AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1124990


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1124990 MtrunA17_Chr7g0265731 98.157 217 4 0 1 217 1 217 8.77e-154 425
Msa1124990 MtrunA17_Chr6g0486051 48.466 163 66 1 55 217 2 146 1.79e-50 160
Msa1124990 MtrunA17_Chr2g0287981 40.876 137 78 2 79 214 62 196 1.23e-29 109
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1124990 AT3G52960.1 62.979 235 68 5 1 217 1 234 3.42e-98 285
Msa1124990 AT1G65980.1 58.282 163 66 1 55 217 2 162 2.92e-62 191
Msa1124990 AT1G60740.1 53.988 163 73 1 55 217 2 162 9.47e-60 185
Msa1124990 AT1G65970.1 53.988 163 73 1 55 217 2 162 3.82e-59 184
Msa1124990 AT1G65990.1 46.309 149 74 2 55 203 2 144 5.72e-37 135
Msa1124990 AT3G06050.1 43.066 137 75 2 79 214 64 198 1.22e-32 117
Msa1124990 AT1G65980.2 59.740 77 31 0 55 131 2 78 1.56e-27 100
Msa1124990 AT3G06050.2 47.945 73 38 0 79 151 64 136 8.39e-20 83.6

Find 59 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGGAGAATCGGAGAGGTTT+TGG 0.170077 7_3:-76263037 None:intergenic
TTTGAGAGGGAGGGTGAATT+TGG 0.195781 7_3:-76262999 None:intergenic
GGAGATGGTGGCGGAGATTT+TGG 0.207407 7_3:-76263065 None:intergenic
AGGTAGGAGAAGGTGGATTC+AGG 0.275143 7_3:-76263103 None:intergenic
GCAGTCCTCTTCGCCGTTCC+AGG 0.310776 7_3:+76263184 Msa1124990:CDS
AACCTGTTGGATTGGGTGTT+AGG 0.351123 7_3:+76263434 Msa1124990:CDS
GTCAAGACGTTATGCTTTGT+TGG 0.388577 7_3:+76263456 Msa1124990:CDS
TGCTCACAGAAACACGTTCC+TGG 0.400832 7_3:+76263223 Msa1124990:CDS
TGTTAGGTCAGAGACGGTTA+TGG 0.417735 7_3:-76263149 None:intergenic
TGATACAATCGCTTGCATTT+CGG 0.418524 7_3:+76263285 Msa1124990:CDS
GGTCAGAGACGGTTATGGTT+TGG 0.420880 7_3:-76263144 None:intergenic
GAATTTGGAAGAGAGGGTTT+TGG 0.429478 7_3:-76262984 None:intergenic
GTGATTTCACAAGAGCGATT+GGG 0.431034 7_3:+76263389 Msa1124990:CDS
AGATAAGAGTGAGGTGGTGG+TGG 0.441187 7_3:-76262954 None:intergenic
GGTAGGAGAAGGTGGATTCA+GGG 0.445681 7_3:-76263102 None:intergenic
GACCTAACACCCAATCCAAC+AGG 0.452953 7_3:-76263436 None:intergenic
TTGAAACGGTTGAATTTGAG+AGG 0.455027 7_3:-76263013 None:intergenic
AGCGATAAACCTGTTGGATT+GGG 0.455914 7_3:+76263427 Msa1124990:CDS
AGCGTGGAAGGAGGATTTGA+AGG 0.464799 7_3:+76263330 Msa1124990:CDS
GCTGATTTCTCCACGAATCC+AGG 0.469358 7_3:-76263241 None:intergenic
GGACTTCACCGGCAGGGTCG+AGG 0.473218 7_3:-76263123 None:intergenic
GGTGATTTCACAAGAGCGAT+TGG 0.474269 7_3:+76263388 Msa1124990:CDS
GAGCGATAAACCTGTTGGAT+TGG 0.482422 7_3:+76263426 Msa1124990:CDS
GGAGGGTGAATTTGGAAGAG+AGG 0.482927 7_3:-76262991 None:intergenic
AACGGTTGAATTTGAGAGGG+AGG 0.500645 7_3:-76263009 None:intergenic
GAGTTTGTCGCCGACGGAGA+TGG 0.504087 7_3:-76263080 None:intergenic
GGGAGATAAGAGTGAGGTGG+TGG 0.509192 7_3:-76262957 None:intergenic
GAGGGTGAATTTGGAAGAGA+GGG 0.514701 7_3:-76262990 None:intergenic
TATGCTTTGTTGGCTGAAGA+TGG 0.518833 7_3:+76263466 Msa1124990:CDS
TTCTCCTACCTCGACCCTGC+CGG 0.521198 7_3:+76263115 Msa1124990:CDS
CATGTTGGTGTGAAAGCTCC+TGG 0.523565 7_3:-76263202 None:intergenic
TTCAGGGAGTTTGTCGCCGA+CGG 0.523891 7_3:-76263086 None:intergenic
ACCGTCTCTGACCTAACAAA+AGG 0.536577 7_3:+76263154 Msa1124990:CDS
ACGGTTGAATTTGAGAGGGA+GGG 0.537771 7_3:-76263008 None:intergenic
GATTTGAGCGATAAACCTGT+TGG 0.550461 7_3:+76263421 Msa1124990:CDS
GGCAGGGTCGAGGTAGGAGA+AGG 0.551945 7_3:-76263113 None:intergenic
GTCGCCGACGGAGATGGTGG+CGG 0.556756 7_3:-76263074 None:intergenic
GGGGAAGAGGAGAATCGGAG+AGG 0.566799 7_3:-76263043 None:intergenic
ATCAGCGGAGCTAAAAGCGA+AGG 0.573209 7_3:+76263258 Msa1124990:CDS
TGATTTCACAAGAGCGATTG+GGG 0.578015 7_3:+76263390 Msa1124990:CDS
TTTGTCGCCGACGGAGATGG+TGG 0.580050 7_3:-76263077 None:intergenic
TGGTTTGGACTTCACCGGCA+GGG 0.580205 7_3:-76263129 None:intergenic
GAAACACGTTCCTGGATTCG+TGG 0.581971 7_3:+76263231 Msa1124990:CDS
GGTTATGGTTTGGACTTCAC+CGG 0.599625 7_3:-76263134 None:intergenic
ATCTCCGCCACCATCTCCGT+CGG 0.611751 7_3:+76263070 Msa1124990:CDS
AGGTGGTGGTGGAAGATGAG+AGG 0.612703 7_3:-76262943 None:intergenic
TGAAACGGTTGAATTTGAGA+GGG 0.618873 7_3:-76263012 None:intergenic
AGGGTCGAGGTAGGAGAAGG+TGG 0.620333 7_3:-76263110 None:intergenic
AAGCTCCTGGAACGGCGAAG+AGG 0.622049 7_3:-76263189 None:intergenic
TTTGGGAGATAAGAGTGAGG+TGG 0.623641 7_3:-76262960 None:intergenic
TTCACCGGCAGGGTCGAGGT+AGG 0.624603 7_3:-76263119 None:intergenic
TGTGATGAAAGCGTGGAAGG+AGG 0.635880 7_3:+76263321 Msa1124990:CDS
GTTTGTGATGAAAGCGTGGA+AGG 0.651012 7_3:+76263318 Msa1124990:CDS
TCAGCGGAGCTAAAAGCGAA+GGG 0.675110 7_3:+76263259 Msa1124990:CDS
ACGTGTTTCTGTGAGCATGT+TGG 0.678748 7_3:-76263217 None:intergenic
TTTGAAGGTGAACGATGAAG+TGG 0.684338 7_3:+76263345 Msa1124990:CDS
ATGCGTTTGTGATGAAAGCG+TGG 0.693181 7_3:+76263314 Msa1124990:CDS
TGGTGTGAAAGCTCCTGGAA+CGG 0.694733 7_3:-76263197 None:intergenic
TGGATTCGTGGAGAAATCAG+CGG 0.698367 7_3:+76263243 Msa1124990:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTTGTTAAGCTTTTCAATT+TGG + chr7_3:76263489-76263508 Msa1124990:CDS 25.0%
! TGTTAAGCTTTTCAATTTGG+AGG + chr7_3:76263492-76263511 Msa1124990:CDS 30.0%
TGAAACGGTTGAATTTGAGA+GGG - chr7_3:76263015-76263034 None:intergenic 35.0%
TTGAAACGGTTGAATTTGAG+AGG - chr7_3:76263016-76263035 None:intergenic 35.0%
!!! CTGCTTTTTTGCCTTTTGTT+AGG - chr7_3:76263168-76263187 None:intergenic 35.0%
TGATACAATCGCTTGCATTT+CGG + chr7_3:76263285-76263304 Msa1124990:CDS 35.0%
! AAGCTTTTCAATTTGGAGGA+AGG + chr7_3:76263496-76263515 Msa1124990:CDS 35.0%
!!! GAAGAGAGGGTTTTGGTTTT+GGG - chr7_3:76262980-76262999 None:intergenic 40.0%
! GAATTTGGAAGAGAGGGTTT+TGG - chr7_3:76262987-76263006 None:intergenic 40.0%
TTTGAAGGTGAACGATGAAG+TGG + chr7_3:76263345-76263364 Msa1124990:CDS 40.0%
! AAGTGGTGCTTTTGTCTGAT+GGG + chr7_3:76263362-76263381 Msa1124990:CDS 40.0%
GTGATTTCACAAGAGCGATT+GGG + chr7_3:76263389-76263408 Msa1124990:CDS 40.0%
TGATTTCACAAGAGCGATTG+GGG + chr7_3:76263390-76263409 Msa1124990:CDS 40.0%
GATTTGAGCGATAAACCTGT+TGG + chr7_3:76263421-76263440 Msa1124990:CDS 40.0%
AGCGATAAACCTGTTGGATT+GGG + chr7_3:76263427-76263446 Msa1124990:CDS 40.0%
GTCAAGACGTTATGCTTTGT+TGG + chr7_3:76263456-76263475 Msa1124990:CDS 40.0%
! TATGCTTTGTTGGCTGAAGA+TGG + chr7_3:76263466-76263485 Msa1124990:CDS 40.0%
! CTTTTCAATTTGGAGGAAGG+TGG + chr7_3:76263499-76263518 Msa1124990:CDS 40.0%
TTTGGGAGATAAGAGTGAGG+TGG - chr7_3:76262963-76262982 None:intergenic 45.0%
!!! GGTTTTGGGAGATAAGAGTG+AGG - chr7_3:76262966-76262985 None:intergenic 45.0%
!!! GGAAGAGAGGGTTTTGGTTT+TGG - chr7_3:76262981-76263000 None:intergenic 45.0%
GAGGGTGAATTTGGAAGAGA+GGG - chr7_3:76262993-76263012 None:intergenic 45.0%
TTTGAGAGGGAGGGTGAATT+TGG - chr7_3:76263002-76263021 None:intergenic 45.0%
ACGGTTGAATTTGAGAGGGA+GGG - chr7_3:76263011-76263030 None:intergenic 45.0%
AACGGTTGAATTTGAGAGGG+AGG - chr7_3:76263012-76263031 None:intergenic 45.0%
!!! GGAGAGGTTTTGGGTTGAAA+CGG - chr7_3:76263030-76263049 None:intergenic 45.0%
! AGGAGAATCGGAGAGGTTTT+GGG - chr7_3:76263039-76263058 None:intergenic 45.0%
!! TTTTGGGGGAAGAGGAGAAT+CGG - chr7_3:76263051-76263070 None:intergenic 45.0%
! GGTTATGGTTTGGACTTCAC+CGG - chr7_3:76263137-76263156 None:intergenic 45.0%
TGTTAGGTCAGAGACGGTTA+TGG - chr7_3:76263152-76263171 None:intergenic 45.0%
ACCGTCTCTGACCTAACAAA+AGG + chr7_3:76263154-76263173 Msa1124990:CDS 45.0%
! GCCTTTTGTTAGGTCAGAGA+CGG - chr7_3:76263158-76263177 None:intergenic 45.0%
! ACGTGTTTCTGTGAGCATGT+TGG - chr7_3:76263220-76263239 None:intergenic 45.0%
TGGATTCGTGGAGAAATCAG+CGG + chr7_3:76263243-76263262 Msa1124990:CDS 45.0%
ATGCGTTTGTGATGAAAGCG+TGG + chr7_3:76263314-76263333 Msa1124990:CDS 45.0%
! GTTTGTGATGAAAGCGTGGA+AGG + chr7_3:76263318-76263337 Msa1124990:CDS 45.0%
! GAAGTGGTGCTTTTGTCTGA+TGG + chr7_3:76263361-76263380 Msa1124990:CDS 45.0%
! GTGCTTTTGTCTGATGGGAA+TGG + chr7_3:76263367-76263386 Msa1124990:CDS 45.0%
GGTGATTTCACAAGAGCGAT+TGG + chr7_3:76263388-76263407 Msa1124990:CDS 45.0%
GAGCGATAAACCTGTTGGAT+TGG + chr7_3:76263426-76263445 Msa1124990:CDS 45.0%
! AACCTGTTGGATTGGGTGTT+AGG + chr7_3:76263434-76263453 Msa1124990:CDS 45.0%
! GGTGGTGCTTTTACTTTCAG+TGG + chr7_3:76263517-76263536 Msa1124990:CDS 45.0%
! AGATAAGAGTGAGGTGGTGG+TGG - chr7_3:76262957-76262976 None:intergenic 50.0%
GGAGGGTGAATTTGGAAGAG+AGG - chr7_3:76262994-76263013 None:intergenic 50.0%
! GAGGAGAATCGGAGAGGTTT+TGG - chr7_3:76263040-76263059 None:intergenic 50.0%
!!! AGATGGTGGCGGAGATTTTG+GGG - chr7_3:76263066-76263085 None:intergenic 50.0%
!!! GAGATGGTGGCGGAGATTTT+GGG - chr7_3:76263067-76263086 None:intergenic 50.0%
! GGTAGGAGAAGGTGGATTCA+GGG - chr7_3:76263105-76263124 None:intergenic 50.0%
! AGGTAGGAGAAGGTGGATTC+AGG - chr7_3:76263106-76263125 None:intergenic 50.0%
GGTCAGAGACGGTTATGGTT+TGG - chr7_3:76263147-76263166 None:intergenic 50.0%
TGGTGTGAAAGCTCCTGGAA+CGG - chr7_3:76263200-76263219 None:intergenic 50.0%
CATGTTGGTGTGAAAGCTCC+TGG - chr7_3:76263205-76263224 None:intergenic 50.0%
TGCTCACAGAAACACGTTCC+TGG + chr7_3:76263223-76263242 Msa1124990:CDS 50.0%
GAAACACGTTCCTGGATTCG+TGG + chr7_3:76263231-76263250 Msa1124990:CDS 50.0%
! GCTGATTTCTCCACGAATCC+AGG - chr7_3:76263244-76263263 None:intergenic 50.0%
ATCAGCGGAGCTAAAAGCGA+AGG + chr7_3:76263258-76263277 Msa1124990:CDS 50.0%
TCAGCGGAGCTAAAAGCGAA+GGG + chr7_3:76263259-76263278 Msa1124990:CDS 50.0%
! TGTGATGAAAGCGTGGAAGG+AGG + chr7_3:76263321-76263340 Msa1124990:CDS 50.0%
AGCGTGGAAGGAGGATTTGA+AGG + chr7_3:76263330-76263349 Msa1124990:CDS 50.0%
GACCTAACACCCAATCCAAC+AGG - chr7_3:76263439-76263458 None:intergenic 50.0%
!! AGGTGGTGGTGGAAGATGAG+AGG - chr7_3:76262946-76262965 None:intergenic 55.0%
GGGAGATAAGAGTGAGGTGG+TGG - chr7_3:76262960-76262979 None:intergenic 55.0%
!!! GATGGTGGCGGAGATTTTGG+GGG - chr7_3:76263065-76263084 None:intergenic 55.0%
!!! GGAGATGGTGGCGGAGATTT+TGG - chr7_3:76263068-76263087 None:intergenic 55.0%
TTCAGGGAGTTTGTCGCCGA+CGG - chr7_3:76263089-76263108 None:intergenic 55.0%
! TGGTTTGGACTTCACCGGCA+GGG - chr7_3:76263132-76263151 None:intergenic 55.0%
! ATGGTTTGGACTTCACCGGC+AGG - chr7_3:76263133-76263152 None:intergenic 55.0%
GGGGAAGAGGAGAATCGGAG+AGG - chr7_3:76263046-76263065 None:intergenic 60.0%
!! GGCGGAGATTTTGGGGGAAG+AGG - chr7_3:76263059-76263078 None:intergenic 60.0%
ATCTCCGCCACCATCTCCGT+CGG + chr7_3:76263070-76263089 Msa1124990:CDS 60.0%
TTTGTCGCCGACGGAGATGG+TGG - chr7_3:76263080-76263099 None:intergenic 60.0%
GAGTTTGTCGCCGACGGAGA+TGG - chr7_3:76263083-76263102 None:intergenic 60.0%
AGGGTCGAGGTAGGAGAAGG+TGG - chr7_3:76263113-76263132 None:intergenic 60.0%
TTCTCCTACCTCGACCCTGC+CGG + chr7_3:76263115-76263134 Msa1124990:CDS 60.0%
AAGCTCCTGGAACGGCGAAG+AGG - chr7_3:76263192-76263211 None:intergenic 60.0%
GGCAGGGTCGAGGTAGGAGA+AGG - chr7_3:76263116-76263135 None:intergenic 65.0%
TTCACCGGCAGGGTCGAGGT+AGG - chr7_3:76263122-76263141 None:intergenic 65.0%
GCAGTCCTCTTCGCCGTTCC+AGG + chr7_3:76263184-76263203 Msa1124990:CDS 65.0%
! GTCGCCGACGGAGATGGTGG+CGG - chr7_3:76263077-76263096 None:intergenic 70.0%
GGACTTCACCGGCAGGGTCG+AGG - chr7_3:76263126-76263145 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 76262914 76263567 76262914 ID=Msa1124990;Name=Msa1124990
chr7_3 mRNA 76262914 76263567 76262914 ID=Msa1124990-mRNA-1;Parent=Msa1124990;Name=Msa1124990-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|-1|0|1|-1|1|1|0|217
chr7_3 exon 76262914 76263567 76262914 ID=Msa1124990-mRNA-1:exon:20704;Parent=Msa1124990-mRNA-1
chr7_3 CDS 76262914 76263567 76262914 ID=Msa1124990-mRNA-1:cds;Parent=Msa1124990-mRNA-1
Gene Sequence

>Msa1124990

ATGGCAACATCACTCTCTTTCTCTAGACTCCTCTCATCTTCCACCACCACCTCACTCTTATCTCCCAAAACCAAAACCCTCTCTTCCAAATTCACCCTCCCTCTCAAATTCAACCGTTTCAACCCAAAACCTCTCCGATTCTCCTCTTCCCCCAAAATCTCCGCCACCATCTCCGTCGGCGACAAACTCCCTGAATCCACCTTCTCCTACCTCGACCCTGCCGGTGAAGTCCAAACCATAACCGTCTCTGACCTAACAAAAGGCAAAAAAGCAGTCCTCTTCGCCGTTCCAGGAGCTTTCACACCAACATGCTCACAGAAACACGTTCCTGGATTCGTGGAGAAATCAGCGGAGCTAAAAGCGAAGGGAGTTGATACAATCGCTTGCATTTCGGTGAACGATGCGTTTGTGATGAAAGCGTGGAAGGAGGATTTGAAGGTGAACGATGAAGTGGTGCTTTTGTCTGATGGGAATGGTGATTTCACAAGAGCGATTGGGGTTGAGCTTGATTTGAGCGATAAACCTGTTGGATTGGGTGTTAGGTCAAGACGTTATGCTTTGTTGGCTGAAGATGGTGTTGTTAAGCTTTTCAATTTGGAGGAAGGTGGTGCTTTTACTTTCAGTGGTGCTGATGATATTCTCAAAGTTCTTTGA

Protein sequence

>Msa1124990

MATSLSFSRLLSSSTTTSLLSPKTKTLSSKFTLPLKFNRFNPKPLRFSSSPKISATISVGDKLPESTFSYLDPAGEVQTITVSDLTKGKKAVLFAVPGAFTPTCSQKHVPGFVEKSAELKAKGVDTIACISVNDAFVMKAWKEDLKVNDEVVLLSDGNGDFTRAIGVELDLSDKPVGLGVRSRRYALLAEDGVVKLFNLEEGGAFTFSGADDILKVL*