 20.0%
!!! CATTCACATTTTATATGATA+CGG - chr2_2:53017153-53017172 None:intergenic 20.0%
!! TGACCCTTTAAATATATATA+AGG - chr2_2:53017226-53017245 None:intergenic 20.0%
!! GAATTCTAAGCAAAATTATA+GGG - chr2_2:53017345-53017364 None:intergenic 20.0%
!! AGAATTCTAAGCAAAATTAT+AGG - chr2_2:53017346-53017365 None:intergenic 20.0%
! TGATAAGTATCTAAGAACTT+GGG - chr2_2:53017126-53017145 None:intergenic 25.0%
!! GCAAGTTTTTAAATATGGAA+GGG - chr2_2:53017278-53017297 None:intergenic 25.0%
!! TGCAAGTTTTTAAATATGGA+AGG - chr2_2:53017279-53017298 None:intergenic 25.0%
!! TGTGTGCAAGTTTTTAAATA+TGG - chr2_2:53017283-53017302 None:intergenic 25.0%
!!! TTCCTGTTTTGAAAAATAAC+TGG - chr2_2:53017431-53017450 None:intergenic 25.0%
!!! TTATTTTTCAAAACAGGAAC+TGG + chr2_2:53017432-53017451 Msa0257250:CDS 25.0%
!!! TATTTTTCAAAACAGGAACT+GGG + chr2_2:53017433-53017452 Msa0257250:CDS 25.0%
! TAAAATGCCAAAGATCAAAA+AGG + chr2_2:53017659-53017678 Msa0257250:CDS 25.0%
! AAAATGCCAAAGATCAAAAA+GGG + chr2_2:53017660-53017679 Msa0257250:CDS 25.0%
! TGATAAGTATCTAAGAACTT+GGG - chr2_2:53017126-53017145 None:intergenic 25.0%
!! GCAAGTTTTTAAATATGGAA+GGG - chr2_2:53017278-53017297 None:intergenic 25.0%
!! TGCAAGTTTTTAAATATGGA+AGG - chr2_2:53017279-53017298 None:intergenic 25.0%
!! TGTGTGCAAGTTTTTAAATA+TGG - chr2_2:53017283-53017302 None:intergenic 25.0%
!!! TTCCTGTTTTGAAAAATAAC+TGG - chr2_2:53017431-53017450 None:intergenic 25.0%
!!! TTATTTTTCAAAACAGGAAC+TGG + chr2_2:53017432-53017451 Msa0257250:CDS 25.0%
!!! TATTTTTCAAAACAGGAACT+GGG + chr2_2:53017433-53017452 Msa0257250:CDS 25.0%
! TAAAATGCCAAAGATCAAAA+AGG + chr2_2:53017659-53017678 Msa0257250:CDS 25.0%
! AAAATGCCAAAGATCAAAAA+GGG + chr2_2:53017660-53017679 Msa0257250:CDS 25.0%
GATAAGTATCTAAGAACTTG+GGG - chr2_2:53017125-53017144 None:intergenic 30.0%
GTGATAAGTATCTAAGAACT+TGG - chr2_2:53017127-53017146 None:intergenic 30.0%
! CACATTTTATATGATACGGA+AGG - chr2_2:53017149-53017168 None:intergenic 30.0%
ATGAGGCAATTGAAAATACT+AGG - chr2_2:53017375-53017394 None:intergenic 30.0%
!!! CACCAGTTATTTTTCAAAAC+AGG + chr2_2:53017426-53017445 Msa0257250:intron 30.0%
! ATTCAAGTCCATGTTGATAA+AGG + chr2_2:53017465-53017484 Msa0257250:CDS 30.0%
! TTCAAGTCCATGTTGATAAA+GGG + chr2_2:53017466-53017485 Msa0257250:CDS 30.0%
GATAAGTATCTAAGAACTTG+GGG - chr2_2:53017125-53017144 None:intergenic 30.0%
GTGATAAGTATCTAAGAACT+TGG - chr2_2:53017127-53017146 None:intergenic 30.0%
! CACATTTTATATGATACGGA+AGG - chr2_2:53017149-53017168 None:intergenic 30.0%
ATGAGGCAATTGAAAATACT+AGG - chr2_2:53017375-53017394 None:intergenic 30.0%
!!! CACCAGTTATTTTTCAAAAC+AGG + chr2_2:53017426-53017445 Msa0257250:intron 30.0%
! ATTCAAGTCCATGTTGATAA+AGG + chr2_2:53017465-53017484 Msa0257250:CDS 30.0%
! TTCAAGTCCATGTTGATAAA+GGG + chr2_2:53017466-53017485 Msa0257250:CDS 30.0%
GATAGGGACTTCAGTATTAT+GGG + chr2_2:53017010-53017029 Msa0257250:intron 35.0%
ATAGGGACTTCAGTATTATG+GGG + chr2_2:53017011-53017030 Msa0257250:intron 35.0%
TTAGAAGCTAGTTATCAACG+GGG - chr2_2:53017093-53017112 None:intergenic 35.0%
CTTAGAAGCTAGTTATCAAC+GGG - chr2_2:53017094-53017113 None:intergenic 35.0%
CCTTAGAAGCTAGTTATCAA+CGG - chr2_2:53017095-53017114 None:intergenic 35.0%
!! CGTTGATAACTAGCTTCTAA+GGG + chr2_2:53017093-53017112 Msa0257250:intron 35.0%
! ATTTCCACTAAGAGTGTGTT+TGG - chr2_2:53017398-53017417 None:intergenic 35.0%
GAGACTCAAAGACAAATGAT+TGG + chr2_2:53017526-53017545 Msa0257250:CDS 35.0%
ACTCAAAGACAAATGATTGG+AGG + chr2_2:53017529-53017548 Msa0257250:CDS 35.0%
GGGAAAATGGATATGTAAGA+AGG + chr2_2:53017565-53017584 Msa0257250:CDS 35.0%
! TCAGAACCCTTTTTGATCTT+TGG - chr2_2:53017669-53017688 None:intergenic 35.0%
GATAGGGACTTCAGTATTAT+GGG + chr2_2:53017010-53017029 Msa0257250:intron 35.0%
ATAGGGACTTCAGTATTATG+GGG + chr2_2:53017011-53017030 Msa0257250:intron 35.0%
TTAGAAGCTAGTTATCAACG+GGG - chr2_2:53017093-53017112 None:intergenic 35.0%
CTTAGAAGCTAGTTATCAAC+GGG - chr2_2:53017094-53017113 None:intergenic 35.0%
CCTTAGAAGCTAGTTATCAA+CGG - chr2_2:53017095-53017114 None:intergenic 35.0%
!! CGTTGATAACTAGCTTCTAA+GGG + chr2_2:53017093-53017112 Msa0257250:intron 35.0%
! ATTTCCACTAAGAGTGTGTT+TGG - chr2_2:53017398-53017417 None:intergenic 35.0%
GAGACTCAAAGACAAATGAT+TGG + chr2_2:53017526-53017545 Msa0257250:CDS 35.0%
ACTCAAAGACAAATGATTGG+AGG + chr2_2:53017529-53017548 Msa0257250:CDS 35.0%
GGGAAAATGGATATGTAAGA+AGG + chr2_2:53017565-53017584 Msa0257250:CDS 35.0%
! TCAGAACCCTTTTTGATCTT+TGG - chr2_2:53017669-53017688 None:intergenic 35.0%
!! TACTCTACGGTGCTATACTT+GGG - chr2_2:53016952-53016971 None:intergenic 40.0%
!! ATACTCTACGGTGCTATACT+TGG - chr2_2:53016953-53016972 None:intergenic 40.0%
GGATAGGGACTTCAGTATTA+TGG + chr2_2:53017009-53017028 Msa0257250:intron 40.0%
! ATCAAGTAGTCTGGGATGTT+CGG + chr2_2:53017048-53017067 Msa0257250:intron 40.0%
!! CCGTTGATAACTAGCTTCTA+AGG + chr2_2:53017092-53017111 Msa0257250:intron 40.0%
! TGATAACTAGCTTCTAAGGG+AGG + chr2_2:53017096-53017115 Msa0257250:intron 40.0%
! GATAACTAGCTTCTAAGGGA+GGG + chr2_2:53017097-53017116 Msa0257250:intron 40.0%
!! ATATGGAAGGGCACTTGTTA+AGG - chr2_2:53017266-53017285 None:intergenic 40.0%
! ACTAAGAGTGTGTTTGGATG+AGG - chr2_2:53017392-53017411 None:intergenic 40.0%
TCATCCAAACACACTCTTAG+TGG + chr2_2:53017391-53017410 Msa0257250:intron 40.0%
! AGTCCATGTTGATAAAGGGA+AGG + chr2_2:53017470-53017489 Msa0257250:CDS 40.0%
AAGACAAATGATTGGAGGTG+TGG + chr2_2:53017534-53017553 Msa0257250:CDS 40.0%
!! TACTCTACGGTGCTATACTT+GGG - chr2_2:53016952-53016971 None:intergenic 40.0%
!! ATACTCTACGGTGCTATACT+TGG - chr2_2:53016953-53016972 None:intergenic 40.0%
GGATAGGGACTTCAGTATTA+TGG + chr2_2:53017009-53017028 Msa0257250:intron 40.0%
! ATCAAGTAGTCTGGGATGTT+CGG + chr2_2:53017048-53017067 Msa0257250:intron 40.0%
!! CCGTTGATAACTAGCTTCTA+AGG + chr2_2:53017092-53017111 Msa0257250:intron 40.0%
! TGATAACTAGCTTCTAAGGG+AGG + chr2_2:53017096-53017115 Msa0257250:intron 40.0%
! GATAACTAGCTTCTAAGGGA+GGG + chr2_2:53017097-53017116 Msa0257250:intron 40.0%
!! ATATGGAAGGGCACTTGTTA+AGG - chr2_2:53017266-53017285 None:intergenic 40.0%
! ACTAAGAGTGTGTTTGGATG+AGG - chr2_2:53017392-53017411 None:intergenic 40.0%
TCATCCAAACACACTCTTAG+TGG + chr2_2:53017391-53017410 Msa0257250:intron 40.0%
! AGTCCATGTTGATAAAGGGA+AGG + chr2_2:53017470-53017489 Msa0257250:CDS 40.0%
AAGACAAATGATTGGAGGTG+TGG + chr2_2:53017534-53017553 Msa0257250:CDS 40.0%
!! TTTTTAGTCAGCCCCTTCGT+AGG - chr2_2:53016927-53016946 None:intergenic 45.0%
TCAGAGACGTTGCTAGGATA+GGG + chr2_2:53016994-53017013 Msa0257250:intron 45.0%
AAGTCCCACATCAAGTAGTC+TGG + chr2_2:53017039-53017058 Msa0257250:intron 45.0%
AGTCCCACATCAAGTAGTCT+GGG + chr2_2:53017040-53017059 Msa0257250:intron 45.0%
CATCCCAGACTACTTGATGT+GGG - chr2_2:53017046-53017065 None:intergenic 45.0%
ACATCCCAGACTACTTGATG+TGG - chr2_2:53017047-53017066 None:intergenic 45.0%
! GATGTTCGGTGAAAGTAGCT+TGG + chr2_2:53017062-53017081 Msa0257250:intron 45.0%
CCACCTTCCCTTTATCAACA+TGG - chr2_2:53017476-53017495 None:intergenic 45.0%
! CCATGTTGATAAAGGGAAGG+TGG + chr2_2:53017473-53017492 Msa0257250:CDS 45.0%
! TGTTGATAAAGGGAAGGTGG+TGG + chr2_2:53017476-53017495 Msa0257250:CDS 45.0%
TGGTGGAAATCAGTGGACAA+TGG + chr2_2:53017493-53017512 Msa0257250:CDS 45.0%
! ATGATTGGAGGTGTGGTCAT+TGG + chr2_2:53017541-53017560 Msa0257250:CDS 45.0%
TGTGGTCATTGGTGGGAAAA+TGG + chr2_2:53017552-53017571 Msa0257250:CDS 45.0%
TTCTTCCAATCTGCATCCTC+TGG - chr2_2:53017600-53017619 None:intergenic 45.0%
! AAGGGTTCTGATCATGCTCA+AGG + chr2_2:53017678-53017697 Msa0257250:CDS 45.0%
!! TTTTTAGTCAGCCCCTTCGT+AGG - chr2_2:53016927-53016946 None:intergenic 45.0%
TCAGAGACGTTGCTAGGATA+GGG + chr2_2:53016994-53017013 Msa0257250:intron 45.0%
AAGTCCCACATCAAGTAGTC+TGG + chr2_2:53017039-53017058 Msa0257250:intron 45.0%
AGTCCCACATCAAGTAGTCT+GGG + chr2_2:53017040-53017059 Msa0257250:intron 45.0%
CATCCCAGACTACTTGATGT+GGG - chr2_2:53017046-53017065 None:intergenic 45.0%
ACATCCCAGACTACTTGATG+TGG - chr2_2:53017047-53017066 None:intergenic 45.0%
! GATGTTCGGTGAAAGTAGCT+TGG + chr2_2:53017062-53017081 Msa0257250:intron 45.0%
CCACCTTCCCTTTATCAACA+TGG - chr2_2:53017476-53017495 None:intergenic 45.0%
! CCATGTTGATAAAGGGAAGG+TGG + chr2_2:53017473-53017492 Msa0257250:CDS 45.0%
! TGTTGATAAAGGGAAGGTGG+TGG + chr2_2:53017476-53017495 Msa0257250:CDS 45.0%
TGGTGGAAATCAGTGGACAA+TGG + chr2_2:53017493-53017512 Msa0257250:CDS 45.0%
! ATGATTGGAGGTGTGGTCAT+TGG + chr2_2:53017541-53017560 Msa0257250:CDS 45.0%
TGTGGTCATTGGTGGGAAAA+TGG + chr2_2:53017552-53017571 Msa0257250:CDS 45.0%
TTCTTCCAATCTGCATCCTC+TGG - chr2_2:53017600-53017619 None:intergenic 45.0%
! AAGGGTTCTGATCATGCTCA+AGG + chr2_2:53017678-53017697 Msa0257250:CDS 45.0%
ATCCTAGCAACGTCTCTGAG+AGG - chr2_2:53016993-53017012 None:intergenic 50.0%
CTCAGAGACGTTGCTAGGAT+AGG + chr2_2:53016993-53017012 Msa0257250:intron 50.0%
! ATTGGAGGTGTGGTCATTGG+TGG + chr2_2:53017544-53017563 Msa0257250:CDS 50.0%
! TTGGAGGTGTGGTCATTGGT+GGG + chr2_2:53017545-53017564 Msa0257250:CDS 50.0%
AAGAAGGCTTGAGATGCCAG+AGG + chr2_2:53017581-53017600 Msa0257250:CDS 50.0%
AGATGCCAGAGGATGCAGAT+TGG + chr2_2:53017592-53017611 Msa0257250:CDS 50.0%
ATCCTAGCAACGTCTCTGAG+AGG - chr2_2:53016993-53017012 None:intergenic 50.0%
CTCAGAGACGTTGCTAGGAT+AGG + chr2_2:53016993-53017012 Msa0257250:intron 50.0%
! ATTGGAGGTGTGGTCATTGG+TGG + chr2_2:53017544-53017563 Msa0257250:CDS 50.0%
! TTGGAGGTGTGGTCATTGGT+GGG + chr2_2:53017545-53017564 Msa0257250:CDS 50.0%
AAGAAGGCTTGAGATGCCAG+AGG + chr2_2:53017581-53017600 Msa0257250:CDS 50.0%
AGATGCCAGAGGATGCAGAT+TGG + chr2_2:53017592-53017611 Msa0257250:CDS 50.0%
! CACCGTAGAGTATCAGCCGT+CGG + chr2_2:53016960-53016979 Msa0257250:intron 55.0%
! ACCGTAGAGTATCAGCCGTC+GGG + chr2_2:53016961-53016980 Msa0257250:intron 55.0%
TCCCGACGGCTGATACTCTA+CGG - chr2_2:53016965-53016984 None:intergenic 55.0%
TCTGAGAGGCAACATCCCGA+CGG - chr2_2:53016979-53016998 None:intergenic 55.0%
TGCCTCTCAGAGACGTTGCT+AGG + chr2_2:53016988-53017007 Msa0257250:intron 55.0%
!! GGGAAGGTGGTGGAAATCAG+TGG + chr2_2:53017486-53017505 Msa0257250:CDS 55.0%
! CACCGTAGAGTATCAGCCGT+CGG + chr2_2:53016960-53016979 Msa0257250:intron 55.0%
! ACCGTAGAGTATCAGCCGTC+GGG + chr2_2:53016961-53016980 Msa0257250:intron 55.0%
TCCCGACGGCTGATACTCTA+CGG - chr2_2:53016965-53016984 None:intergenic 55.0%
TCTGAGAGGCAACATCCCGA+CGG - chr2_2:53016979-53016998 None:intergenic 55.0%
TGCCTCTCAGAGACGTTGCT+AGG + chr2_2:53016988-53017007 Msa0257250:intron 55.0%
!! GGGAAGGTGGTGGAAATCAG+TGG + chr2_2:53017486-53017505 Msa0257250:CDS 55.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 53016915 53017704 53016915 ID=Msa0257250;Name=Msa0257250
chr2_2 mRNA 53016915 53017704 53016915 ID=Msa0257250-mRNA-1;Parent=Msa0257250;Name=Msa0257250-mRNA-1;_AED=0.50;_eAED=0.51;_QI=0|0|0|0.5|1|1|2|0|103
chr2_2 exon 53016915 53016953 53016915 ID=Msa0257250-mRNA-1:exon:15927;Parent=Msa0257250-mRNA-1
chr2_2 exon 53017432 53017704 53017432 ID=Msa0257250-mRNA-1:exon:15928;Parent=Msa0257250-mRNA-1
chr2_2 CDS 53016915 53016953 53016915 ID=Msa0257250-mRNA-1:cds;Parent=Msa0257250-mRNA-1
chr2_2 CDS 53017432 53017704 53017432 ID=Msa0257250-mRNA-1:cds;Parent=Msa0257250-mRNA-1
Gene Sequence

>Msa0257250

ATGGCAATACCTACGAAGGGGCTGACTAAAAAAGCCCAATTATTTTTCAAAACAGGAACTGGGAAAAACAACATTCAAGTCCATGTTGATAAAGGGAAGGTGGTGGAAATCAGTGGACAATGGAAGCAGCAAAGAGACTCAAAGACAAATGATTGGAGGTGTGGTCATTGGTGGGAAAATGGATATGTAAGAAGGCTTGAGATGCCAGAGGATGCAGATTGGAAGAATATACAAGCATTCATATATAATGACATATTCTTAGAAATTAAAATGCCAAAGATCAAAAAGGGTTCTGATCATGCTCAAGGATAA

Protein sequence

>Msa0257250

MAIPTKGLTKKAQLFFKTGTGKNNIQVHVDKGKVVEISGQWKQQRDSKTNDWRCGHWWENGYVRRLEMPEDADWKNIQAFIYNDIFLEIKMPKIKKGSDHAQG*