AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1368430


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1368430 MtrunA17_Chr6g0455061 90.530 264 23 1 1 264 1 262 6.11e-175 482
Msa1368430 MtrunA17_Chr3g0144851 91.667 264 21 1 1 264 1 263 5.87e-173 477
Msa1368430 MtrunA17_Chr4g0035301 42.045 264 94 15 3 254 5 221 9.84e-32 117
Msa1368430 MtrunA17_Chr4g0035291 38.735 253 95 11 10 254 9 209 5.72e-26 101
Msa1368430 MtrunA17_Chr4g0035281 36.150 213 79 8 49 253 2 165 1.01e-24 97.1
Msa1368430 MtrunA17_Chr8g0372841 29.661 236 141 8 22 255 12 224 9.03e-21 88.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1368430 AT5G66440.1 27.473 273 147 7 1 256 1 239 7.26e-21 89.0
Msa1368430 AT4G34560.1 32.178 202 91 8 64 263 63 220 1.71e-16 76.6
Msa1368430 AT2G21560.1 26.374 273 173 10 1 254 1 264 4.09e-12 65.1

Find 29 sgRNAs with CRISPR-Local

Find 84 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAGATTAGCTAGGAATAAA+TGG 0.252040 tig0018646:+115559 None:intergenic
AATGAAGTTGGAAGAGAAAC+AGG 0.271425 tig0018646:-115861 Msa1368430:CDS
TCGTTGCTCATTCCATCTTC+AGG 0.330037 tig0018646:+115650 None:intergenic
GAAAGATTGCTAATTTGTTT+CGG 0.382950 tig0018646:-116273 Msa1368430:CDS
GTGATAACGATAAGAGTAAG+AGG 0.395005 tig0018646:-115715 Msa1368430:CDS
ATCACACTCATTGCTCAATC+TGG 0.403087 tig0018646:-116106 Msa1368430:CDS
TCAAAGCCAATGGTAGTTGT+TGG 0.417819 tig0018646:+116203 None:intergenic
TGGAAGTGAAGGGATATAGA+AGG 0.441385 tig0018646:-115817 Msa1368430:CDS
AAAGTTGAGAACAACGTAAA+GGG 0.443322 tig0018646:-115956 Msa1368430:CDS
AGATGATAATAGAATGAAGT+TGG 0.450200 tig0018646:-115873 Msa1368430:CDS
TTCATTCCAACAACTACCAT+TGG 0.464826 tig0018646:-116209 Msa1368430:CDS
AGAGATGGGTTTGGAAGTGA+AGG 0.496963 tig0018646:-115828 Msa1368430:CDS
TCGAGTTTATATCCTGAAGA+TGG 0.500432 tig0018646:-115662 Msa1368430:CDS
GGGATATAGAAGGTGTCAAT+CGG 0.514951 tig0018646:-115807 Msa1368430:CDS
CTTGAGTTCTTCAAAGCCAA+TGG 0.531388 tig0018646:+116193 None:intergenic
AAAAGTTGAGAACAACGTAA+AGG 0.543362 tig0018646:-115957 Msa1368430:CDS
TAGAATAAACGATGGATGCA+TGG 0.556637 tig0018646:-115930 Msa1368430:CDS
ATCGGAAATTGAGTTGGTGA+GGG 0.576160 tig0018646:-115789 Msa1368430:CDS
AACATGTATCAGAAAATCCA+AGG 0.585434 tig0018646:-116004 Msa1368430:CDS
AATCGGAAATTGAGTTGGTG+AGG 0.606720 tig0018646:-115790 Msa1368430:CDS
GTGTCAATCGGAAATTGAGT+TGG 0.619603 tig0018646:-115795 Msa1368430:CDS
TCTTGCAATAAATGCCTCCA+CGG 0.627372 tig0018646:+115613 None:intergenic
TGTGAATAGTGATGATGTGA+AGG 0.638060 tig0018646:-115765 Msa1368430:CDS
AGGATCAAAGAGTGTTGCAA+AGG 0.643836 tig0018646:-115745 Msa1368430:CDS
GAGATGGGTTTGGAAGTGAA+GGG 0.651077 tig0018646:-115827 Msa1368430:CDS
TCGGAAATTGAGTTGGTGAG+GGG 0.662410 tig0018646:-115788 Msa1368430:CDS
CGAATTTCGTCGCACCGTGG+AGG 0.663215 tig0018646:-115627 Msa1368430:CDS
AAGGGTCGTAGAATAAACGA+TGG 0.676337 tig0018646:-115938 Msa1368430:CDS
CGACGAATTTCGTCGCACCG+TGG 0.721139 tig0018646:-115630 Msa1368430:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAAAGATTGCTAATTTGTTT+CGG - tig0018646:115638-115657 Msa1368430:CDS 25.0%
!!! TTGTGTTGATTTTGATTTCA+AGG - tig0018646:115677-115696 Msa1368430:CDS 25.0%
! AGATGATAATAGAATGAAGT+TGG - tig0018646:116038-116057 Msa1368430:CDS 25.0%
!!! GAAAGATTGCTAATTTGTTT+CGG - tig0018646:115638-115657 Msa1368430:CDS 25.0%
!!! TTGTGTTGATTTTGATTTCA+AGG - tig0018646:115677-115696 Msa1368430:CDS 25.0%
! AGATGATAATAGAATGAAGT+TGG - tig0018646:116038-116057 Msa1368430:CDS 25.0%
!! ACGATGTTTTTGAACTTTGT+TGG + tig0018646:115611-115630 None:intergenic 30.0%
! AACTCAAGTGAATATTTTCG+AGG - tig0018646:115733-115752 Msa1368430:CDS 30.0%
AACATGTATCAGAAAATCCA+AGG - tig0018646:115907-115926 Msa1368430:CDS 30.0%
!! AGAAAATCCAAGGTTTTGAT+CGG - tig0018646:115917-115936 Msa1368430:CDS 30.0%
AAAAGTTGAGAACAACGTAA+AGG - tig0018646:115954-115973 Msa1368430:CDS 30.0%
AAAGTTGAGAACAACGTAAA+GGG - tig0018646:115955-115974 Msa1368430:CDS 30.0%
!! ACGATGTTTTTGAACTTTGT+TGG + tig0018646:115611-115630 None:intergenic 30.0%
! AACTCAAGTGAATATTTTCG+AGG - tig0018646:115733-115752 Msa1368430:CDS 30.0%
AACATGTATCAGAAAATCCA+AGG - tig0018646:115907-115926 Msa1368430:CDS 30.0%
!! AGAAAATCCAAGGTTTTGAT+CGG - tig0018646:115917-115936 Msa1368430:CDS 30.0%
AAAAGTTGAGAACAACGTAA+AGG - tig0018646:115954-115973 Msa1368430:CDS 30.0%
AAAGTTGAGAACAACGTAAA+GGG - tig0018646:115955-115974 Msa1368430:CDS 30.0%
TTCATTCCAACAACTACCAT+TGG - tig0018646:115702-115721 Msa1368430:CDS 35.0%
AAAAACAAAACCAGGACCAA+CGG + tig0018646:115764-115783 None:intergenic 35.0%
CCAACAAGAAAAACAAAACC+AGG + tig0018646:115772-115791 None:intergenic 35.0%
!!! CCTGGTTTTGTTTTTCTTGT+TGG - tig0018646:115769-115788 Msa1368430:CDS 35.0%
! GAACTTCTTCTTCTTTTTGC+AGG + tig0018646:115850-115869 None:intergenic 35.0%
!!! GTTTTTTCCGATCAAAACCT+TGG + tig0018646:115927-115946 None:intergenic 35.0%
TAGAATAAACGATGGATGCA+TGG - tig0018646:115981-116000 Msa1368430:CDS 35.0%
AATGAAGTTGGAAGAGAAAC+AGG - tig0018646:116050-116069 Msa1368430:CDS 35.0%
ACAGGAGATAAAAACAGAGA+TGG - tig0018646:116068-116087 Msa1368430:CDS 35.0%
CAGGAGATAAAAACAGAGAT+GGG - tig0018646:116069-116088 Msa1368430:CDS 35.0%
! GATAAAAACAGAGATGGGTT+TGG - tig0018646:116074-116093 Msa1368430:CDS 35.0%
! TGTGAATAGTGATGATGTGA+AGG - tig0018646:116146-116165 Msa1368430:CDS 35.0%
! GTGATAACGATAAGAGTAAG+AGG - tig0018646:116196-116215 Msa1368430:CDS 35.0%
TCGAGTTTATATCCTGAAGA+TGG - tig0018646:116249-116268 Msa1368430:CDS 35.0%
TTCATTCCAACAACTACCAT+TGG - tig0018646:115702-115721 Msa1368430:CDS 35.0%
AAAAACAAAACCAGGACCAA+CGG + tig0018646:115764-115783 None:intergenic 35.0%
CCAACAAGAAAAACAAAACC+AGG + tig0018646:115772-115791 None:intergenic 35.0%
!!! CCTGGTTTTGTTTTTCTTGT+TGG - tig0018646:115769-115788 Msa1368430:CDS 35.0%
! GAACTTCTTCTTCTTTTTGC+AGG + tig0018646:115850-115869 None:intergenic 35.0%
!!! GTTTTTTCCGATCAAAACCT+TGG + tig0018646:115927-115946 None:intergenic 35.0%
TAGAATAAACGATGGATGCA+TGG - tig0018646:115981-116000 Msa1368430:CDS 35.0%
AATGAAGTTGGAAGAGAAAC+AGG - tig0018646:116050-116069 Msa1368430:CDS 35.0%
ACAGGAGATAAAAACAGAGA+TGG - tig0018646:116068-116087 Msa1368430:CDS 35.0%
CAGGAGATAAAAACAGAGAT+GGG - tig0018646:116069-116088 Msa1368430:CDS 35.0%
! GATAAAAACAGAGATGGGTT+TGG - tig0018646:116074-116093 Msa1368430:CDS 35.0%
! TGTGAATAGTGATGATGTGA+AGG - tig0018646:116146-116165 Msa1368430:CDS 35.0%
! GTGATAACGATAAGAGTAAG+AGG - tig0018646:116196-116215 Msa1368430:CDS 35.0%
TCGAGTTTATATCCTGAAGA+TGG - tig0018646:116249-116268 Msa1368430:CDS 35.0%
TCAAAGCCAATGGTAGTTGT+TGG + tig0018646:115711-115730 None:intergenic 40.0%
CTTGAGTTCTTCAAAGCCAA+TGG + tig0018646:115721-115740 None:intergenic 40.0%
!! TATTTTCGAGGTTTTGCCGT+TGG - tig0018646:115745-115764 Msa1368430:CDS 40.0%
ATCACACTCATTGCTCAATC+TGG - tig0018646:115805-115824 Msa1368430:CDS 40.0%
AAGGGTCGTAGAATAAACGA+TGG - tig0018646:115973-115992 Msa1368430:CDS 40.0%
TGGAAGTGAAGGGATATAGA+AGG - tig0018646:116094-116113 Msa1368430:CDS 40.0%
!! GGGATATAGAAGGTGTCAAT+CGG - tig0018646:116104-116123 Msa1368430:CDS 40.0%
GTGTCAATCGGAAATTGAGT+TGG - tig0018646:116116-116135 Msa1368430:CDS 40.0%
!! AATCGGAAATTGAGTTGGTG+AGG - tig0018646:116121-116140 Msa1368430:CDS 40.0%
!! ATCGGAAATTGAGTTGGTGA+GGG - tig0018646:116122-116141 Msa1368430:CDS 40.0%
!! AGGATCAAAGAGTGTTGCAA+AGG - tig0018646:116166-116185 Msa1368430:CDS 40.0%
TCTTGCAATAAATGCCTCCA+CGG + tig0018646:116301-116320 None:intergenic 40.0%
TCAAAGCCAATGGTAGTTGT+TGG + tig0018646:115711-115730 None:intergenic 40.0%
CTTGAGTTCTTCAAAGCCAA+TGG + tig0018646:115721-115740 None:intergenic 40.0%
!! TATTTTCGAGGTTTTGCCGT+TGG - tig0018646:115745-115764 Msa1368430:CDS 40.0%
ATCACACTCATTGCTCAATC+TGG - tig0018646:115805-115824 Msa1368430:CDS 40.0%
AAGGGTCGTAGAATAAACGA+TGG - tig0018646:115973-115992 Msa1368430:CDS 40.0%
TGGAAGTGAAGGGATATAGA+AGG - tig0018646:116094-116113 Msa1368430:CDS 40.0%
!! GGGATATAGAAGGTGTCAAT+CGG - tig0018646:116104-116123 Msa1368430:CDS 40.0%
GTGTCAATCGGAAATTGAGT+TGG - tig0018646:116116-116135 Msa1368430:CDS 40.0%
!! AATCGGAAATTGAGTTGGTG+AGG - tig0018646:116121-116140 Msa1368430:CDS 40.0%
!! ATCGGAAATTGAGTTGGTGA+GGG - tig0018646:116122-116141 Msa1368430:CDS 40.0%
!! AGGATCAAAGAGTGTTGCAA+AGG - tig0018646:116166-116185 Msa1368430:CDS 40.0%
TCTTGCAATAAATGCCTCCA+CGG + tig0018646:116301-116320 None:intergenic 40.0%
! AGAGATGGGTTTGGAAGTGA+AGG - tig0018646:116083-116102 Msa1368430:CDS 45.0%
! GAGATGGGTTTGGAAGTGAA+GGG - tig0018646:116084-116103 Msa1368430:CDS 45.0%
!! TCGGAAATTGAGTTGGTGAG+GGG - tig0018646:116123-116142 Msa1368430:CDS 45.0%
TCGTTGCTCATTCCATCTTC+AGG + tig0018646:116264-116283 None:intergenic 45.0%
! AGAGATGGGTTTGGAAGTGA+AGG - tig0018646:116083-116102 Msa1368430:CDS 45.0%
! GAGATGGGTTTGGAAGTGAA+GGG - tig0018646:116084-116103 Msa1368430:CDS 45.0%
!! TCGGAAATTGAGTTGGTGAG+GGG - tig0018646:116123-116142 Msa1368430:CDS 45.0%
TCGTTGCTCATTCCATCTTC+AGG + tig0018646:116264-116283 None:intergenic 45.0%
! CGAGGTTTTGCCGTTGGTCC+TGG - tig0018646:115751-115770 Msa1368430:CDS 60.0%
CGACGAATTTCGTCGCACCG+TGG - tig0018646:116281-116300 Msa1368430:CDS 60.0%
CGAATTTCGTCGCACCGTGG+AGG - tig0018646:116284-116303 Msa1368430:CDS 60.0%
! CGAGGTTTTGCCGTTGGTCC+TGG - tig0018646:115751-115770 Msa1368430:CDS 60.0%
CGACGAATTTCGTCGCACCG+TGG - tig0018646:116281-116300 Msa1368430:CDS 60.0%
CGAATTTCGTCGCACCGTGG+AGG - tig0018646:116284-116303 Msa1368430:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0018646 gene 115568 116365 115568 ID=Msa1368430;Name=Msa1368430
tig0018646 mRNA 115568 116365 115568 ID=Msa1368430-mRNA-1;Parent=Msa1368430;Name=Msa1368430-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|265
tig0018646 exon 115568 116365 115568 ID=Msa1368430-mRNA-1:exon:482;Parent=Msa1368430-mRNA-1
tig0018646 CDS 115568 116365 115568 ID=Msa1368430-mRNA-1:cds;Parent=Msa1368430-mRNA-1
Gene Sequence

>Msa1368430

ATGGGTTCAATCAATTTACACAAACACAAAGCAGAGAAATCCAACAAAGTTCAAAAACATCGTCATCTTAGAAAGATTGCTAATTTGTTTCGGTATTTAGAGATGTGTGTTGTGTTGATTTTGATTTCAAGGCTTTCATTCCAACAACTACCATTGGCTTTGAAGAACTCAAGTGAATATTTTCGAGGTTTTGCCGTTGGTCCTGGTTTTGTTTTTCTTGTTGGAAACATTATCATCATCACACTCATTGCTCAATCTGGTCACTTCTCACAACATGATCCTGCAAAAAGAAGAAGAAGTTCAGAACATGATCTTTATCTCGAGTTTCTCAAGAATAGCAACATGTATCAGAAAATCCAAGGTTTTGATCGGAAAAAACTGAGCGTAAAAGTTGAGAACAACGTAAAGGGTCGTAGAATAAACGATGGATGCATGGTGAAATTCTCTGAGAAAGAGAGTAAAAAGAGTGAAGATGATAATAGAATGAAGTTGGAAGAGAAACAGGAGATAAAAACAGAGATGGGTTTGGAAGTGAAGGGATATAGAAGGTGTCAATCGGAAATTGAGTTGGTGAGGGGTGTGAATAGTGATGATGTGAAGGATCAAAGAGTGTTGCAAAGGTGTGAGAGTGATAACGATAAGAGTAAGAGGAAAAACATTGAAGTTGATAAAGTGAAAAAATCGAGTTTATATCCTGAAGATGGAATGAGCAACGACGAATTTCGTCGCACCGTGGAGGCATTTATTGCAAGACAACAGAAGCTACGAATAAACGAAGTACAAACCATTTATTCCTAG

Protein sequence

>Msa1368430

MGSINLHKHKAEKSNKVQKHRHLRKIANLFRYLEMCVVLILISRLSFQQLPLALKNSSEYFRGFAVGPGFVFLVGNIIIITLIAQSGHFSQHDPAKRRRSSEHDLYLEFLKNSNMYQKIQGFDRKKLSVKVENNVKGRRINDGCMVKFSEKESKKSEDDNRMKLEEKQEIKTEMGLEVKGYRRCQSEIELVRGVNSDDVKDQRVLQRCESDNDKSKRKNIEVDKVKKSSLYPEDGMSNDEFRRTVEAFIARQQKLRINEVQTIYS*