AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0755830


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0755830 MtrunA17_Chr5g0400761 93.893 131 7 1 1 130 1 131 7.04e-90 256
Msa0755830 MtrunA17_Chr4g0054461 65.625 96 33 0 35 130 7 102 2.13e-44 140
Msa0755830 MtrunA17_Chr3g0140691 59.155 71 26 2 61 130 30 98 3.09e-23 86.7
Msa0755830 MtrunA17_Chr3g0123851 39.474 76 42 2 59 130 46 121 3.74e-13 61.6
Msa0755830 MtrunA17_Chr8g0381891 39.474 76 42 2 59 130 48 123 1.03e-11 57.8
Msa0755830 MtrunA17_Chr4g0063871 32.000 125 68 4 6 130 7 114 1.89e-11 57.0
Msa0755830 MtrunA17_Chr2g0330071 30.216 139 65 5 11 130 3 128 3.98e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0755830 AT4G37810.1 47.706 109 49 3 30 130 20 128 9.72e-26 94.4
Msa0755830 AT5G10310.2 40.244 82 35 3 59 130 51 128 2.97e-11 57.0
Msa0755830 AT5G10310.1 40.244 82 35 3 59 130 45 122 3.80e-11 56.6

Find 39 sgRNAs with CRISPR-Local

Find 102 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGCACCTTGTATCACATTT+TGG 0.211299 5_2:+9639136 None:intergenic
GAATATCATCATGTCATTTA+TGG 0.231378 5_2:-9639642 Msa0755830:CDS
CATCTAAATGAGCTACATTA+TGG 0.294334 5_2:+9638930 None:intergenic
GTCATTGCTCGAGGATTTGC+TGG 0.332737 5_2:+9639082 None:intergenic
CATTTGCATTTCCAACTCAT+AGG 0.395492 5_2:+9638989 None:intergenic
TAGAGAAAGGTGTTCAAGAA+AGG 0.412468 5_2:+9639690 None:intergenic
CCAACTCATAGGTTTATAGT+TGG 0.415908 5_2:+9639000 None:intergenic
AGGGAGAATTCTTTAGAGAA+AGG 0.416869 5_2:+9639677 None:intergenic
TATGAGAAAGAGAAGAGAAA+TGG 0.420044 5_2:+9639599 None:intergenic
TGTTGATTTGTGCAGACAAT+AGG 0.427844 5_2:-9639202 Msa0755830:intron
AGTTTCAAGCTTGACACAAA+AGG 0.454396 5_2:-9639577 Msa0755830:CDS
AGAGAAAGGTGTTCAAGAAA+GGG 0.460515 5_2:+9639691 None:intergenic
TGATATTCATTCCTCATTTG+AGG 0.464024 5_2:+9639657 None:intergenic
TTATGGAACAAATCAAATCA+AGG 0.478334 5_2:+9638947 None:intergenic
GATATTCATTCCTCATTTGA+GGG 0.488619 5_2:+9639658 None:intergenic
GTTTCAAGCTTGACACAAAA+GGG 0.500719 5_2:-9639576 Msa0755830:CDS
ATCTTTCCTGTCATTGCTCG+AGG 0.500929 5_2:+9639073 None:intergenic
GCAACTGCAGACAGAGTTGA+AGG 0.512648 5_2:+9639046 None:intergenic
GTAGCTCATTTAGATGATCA+AGG 0.537745 5_2:-9638923 Msa0755830:three_prime_UTR
GCAAATCCTCGAGCAATGAC+AGG 0.547611 5_2:-9639079 Msa0755830:CDS
GTGATGGTGAGGAAGCAGAT+AGG 0.550422 5_2:-9639169 Msa0755830:CDS
AAAGAATTCTCCCTCAAATG+AGG 0.557496 5_2:-9639668 Msa0755830:exon
CCAACTATAAACCTATGAGT+TGG 0.573239 5_2:-9639000 Msa0755830:CDS
GGCCACCAAAATGTGATACA+AGG 0.578748 5_2:-9639141 Msa0755830:CDS
TGTCTGCAGTTGCTTATGCT+AGG 0.585427 5_2:-9639036 Msa0755830:CDS
TTACCTGGTGAAAACCATGT+TGG 0.587700 5_2:+9639431 None:intergenic
GTGATAACAAGGTGATGGTG+AGG 0.587937 5_2:-9639180 Msa0755830:CDS
TATGGAACAAATCAAATCAA+GGG 0.596622 5_2:+9638948 None:intergenic
CTGCAGTTGCTTATGCTAGG+AGG 0.607524 5_2:-9639033 Msa0755830:CDS
ATGAGTTGGAAATGCAAATG+TGG 0.611058 5_2:-9638986 Msa0755830:CDS
AGAAAGACTTTGAACCAACA+TGG 0.614586 5_2:-9639445 Msa0755830:CDS
CAAAAGGGACTTGTAACTGA+AGG 0.617750 5_2:-9639561 Msa0755830:intron
AATAGGTGATAACAAGGTGA+TGG 0.620627 5_2:-9639185 Msa0755830:CDS
TGAGGAAGCAGATAGGATCA+AGG 0.622434 5_2:-9639162 Msa0755830:CDS
GATACAAGGTGCAGATTCTG+TGG 0.657438 5_2:-9639127 Msa0755830:CDS
GCAGACAATAGGTGATAACA+AGG 0.666495 5_2:-9639191 Msa0755830:intron
CAGATTCTGTGGTCACTGCG+AGG 0.669680 5_2:-9639116 Msa0755830:CDS
TGAGTTGGAAATGCAAATGT+GGG 0.678868 5_2:-9638985 Msa0755830:CDS
CAACTGCAGACAGAGTTGAA+GGG 0.720563 5_2:+9639047 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAATTATTTTTCTCATTTG+AGG - chr5_2:9639207-9639226 Msa0755830:intron 15.0%
!!! TTAATTATTTTTCTCATTTG+AGG - chr5_2:9639207-9639226 Msa0755830:intron 15.0%
!! AAATGTAAACAAAATTTACC+TGG + chr5_2:9639139-9639158 None:intergenic 20.0%
!! AAGTTATAAGAATTTAGAAG+AGG + chr5_2:9639178-9639197 None:intergenic 20.0%
!! AAATGTAAACAAAATTTACC+TGG + chr5_2:9639139-9639158 None:intergenic 20.0%
!! AAGTTATAAGAATTTAGAAG+AGG + chr5_2:9639178-9639197 None:intergenic 20.0%
!! GAATATCATCATGTCATTTA+TGG - chr5_2:9638910-9638929 Msa0755830:three_prime_UTR 25.0%
! TTGAAGTAAGAGTTATAAGT+TGG + chr5_2:9639041-9639060 None:intergenic 25.0%
! TATGGAACAAATCAAATCAA+GGG + chr5_2:9639607-9639626 None:intergenic 25.0%
! TTATGGAACAAATCAAATCA+AGG + chr5_2:9639608-9639627 None:intergenic 25.0%
!! GAATATCATCATGTCATTTA+TGG - chr5_2:9638910-9638929 Msa0755830:three_prime_UTR 25.0%
! TTGAAGTAAGAGTTATAAGT+TGG + chr5_2:9639041-9639060 None:intergenic 25.0%
! TATGGAACAAATCAAATCAA+GGG + chr5_2:9639607-9639626 None:intergenic 25.0%
! TTATGGAACAAATCAAATCA+AGG + chr5_2:9639608-9639627 None:intergenic 25.0%
GATATTCATTCCTCATTTGA+GGG + chr5_2:9638897-9638916 None:intergenic 30.0%
TGATATTCATTCCTCATTTG+AGG + chr5_2:9638898-9638917 None:intergenic 30.0%
TATGAGAAAGAGAAGAGAAA+TGG + chr5_2:9638956-9638975 None:intergenic 30.0%
ATAAGAATTTAGAAGAGGCA+GGG + chr5_2:9639173-9639192 None:intergenic 30.0%
TATAAGAATTTAGAAGAGGC+AGG + chr5_2:9639174-9639193 None:intergenic 30.0%
CTAATTAAGATGAGTGATGT+AGG - chr5_2:9639313-9639332 Msa0755830:intron 30.0%
CATCTAAATGAGCTACATTA+TGG + chr5_2:9639625-9639644 None:intergenic 30.0%
GATATTCATTCCTCATTTGA+GGG + chr5_2:9638897-9638916 None:intergenic 30.0%
TGATATTCATTCCTCATTTG+AGG + chr5_2:9638898-9638917 None:intergenic 30.0%
TATGAGAAAGAGAAGAGAAA+TGG + chr5_2:9638956-9638975 None:intergenic 30.0%
ATAAGAATTTAGAAGAGGCA+GGG + chr5_2:9639173-9639192 None:intergenic 30.0%
TATAAGAATTTAGAAGAGGC+AGG + chr5_2:9639174-9639193 None:intergenic 30.0%
CTAATTAAGATGAGTGATGT+AGG - chr5_2:9639313-9639332 Msa0755830:intron 30.0%
CATCTAAATGAGCTACATTA+TGG + chr5_2:9639625-9639644 None:intergenic 30.0%
!! AGAGAAAGGTGTTCAAGAAA+GGG + chr5_2:9638864-9638883 None:intergenic 35.0%
!! TAGAGAAAGGTGTTCAAGAA+AGG + chr5_2:9638865-9638884 None:intergenic 35.0%
! AGGGAGAATTCTTTAGAGAA+AGG + chr5_2:9638878-9638897 None:intergenic 35.0%
AAAGAATTCTCCCTCAAATG+AGG - chr5_2:9638884-9638903 Msa0755830:three_prime_UTR 35.0%
AGTTTCAAGCTTGACACAAA+AGG - chr5_2:9638975-9638994 Msa0755830:CDS 35.0%
GTTTCAAGCTTGACACAAAA+GGG - chr5_2:9638976-9638995 Msa0755830:CDS 35.0%
AGAAAGACTTTGAACCAACA+TGG - chr5_2:9639107-9639126 Msa0755830:CDS 35.0%
!! TGTTGATTTGTGCAGACAAT+AGG - chr5_2:9639350-9639369 Msa0755830:intron 35.0%
AATAGGTGATAACAAGGTGA+TGG - chr5_2:9639367-9639386 Msa0755830:intron 35.0%
CCAACTCATAGGTTTATAGT+TGG + chr5_2:9639555-9639574 None:intergenic 35.0%
CCAACTATAAACCTATGAGT+TGG - chr5_2:9639552-9639571 Msa0755830:intron 35.0%
CATTTGCATTTCCAACTCAT+AGG + chr5_2:9639566-9639585 None:intergenic 35.0%
! ATGAGTTGGAAATGCAAATG+TGG - chr5_2:9639566-9639585 Msa0755830:CDS 35.0%
! TGAGTTGGAAATGCAAATGT+GGG - chr5_2:9639567-9639586 Msa0755830:CDS 35.0%
GTAGCTCATTTAGATGATCA+AGG - chr5_2:9639629-9639648 Msa0755830:CDS 35.0%
!! AGAGAAAGGTGTTCAAGAAA+GGG + chr5_2:9638864-9638883 None:intergenic 35.0%
!! TAGAGAAAGGTGTTCAAGAA+AGG + chr5_2:9638865-9638884 None:intergenic 35.0%
! AGGGAGAATTCTTTAGAGAA+AGG + chr5_2:9638878-9638897 None:intergenic 35.0%
AAAGAATTCTCCCTCAAATG+AGG - chr5_2:9638884-9638903 Msa0755830:three_prime_UTR 35.0%
AGTTTCAAGCTTGACACAAA+AGG - chr5_2:9638975-9638994 Msa0755830:CDS 35.0%
GTTTCAAGCTTGACACAAAA+GGG - chr5_2:9638976-9638995 Msa0755830:CDS 35.0%
AGAAAGACTTTGAACCAACA+TGG - chr5_2:9639107-9639126 Msa0755830:CDS 35.0%
!! TGTTGATTTGTGCAGACAAT+AGG - chr5_2:9639350-9639369 Msa0755830:intron 35.0%
AATAGGTGATAACAAGGTGA+TGG - chr5_2:9639367-9639386 Msa0755830:intron 35.0%
CCAACTCATAGGTTTATAGT+TGG + chr5_2:9639555-9639574 None:intergenic 35.0%
CCAACTATAAACCTATGAGT+TGG - chr5_2:9639552-9639571 Msa0755830:intron 35.0%
CATTTGCATTTCCAACTCAT+AGG + chr5_2:9639566-9639585 None:intergenic 35.0%
! ATGAGTTGGAAATGCAAATG+TGG - chr5_2:9639566-9639585 Msa0755830:CDS 35.0%
! TGAGTTGGAAATGCAAATGT+GGG - chr5_2:9639567-9639586 Msa0755830:CDS 35.0%
GTAGCTCATTTAGATGATCA+AGG - chr5_2:9639629-9639648 Msa0755830:CDS 35.0%
CAAAAGGGACTTGTAACTGA+AGG - chr5_2:9638991-9639010 Msa0755830:CDS 40.0%
TCTTCTTCTTCTGCTCTTAC+AGG - chr5_2:9639083-9639102 Msa0755830:CDS 40.0%
TTACCTGGTGAAAACCATGT+TGG + chr5_2:9639124-9639143 None:intergenic 40.0%
AGACTGAGTAAACGAGTTGT+CGG + chr5_2:9639290-9639309 None:intergenic 40.0%
GCAGACAATAGGTGATAACA+AGG - chr5_2:9639361-9639380 Msa0755830:intron 40.0%
! CACCTTGTATCACATTTTGG+TGG + chr5_2:9639416-9639435 None:intergenic 40.0%
! CTGCACCTTGTATCACATTT+TGG + chr5_2:9639419-9639438 None:intergenic 40.0%
CAAAAGGGACTTGTAACTGA+AGG - chr5_2:9638991-9639010 Msa0755830:CDS 40.0%
TCTTCTTCTTCTGCTCTTAC+AGG - chr5_2:9639083-9639102 Msa0755830:CDS 40.0%
TTACCTGGTGAAAACCATGT+TGG + chr5_2:9639124-9639143 None:intergenic 40.0%
AGACTGAGTAAACGAGTTGT+CGG + chr5_2:9639290-9639309 None:intergenic 40.0%
GCAGACAATAGGTGATAACA+AGG - chr5_2:9639361-9639380 Msa0755830:intron 40.0%
! CACCTTGTATCACATTTTGG+TGG + chr5_2:9639416-9639435 None:intergenic 40.0%
! CTGCACCTTGTATCACATTT+TGG + chr5_2:9639419-9639438 None:intergenic 40.0%
! GAACCAACATGGTTTTCACC+AGG - chr5_2:9639118-9639137 Msa0755830:CDS 45.0%
! GTGATAACAAGGTGATGGTG+AGG - chr5_2:9639372-9639391 Msa0755830:intron 45.0%
TGAGGAAGCAGATAGGATCA+AGG - chr5_2:9639390-9639409 Msa0755830:intron 45.0%
GGCCACCAAAATGTGATACA+AGG - chr5_2:9639411-9639430 Msa0755830:intron 45.0%
GATACAAGGTGCAGATTCTG+TGG - chr5_2:9639425-9639444 Msa0755830:intron 45.0%
ATCTTTCCTGTCATTGCTCG+AGG + chr5_2:9639482-9639501 None:intergenic 45.0%
CAACTGCAGACAGAGTTGAA+GGG + chr5_2:9639508-9639527 None:intergenic 45.0%
TGTCTGCAGTTGCTTATGCT+AGG - chr5_2:9639516-9639535 Msa0755830:intron 45.0%
! GAACCAACATGGTTTTCACC+AGG - chr5_2:9639118-9639137 Msa0755830:CDS 45.0%
! GTGATAACAAGGTGATGGTG+AGG - chr5_2:9639372-9639391 Msa0755830:intron 45.0%
TGAGGAAGCAGATAGGATCA+AGG - chr5_2:9639390-9639409 Msa0755830:intron 45.0%
GGCCACCAAAATGTGATACA+AGG - chr5_2:9639411-9639430 Msa0755830:intron 45.0%
GATACAAGGTGCAGATTCTG+TGG - chr5_2:9639425-9639444 Msa0755830:intron 45.0%
ATCTTTCCTGTCATTGCTCG+AGG + chr5_2:9639482-9639501 None:intergenic 45.0%
CAACTGCAGACAGAGTTGAA+GGG + chr5_2:9639508-9639527 None:intergenic 45.0%
TGTCTGCAGTTGCTTATGCT+AGG - chr5_2:9639516-9639535 Msa0755830:intron 45.0%
!! TAAACGAGTTGTCGGCTCAG+TGG + chr5_2:9639282-9639301 None:intergenic 50.0%
! GTGATGGTGAGGAAGCAGAT+AGG - chr5_2:9639383-9639402 Msa0755830:intron 50.0%
GTCATTGCTCGAGGATTTGC+TGG + chr5_2:9639473-9639492 None:intergenic 50.0%
GCAAATCCTCGAGCAATGAC+AGG - chr5_2:9639473-9639492 Msa0755830:intron 50.0%
GCAACTGCAGACAGAGTTGA+AGG + chr5_2:9639509-9639528 None:intergenic 50.0%
CTGCAGTTGCTTATGCTAGG+AGG - chr5_2:9639519-9639538 Msa0755830:intron 50.0%
!! TAAACGAGTTGTCGGCTCAG+TGG + chr5_2:9639282-9639301 None:intergenic 50.0%
! GTGATGGTGAGGAAGCAGAT+AGG - chr5_2:9639383-9639402 Msa0755830:intron 50.0%
GTCATTGCTCGAGGATTTGC+TGG + chr5_2:9639473-9639492 None:intergenic 50.0%
GCAAATCCTCGAGCAATGAC+AGG - chr5_2:9639473-9639492 Msa0755830:intron 50.0%
GCAACTGCAGACAGAGTTGA+AGG + chr5_2:9639509-9639528 None:intergenic 50.0%
CTGCAGTTGCTTATGCTAGG+AGG - chr5_2:9639519-9639538 Msa0755830:intron 50.0%
CAGATTCTGTGGTCACTGCG+AGG - chr5_2:9639436-9639455 Msa0755830:CDS 55.0%
CAGATTCTGTGGTCACTGCG+AGG - chr5_2:9639436-9639455 Msa0755830:CDS 55.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 9638853 9639721 9638853 ID=Msa0755830;Name=Msa0755830
chr5_2 mRNA 9638853 9639721 9638853 ID=Msa0755830-mRNA-1;Parent=Msa0755830;Name=Msa0755830-mRNA-1;_AED=0.03;_eAED=0.03;_QI=48|1|1|1|1|1|3|111|130
chr5_2 exon 9638853 9639209 9638853 ID=Msa0755830-mRNA-1:exon:4508;Parent=Msa0755830-mRNA-1
chr5_2 exon 9639435 9639469 9639435 ID=Msa0755830-mRNA-1:exon:4507;Parent=Msa0755830-mRNA-1
chr5_2 exon 9639562 9639721 9639562 ID=Msa0755830-mRNA-1:exon:4506;Parent=Msa0755830-mRNA-1
chr5_2 five_prime_UTR 9639674 9639721 9639674 ID=Msa0755830-mRNA-1:five_prime_utr;Parent=Msa0755830-mRNA-1
chr5_2 CDS 9639562 9639673 9639562 ID=Msa0755830-mRNA-1:cds;Parent=Msa0755830-mRNA-1
chr5_2 CDS 9639435 9639469 9639435 ID=Msa0755830-mRNA-1:cds;Parent=Msa0755830-mRNA-1
chr5_2 CDS 9638964 9639209 9638964 ID=Msa0755830-mRNA-1:cds;Parent=Msa0755830-mRNA-1
chr5_2 three_prime_UTR 9638853 9638963 9638853 ID=Msa0755830-mRNA-1:three_prime_utr;Parent=Msa0755830-mRNA-1
Gene Sequence

>Msa0755830

ATGAGGAATGAATATCATCATGTCATTTATGGTCAAAGATTCATTTTCATTACCATTTCTCTTCTCTTTCTCATAGTTTCAAGCTTGACACAAAAGGGACTTGTAACTGAAGGTAGAAAGACTTTGAACCAACATGGTTTTCACCAGACAATAGGTGATAACAAGGTGATGGTGAGGAAGCAGATAGGATCAAGGCCACCAAAATGTGATACAAGGTGCAGATTCTGTGGTCACTGCGAGGCTATTCAAGTTCCAGCAAATCCTCGAGCAATGACAGGAAAGATCAACCCTTCAACTCTGTCTGCAGTTGCTTATGCTAGGAGGCAAGATAATTCCAACTATAAACCTATGAGTTGGAAATGCAAATGTGGGAACATTATTTTCAACCCTTGA

Protein sequence

>Msa0755830

MRNEYHHVIYGQRFIFITISLLFLIVSSLTQKGLVTEGRKTLNQHGFHQTIGDNKVMVRKQIGSRPPKCDTRCRFCGHCEAIQVPANPRAMTGKINPSTLSAVAYARRQDNSNYKPMSWKCKCGNIIFNP*