AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene58372

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene58372.t1 MTR_2g078620 98.221 281 5 0 1 281 42 322 0.0 565
MS.gene58372.t1 MTR_2g083910 47.059 102 42 5 184 278 134 230 8.34e-19 83.6
MS.gene58372.t1 MTR_2g083910 47.059 102 42 5 184 278 134 230 1.60e-18 83.2
MS.gene58372.t1 MTR_2g016760 39.053 169 83 5 126 279 66 229 1.90e-17 81.6
MS.gene58372.t1 MTR_8g086820 41.322 121 52 5 175 279 123 240 4.22e-17 79.0
MS.gene58372.t1 MTR_4g080340 40.367 109 47 3 188 278 128 236 3.13e-13 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene58372.t1 AT2G42760 38.095 126 42 7 184 279 145 264 2.36e-11 63.2

Find 52 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACATCTTATTTCCCCAATT+TGG 0.135591 2.3:-19253927 None:intergenic
TCTTCTTCTTTCACTCTAAT+TGG 0.176697 2.3:-19252615 None:intergenic
CAACTCCTCCTGTTCCAAAT+TGG 0.187842 2.3:+19253913 MS.gene58372:CDS
CTTAAACAAAGAGGGTATTT+TGG 0.192411 2.3:+19253656 MS.gene58372:CDS
TGGAGGCAAGTTGTCATTAT+TGG 0.201109 2.3:-19252877 None:intergenic
AGTTCAAGGGTTCAAGGATT+TGG 0.219405 2.3:+19253746 MS.gene58372:CDS
GGTGCTCTTTGCAGCTTCTT+AGG 0.231368 2.3:-19252582 None:intergenic
CAAGAAACTGATTCAAGAAT+TGG 0.268407 2.3:+19252825 MS.gene58372:CDS
AACTCCTCCTGTTCCAAATT+GGG 0.290556 2.3:+19253914 MS.gene58372:CDS
GTTCAAGGGTTCAAGGATTT+GGG 0.318307 2.3:+19253747 MS.gene58372:CDS
GGAGGCAAGTTGTCATTATT+GGG 0.324183 2.3:-19252876 None:intergenic
CCATCTTTGCCTCCAACAAT+AGG 0.347224 2.3:+19252786 MS.gene58372:CDS
ACTCTAATTGGTGGCATTGA+TGG 0.367540 2.3:-19252603 None:intergenic
AGCTTAGCTAACATAATTCC+TGG 0.370469 2.3:+19253801 MS.gene58372:CDS
GCCTCCAAGGTTAACCTCTA+AGG 0.388438 2.3:+19252893 MS.gene58372:CDS
TCCTCTCTCCCTATTGTTGG+AGG 0.400398 2.3:-19252795 None:intergenic
AGGATGAACAAAATCACTAT+TGG 0.403416 2.3:-19252562 None:intergenic
TCCTAAATCAGAAAACAATA+AGG 0.414045 2.3:+19253694 MS.gene58372:CDS
TTATTTCCCCAATTTGGAAC+AGG 0.427610 2.3:-19253921 None:intergenic
ATATAAAACCAAAGATGTTA+AGG 0.433545 2.3:+19252463 None:intergenic
GGAATTATGTTAGCTAAGCT+TGG 0.440726 2.3:-19253798 None:intergenic
TCTTCTTTCACTCTAATTGG+TGG 0.448745 2.3:-19252612 None:intergenic
CCTATTGTTGGAGGCAAAGA+TGG 0.449300 2.3:-19252786 None:intergenic
CTTGAGTATGAAGAAGTTCA+AGG 0.460785 2.3:+19253732 MS.gene58372:CDS
ATAGAAGTGATAGCAATAGA+AGG 0.463972 2.3:+19252742 MS.gene58372:CDS
ATTAGTCTTGTTGAAGGGTA+AGG 0.475567 2.3:-19252498 None:intergenic
CATCTTTGCCTCCAACAATA+GGG 0.480386 2.3:+19252787 MS.gene58372:CDS
ACCTTAGAGGTTAACCTTGG+AGG 0.482914 2.3:-19252894 None:intergenic
GAGCTGATTAGTCTTGTTGA+AGG 0.486253 2.3:-19252504 None:intergenic
ATCGGATTCTGCTATGCATA+AGG 0.492617 2.3:+19252677 MS.gene58372:CDS
TGAAGAAGTTCAAGGGTTCA+AGG 0.522733 2.3:+19253740 MS.gene58372:CDS
AGTACCTTAGAGGTTAACCT+TGG 0.525551 2.3:-19252897 None:intergenic
AACCATGCTTCTGATAAGTA+AGG 0.533103 2.3:-19253876 None:intergenic
TCATTATTGGGAGGTGTCGA+TGG 0.539813 2.3:-19252864 None:intergenic
ATAATGACAACTTGCCTCCA+AGG 0.544515 2.3:+19252880 MS.gene58372:CDS
TTACTTATCAGAAGCATGGT+TGG 0.557791 2.3:+19253878 MS.gene58372:CDS
TGAACAAAATCACTATTGGA+TGG 0.561406 2.3:-19252558 None:intergenic
CATCATTGTGCAAAGATGAA+AGG 0.561895 2.3:+19252711 MS.gene58372:CDS
ACTCCTCCTGTTCCAAATTG+GGG 0.566945 2.3:+19253915 MS.gene58372:CDS
CTTCATACTCAAGATCACTT+AGG 0.571003 2.3:-19253722 None:intergenic
CAGCATTCCAAGAAGTAGAC+CGG 0.572646 2.3:+19253611 MS.gene58372:CDS
GACCTTACTTATCAGAAGCA+TGG 0.574521 2.3:+19253874 MS.gene58372:CDS
GTTGAAAGCTTAAACAAAGA+GGG 0.576048 2.3:+19253648 MS.gene58372:CDS
AGCTGATTAGTCTTGTTGAA+GGG 0.577448 2.3:-19252503 None:intergenic
TTTCCCCAATTTGGAACAGG+AGG 0.577483 2.3:-19253918 None:intergenic
GATTCTGCTATGCATAAGGC+AGG 0.577729 2.3:+19252681 MS.gene58372:CDS
GCCTCCAACAATAGGGAGAG+AGG 0.599344 2.3:+19252794 MS.gene58372:CDS
AGTTGAAAGCTTAAACAAAG+AGG 0.608171 2.3:+19253647 MS.gene58372:CDS
TTGAGTATGAAGAAGTTCAA+GGG 0.610506 2.3:+19253733 MS.gene58372:CDS
GAGGAAGATAAAGCAGCAAG+AGG 0.618815 2.3:+19253852 MS.gene58372:CDS
CAAATTGGTGCATCAAACAT+CGG 0.624498 2.3:+19252659 MS.gene58372:CDS
GGCAAGTTGTCATTATTGGG+AGG 0.626871 2.3:-19252873 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTTAAATGCTAAAATTATT+TGG - chr2.3:19253229-19253248 None:intergenic 15.0%
!! AACACCAATTAATACAAATA+TGG + chr2.3:19253195-19253214 MS.gene58372:intron 20.0%
!! ATGATCAATCAAAATATGAT+TGG - chr2.3:19253423-19253442 None:intergenic 20.0%
!! GAAGAAAAAGATGATAAAAA+AGG + chr2.3:19252633-19252652 MS.gene58372:CDS 20.0%
!! GACATAATGATTTAAAAAGA+GGG - chr2.3:19253128-19253147 None:intergenic 20.0%
!! TAATATCAATCATAAACTCT+TGG - chr2.3:19253155-19253174 None:intergenic 20.0%
!! TGACATAATGATTTAAAAAG+AGG - chr2.3:19253129-19253148 None:intergenic 20.0%
!! TTAATACAAATATGGCTAAA+AGG + chr2.3:19253203-19253222 MS.gene58372:intron 20.0%
!! TTAGCCATATTTGTATTAAT+TGG - chr2.3:19253202-19253221 None:intergenic 20.0%
!!! GAAAAAACATATCAAGTTTT+GGG + chr2.3:19253962-19253981 MS.gene58372:CDS 20.0%
!!! TGAAAAAACATATCAAGTTT+TGG + chr2.3:19253961-19253980 MS.gene58372:CDS 20.0%
! ATAGCATCAGAAATAGAAAA+GGG + chr2.3:19253255-19253274 MS.gene58372:intron 25.0%
! ATATTTGAACATAGCATGAT+AGG - chr2.3:19253330-19253349 None:intergenic 25.0%
! CGAAGAATTGTGATTTAATA+TGG + chr2.3:19253031-19253050 MS.gene58372:intron 25.0%
! TAATGATTTAAAAAGAGGGT+AGG - chr2.3:19253124-19253143 None:intergenic 25.0%
! TCCTAAATCAGAAAACAATA+AGG + chr2.3:19253694-19253713 MS.gene58372:CDS 25.0%
! TGATAAAAAAGGAAGCAAAT+TGG + chr2.3:19252644-19252663 MS.gene58372:CDS 25.0%
!! TCCTTATTGTTTTCTGATTT+AGG - chr2.3:19253698-19253717 None:intergenic 25.0%
!! TGATTTTTATAGTACCTTAG+AGG - chr2.3:19252910-19252929 None:intergenic 25.0%
!!! TATTAATTGGTGTTACTTCT+TGG - chr2.3:19253189-19253208 None:intergenic 25.0%
AATATCGCTTATTGTTACGA+AGG - chr2.3:19253499-19253518 None:intergenic 30.0%
ACAAAAAAAGAGAAGAATGC+AGG + chr2.3:19253381-19253400 MS.gene58372:intron 30.0%
AGGATGAACAAAATCACTAT+TGG - chr2.3:19252565-19252584 None:intergenic 30.0%
AGTTGAAAGCTTAAACAAAG+AGG + chr2.3:19253647-19253666 MS.gene58372:CDS 30.0%
ATAGAAGTGATAGCAATAGA+AGG + chr2.3:19252742-19252761 MS.gene58372:CDS 30.0%
ATGCAACAATAATACGTGAA+AGG - chr2.3:19253465-19253484 None:intergenic 30.0%
ATTTAATATGGCAAGTAGTC+TGG + chr2.3:19253043-19253062 MS.gene58372:intron 30.0%
CATAGCATCAGAAATAGAAA+AGG + chr2.3:19253254-19253273 MS.gene58372:intron 30.0%
GAAAAATAGAGATGAAAGTG+AGG + chr2.3:19253833-19253852 MS.gene58372:CDS 30.0%
GTTGAAAGCTTAAACAAAGA+GGG + chr2.3:19253648-19253667 MS.gene58372:CDS 30.0%
TCTTCTTCTTTCACTCTAAT+TGG - chr2.3:19252618-19252637 None:intergenic 30.0%
TGAACAAAATCACTATTGGA+TGG - chr2.3:19252561-19252580 None:intergenic 30.0%
TTGAGTATGAAGAAGTTCAA+GGG + chr2.3:19253733-19253752 MS.gene58372:CDS 30.0%
! CAAGAAACTGATTCAAGAAT+TGG + chr2.3:19252825-19252844 MS.gene58372:CDS 30.0%
!!! CTTAAACAAAGAGGGTATTT+TGG + chr2.3:19253656-19253675 MS.gene58372:CDS 30.0%
AACCATGCTTCTGATAAGTA+AGG - chr2.3:19253879-19253898 None:intergenic 35.0%
AGAGAAGAATGCAGGAATAT+AGG + chr2.3:19253389-19253408 MS.gene58372:intron 35.0%
AGCTTAGCTAACATAATTCC+TGG + chr2.3:19253801-19253820 MS.gene58372:CDS 35.0%
CAAATTGGTGCATCAAACAT+CGG + chr2.3:19252659-19252678 MS.gene58372:CDS 35.0%
CATCATTGTGCAAAGATGAA+AGG + chr2.3:19252711-19252730 MS.gene58372:CDS 35.0%
CTTCATACTCAAGATCACTT+AGG - chr2.3:19253725-19253744 None:intergenic 35.0%
CTTGAGTATGAAGAAGTTCA+AGG + chr2.3:19253732-19253751 MS.gene58372:CDS 35.0%
GGAATTATGTTAGCTAAGCT+TGG - chr2.3:19253801-19253820 None:intergenic 35.0%
TCTTCTTTCACTCTAATTGG+TGG - chr2.3:19252615-19252634 None:intergenic 35.0%
! AATCAGCTCAGAACTTTTGA+AGG + chr2.3:19252518-19252537 MS.gene58372:CDS 35.0%
! GACATCTTATTTCCCCAATT+TGG - chr2.3:19253930-19253949 None:intergenic 35.0%
! TTACTTATCAGAAGCATGGT+TGG + chr2.3:19253878-19253897 MS.gene58372:CDS 35.0%
! TTATTTCCCCAATTTGGAAC+AGG - chr2.3:19253924-19253943 None:intergenic 35.0%
!! AGCTGATTAGTCTTGTTGAA+GGG - chr2.3:19252506-19252525 None:intergenic 35.0%
!! ATTAGTCTTGTTGAAGGGTA+AGG - chr2.3:19252501-19252520 None:intergenic 35.0%
!! CTATTTTTCTCTTGCAAACC+AGG - chr2.3:19253822-19253841 None:intergenic 35.0%
!! TATTTTGGAGATGAGGAGAA+AGG + chr2.3:19253671-19253690 MS.gene58372:CDS 35.0%
!!! TCAACTTCGATGTTTTTAGC+CGG - chr2.3:19253633-19253652 None:intergenic 35.0%
AACTCCTCCTGTTCCAAATT+GGG + chr2.3:19253914-19253933 MS.gene58372:CDS 40.0%
AGTACCTTAGAGGTTAACCT+TGG - chr2.3:19252900-19252919 None:intergenic 40.0%
AGTTCAAGGGTTCAAGGATT+TGG + chr2.3:19253746-19253765 MS.gene58372:CDS 40.0%
ATAATGACAACTTGCCTCCA+AGG + chr2.3:19252880-19252899 MS.gene58372:CDS 40.0%
ATATGGCAAGTAGTCTGGTA+CGG + chr2.3:19253048-19253067 MS.gene58372:intron 40.0%
ATCGGATTCTGCTATGCATA+AGG + chr2.3:19252677-19252696 MS.gene58372:CDS 40.0%
CATCTTTGCCTCCAACAATA+GGG + chr2.3:19252787-19252806 MS.gene58372:CDS 40.0%
GACCTTACTTATCAGAAGCA+TGG + chr2.3:19253874-19253893 MS.gene58372:CDS 40.0%
GGAGGCAAGTTGTCATTATT+GGG - chr2.3:19252879-19252898 None:intergenic 40.0%
GTTCAAGGGTTCAAGGATTT+GGG + chr2.3:19253747-19253766 MS.gene58372:CDS 40.0%
TCGTTTATGATTAAGCGCGT+AGG + chr2.3:19252975-19252994 MS.gene58372:intron 40.0%
TGAAGAAGTTCAAGGGTTCA+AGG + chr2.3:19253740-19253759 MS.gene58372:CDS 40.0%
TGGAGGCAAGTTGTCATTAT+TGG - chr2.3:19252880-19252899 None:intergenic 40.0%
! ACTCTAATTGGTGGCATTGA+TGG - chr2.3:19252606-19252625 None:intergenic 40.0%
! TTTTCCTCTCTCCCTATTGT+TGG - chr2.3:19252801-19252820 None:intergenic 40.0%
!! GAGCTGATTAGTCTTGTTGA+AGG - chr2.3:19252507-19252526 None:intergenic 40.0%
!! TTTTTAGCCGGTCTACTTCT+TGG - chr2.3:19253621-19253640 None:intergenic 40.0%
!!! AAGAGGGTATTTTGGAGATG+AGG + chr2.3:19253664-19253683 MS.gene58372:CDS 40.0%
ACCTTAGAGGTTAACCTTGG+AGG - chr2.3:19252897-19252916 None:intergenic 45.0%
ACTCCTCCTGTTCCAAATTG+GGG + chr2.3:19253915-19253934 MS.gene58372:CDS 45.0%
CAACTCCTCCTGTTCCAAAT+TGG + chr2.3:19253913-19253932 MS.gene58372:CDS 45.0%
CAGCATTCCAAGAAGTAGAC+CGG + chr2.3:19253611-19253630 MS.gene58372:CDS 45.0%
CCATCTTTGCCTCCAACAAT+AGG + chr2.3:19252786-19252805 MS.gene58372:CDS 45.0%
CCTATTGTTGGAGGCAAAGA+TGG - chr2.3:19252789-19252808 None:intergenic 45.0%
GAGGAAGATAAAGCAGCAAG+AGG + chr2.3:19253852-19253871 MS.gene58372:CDS 45.0%
GATTCTGCTATGCATAAGGC+AGG + chr2.3:19252681-19252700 MS.gene58372:CDS 45.0%
GGCAAGTTGTCATTATTGGG+AGG - chr2.3:19252876-19252895 None:intergenic 45.0%
! TTTCCCCAATTTGGAACAGG+AGG - chr2.3:19253921-19253940 None:intergenic 45.0%
!! TCATTATTGGGAGGTGTCGA+TGG - chr2.3:19252867-19252886 None:intergenic 45.0%
!! TGGTGTTACTTCTTGGTGCT+AGG - chr2.3:19253182-19253201 None:intergenic 45.0%
!!! AGGTGTCGATGGTTGTTTTC+GGG - chr2.3:19252856-19252875 None:intergenic 45.0%
!!! GAGGTGTCGATGGTTGTTTT+CGG - chr2.3:19252857-19252876 None:intergenic 45.0%
AACTGCAACGTGACCGTGAT+TGG - chr2.3:19253076-19253095 None:intergenic 50.0%
GCCTCCAAGGTTAACCTCTA+AGG + chr2.3:19252893-19252912 MS.gene58372:CDS 50.0%
GGTGCTCTTTGCAGCTTCTT+AGG - chr2.3:19252585-19252604 None:intergenic 50.0%
GTCTGGTACGGTTCCAATCA+CGG + chr2.3:19253060-19253079 MS.gene58372:intron 50.0%
TCCTCTCTCCCTATTGTTGG+AGG - chr2.3:19252798-19252817 None:intergenic 50.0%
CACGGTCACGTTGCAGTTAC+AGG + chr2.3:19253078-19253097 MS.gene58372:intron 55.0%
GCCTCCAACAATAGGGAGAG+AGG + chr2.3:19252794-19252813 MS.gene58372:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 19252477 19254013 19252477 ID=MS.gene58372
chr2.3 mRNA 19252477 19254013 19252477 ID=MS.gene58372.t1;Parent=MS.gene58372
chr2.3 exon 19252477 19252914 19252477 ID=MS.gene58372.t1.exon1;Parent=MS.gene58372.t1
chr2.3 CDS 19252477 19252914 19252477 ID=cds.MS.gene58372.t1;Parent=MS.gene58372.t1
chr2.3 exon 19253606 19254013 19253606 ID=MS.gene58372.t1.exon2;Parent=MS.gene58372.t1
chr2.3 CDS 19253606 19254013 19253606 ID=cds.MS.gene58372.t1;Parent=MS.gene58372.t1
Gene Sequence

>MS.gene58372

ATGTTAAGGTGTCATTCTGATCCTTACCCTTCAACAAGACTAATCAGCTCAGAACTTTTGAAGGATTCATCAGCAAGTAAACCATCCAATAGTGATTTTGTTCATCCTAAGAAGCTGCAAAGAGCACCATCAATGCCACCAATTAGAGTGAAAGAAGAAGAAAAAGATGATAAAAAAGGAAGCAAATTGGTGCATCAAACATCGGATTCTGCTATGCATAAGGCAGGTAGTAAACATCATTGTGCAAAGATGAAAGGACTTGATCATAGAAGTGATAGCAATAGAAGGAAAAGCAAATTGCTAAGAACACCATCTTTGCCTCCAACAATAGGGAGAGAGGAAAAGTTTCAAGAAACTGATTCAAGAATTGGAAGATCCCGAAAACAACCATCGACACCTCCCAATAATGACAACTTGCCTCCAAGGTTAACCTCTAAGGTACTATAAAAATCATCTTGCTTTTATAAAGATCTAAGTAATGTATAGACTTTTTTTTTTTCGTTTATGATTAAGCGCGTAGGTTTTAAATTGTGATTTGTCGTGCTTCAATATTGCGAAGAATTGTGATTTAATATGGCAAGTAGTCTGGTACGGTTCCAATCACGGTCACGTTGCAGTTACAGGAAATGAAATACATTATGTCGCCTACCCTCTTTTTAAATCATTATGTCACATCCAAGAGTTTATGATTGATATTATGTGCCTAGCACCAAGAAGTAACACCAATTAATACAAATATGGCTAAAAGGCCAAATAATTTTAGCATTTAAGTAAAATCATAGCATCAGAAATAGAAAAGGGCAGAGTAGCACATTTAGCTTGCTGCAACATTTTAAGAAAAGTCATTAGTCCTATCATGCTATGTTCAAATATAGAGCAATGTTATTTCTTACAAATGATTTTTACAAAAAAAGAGAAGAATGCAGGAATATAGGATATTTAACCAATCATATTTTGATTGATCATACGCGAGAAAGCGTCACTTCCTTTCACGTATTATTGTTGCATTTCTTGATACTCCTTCGTAACAATAAGCGATATTCTTGAATATAAGTACTTCAAATTTCAAATTGATTCGAATGTTTATGAAGCGAACTCATTGTATATGTTTTGCGATGCTTGATGACAGAGTTGCAGCATTCCAAGAAGTAGACCGGCTAAAAACATCGAAGTTGAAAGCTTAAACAAAGAGGGTATTTTGGAGATGAGGAGAAAGGTCCTAAATCAGAAAACAATAAGGAGAAGCCTAAGTGATCTTGAGTATGAAGAAGTTCAAGGGTTCAAGGATTTGGGATTCTCATTTGAGAAAGAAGCTTTAAGTCCAAGCTTAGCTAACATAATTCCTGGTTTGCAAGAGAAAAATAGAGATGAAAGTGAGGAAGATAAAGCAGCAAGAGGACCTTACTTATCAGAAGCATGGTTGGTGCAAAGTTGTGCAACTCCTCCTGTTCCAAATTGGGGAAATAAGATGTCTGCAGATGACATGAAAAAACATATCAAGTTTTGGGCTAGAGCTGTTGCTTCAACTAAATGTTGA
Protein sequence

>MS.gene58372.t1

MLRCHSDPYPSTRLISSELLKDSSASKPSNSDFVHPKKLQRAPSMPPIRVKEEEKDDKKGSKLVHQTSDSAMHKAGSKHHCAKMKGLDHRSDSNRRKSKLLRTPSLPPTIGREEKFQETDSRIGRSRKQPSTPPNNDNLPPRLTSKSCSIPRSRPAKNIEVESLNKEGILEMRRKVLNQKTIRRSLSDLEYEEVQGFKDLGFSFEKEALSPSLANIIPGLQEKNRDESEEDKAARGPYLSEAWLVQSCATPPVPNWGNKMSADDMKKHIKFWARAVASTKC