AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0440990

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0440990 MtrunA17_Chr3g0078241 98.837 86 1 0 1 86 384 469 2.18e-54 174
Msa0440990 MtrunA17_Chr2g0303951 75.294 85 21 0 1 85 385 469 1.21e-42 144
Msa0440990 MtrunA17_Chr5g0419741 58.025 81 34 0 1 81 214 294 1.02e-28 104
Msa0440990 MtrunA17_Chr3g0122541 69.512 82 25 0 1 82 367 448 5.80e-28 104
Msa0440990 MtrunA17_Chr3g0122521 63.415 82 30 0 1 82 106 187 8.11e-25 92.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0440990 AT4G18140.4 74.118 85 22 0 1 85 357 441 1.21e-40 138
Msa0440990 AT4G18140.6 74.118 85 22 0 1 85 357 441 1.21e-40 138
Msa0440990 AT4G18140.5 74.118 85 22 0 1 85 357 441 1.21e-40 138
Msa0440990 AT4G18140.1 73.494 83 22 0 1 83 357 439 1.17e-39 135
Msa0440990 AT4G18140.2 73.494 83 22 0 1 83 357 439 1.17e-39 135
Msa0440990 AT4G18140.3 74.390 82 21 0 1 82 357 438 2.46e-39 135
Msa0440990 AT5G46410.3 71.765 85 24 0 1 85 369 453 9.19e-39 133
Msa0440990 AT5G46410.1 71.765 85 24 0 1 85 369 453 9.19e-39 133
Msa0440990 AT5G46410.2 71.765 85 24 0 1 85 372 456 9.67e-39 133
Msa0440990 AT5G11860.3 66.667 81 27 0 1 81 200 280 1.04e-34 120
Msa0440990 AT5G11860.5 66.667 81 27 0 1 81 200 280 1.04e-34 120
Msa0440990 AT5G11860.1 66.667 81 27 0 1 81 200 280 1.04e-34 120
Msa0440990 AT5G11860.4 66.667 81 27 0 1 81 200 280 1.04e-34 120
Msa0440990 AT5G11860.2 66.667 81 27 0 1 81 200 280 1.04e-34 120
Msa0440990 AT1G29780.1 39.286 84 50 1 1 83 138 221 3.98e-14 64.7
Msa0440990 AT1G29770.1 36.471 85 53 1 1 84 192 276 2.56e-12 60.5

Find 30 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATTTCTTTACTTCCCTTTC+TGG 0.097640 3_3:+9131072 Msa0440990:CDS
ACCAAAGATTTGACAGTTCT+TGG 0.197757 3_3:+9130564 Msa0440990:CDS
ACAGAGGCTGTGTTAATTAA+TGG 0.241927 3_3:+9131421 Msa0440990:three_prime_UTR
TTCAGAAATAGCTATGATTC+TGG 0.252842 3_3:+9131294 Msa0440990:three_prime_UTR
TCAAATTTCTCTGCGATAAT+CGG 0.313863 3_3:-9131124 None:intergenic
TCCAAGAACTGTCAAATCTT+TGG 0.348444 3_3:-9130565 Msa0440980:intron
TCAGAAATAGCTATGATTCT+GGG 0.405810 3_3:+9131295 Msa0440990:three_prime_UTR
CAGAGGCTGTGTTAATTAAT+GGG 0.406909 3_3:+9131422 Msa0440990:three_prime_UTR
TCATCAAACCAACTCTCAAT+AGG 0.412269 3_3:-9131031 None:intergenic
CTATGAAGGGCGAGGAGGTC+CGG 0.436459 3_3:-9131176 None:intergenic
CTGAGGAGAGTTGTCTACTA+TGG 0.448136 3_3:-9130607 Msa0440980:intron
TCAGACTGCAAGTTAACAAT+GGG 0.500724 3_3:+9131005 Msa0440990:CDS
TCAACGAGTTTCTCCAGAAA+GGG 0.501744 3_3:-9131085 None:intergenic
ATAATCGACTAATTCTATGA+AGG 0.502725 3_3:-9131190 None:intergenic
AATGTGCAAGACAACTAGGC+AGG 0.526575 3_3:-9131250 None:intergenic
ATGGGATTCCTATTGAGAGT+TGG 0.527202 3_3:+9131023 Msa0440990:CDS
CTTGATAGATGCACGAATCT+CGG 0.530294 3_3:-9130530 Msa0440980:intron
CATAGTAGACAACTCTCCTC+AGG 0.530342 3_3:+9130608 Msa0440990:CDS
GAAATCAAAGCAGAATCAGA+TGG 0.530841 3_3:-9131055 None:intergenic
ATCAACGAGTTTCTCCAGAA+AGG 0.548402 3_3:-9131086 None:intergenic
TAATCGACTAATTCTATGAA+GGG 0.551086 3_3:-9131189 None:intergenic
CTAAAATGTGCAAGACAACT+AGG 0.557100 3_3:-9131254 None:intergenic
GACTAATTCTATGAAGGGCG+AGG 0.578931 3_3:-9131184 None:intergenic
TCTGGAGAAACTCGTTGATG+TGG 0.587394 3_3:+9131090 Msa0440990:CDS
CAGAAATAGCTATGATTCTG+GGG 0.589495 3_3:+9131296 Msa0440990:three_prime_UTR
TTCAGACTGCAAGTTAACAA+TGG 0.590311 3_3:+9131004 Msa0440990:CDS
ATGTGCAAGACAACTAGGCA+GGG 0.600660 3_3:-9131249 None:intergenic
GATTCGTGCATCTATCAAGA+TGG 0.603464 3_3:+9130534 Msa0440990:CDS
TAATTCTATGAAGGGCGAGG+AGG 0.669597 3_3:-9131181 None:intergenic
CTTACTGAACTACAGTACAG+AGG 0.727146 3_3:+9131405 Msa0440990:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATAATTTTATTTCAAGTTT+TGG + chr3_3:9131359-9131378 Msa0440990:three_prime_UTR 10.0%
!!! AATAATTTTATTTCAAGTTT+TGG + chr3_3:9131359-9131378 Msa0440990:three_prime_UTR 10.0%
!! ATTTCAATATTATTTACCAT+AGG - chr3_3:9130958-9130977 None:intergenic 15.0%
!! ATTTCAATATTATTTACCAT+AGG - chr3_3:9130958-9130977 None:intergenic 15.0%
!!! AGATATAATGCCAAATATTT+TGG - chr3_3:9130695-9130714 None:intergenic 20.0%
!! GCATAATATAAATGTATCAT+TGG + chr3_3:9130841-9130860 Msa0440990:intron 20.0%
!!! AATTAGTTTTGCATATATTC+CGG + chr3_3:9131157-9131176 Msa0440990:exon 20.0%
!!! AGATATAATGCCAAATATTT+TGG - chr3_3:9130695-9130714 None:intergenic 20.0%
!! GCATAATATAAATGTATCAT+TGG + chr3_3:9130841-9130860 Msa0440990:intron 20.0%
!!! AATTAGTTTTGCATATATTC+CGG + chr3_3:9131157-9131176 Msa0440990:exon 20.0%
! AACCTATTATAACATGAAGA+CGG - chr3_3:9130642-9130661 Msa0440980:intron 25.0%
! CATTCATGATCCAAAATATT+TGG + chr3_3:9130682-9130701 Msa0440990:intron 25.0%
! GAAAATTAGTCATCTAAATG+AGG - chr3_3:9130776-9130795 None:intergenic 25.0%
! TATAGGAGATTCATGAAAAT+TGG - chr3_3:9130802-9130821 None:intergenic 25.0%
! TCATAATGTAAATGCATCAT+TGG + chr3_3:9130886-9130905 Msa0440990:intron 25.0%
!! ATAGTCCTTTTATATTTGTC+TGG + chr3_3:9130918-9130937 Msa0440990:intron 25.0%
! TTACCATAGGCAATAAATAA+AGG - chr3_3:9130945-9130964 None:intergenic 25.0%
! TAATCGACTAATTCTATGAA+GGG - chr3_3:9131192-9131211 None:intergenic 25.0%
! ATAATCGACTAATTCTATGA+AGG - chr3_3:9131193-9131212 None:intergenic 25.0%
! AACCTATTATAACATGAAGA+CGG - chr3_3:9130642-9130661 Msa0440980:intron 25.0%
! CATTCATGATCCAAAATATT+TGG + chr3_3:9130682-9130701 Msa0440990:intron 25.0%
! GAAAATTAGTCATCTAAATG+AGG - chr3_3:9130776-9130795 None:intergenic 25.0%
! TATAGGAGATTCATGAAAAT+TGG - chr3_3:9130802-9130821 None:intergenic 25.0%
! TCATAATGTAAATGCATCAT+TGG + chr3_3:9130886-9130905 Msa0440990:intron 25.0%
!! ATAGTCCTTTTATATTTGTC+TGG + chr3_3:9130918-9130937 Msa0440990:intron 25.0%
! TTACCATAGGCAATAAATAA+AGG - chr3_3:9130945-9130964 None:intergenic 25.0%
! TAATCGACTAATTCTATGAA+GGG - chr3_3:9131192-9131211 None:intergenic 25.0%
! ATAATCGACTAATTCTATGA+AGG - chr3_3:9131193-9131212 None:intergenic 25.0%
TAAAATCGCGAATGATGTAT+AGG - chr3_3:9130819-9130838 None:intergenic 30.0%
GCATTTACATTATGATGTGA+AGG - chr3_3:9130881-9130900 None:intergenic 30.0%
AAGGACCAGACAAATATAAA+AGG - chr3_3:9130926-9130945 None:intergenic 30.0%
TCAAACTTCTGTTCATGTTT+AGG + chr3_3:9130979-9130998 Msa0440990:intron 30.0%
TCAAATTTCTCTGCGATAAT+CGG - chr3_3:9131127-9131146 None:intergenic 30.0%
TTCAGAAATAGCTATGATTC+TGG + chr3_3:9131294-9131313 Msa0440990:three_prime_UTR 30.0%
TCAGAAATAGCTATGATTCT+GGG + chr3_3:9131295-9131314 Msa0440990:three_prime_UTR 30.0%
TAAAATCGCGAATGATGTAT+AGG - chr3_3:9130819-9130838 None:intergenic 30.0%
GCATTTACATTATGATGTGA+AGG - chr3_3:9130881-9130900 None:intergenic 30.0%
AAGGACCAGACAAATATAAA+AGG - chr3_3:9130926-9130945 None:intergenic 30.0%
TCAAACTTCTGTTCATGTTT+AGG + chr3_3:9130979-9130998 Msa0440990:intron 30.0%
TCAAATTTCTCTGCGATAAT+CGG - chr3_3:9131127-9131146 None:intergenic 30.0%
TTCAGAAATAGCTATGATTC+TGG + chr3_3:9131294-9131313 Msa0440990:three_prime_UTR 30.0%
TCAGAAATAGCTATGATTCT+GGG + chr3_3:9131295-9131314 Msa0440990:three_prime_UTR 30.0%
ACCAAAGATTTGACAGTTCT+TGG + chr3_3:9130564-9130583 Msa0440990:CDS 35.0%
TCCAAGAACTGTCAAATCTT+TGG - chr3_3:9130568-9130587 Msa0440980:intron 35.0%
CTATTATAACATGAAGACGG+AGG - chr3_3:9130639-9130658 Msa0440980:intron 35.0%
CTCCGTCTTCATGTTATAAT+AGG + chr3_3:9130637-9130656 Msa0440990:intron 35.0%
!! GTCATCTAAATGAGGCATTT+TGG - chr3_3:9130768-9130787 None:intergenic 35.0%
! GGTCCTTTATTTATTGCCTA+TGG + chr3_3:9130939-9130958 Msa0440990:intron 35.0%
TTCAGACTGCAAGTTAACAA+TGG + chr3_3:9131004-9131023 Msa0440990:CDS 35.0%
TCAGACTGCAAGTTAACAAT+GGG + chr3_3:9131005-9131024 Msa0440990:CDS 35.0%
TCATCAAACCAACTCTCAAT+AGG - chr3_3:9131034-9131053 None:intergenic 35.0%
GAAATCAAAGCAGAATCAGA+TGG - chr3_3:9131058-9131077 None:intergenic 35.0%
GATTTCTTTACTTCCCTTTC+TGG + chr3_3:9131072-9131091 Msa0440990:CDS 35.0%
CTAAAATGTGCAAGACAACT+AGG - chr3_3:9131257-9131276 None:intergenic 35.0%
CAGAAATAGCTATGATTCTG+GGG + chr3_3:9131296-9131315 Msa0440990:three_prime_UTR 35.0%
ACAGAGGCTGTGTTAATTAA+TGG + chr3_3:9131421-9131440 Msa0440990:three_prime_UTR 35.0%
CAGAGGCTGTGTTAATTAAT+GGG + chr3_3:9131422-9131441 Msa0440990:three_prime_UTR 35.0%
ACCAAAGATTTGACAGTTCT+TGG + chr3_3:9130564-9130583 Msa0440990:CDS 35.0%
TCCAAGAACTGTCAAATCTT+TGG - chr3_3:9130568-9130587 Msa0440980:intron 35.0%
CTATTATAACATGAAGACGG+AGG - chr3_3:9130639-9130658 Msa0440980:intron 35.0%
CTCCGTCTTCATGTTATAAT+AGG + chr3_3:9130637-9130656 Msa0440990:intron 35.0%
!! GTCATCTAAATGAGGCATTT+TGG - chr3_3:9130768-9130787 None:intergenic 35.0%
! GGTCCTTTATTTATTGCCTA+TGG + chr3_3:9130939-9130958 Msa0440990:intron 35.0%
TTCAGACTGCAAGTTAACAA+TGG + chr3_3:9131004-9131023 Msa0440990:CDS 35.0%
TCAGACTGCAAGTTAACAAT+GGG + chr3_3:9131005-9131024 Msa0440990:CDS 35.0%
TCATCAAACCAACTCTCAAT+AGG - chr3_3:9131034-9131053 None:intergenic 35.0%
GAAATCAAAGCAGAATCAGA+TGG - chr3_3:9131058-9131077 None:intergenic 35.0%
GATTTCTTTACTTCCCTTTC+TGG + chr3_3:9131072-9131091 Msa0440990:CDS 35.0%
CTAAAATGTGCAAGACAACT+AGG - chr3_3:9131257-9131276 None:intergenic 35.0%
CAGAAATAGCTATGATTCTG+GGG + chr3_3:9131296-9131315 Msa0440990:three_prime_UTR 35.0%
ACAGAGGCTGTGTTAATTAA+TGG + chr3_3:9131421-9131440 Msa0440990:three_prime_UTR 35.0%
CAGAGGCTGTGTTAATTAAT+GGG + chr3_3:9131422-9131441 Msa0440990:three_prime_UTR 35.0%
GATTCGTGCATCTATCAAGA+TGG + chr3_3:9130534-9130553 Msa0440990:CDS 40.0%
!!! CTACTATGGCTACTTTTGCT+AGG - chr3_3:9130596-9130615 Msa0440980:intron 40.0%
ATGGGATTCCTATTGAGAGT+TGG + chr3_3:9131023-9131042 Msa0440990:CDS 40.0%
TCAACGAGTTTCTCCAGAAA+GGG - chr3_3:9131088-9131107 None:intergenic 40.0%
ATCAACGAGTTTCTCCAGAA+AGG - chr3_3:9131089-9131108 None:intergenic 40.0%
CTTACTGAACTACAGTACAG+AGG + chr3_3:9131405-9131424 Msa0440990:three_prime_UTR 40.0%
CTTGATAGATGCACGAATCT+CGG - chr3_3:9130533-9130552 Msa0440980:intron 40.0%
GATTCGTGCATCTATCAAGA+TGG + chr3_3:9130534-9130553 Msa0440990:CDS 40.0%
!!! CTACTATGGCTACTTTTGCT+AGG - chr3_3:9130596-9130615 Msa0440980:intron 40.0%
ATGGGATTCCTATTGAGAGT+TGG + chr3_3:9131023-9131042 Msa0440990:CDS 40.0%
TCAACGAGTTTCTCCAGAAA+GGG - chr3_3:9131088-9131107 None:intergenic 40.0%
ATCAACGAGTTTCTCCAGAA+AGG - chr3_3:9131089-9131108 None:intergenic 40.0%
CTTACTGAACTACAGTACAG+AGG + chr3_3:9131405-9131424 Msa0440990:three_prime_UTR 40.0%
CTGAGGAGAGTTGTCTACTA+TGG - chr3_3:9130610-9130629 Msa0440980:intron 45.0%
CATAGTAGACAACTCTCCTC+AGG + chr3_3:9130608-9130627 Msa0440990:CDS 45.0%
TCTGGAGAAACTCGTTGATG+TGG + chr3_3:9131090-9131109 Msa0440990:CDS 45.0%
TAATTCTATGAAGGGCGAGG+AGG - chr3_3:9131184-9131203 None:intergenic 45.0%
GACTAATTCTATGAAGGGCG+AGG - chr3_3:9131187-9131206 None:intergenic 45.0%
ATGTGCAAGACAACTAGGCA+GGG - chr3_3:9131252-9131271 None:intergenic 45.0%
AATGTGCAAGACAACTAGGC+AGG - chr3_3:9131253-9131272 None:intergenic 45.0%
CTGAGGAGAGTTGTCTACTA+TGG - chr3_3:9130610-9130629 Msa0440980:intron 45.0%
CATAGTAGACAACTCTCCTC+AGG + chr3_3:9130608-9130627 Msa0440990:CDS 45.0%
TCTGGAGAAACTCGTTGATG+TGG + chr3_3:9131090-9131109 Msa0440990:CDS 45.0%
TAATTCTATGAAGGGCGAGG+AGG - chr3_3:9131184-9131203 None:intergenic 45.0%
GACTAATTCTATGAAGGGCG+AGG - chr3_3:9131187-9131206 None:intergenic 45.0%
ATGTGCAAGACAACTAGGCA+GGG - chr3_3:9131252-9131271 None:intergenic 45.0%
AATGTGCAAGACAACTAGGC+AGG - chr3_3:9131253-9131272 None:intergenic 45.0%
GAAGACGGAGGAAATACCTG+AGG - chr3_3:9130627-9130646 Msa0440980:intron 50.0%
GAAGACGGAGGAAATACCTG+AGG - chr3_3:9130627-9130646 Msa0440980:intron 50.0%
CTATGAAGGGCGAGGAGGTC+CGG - chr3_3:9131179-9131198 None:intergenic 60.0%
CTATGAAGGGCGAGGAGGTC+CGG - chr3_3:9131179-9131198 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 9130531 9131478 9130531 ID=Msa0440990;Name=Msa0440990
chr3_3 mRNA 9130531 9131478 9130531 ID=Msa0440990-mRNA-1;Parent=Msa0440990;Name=Msa0440990-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|1|0.5|1|1|1|2|316|86
chr3_3 exon 9130531 9130629 9130531 ID=Msa0440990-mRNA-1:exon:1839;Parent=Msa0440990-mRNA-1
chr3_3 exon 9131001 9131478 9131001 ID=Msa0440990-mRNA-1:exon:1840;Parent=Msa0440990-mRNA-1
chr3_3 CDS 9130531 9130629 9130531 ID=Msa0440990-mRNA-1:cds;Parent=Msa0440990-mRNA-1
chr3_3 CDS 9131001 9131162 9131001 ID=Msa0440990-mRNA-1:cds;Parent=Msa0440990-mRNA-1
chr3_3 three_prime_UTR 9131163 9131478 9131163 ID=Msa0440990-mRNA-1:three_prime_utr;Parent=Msa0440990-mRNA-1
Gene Sequence

>Msa0440990

CGAGATTCGTGCATCTATCAAGATGGCACTTTCACCAAAGATTTGACAGTTCTTGGACTTGACCTAGCAAAAGTAGCCATAGTAGACAACTCTCCTCAGGTGTTCAGACTGCAAGTTAACAATGGGATTCCTATTGAGAGTTGGTTTGATGATCCATCTGATTCTGCTTTGATTTCTTTACTTCCCTTTCTGGAGAAACTCGTTGATGTGGACGATGTTCGACCGATTATCGCAGAGAAATTTGAGAACAAGAAGAATTAG
Protein sequence

>Msa0440990

RDSCIYQDGTFTKDLTVLGLDLAKVAIVDNSPQVFRLQVNNGIPIESWFDDPSDSALISLLPFLEKLVDVDDVRPIIAEKFENKKN*