AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0797530


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0797530 MtrunA17_Chr5g0400761 94.656 131 6 1 1 130 1 131 8.29e-91 258
Msa0797530 MtrunA17_Chr4g0054461 65.625 96 33 0 35 130 7 102 2.09e-44 140
Msa0797530 MtrunA17_Chr3g0140691 59.155 71 26 2 61 130 30 98 3.09e-23 86.7
Msa0797530 MtrunA17_Chr3g0123851 39.474 76 42 2 59 130 46 121 4.39e-13 61.2
Msa0797530 MtrunA17_Chr4g0063871 32.000 125 68 4 6 130 7 114 1.02e-11 57.8
Msa0797530 MtrunA17_Chr8g0381891 39.474 76 42 2 59 130 48 123 1.05e-11 57.8
Msa0797530 MtrunA17_Chr2g0330071 30.216 139 65 5 11 130 3 128 6.49e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0797530 AT4G37810.1 47.706 109 49 3 30 130 20 128 9.62e-26 94.4
Msa0797530 AT5G10310.2 40.244 82 35 3 59 130 51 128 3.07e-11 57.0
Msa0797530 AT5G10310.1 40.244 82 35 3 59 130 45 122 4.10e-11 56.6

Find 39 sgRNAs with CRISPR-Local

Find 106 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGCACCTTGTATCACATTT+TGG 0.211299 5_3:+9709218 None:intergenic
GAATATCATCATGTCATTTA+TGG 0.231378 5_3:-9709746 Msa0797530:CDS
CATCTAAATGAGCTACATTA+TGG 0.294334 5_3:+9709012 None:intergenic
GTCATTGCTCGAGGATTTGC+TGG 0.332737 5_3:+9709164 None:intergenic
CATTTGCATTTCCAACTCAT+AGG 0.395492 5_3:+9709071 None:intergenic
TAGAGAAAGGTGTTCAAGAA+AGG 0.412468 5_3:+9709794 None:intergenic
CCAACTCATAGGTTTATAGT+TGG 0.415908 5_3:+9709082 None:intergenic
AGGGAGAATTCTTTAGAGAA+AGG 0.416869 5_3:+9709781 None:intergenic
TATGAGAAAGAGAAGAGAAA+TGG 0.420044 5_3:+9709703 None:intergenic
TGTTGATTTGTGCAGACAAT+AGG 0.427844 5_3:-9709284 Msa0797530:intron
AGTTTCAAGCTTGACACAAA+AGG 0.454396 5_3:-9709681 Msa0797530:CDS
AGAGAAAGGTGTTCAAGAAA+GGG 0.460515 5_3:+9709795 None:intergenic
TGATATTCATTCCTCATTTG+AGG 0.464024 5_3:+9709761 None:intergenic
GCAACTGCAGAGAGAGTTGA+AGG 0.477572 5_3:+9709128 None:intergenic
TTATGGAACAAATCAAATCA+AGG 0.478334 5_3:+9709029 None:intergenic
GATATTCATTCCTCATTTGA+GGG 0.488619 5_3:+9709762 None:intergenic
GTTTCAAGCTTGACACAAAA+GGG 0.500719 5_3:-9709680 Msa0797530:CDS
ATCTTTCCTGTCATTGCTCG+AGG 0.500929 5_3:+9709155 None:intergenic
GTAGCTCATTTAGATGATCA+AGG 0.537745 5_3:-9709005 Msa0797530:three_prime_UTR
GCAAATCCTCGAGCAATGAC+AGG 0.547611 5_3:-9709161 Msa0797530:CDS
GTGATGGTGAGGAAGCAGAT+AGG 0.550422 5_3:-9709251 Msa0797530:CDS
AAAGAATTCTCCCTCAAATG+AGG 0.557496 5_3:-9709772 Msa0797530:exon
CCAACTATAAACCTATGAGT+TGG 0.573239 5_3:-9709082 Msa0797530:CDS
GGCCACCAAAATGTGATACA+AGG 0.578748 5_3:-9709223 Msa0797530:CDS
TCTCTGCAGTTGCTTATGCT+AGG 0.585427 5_3:-9709118 Msa0797530:CDS
TTACCTGGTGAAAACCATGT+TGG 0.587700 5_3:+9709535 None:intergenic
GTGATAACAAGGTGATGGTG+AGG 0.587937 5_3:-9709262 Msa0797530:CDS
TATGGAACAAATCAAATCAA+GGG 0.596622 5_3:+9709030 None:intergenic
CTGCAGTTGCTTATGCTAGG+AGG 0.607524 5_3:-9709115 Msa0797530:CDS
ATGAGTTGGAAATGCAAATG+TGG 0.611058 5_3:-9709068 Msa0797530:CDS
AGAAAGACTTTGAACCAACA+TGG 0.614586 5_3:-9709549 Msa0797530:CDS
CAAAAGGGACTTGTAACTGA+AGG 0.617750 5_3:-9709665 Msa0797530:intron
AATAGGTGATAACAAGGTGA+TGG 0.620627 5_3:-9709267 Msa0797530:CDS
TGAGGAAGCAGATAGGATCA+AGG 0.622434 5_3:-9709244 Msa0797530:CDS
GATACAAGGTGCAGATTCTG+TGG 0.657438 5_3:-9709209 Msa0797530:CDS
GCAGACAATAGGTGATAACA+AGG 0.666495 5_3:-9709273 Msa0797530:intron
CAGATTCTGTGGTCACTGCG+AGG 0.669680 5_3:-9709198 Msa0797530:CDS
TGAGTTGGAAATGCAAATGT+GGG 0.678868 5_3:-9709067 Msa0797530:CDS
CAACTGCAGAGAGAGTTGAA+GGG 0.724322 5_3:+9709129 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAAGTTATAAGAATT+TGG + chr5_3:9709266-9709285 None:intergenic 10.0%
!! AAAAAAAAGTTATAAGAATT+TGG + chr5_3:9709266-9709285 None:intergenic 10.0%
!!! TTAATTATTTTTCTCATTTG+AGG - chr5_3:9709289-9709308 Msa0797530:intron 15.0%
!!! TTAATTATTTTTCTCATTTG+AGG - chr5_3:9709289-9709308 Msa0797530:intron 15.0%
!! AAATGTAAACAAAATTTACC+TGG + chr5_3:9709221-9709240 None:intergenic 20.0%
!! AAATGTAAACAAAATTTACC+TGG + chr5_3:9709221-9709240 None:intergenic 20.0%
!! GAATATCATCATGTCATTTA+TGG - chr5_3:9708992-9709011 Msa0797530:three_prime_UTR 25.0%
! TTGAAGTAAGAGTTATAAGT+TGG + chr5_3:9709123-9709142 None:intergenic 25.0%
! AAGTTATAAGAATTTGGAAG+AGG + chr5_3:9709260-9709279 None:intergenic 25.0%
! TATGGAACAAATCAAATCAA+GGG + chr5_3:9709711-9709730 None:intergenic 25.0%
! TTATGGAACAAATCAAATCA+AGG + chr5_3:9709712-9709731 None:intergenic 25.0%
!! GAATATCATCATGTCATTTA+TGG - chr5_3:9708992-9709011 Msa0797530:three_prime_UTR 25.0%
! TTGAAGTAAGAGTTATAAGT+TGG + chr5_3:9709123-9709142 None:intergenic 25.0%
! AAGTTATAAGAATTTGGAAG+AGG + chr5_3:9709260-9709279 None:intergenic 25.0%
! TATGGAACAAATCAAATCAA+GGG + chr5_3:9709711-9709730 None:intergenic 25.0%
! TTATGGAACAAATCAAATCA+AGG + chr5_3:9709712-9709731 None:intergenic 25.0%
GATATTCATTCCTCATTTGA+GGG + chr5_3:9708979-9708998 None:intergenic 30.0%
TGATATTCATTCCTCATTTG+AGG + chr5_3:9708980-9708999 None:intergenic 30.0%
TATGAGAAAGAGAAGAGAAA+TGG + chr5_3:9709038-9709057 None:intergenic 30.0%
CTAATTAAGATGAGTGATGT+AGG - chr5_3:9709417-9709436 Msa0797530:intron 30.0%
CATCTAAATGAGCTACATTA+TGG + chr5_3:9709729-9709748 None:intergenic 30.0%
GATATTCATTCCTCATTTGA+GGG + chr5_3:9708979-9708998 None:intergenic 30.0%
TGATATTCATTCCTCATTTG+AGG + chr5_3:9708980-9708999 None:intergenic 30.0%
TATGAGAAAGAGAAGAGAAA+TGG + chr5_3:9709038-9709057 None:intergenic 30.0%
CTAATTAAGATGAGTGATGT+AGG - chr5_3:9709417-9709436 Msa0797530:intron 30.0%
CATCTAAATGAGCTACATTA+TGG + chr5_3:9709729-9709748 None:intergenic 30.0%
!! AGAGAAAGGTGTTCAAGAAA+GGG + chr5_3:9708946-9708965 None:intergenic 35.0%
!! TAGAGAAAGGTGTTCAAGAA+AGG + chr5_3:9708947-9708966 None:intergenic 35.0%
! AGGGAGAATTCTTTAGAGAA+AGG + chr5_3:9708960-9708979 None:intergenic 35.0%
AAAGAATTCTCCCTCAAATG+AGG - chr5_3:9708966-9708985 Msa0797530:three_prime_UTR 35.0%
AGTTTCAAGCTTGACACAAA+AGG - chr5_3:9709057-9709076 Msa0797530:CDS 35.0%
GTTTCAAGCTTGACACAAAA+GGG - chr5_3:9709058-9709077 Msa0797530:CDS 35.0%
AGAAAGACTTTGAACCAACA+TGG - chr5_3:9709189-9709208 Msa0797530:CDS 35.0%
ATAAGAATTTGGAAGAGGCA+GGG + chr5_3:9709255-9709274 None:intergenic 35.0%
TATAAGAATTTGGAAGAGGC+AGG + chr5_3:9709256-9709275 None:intergenic 35.0%
!! TGTTGATTTGTGCAGACAAT+AGG - chr5_3:9709454-9709473 Msa0797530:intron 35.0%
AATAGGTGATAACAAGGTGA+TGG - chr5_3:9709471-9709490 Msa0797530:intron 35.0%
CCAACTCATAGGTTTATAGT+TGG + chr5_3:9709659-9709678 None:intergenic 35.0%
CCAACTATAAACCTATGAGT+TGG - chr5_3:9709656-9709675 Msa0797530:intron 35.0%
CATTTGCATTTCCAACTCAT+AGG + chr5_3:9709670-9709689 None:intergenic 35.0%
! ATGAGTTGGAAATGCAAATG+TGG - chr5_3:9709670-9709689 Msa0797530:CDS 35.0%
! TGAGTTGGAAATGCAAATGT+GGG - chr5_3:9709671-9709690 Msa0797530:CDS 35.0%
GTAGCTCATTTAGATGATCA+AGG - chr5_3:9709733-9709752 Msa0797530:CDS 35.0%
!! AGAGAAAGGTGTTCAAGAAA+GGG + chr5_3:9708946-9708965 None:intergenic 35.0%
!! TAGAGAAAGGTGTTCAAGAA+AGG + chr5_3:9708947-9708966 None:intergenic 35.0%
! AGGGAGAATTCTTTAGAGAA+AGG + chr5_3:9708960-9708979 None:intergenic 35.0%
AAAGAATTCTCCCTCAAATG+AGG - chr5_3:9708966-9708985 Msa0797530:three_prime_UTR 35.0%
AGTTTCAAGCTTGACACAAA+AGG - chr5_3:9709057-9709076 Msa0797530:CDS 35.0%
GTTTCAAGCTTGACACAAAA+GGG - chr5_3:9709058-9709077 Msa0797530:CDS 35.0%
AGAAAGACTTTGAACCAACA+TGG - chr5_3:9709189-9709208 Msa0797530:CDS 35.0%
ATAAGAATTTGGAAGAGGCA+GGG + chr5_3:9709255-9709274 None:intergenic 35.0%
TATAAGAATTTGGAAGAGGC+AGG + chr5_3:9709256-9709275 None:intergenic 35.0%
!! TGTTGATTTGTGCAGACAAT+AGG - chr5_3:9709454-9709473 Msa0797530:intron 35.0%
AATAGGTGATAACAAGGTGA+TGG - chr5_3:9709471-9709490 Msa0797530:intron 35.0%
CCAACTCATAGGTTTATAGT+TGG + chr5_3:9709659-9709678 None:intergenic 35.0%
CCAACTATAAACCTATGAGT+TGG - chr5_3:9709656-9709675 Msa0797530:intron 35.0%
CATTTGCATTTCCAACTCAT+AGG + chr5_3:9709670-9709689 None:intergenic 35.0%
! ATGAGTTGGAAATGCAAATG+TGG - chr5_3:9709670-9709689 Msa0797530:CDS 35.0%
! TGAGTTGGAAATGCAAATGT+GGG - chr5_3:9709671-9709690 Msa0797530:CDS 35.0%
GTAGCTCATTTAGATGATCA+AGG - chr5_3:9709733-9709752 Msa0797530:CDS 35.0%
CAAAAGGGACTTGTAACTGA+AGG - chr5_3:9709073-9709092 Msa0797530:CDS 40.0%
TCTTCTTCTTCTGCTCTTAC+AGG - chr5_3:9709165-9709184 Msa0797530:CDS 40.0%
TTACCTGGTGAAAACCATGT+TGG + chr5_3:9709206-9709225 None:intergenic 40.0%
GTAAGAGTTTGTCAACTCAG+TGG + chr5_3:9709364-9709383 None:intergenic 40.0%
AGACTGAGTAAACGAGTTGT+CGG + chr5_3:9709394-9709413 None:intergenic 40.0%
GCAGACAATAGGTGATAACA+AGG - chr5_3:9709465-9709484 Msa0797530:intron 40.0%
! CACCTTGTATCACATTTTGG+TGG + chr5_3:9709520-9709539 None:intergenic 40.0%
! CTGCACCTTGTATCACATTT+TGG + chr5_3:9709523-9709542 None:intergenic 40.0%
CAAAAGGGACTTGTAACTGA+AGG - chr5_3:9709073-9709092 Msa0797530:CDS 40.0%
TCTTCTTCTTCTGCTCTTAC+AGG - chr5_3:9709165-9709184 Msa0797530:CDS 40.0%
TTACCTGGTGAAAACCATGT+TGG + chr5_3:9709206-9709225 None:intergenic 40.0%
GTAAGAGTTTGTCAACTCAG+TGG + chr5_3:9709364-9709383 None:intergenic 40.0%
AGACTGAGTAAACGAGTTGT+CGG + chr5_3:9709394-9709413 None:intergenic 40.0%
GCAGACAATAGGTGATAACA+AGG - chr5_3:9709465-9709484 Msa0797530:intron 40.0%
! CACCTTGTATCACATTTTGG+TGG + chr5_3:9709520-9709539 None:intergenic 40.0%
! CTGCACCTTGTATCACATTT+TGG + chr5_3:9709523-9709542 None:intergenic 40.0%
! GAACCAACATGGTTTTCACC+AGG - chr5_3:9709200-9709219 Msa0797530:CDS 45.0%
! GTGATAACAAGGTGATGGTG+AGG - chr5_3:9709476-9709495 Msa0797530:intron 45.0%
TGAGGAAGCAGATAGGATCA+AGG - chr5_3:9709494-9709513 Msa0797530:intron 45.0%
GGCCACCAAAATGTGATACA+AGG - chr5_3:9709515-9709534 Msa0797530:intron 45.0%
GATACAAGGTGCAGATTCTG+TGG - chr5_3:9709529-9709548 Msa0797530:intron 45.0%
ATCTTTCCTGTCATTGCTCG+AGG + chr5_3:9709586-9709605 None:intergenic 45.0%
CAACTGCAGAGAGAGTTGAA+GGG + chr5_3:9709612-9709631 None:intergenic 45.0%
TCTCTGCAGTTGCTTATGCT+AGG - chr5_3:9709620-9709639 Msa0797530:intron 45.0%
! GAACCAACATGGTTTTCACC+AGG - chr5_3:9709200-9709219 Msa0797530:CDS 45.0%
! GTGATAACAAGGTGATGGTG+AGG - chr5_3:9709476-9709495 Msa0797530:intron 45.0%
TGAGGAAGCAGATAGGATCA+AGG - chr5_3:9709494-9709513 Msa0797530:intron 45.0%
GGCCACCAAAATGTGATACA+AGG - chr5_3:9709515-9709534 Msa0797530:intron 45.0%
GATACAAGGTGCAGATTCTG+TGG - chr5_3:9709529-9709548 Msa0797530:intron 45.0%
ATCTTTCCTGTCATTGCTCG+AGG + chr5_3:9709586-9709605 None:intergenic 45.0%
CAACTGCAGAGAGAGTTGAA+GGG + chr5_3:9709612-9709631 None:intergenic 45.0%
TCTCTGCAGTTGCTTATGCT+AGG - chr5_3:9709620-9709639 Msa0797530:intron 45.0%
!! TAAACGAGTTGTCGGCTCAG+TGG + chr5_3:9709386-9709405 None:intergenic 50.0%
! GTGATGGTGAGGAAGCAGAT+AGG - chr5_3:9709487-9709506 Msa0797530:intron 50.0%
GTCATTGCTCGAGGATTTGC+TGG + chr5_3:9709577-9709596 None:intergenic 50.0%
GCAAATCCTCGAGCAATGAC+AGG - chr5_3:9709577-9709596 Msa0797530:intron 50.0%
GCAACTGCAGAGAGAGTTGA+AGG + chr5_3:9709613-9709632 None:intergenic 50.0%
CTGCAGTTGCTTATGCTAGG+AGG - chr5_3:9709623-9709642 Msa0797530:intron 50.0%
!! TAAACGAGTTGTCGGCTCAG+TGG + chr5_3:9709386-9709405 None:intergenic 50.0%
! GTGATGGTGAGGAAGCAGAT+AGG - chr5_3:9709487-9709506 Msa0797530:intron 50.0%
GTCATTGCTCGAGGATTTGC+TGG + chr5_3:9709577-9709596 None:intergenic 50.0%
GCAAATCCTCGAGCAATGAC+AGG - chr5_3:9709577-9709596 Msa0797530:intron 50.0%
GCAACTGCAGAGAGAGTTGA+AGG + chr5_3:9709613-9709632 None:intergenic 50.0%
CTGCAGTTGCTTATGCTAGG+AGG - chr5_3:9709623-9709642 Msa0797530:intron 50.0%
CAGATTCTGTGGTCACTGCG+AGG - chr5_3:9709540-9709559 Msa0797530:CDS 55.0%
CAGATTCTGTGGTCACTGCG+AGG - chr5_3:9709540-9709559 Msa0797530:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 9708935 9709825 9708935 ID=Msa0797530;Name=Msa0797530
chr5_3 mRNA 9708935 9709825 9708935 ID=Msa0797530-mRNA-1;Parent=Msa0797530;Name=Msa0797530-mRNA-1;_AED=0.01;_eAED=0.01;_QI=48|1|1|1|1|1|3|111|130
chr5_3 exon 9708935 9709291 9708935 ID=Msa0797530-mRNA-1:exon:4178;Parent=Msa0797530-mRNA-1
chr5_3 exon 9709539 9709573 9709539 ID=Msa0797530-mRNA-1:exon:4177;Parent=Msa0797530-mRNA-1
chr5_3 exon 9709666 9709825 9709666 ID=Msa0797530-mRNA-1:exon:4176;Parent=Msa0797530-mRNA-1
chr5_3 five_prime_UTR 9709778 9709825 9709778 ID=Msa0797530-mRNA-1:five_prime_utr;Parent=Msa0797530-mRNA-1
chr5_3 CDS 9709666 9709777 9709666 ID=Msa0797530-mRNA-1:cds;Parent=Msa0797530-mRNA-1
chr5_3 CDS 9709539 9709573 9709539 ID=Msa0797530-mRNA-1:cds;Parent=Msa0797530-mRNA-1
chr5_3 CDS 9709046 9709291 9709046 ID=Msa0797530-mRNA-1:cds;Parent=Msa0797530-mRNA-1
chr5_3 three_prime_UTR 9708935 9709045 9708935 ID=Msa0797530-mRNA-1:three_prime_utr;Parent=Msa0797530-mRNA-1
Gene Sequence

>Msa0797530

ATGAGGAATGAATATCATCATGTCATTTATGGTCAAAGATTCAGTTTCATTACCATTTCTCTTCTCTTTCTCATAGTTTCAAGCTTGACACAAAAGGGACTTGTAACTGAAGGTAGAAAGACTTTGAACCAACATGGTTTTCACCAGACAATAGGTGATAACAAGGTGATGGTGAGGAAGCAGATAGGATCAAGGCCACCAAAATGTGATACAAGGTGCAGATTCTGTGGTCACTGCGAGGCTATTCAAGTTCCAGCAAATCCTCGAGCAATGACAGGAAAGATCAACCCTTCAACTCTCTCTGCAGTTGCTTATGCTAGGAGGCAAGATAATTCCAACTATAAACCTATGAGTTGGAAATGCAAATGTGGGAACATTATTTTCAACCCTTGA

Protein sequence

>Msa0797530

MRNEYHHVIYGQRFSFITISLLFLIVSSLTQKGLVTEGRKTLNQHGFHQTIGDNKVMVRKQIGSRPPKCDTRCRFCGHCEAIQVPANPRAMTGKINPSTLSAVAYARRQDNSNYKPMSWKCKCGNIIFNP*