AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1167370


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1167370 MtrunA17_Chr7g0265731 98.157 217 4 0 1 217 1 217 8.77e-154 425
Msa1167370 MtrunA17_Chr6g0486051 48.466 163 66 1 55 217 2 146 1.79e-50 160
Msa1167370 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
Msa1167370 AT3G52960.1 62.979 235 68 5 1 217 1 234 3.42e-98 285
Msa1167370 AT1G65980.1 58.282 163 66 1 55 217 2 162 2.92e-62 191
Msa1167370 AT1G60740.1 53.988 163 73 1 55 217 2 162 9.47e-60 185
Msa1167370 AT1G65970.1 53.988 163 73 1 55 217 2 162 3.82e-59 184
Msa1167370 AT1G65990.1 46.309 149 74 2 55 203 2 144 5.72e-37 135
Msa1167370 AT3G06050.1 43.066 137 75 2 79 214 64 198 1.22e-32 117
Msa1167370 AT1G65980.2 59.740 77 31 0 55 131 2 78 1.56e-27 100
Msa1167370 AT3G06050.2 47.945 73 38 0 79 151 64 136 8.39e-20 83.6

Find 58 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAGGAGAATCGGAGAGGTTT+TGG 0.170077 7_4:-59819610 None:intergenic
GGAGATGGTGGCGGAGATTT+TGG 0.207407 7_4:-59819638 None:intergenic
AGGTAGGAGAAGGTGGATTC+AGG 0.275143 7_4:-59819676 None:intergenic
GCAGTCCTCTTCGCCGTTCC+AGG 0.310776 7_4:+59819757 Msa1167370:CDS
AACCTGTTGGATTGGGTGTT+AGG 0.351123 7_4:+59820007 Msa1167370:CDS
GTCAAGACGTTATGCTTTGT+TGG 0.388577 7_4:+59820029 Msa1167370:CDS
TGCTCACAGAAACACGTTCC+TGG 0.400832 7_4:+59819796 Msa1167370:CDS
TGTTAGGTCAGAGACGGTTA+TGG 0.417735 7_4:-59819722 None:intergenic
GGAGGGTGAATTTGGAAGAG+AGG 0.418378 7_4:-59819564 None:intergenic
TGATACAATCGCTTGCATTT+CGG 0.418524 7_4:+59819858 Msa1167370:CDS
GGTCAGAGACGGTTATGGTT+TGG 0.420880 7_4:-59819717 None:intergenic
GAATTTGGAAGAGAGGGTTT+TGG 0.429478 7_4:-59819557 None:intergenic
GTGATTTCACAAGAGCGATT+GGG 0.431034 7_4:+59819962 Msa1167370:CDS
GGTTGAAACGGTTGAATTTG+AGG 0.432097 7_4:-59819588 None:intergenic
AGATAAGAGTGAGGTGGTGG+TGG 0.441187 7_4:-59819527 None:intergenic
GGTAGGAGAAGGTGGATTCA+GGG 0.445681 7_4:-59819675 None:intergenic
GACCTAACACCCAATCCAAC+AGG 0.452953 7_4:-59820009 None:intergenic
AGCGATAAACCTGTTGGATT+GGG 0.455914 7_4:+59820000 Msa1167370:CDS
AGCGTGGAAGGAGGATTTGA+AGG 0.464799 7_4:+59819903 Msa1167370:CDS
GCTGATTTCTCCACGAATCC+AGG 0.469358 7_4:-59819814 None:intergenic
GGACTTCACCGGCAGGGTCG+AGG 0.473218 7_4:-59819696 None:intergenic
GGTGATTTCACAAGAGCGAT+TGG 0.474269 7_4:+59819961 Msa1167370:CDS
GAGCGATAAACCTGTTGGAT+TGG 0.482422 7_4:+59819999 Msa1167370:CDS
GTTGAAACGGTTGAATTTGA+GGG 0.495346 7_4:-59819587 None:intergenic
GAGTTTGTCGCCGACGGAGA+TGG 0.504087 7_4:-59819653 None:intergenic
GGGAGATAAGAGTGAGGTGG+TGG 0.509192 7_4:-59819530 None:intergenic
TATGCTTTGTTGGCTGAAGA+TGG 0.518833 7_4:+59820039 Msa1167370:CDS
TTCTCCTACCTCGACCCTGC+CGG 0.521198 7_4:+59819688 Msa1167370:CDS
CATGTTGGTGTGAAAGCTCC+TGG 0.523565 7_4:-59819775 None:intergenic
TTCAGGGAGTTTGTCGCCGA+CGG 0.523891 7_4:-59819659 None:intergenic
TTGAAACGGTTGAATTTGAG+GGG 0.530800 7_4:-59819586 None:intergenic
ACCGTCTCTGACCTAACAAA+AGG 0.536577 7_4:+59819727 Msa1167370:CDS
GATTTGAGCGATAAACCTGT+TGG 0.550461 7_4:+59819994 Msa1167370:CDS
GGCAGGGTCGAGGTAGGAGA+AGG 0.551945 7_4:-59819686 None:intergenic
GAGGGTGAATTTGGAAGAGA+GGG 0.554835 7_4:-59819563 None:intergenic
GTCGCCGACGGAGATGGTGG+CGG 0.556756 7_4:-59819647 None:intergenic
GGGGAAGAGGAGAATCGGAG+AGG 0.566799 7_4:-59819616 None:intergenic
ATCAGCGGAGCTAAAAGCGA+AGG 0.573209 7_4:+59819831 Msa1167370:CDS
TGATTTCACAAGAGCGATTG+GGG 0.578015 7_4:+59819963 Msa1167370:CDS
TTTGTCGCCGACGGAGATGG+TGG 0.580050 7_4:-59819650 None:intergenic
TGGTTTGGACTTCACCGGCA+GGG 0.580205 7_4:-59819702 None:intergenic
GAAACACGTTCCTGGATTCG+TGG 0.581971 7_4:+59819804 Msa1167370:CDS
GGTTATGGTTTGGACTTCAC+CGG 0.599625 7_4:-59819707 None:intergenic
ATCTCCGCCACCATCTCCGT+CGG 0.611751 7_4:+59819643 Msa1167370:CDS
TGAAACGGTTGAATTTGAGG+GGG 0.612339 7_4:-59819585 None:intergenic
AGGTGGTGGTGGAAGATGAG+AGG 0.612703 7_4:-59819516 None:intergenic
AGGGTCGAGGTAGGAGAAGG+TGG 0.620333 7_4:-59819683 None:intergenic
AAGCTCCTGGAACGGCGAAG+AGG 0.622049 7_4:-59819762 None:intergenic
TTTGGGAGATAAGAGTGAGG+TGG 0.623641 7_4:-59819533 None:intergenic
TTCACCGGCAGGGTCGAGGT+AGG 0.624603 7_4:-59819692 None:intergenic
TGTGATGAAAGCGTGGAAGG+AGG 0.635880 7_4:+59819894 Msa1167370:CDS
GTTTGTGATGAAAGCGTGGA+AGG 0.651012 7_4:+59819891 Msa1167370:CDS
TCAGCGGAGCTAAAAGCGAA+GGG 0.675110 7_4:+59819832 Msa1167370:CDS
ACGTGTTTCTGTGAGCATGT+TGG 0.678748 7_4:-59819790 None:intergenic
TTTGAAGGTGAACGATGAAG+TGG 0.684338 7_4:+59819918 Msa1167370:CDS
ATGCGTTTGTGATGAAAGCG+TGG 0.693181 7_4:+59819887 Msa1167370:CDS
TGGTGTGAAAGCTCCTGGAA+CGG 0.694733 7_4:-59819770 None:intergenic
TGGATTCGTGGAGAAATCAG+CGG 0.698367 7_4:+59819816 Msa1167370:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTTGTTAAGCTTTTCAATT+TGG + chr7_4:59820062-59820081 Msa1167370:CDS 25.0%
! TGTTAAGCTTTTCAATTTGG+AGG + chr7_4:59820065-59820084 Msa1167370:CDS 30.0%
TTGAAACGGTTGAATTTGAG+GGG - chr7_4:59819589-59819608 None:intergenic 35.0%
GTTGAAACGGTTGAATTTGA+GGG - chr7_4:59819590-59819609 None:intergenic 35.0%
!!! CTGCTTTTTTGCCTTTTGTT+AGG - chr7_4:59819741-59819760 None:intergenic 35.0%
TGATACAATCGCTTGCATTT+CGG + chr7_4:59819858-59819877 Msa1167370:CDS 35.0%
! AAGCTTTTCAATTTGGAGGA+AGG + chr7_4:59820069-59820088 Msa1167370:CDS 35.0%
!!! GAAGAGAGGGTTTTGGTTTT+GGG - chr7_4:59819553-59819572 None:intergenic 40.0%
! GAATTTGGAAGAGAGGGTTT+TGG - chr7_4:59819560-59819579 None:intergenic 40.0%
TGAAACGGTTGAATTTGAGG+GGG - chr7_4:59819588-59819607 None:intergenic 40.0%
GGTTGAAACGGTTGAATTTG+AGG - chr7_4:59819591-59819610 None:intergenic 40.0%
TTTGAAGGTGAACGATGAAG+TGG + chr7_4:59819918-59819937 Msa1167370:CDS 40.0%
! AAGTGGTGCTTTTGTCTGAT+GGG + chr7_4:59819935-59819954 Msa1167370:CDS 40.0%
GTGATTTCACAAGAGCGATT+GGG + chr7_4:59819962-59819981 Msa1167370:CDS 40.0%
TGATTTCACAAGAGCGATTG+GGG + chr7_4:59819963-59819982 Msa1167370:CDS 40.0%
GATTTGAGCGATAAACCTGT+TGG + chr7_4:59819994-59820013 Msa1167370:CDS 40.0%
AGCGATAAACCTGTTGGATT+GGG + chr7_4:59820000-59820019 Msa1167370:CDS 40.0%
GTCAAGACGTTATGCTTTGT+TGG + chr7_4:59820029-59820048 Msa1167370:CDS 40.0%
! TATGCTTTGTTGGCTGAAGA+TGG + chr7_4:59820039-59820058 Msa1167370:CDS 40.0%
! CTTTTCAATTTGGAGGAAGG+TGG + chr7_4:59820072-59820091 Msa1167370:CDS 40.0%
TTTGGGAGATAAGAGTGAGG+TGG - chr7_4:59819536-59819555 None:intergenic 45.0%
!!! GGTTTTGGGAGATAAGAGTG+AGG - chr7_4:59819539-59819558 None:intergenic 45.0%
!!! GGAAGAGAGGGTTTTGGTTT+TGG - chr7_4:59819554-59819573 None:intergenic 45.0%
GAGGGTGAATTTGGAAGAGA+GGG - chr7_4:59819566-59819585 None:intergenic 45.0%
!!! GGAGAGGTTTTGGGTTGAAA+CGG - chr7_4:59819603-59819622 None:intergenic 45.0%
! AGGAGAATCGGAGAGGTTTT+GGG - chr7_4:59819612-59819631 None:intergenic 45.0%
!! TTTTGGGGGAAGAGGAGAAT+CGG - chr7_4:59819624-59819643 None:intergenic 45.0%
! GGTTATGGTTTGGACTTCAC+CGG - chr7_4:59819710-59819729 None:intergenic 45.0%
TGTTAGGTCAGAGACGGTTA+TGG - chr7_4:59819725-59819744 None:intergenic 45.0%
ACCGTCTCTGACCTAACAAA+AGG + chr7_4:59819727-59819746 Msa1167370:CDS 45.0%
! GCCTTTTGTTAGGTCAGAGA+CGG - chr7_4:59819731-59819750 None:intergenic 45.0%
! ACGTGTTTCTGTGAGCATGT+TGG - chr7_4:59819793-59819812 None:intergenic 45.0%
TGGATTCGTGGAGAAATCAG+CGG + chr7_4:59819816-59819835 Msa1167370:CDS 45.0%
ATGCGTTTGTGATGAAAGCG+TGG + chr7_4:59819887-59819906 Msa1167370:CDS 45.0%
! GTTTGTGATGAAAGCGTGGA+AGG + chr7_4:59819891-59819910 Msa1167370:CDS 45.0%
! GAAGTGGTGCTTTTGTCTGA+TGG + chr7_4:59819934-59819953 Msa1167370:CDS 45.0%
! GTGCTTTTGTCTGATGGGAA+TGG + chr7_4:59819940-59819959 Msa1167370:CDS 45.0%
GGTGATTTCACAAGAGCGAT+TGG + chr7_4:59819961-59819980 Msa1167370:CDS 45.0%
GAGCGATAAACCTGTTGGAT+TGG + chr7_4:59819999-59820018 Msa1167370:CDS 45.0%
! AACCTGTTGGATTGGGTGTT+AGG + chr7_4:59820007-59820026 Msa1167370:CDS 45.0%
! GGTGGTGCTTTTACTTTCAG+TGG + chr7_4:59820090-59820109 Msa1167370:CDS 45.0%
! AGATAAGAGTGAGGTGGTGG+TGG - chr7_4:59819530-59819549 None:intergenic 50.0%
GGAGGGTGAATTTGGAAGAG+AGG - chr7_4:59819567-59819586 None:intergenic 50.0%
TTTGAGGGGGAGGGTGAATT+TGG - chr7_4:59819575-59819594 None:intergenic 50.0%
ACGGTTGAATTTGAGGGGGA+GGG - chr7_4:59819584-59819603 None:intergenic 50.0%
AACGGTTGAATTTGAGGGGG+AGG - chr7_4:59819585-59819604 None:intergenic 50.0%
! GAGGAGAATCGGAGAGGTTT+TGG - chr7_4:59819613-59819632 None:intergenic 50.0%
!!! AGATGGTGGCGGAGATTTTG+GGG - chr7_4:59819639-59819658 None:intergenic 50.0%
!!! GAGATGGTGGCGGAGATTTT+GGG - chr7_4:59819640-59819659 None:intergenic 50.0%
! GGTAGGAGAAGGTGGATTCA+GGG - chr7_4:59819678-59819697 None:intergenic 50.0%
! AGGTAGGAGAAGGTGGATTC+AGG - chr7_4:59819679-59819698 None:intergenic 50.0%
GGTCAGAGACGGTTATGGTT+TGG - chr7_4:59819720-59819739 None:intergenic 50.0%
TGGTGTGAAAGCTCCTGGAA+CGG - chr7_4:59819773-59819792 None:intergenic 50.0%
CATGTTGGTGTGAAAGCTCC+TGG - chr7_4:59819778-59819797 None:intergenic 50.0%
TGCTCACAGAAACACGTTCC+TGG + chr7_4:59819796-59819815 Msa1167370:CDS 50.0%
GAAACACGTTCCTGGATTCG+TGG + chr7_4:59819804-59819823 Msa1167370:CDS 50.0%
! GCTGATTTCTCCACGAATCC+AGG - chr7_4:59819817-59819836 None:intergenic 50.0%
ATCAGCGGAGCTAAAAGCGA+AGG + chr7_4:59819831-59819850 Msa1167370:CDS 50.0%
TCAGCGGAGCTAAAAGCGAA+GGG + chr7_4:59819832-59819851 Msa1167370:CDS 50.0%
! TGTGATGAAAGCGTGGAAGG+AGG + chr7_4:59819894-59819913 Msa1167370:CDS 50.0%
AGCGTGGAAGGAGGATTTGA+AGG + chr7_4:59819903-59819922 Msa1167370:CDS 50.0%
GACCTAACACCCAATCCAAC+AGG - chr7_4:59820012-59820031 None:intergenic 50.0%
!! AGGTGGTGGTGGAAGATGAG+AGG - chr7_4:59819519-59819538 None:intergenic 55.0%
GGGAGATAAGAGTGAGGTGG+TGG - chr7_4:59819533-59819552 None:intergenic 55.0%
!!! GATGGTGGCGGAGATTTTGG+GGG - chr7_4:59819638-59819657 None:intergenic 55.0%
!!! GGAGATGGTGGCGGAGATTT+TGG - chr7_4:59819641-59819660 None:intergenic 55.0%
TTCAGGGAGTTTGTCGCCGA+CGG - chr7_4:59819662-59819681 None:intergenic 55.0%
! TGGTTTGGACTTCACCGGCA+GGG - chr7_4:59819705-59819724 None:intergenic 55.0%
! ATGGTTTGGACTTCACCGGC+AGG - chr7_4:59819706-59819725 None:intergenic 55.0%
GGGGAAGAGGAGAATCGGAG+AGG - chr7_4:59819619-59819638 None:intergenic 60.0%
!! GGCGGAGATTTTGGGGGAAG+AGG - chr7_4:59819632-59819651 None:intergenic 60.0%
ATCTCCGCCACCATCTCCGT+CGG + chr7_4:59819643-59819662 Msa1167370:CDS 60.0%
TTTGTCGCCGACGGAGATGG+TGG - chr7_4:59819653-59819672 None:intergenic 60.0%
GAGTTTGTCGCCGACGGAGA+TGG - chr7_4:59819656-59819675 None:intergenic 60.0%
AGGGTCGAGGTAGGAGAAGG+TGG - chr7_4:59819686-59819705 None:intergenic 60.0%
TTCTCCTACCTCGACCCTGC+CGG + chr7_4:59819688-59819707 Msa1167370:CDS 60.0%
AAGCTCCTGGAACGGCGAAG+AGG - chr7_4:59819765-59819784 None:intergenic 60.0%
GGCAGGGTCGAGGTAGGAGA+AGG - chr7_4:59819689-59819708 None:intergenic 65.0%
TTCACCGGCAGGGTCGAGGT+AGG - chr7_4:59819695-59819714 None:intergenic 65.0%
GCAGTCCTCTTCGCCGTTCC+AGG + chr7_4:59819757-59819776 Msa1167370:CDS 65.0%
! GTCGCCGACGGAGATGGTGG+CGG - chr7_4:59819650-59819669 None:intergenic 70.0%
GGACTTCACCGGCAGGGTCG+AGG - chr7_4:59819699-59819718 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 59819487 59820140 59819487 ID=Msa1167370;Name=Msa1167370
chr7_4 mRNA 59819487 59820140 59819487 ID=Msa1167370-mRNA-1;Parent=Msa1167370;Name=Msa1167370-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|-1|0|1|-1|1|1|0|217
chr7_4 exon 59819487 59820140 59819487 ID=Msa1167370-mRNA-1:exon:18582;Parent=Msa1167370-mRNA-1
chr7_4 CDS 59819487 59820140 59819487 ID=Msa1167370-mRNA-1:cds;Parent=Msa1167370-mRNA-1
Gene Sequence

>Msa1167370

ATGGCAACATCACTCTCTTTCTCTAGACTCCTCTCATCTTCCACCACCACCTCACTCTTATCTCCCAAAACCAAAACCCTCTCTTCCAAATTCACCCTCCCCCTCAAATTCAACCGTTTCAACCCAAAACCTCTCCGATTCTCCTCTTCCCCCAAAATCTCCGCCACCATCTCCGTCGGCGACAAACTCCCTGAATCCACCTTCTCCTACCTCGACCCTGCCGGTGAAGTCCAAACCATAACCGTCTCTGACCTAACAAAAGGCAAAAAAGCAGTCCTCTTCGCCGTTCCAGGAGCTTTCACACCAACATGCTCACAGAAACACGTTCCTGGATTCGTGGAGAAATCAGCGGAGCTAAAAGCGAAGGGAGTTGATACAATCGCTTGCATTTCGGTGAACGATGCGTTTGTGATGAAAGCGTGGAAGGAGGATTTGAAGGTGAACGATGAAGTGGTGCTTTTGTCTGATGGGAATGGTGATTTCACAAGAGCGATTGGGGTTGAGCTTGATTTGAGCGATAAACCTGTTGGATTGGGTGTTAGGTCAAGACGTTATGCTTTGTTGGCTGAAGATGGTGTTGTTAAGCTTTTCAATTTGGAGGAAGGTGGTGCTTTTACTTTCAGTGGTGCTGATGATATTCTCAAAGTTCTTTGA

Protein sequence

>Msa1167370

MATSLSFSRLLSSSTTTSLLSPKTKTLSSKFTLPLKFNRFNPKPLRFSSSPKISATISVGDKLPESTFSYLDPAGEVQTITVSDLTKGKKAVLFAVPGAFTPTCSQKHVPGFVEKSAELKAKGVDTIACISVNDAFVMKAWKEDLKVNDEVVLLSDGNGDFTRAIGVELDLSDKPVGLGVRSRRYALLAEDGVVKLFNLEEGGAFTFSGADDILKVL*