AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene073036


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073036.t1 MTR_3g109200 88.298 188 17 1 1 183 1 188 5.54e-119 334
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene073036.t1 AT4G31310 57.927 164 67 1 21 182 10 173 2.80e-62 191
MS.gene073036.t1 AT4G31310 57.927 164 67 1 21 182 8 171 3.02e-62 190
MS.gene073036.t1 AT2G24390 59.028 144 58 1 21 163 8 151 2.11e-60 185
MS.gene073036.t1 AT2G24390 57.639 144 56 2 21 163 8 147 5.96e-57 176
MS.gene073036.t1 AT2G24390 57.639 144 58 2 21 163 8 149 1.38e-55 172
MS.gene073036.t1 AT5G39730 42.857 154 88 0 12 165 1 154 3.51e-43 142
MS.gene073036.t1 AT3G28950 46.207 145 75 1 14 158 2 143 2.00e-41 137
MS.gene073036.t1 AT3G28940 38.994 159 96 1 14 172 3 160 3.44e-40 134
MS.gene073036.t1 AT5G39720 42.069 145 84 0 19 163 8 152 5.15e-40 134
MS.gene073036.t1 AT3G28930 37.805 164 101 1 14 177 3 165 2.91e-39 132
MS.gene073036.t1 AT3G28930 37.805 164 101 1 14 177 3 165 2.91e-39 132
MS.gene073036.t1 AT5G39720 45.763 118 64 0 19 136 8 125 6.95e-34 117
MS.gene073036.t1 AT3G28930 40.650 123 73 0 14 136 3 125 1.57e-30 108

Find 35 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGTTTGTTCAGGTTCTTCT+TGG 0.166206 3.3:-89179876 MS.gene073036:intron
CAGGTTCTTCTTGGCATCTC+TGG 0.306327 3.3:-89179867 MS.gene073036:CDS
GCATATAAATCAGGATCATT+TGG 0.367836 3.3:+89179570 None:intergenic
TGCGAGTTTATGCTTATGTT+TGG 0.368761 3.3:-89179599 MS.gene073036:CDS
GTGACTTTGTTAGTCTGAAC+GGG 0.387086 3.3:+89179987 None:intergenic
CTCCTTGCCGATGAGGTTGT+TGG 0.399169 3.3:-89180195 MS.gene073036:CDS
TCCCACTCAGCATATAAATC+AGG 0.440243 3.3:+89179561 None:intergenic
GTTTCATAAGTCTGAACTCT+TGG 0.441481 3.3:+89178626 None:intergenic
GAGAGGGTAGCGGGTGAAGA+TGG 0.459964 3.3:+89180150 None:intergenic
GTCTGAACGGGGAGGATAGC+GGG 0.472073 3.3:+89179999 None:intergenic
GTATTGAATACTAGCGTAGT+TGG 0.505562 3.3:-89180270 MS.gene073036:CDS
AACTAGTCGGAGAGGGTAGC+GGG 0.511024 3.3:+89180141 None:intergenic
TAACTAGTCGGAGAGGGTAG+CGG 0.538096 3.3:+89180140 None:intergenic
AATACTAGCGTAGTTGGAGT+TGG 0.545688 3.3:-89180264 MS.gene073036:CDS
TGATAGCTTCATGCAACAGT+TGG 0.549800 3.3:-89178666 MS.gene073036:CDS
AGGGTAGCGGGTGAAGATGG+AGG 0.557542 3.3:+89180153 None:intergenic
AGTGACTTTGTTAGTCTGAA+CGG 0.558317 3.3:+89179986 None:intergenic
AGTCACAGATTTAAGATCAA+AGG 0.574334 3.3:-89180032 MS.gene073036:CDS
TCCTGATTTATATGCTGAGT+GGG 0.577694 3.3:-89179562 MS.gene073036:CDS
GGGTAGCGGGTGAAGATGGA+GGG 0.580662 3.3:+89180154 None:intergenic
GAGGGCGCCAACAACCTCAT+CGG 0.585470 3.3:+89180188 None:intergenic
CGCCAACAACCTCATCGGCA+AGG 0.589069 3.3:+89180193 None:intergenic
TGGAAGCCTCCTTGCCGATG+AGG 0.589141 3.3:-89180202 MS.gene073036:CDS
GTTCAGACTAACAAAGTCAC+TGG 0.597618 3.3:-89179984 MS.gene073036:CDS
ATGGAGGGACGCGTTTCAAG+AGG 0.602241 3.3:+89180169 None:intergenic
TGTAAGCATCAAGGGTCAAG+TGG 0.602850 3.3:+89178578 None:intergenic
GTATACTAGAACTCAAGTTG+AGG 0.624240 3.3:-89179805 MS.gene073036:CDS
TGGAGGGACGCGTTTCAAGA+GGG 0.634749 3.3:+89180170 None:intergenic
AAGAACTAACTAGTCGGAGA+GGG 0.647103 3.3:+89180134 None:intergenic
AAAGAACTAACTAGTCGGAG+AGG 0.650218 3.3:+89180133 None:intergenic
AGTCTGAACGGGGAGGATAG+CGG 0.662008 3.3:+89179998 None:intergenic
CAACAACCTCATCGGCAAGG+AGG 0.666134 3.3:+89180196 None:intergenic
CTTTGTTAGTCTGAACGGGG+AGG 0.697174 3.3:+89179991 None:intergenic
TGACTTTGTTAGTCTGAACG+GGG 0.700303 3.3:+89179988 None:intergenic
ATCCTGATTTATATGCTGAG+TGG 0.708885 3.3:-89179563 MS.gene073036:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAGAATTAATTAATTAAATT+TGG + chr3.3:89178972-89178991 None:intergenic 10.0%
!! TTAATTAATTAAATTTGGTA+AGG + chr3.3:89178967-89178986 None:intergenic 10.0%
!! ATTATTGATGAAATTTAACA+TGG + chr3.3:89179153-89179172 None:intergenic 15.0%
!! TAATAGGAAATTATTTGTAC+AGG - chr3.3:89179228-89179247 MS.gene073036:intron 20.0%
!! TATTAAGTAAGAACTTTGTT+TGG - chr3.3:89179502-89179521 MS.gene073036:intron 20.0%
!! TTAATTAATTCTGTTTGTTC+AGG - chr3.3:89178979-89178998 MS.gene073036:intron 20.0%
!!! TACAATAGAATGAATTTGTT+TGG + chr3.3:89179344-89179363 None:intergenic 20.0%
!!! TACTCAGCTTTTTATTTTAT+AGG + chr3.3:89179851-89179870 None:intergenic 20.0%
!!! TATTTTGAAGTCTCTTATTT+TGG - chr3.3:89179973-89179992 MS.gene073036:intron 20.0%
!!! TTTAGAACAAGAATCTTAAT+AGG - chr3.3:89179212-89179231 MS.gene073036:intron 20.0%
! AAGAACTTTCTTCTTGAATA+GGG + chr3.3:89180109-89180128 None:intergenic 25.0%
! AATAAGAGACTTCAAAATAC+AGG + chr3.3:89179972-89179991 None:intergenic 25.0%
! GATTACTAAACAAAAAGGTT+TGG + chr3.3:89179721-89179740 None:intergenic 25.0%
! GGCTTAAGTAAATAATTAAG+TGG + chr3.3:89179462-89179481 None:intergenic 25.0%
! TAAGAACTTTCTTCTTGAAT+AGG + chr3.3:89180110-89180129 None:intergenic 25.0%
! TGAGAAGAAAATTATCTGTA+AGG + chr3.3:89179782-89179801 None:intergenic 25.0%
!! CTTAACTGTTAATTTGAGAT+TGG - chr3.3:89179632-89179651 MS.gene073036:intron 25.0%
!! TTGCTGATTACTAAACAAAA+AGG + chr3.3:89179726-89179745 None:intergenic 25.0%
!!! AATCACAACGTTTTTGTTTA+TGG - chr3.3:89178643-89178662 MS.gene073036:CDS 25.0%
!!! TCTTATTTTCTTCGTATGTT+GGG - chr3.3:89179417-89179436 MS.gene073036:intron 25.0%
!!! TTTTTGTTTAGTAATCAGCA+AGG - chr3.3:89179725-89179744 MS.gene073036:intron 25.0%
ACATACGAAGAAAATAAGAG+AGG + chr3.3:89179416-89179435 None:intergenic 30.0%
ATAATTCTTCCTACCAGTTT+AGG - chr3.3:89179363-89179382 MS.gene073036:intron 30.0%
ATATCATTTCATCCCTAAAC+TGG + chr3.3:89179379-89179398 None:intergenic 30.0%
ATCTGAGAAATTCTTCTTCT+GGG - chr3.3:89179674-89179693 MS.gene073036:intron 30.0%
GCATATAAATCAGGATCATT+TGG + chr3.3:89179298-89179317 None:intergenic 30.0%
TAATTAAGTGGCAAATGATG+AGG + chr3.3:89179450-89179469 None:intergenic 30.0%
TAATTCTTCCTACCAGTTTA+GGG - chr3.3:89179364-89179383 MS.gene073036:intron 30.0%
TATCTGAGAAATTCTTCTTC+TGG - chr3.3:89179673-89179692 MS.gene073036:intron 30.0%
TCTTCTCAGCACAAAATAAA+AGG - chr3.3:89179794-89179813 MS.gene073036:CDS 30.0%
TCTTTCATTCAGTAAACGAT+CGG - chr3.3:89179572-89179591 MS.gene073036:CDS 30.0%
! ACTGTTAATTTGAGATTGGA+TGG - chr3.3:89179636-89179655 MS.gene073036:intron 30.0%
! AGTCACAGATTTAAGATCAA+AGG - chr3.3:89178833-89178852 MS.gene073036:intron 30.0%
! ATCGTTTTCTTGCTTATAGA+AGG + chr3.3:89180264-89180283 None:intergenic 30.0%
! CTGTTAATTTGAGATTGGAT+GGG - chr3.3:89179637-89179656 MS.gene073036:intron 30.0%
! TCTAAAAGCACAAAATGTTC+AGG + chr3.3:89179198-89179217 None:intergenic 30.0%
! TTGTTTGGTGATTTAGAAAC+TGG - chr3.3:89179517-89179536 MS.gene073036:intron 30.0%
!!! CTCTTATTTTCTTCGTATGT+TGG - chr3.3:89179416-89179435 MS.gene073036:intron 30.0%
!!! TCAAGTTGAGGTTTTCTTAA+TGG - chr3.3:89179072-89179091 MS.gene073036:intron 30.0%
AAATTCTTCTTCTGGGTTGT+TGG - chr3.3:89179681-89179700 MS.gene073036:intron 35.0%
AACAACGCAATCATGAACAA+AGG + chr3.3:89179483-89179502 None:intergenic 35.0%
AACTTTCTTCTTGAATAGGG+AGG + chr3.3:89180106-89180125 None:intergenic 35.0%
AATTCTTCTTCTGGGTTGTT+GGG - chr3.3:89179682-89179701 MS.gene073036:intron 35.0%
ACTTTCTTCTTGAATAGGGA+GGG + chr3.3:89180105-89180124 None:intergenic 35.0%
ATCCTGATTTATATGCTGAG+TGG - chr3.3:89179302-89179321 MS.gene073036:intron 35.0%
ATTCACAGAAACTACTATGC+AGG + chr3.3:89180006-89180025 None:intergenic 35.0%
GAGTCAAAGAACTAACTAGT+CGG + chr3.3:89178740-89178759 None:intergenic 35.0%
GTATTGAATACTAGCGTAGT+TGG - chr3.3:89178595-89178614 MS.gene073036:CDS 35.0%
GTTTCATAAGTCTGAACTCT+TGG + chr3.3:89180242-89180261 None:intergenic 35.0%
TCCTGATTTATATGCTGAGT+GGG - chr3.3:89179303-89179322 MS.gene073036:intron 35.0%
TCCTTCAATGTCAAAACATC+AGG + chr3.3:89180140-89180159 None:intergenic 35.0%
TCTCAGCACAAAATAAAAGG+TGG - chr3.3:89179797-89179816 MS.gene073036:CDS 35.0%
TGCGAGTTTATGCTTATGTT+TGG - chr3.3:89179266-89179285 MS.gene073036:intron 35.0%
! AGTGACTTTGTTAGTCTGAA+CGG + chr3.3:89178882-89178901 None:intergenic 35.0%
! GTATACTAGAACTCAAGTTG+AGG - chr3.3:89179060-89179079 MS.gene073036:intron 35.0%
! TATCTGTAAGGTGTTCATCA+AGG + chr3.3:89179770-89179789 None:intergenic 35.0%
! TGCTTGATAGTAAACATCTG+AGG - chr3.3:89179883-89179902 MS.gene073036:intron 35.0%
!! AACATCTGAGGTTTTAGTCT+AGG - chr3.3:89179895-89179914 MS.gene073036:intron 35.0%
!! CGATATTTTAGATGAGTTCG+AGG - chr3.3:89179030-89179049 MS.gene073036:intron 35.0%
!!! ATGTTTTGACATTGAAGGAG+TGG - chr3.3:89180141-89180160 MS.gene073036:intron 35.0%
!!! TCCTGATGTTTTGACATTGA+AGG - chr3.3:89180136-89180155 MS.gene073036:intron 35.0%
!!! TGAACTCTTGGTTTTGATTC+TGG + chr3.3:89180230-89180249 None:intergenic 35.0%
AAAGAACTAACTAGTCGGAG+AGG + chr3.3:89178735-89178754 None:intergenic 40.0%
AAGAACTAACTAGTCGGAGA+GGG + chr3.3:89178734-89178753 None:intergenic 40.0%
AATACTAGCGTAGTTGGAGT+TGG - chr3.3:89178601-89178620 MS.gene073036:CDS 40.0%
ATTCTTCTTCTGGGTTGTTG+GGG - chr3.3:89179683-89179702 MS.gene073036:intron 40.0%
CATTTCATCCCTAAACTGGT+AGG + chr3.3:89179375-89179394 None:intergenic 40.0%
GGTGATTTAGAAACTGGATC+CGG - chr3.3:89179523-89179542 MS.gene073036:intron 40.0%
GTTCAGACTAACAAAGTCAC+TGG - chr3.3:89178881-89178900 MS.gene073036:intron 40.0%
GTTCAGGATCATGATGACTT+TGG + chr3.3:89179182-89179201 None:intergenic 40.0%
TCCCACTCAGCATATAAATC+AGG + chr3.3:89179307-89179326 None:intergenic 40.0%
TGATAGCTTCATGCAACAGT+TGG - chr3.3:89180199-89180218 MS.gene073036:CDS 40.0%
! AAACATACTTTTCCCACTGC+AGG + chr3.3:89179553-89179572 None:intergenic 40.0%
! AACATACTTTTCCCACTGCA+GGG + chr3.3:89179552-89179571 None:intergenic 40.0%
! ATATGCTGAGTGGGATTTTG+AGG - chr3.3:89179312-89179331 MS.gene073036:intron 40.0%
! CTGTTTGTTCAGGTTCTTCT+TGG - chr3.3:89178989-89179008 MS.gene073036:intron 40.0%
! GTGACTTTGTTAGTCTGAAC+GGG + chr3.3:89178881-89178900 None:intergenic 40.0%
! TGACTTTGTTAGTCTGAACG+GGG + chr3.3:89178880-89178899 None:intergenic 40.0%
AGGACAGACTCTTTCTCTCA+TGG + chr3.3:89179952-89179971 None:intergenic 45.0%
CAGGTTCTTCTTGGCATCTC+TGG - chr3.3:89178998-89179017 MS.gene073036:intron 50.0%
CTTGAATAGGGAGGGATGCA+TGG + chr3.3:89180097-89180116 None:intergenic 50.0%
TAACTAGTCGGAGAGGGTAG+CGG + chr3.3:89178728-89178747 None:intergenic 50.0%
! CTTTGTTAGTCTGAACGGGG+AGG + chr3.3:89178877-89178896 None:intergenic 50.0%
! TTTTCCCACTGCAGGGAATC+CGG + chr3.3:89179545-89179564 None:intergenic 50.0%
AACTAGTCGGAGAGGGTAGC+GGG + chr3.3:89178727-89178746 None:intergenic 55.0%
AGTCTGAACGGGGAGGATAG+CGG + chr3.3:89178870-89178889 None:intergenic 55.0%
ATGGAGGGACGCGTTTCAAG+AGG + chr3.3:89178699-89178718 None:intergenic 55.0%
CAACAACCTCATCGGCAAGG+AGG + chr3.3:89178672-89178691 None:intergenic 55.0%
CTCCTTGCCGATGAGGTTGT+TGG - chr3.3:89178670-89178689 MS.gene073036:CDS 55.0%
TGGAGGGACGCGTTTCAAGA+GGG + chr3.3:89178698-89178717 None:intergenic 55.0%
CGCCAACAACCTCATCGGCA+AGG + chr3.3:89178675-89178694 None:intergenic 60.0%
GGATCCGGATTCCCTGCAGT+GGG - chr3.3:89179538-89179557 MS.gene073036:intron 60.0%
GTCTGAACGGGGAGGATAGC+GGG + chr3.3:89178869-89178888 None:intergenic 60.0%
TGGAAGCCTCCTTGCCGATG+AGG - chr3.3:89178663-89178682 MS.gene073036:CDS 60.0%
TGGATCCGGATTCCCTGCAG+TGG - chr3.3:89179537-89179556 MS.gene073036:intron 60.0%
!! AGGGTAGCGGGTGAAGATGG+AGG + chr3.3:89178715-89178734 None:intergenic 60.0%
!! GAGAGGGTAGCGGGTGAAGA+TGG + chr3.3:89178718-89178737 None:intergenic 60.0%
!! GAGGGCGCCAACAACCTCAT+CGG + chr3.3:89178680-89178699 None:intergenic 60.0%
!! GGGTAGCGGGTGAAGATGGA+GGG + chr3.3:89178714-89178733 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 89178586 89180301 89178586 ID=MS.gene073036
chr3.3 mRNA 89178586 89180301 89178586 ID=MS.gene073036.t1;Parent=MS.gene073036
chr3.3 exon 89180144 89180301 89180144 ID=MS.gene073036.t1.exon1;Parent=MS.gene073036.t1
chr3.3 CDS 89180144 89180301 89180144 ID=cds.MS.gene073036.t1;Parent=MS.gene073036.t1
chr3.3 exon 89179980 89180052 89179980 ID=MS.gene073036.t1.exon2;Parent=MS.gene073036.t1
chr3.3 CDS 89179980 89180052 89179980 ID=cds.MS.gene073036.t1;Parent=MS.gene073036.t1
chr3.3 exon 89179794 89179886 89179794 ID=MS.gene073036.t1.exon3;Parent=MS.gene073036.t1
chr3.3 CDS 89179794 89179886 89179794 ID=cds.MS.gene073036.t1;Parent=MS.gene073036.t1
chr3.3 exon 89179554 89179637 89179554 ID=MS.gene073036.t1.exon4;Parent=MS.gene073036.t1
chr3.3 CDS 89179554 89179637 89179554 ID=cds.MS.gene073036.t1;Parent=MS.gene073036.t1
chr3.3 exon 89178586 89178729 89178586 ID=MS.gene073036.t1.exon5;Parent=MS.gene073036.t1
chr3.3 CDS 89178586 89178729 89178586 ID=cds.MS.gene073036.t1;Parent=MS.gene073036.t1
Gene Sequence

>MS.gene073036

ATGAGCGTGGTATTGAATACTAGCGTAGTTGGAGTTGGTACTCAGAATCAGAATCAGAATCACAACGTTTTTGTTTATGGAAGCCTCCTTGCCGATGAGGTTGTTGGCGCCCTCTTGAAACGCGTCCCTCCATCTTCACCCGCTACCCTCTCCGACTAGTTAGTTCTTTGACTCGTTAATCAATATCAATTATTTCTCTTATTCTTCTTTGATTTATGTTTTATTAAAATAAGATGAAATTGAATACAGTCACAGATTTAAGATCAAAGGTCGTGTTTATCCCGCTATCCTCCCCGTTCAGACTAACAAAGTCACTGGCAGAGTAAGATAATCAATTCTATTCAACAATTCTTGCACACTCTTAATTATTGCATTCAACCTTACCAAATTTAATTAATTAATTCTGTTTGTTCAGGTTCTTCTTGGCATCTCTGGAGTTGAACTCGATATTTTAGATGAGTTCGAGGATGTTGAGTATACTAGAACTCAAGTTGAGGTTTTCTTAATGGTAACTAAAATTCGTATATAAACAAATTCATTTTATTTTTATTTTTATGTTTGATTCCATGTTAAATTTCATCAATAATTGATTTCCAAAGTCATCATGATCCTGAACATTTTGTGCTTTTAGAACAAGAATCTTAATAGGAAATTATTTGTACAGGATAATTCTGAAAACTTGCGAGTTTATGCTTATGTTTGGAGCAATCCAAATGATCCTGATTTATATGCTGAGTGGGATTTTGAGGTATTTTCCAAACAAATTCATTCTATTGTATAATTCTTCCTACCAGTTTAGGGATGAAATGATATTCAATATATTTATTCCTCTCTTATTTTCTTCGTATGTTGGGACAATTACCTCATCATTTGCCACTTAATTATTTACTTAAGCCTTTGTTCATGATTGCGTTGTTATTAAGTAAGAACTTTGTTTGGTGATTTAGAAACTGGATCCGGATTCCCTGCAGTGGGAAAAGTATGTTTCTTTCATTCAGTAAACGATCGGTTTAGATTTTACAATAACAAAATCAGTTTTAAATGATCTTAACTGTTAATTTGAGATTGGATGGGTTGATATAAAAAATATCTGAGAAATTCTTCTTCTGGGTTGTTGGGGTAGACAGATTTTCCAAACCTTTTTGTTTAGTAATCAGCAAGGCAAAATAATGATTTAAGTTCCTTGATGAACACCTTACAGATAATTTTCTTCTCAGCACAAAATAAAAGGTGGATCGCACTGTGTTAGTTGTGTTTTGACTCCTATAAAATAAAAAGCTGAGTATGTATGTATAAATGCTTGATAGTAAACATCTGAGGTTTTAGTCTAGGTTAATTTATGTTATTGATTCATTATAGATATCCATGAGAGAAAGAGTCTGTCCTGTATTTTGAAGTCTCTTATTTTGGCTTACAACCTGCATAGTAGTTTCTGTGAATGTCTTTGATCTTCACATGCTCTTTTAATTTATTCGTTTCTAATTCTAGATTCAAATTTAAATATCTTTCCATGCATCCCTCCCTATTCAAGAAGAAAGTTCTTATTCTCTTCCTGATGTTTTGACATTGAAGGAGTGGAAAAAAGATCACATGAATGATTTCGTCAAGATGACTGATAGCTTCATGCAACAGTTGGAATTGCCAGAATCAAAACCAAGAGTTCAGACTTATGAAACCTTCTATAAGCAAGAAAACGATAAGCCACTTGACCCTTGA

Protein sequence

>MS.gene073036.t1

MSVVLNTSVVGVGTQNQNQNHNVFVYGSLLADEVVGALLKRVPPSSPATLSDYHRFKIKGRVYPAILPVQTNKVTGRVLLGISGVELDILDEFEDVEYTRTQVEVFLMDNSENLRVYAYVWSNPNDPDLYAEWDFEEWKKDHMNDFVKMTDSFMQQLELPESKPRVQTYETFYKQENDKPLDP