AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene01133

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01133.t1 MTR_7g100280 100.000 105 0 0 1 105 1 105 1.57e-71 208
MS.gene01133.t1 MTR_4g094308 100.000 105 0 0 1 105 1 105 1.57e-71 208
MS.gene01133.t1 MTR_2g008180 100.000 105 0 0 1 105 1 105 1.57e-71 208
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene01133.t1 AT4G14320 92.381 105 8 0 1 105 1 105 1.00e-66 196
MS.gene01133.t1 AT3G23390 92.381 105 8 0 1 105 1 105 1.00e-66 196
MS.gene01133.t1 AT4G14320 91.398 93 8 0 1 93 1 93 3.30e-57 174

Find 25 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTTACCCTTCTTGTATT+GGG 0.247979 2.1:-74375880 None:intergenic
TATCTTTACCCTTCTTGTAT+TGG 0.312780 2.1:-74375881 None:intergenic
CAAGGGAACTTCTCTCTTCT+AGG 0.380957 2.1:+74376884 MS.gene01133:CDS
GATCGCAAACAGTCTGGTTA+TGG 0.387570 2.1:+74375933 MS.gene01133:CDS
TGTTCTGAGGTTGCAATGCC+AGG 0.411690 2.1:+74376673 MS.gene01133:CDS
GCATTCCTTGCTCTTGCAGT+AGG 0.441918 2.1:-74375832 None:intergenic
TGAGATTGGTGGTGATAAGA+AGG 0.451732 2.1:+74376860 MS.gene01133:CDS
GAGAAACATGCTTGCAGCCC+TGG 0.453437 2.1:-74376691 None:intergenic
CGTTACGATCGCAAACAGTC+TGG 0.464861 2.1:+74375927 MS.gene01133:CDS
TGTTTCTCAACATGCAATCA+AGG 0.468902 2.1:+74376706 MS.gene01133:CDS
GTTACCTTCTTGTGAAAGAC+GGG 0.495280 2.1:-74375969 None:intergenic
GAGATTGGTGGTGATAAGAA+GGG 0.526133 2.1:+74376861 MS.gene01133:CDS
CAAGGTTACCCAATACAAGA+AGG 0.553515 2.1:+74375872 MS.gene01133:CDS
CGCAAACAGTCTGGTTATGG+TGG 0.554816 2.1:+74375936 MS.gene01133:CDS
TGGTGGTGATAAGAAGGGCA+AGG 0.556388 2.1:+74376866 MS.gene01133:CDS
AAAGATAGCATCGCCGCTCA+AGG 0.571046 2.1:+74375897 MS.gene01133:CDS
AGTTACCTTCTTGTGAAAGA+CGG 0.572609 2.1:-74375970 None:intergenic
CAAGAAGCATACACTTCACA+AGG 0.596444 2.1:+74375854 MS.gene01133:CDS
GAAAACCTACTGCAAGAGCA+AGG 0.601503 2.1:+74375827 MS.gene01133:CDS
CCACTAAGAAAATTGTTCTG+AGG 0.602363 2.1:+74376660 MS.gene01133:CDS
TAAGCCCGTCTTTCACAAGA+AGG 0.606865 2.1:+74375965 MS.gene01133:CDS
AAGGTTACCCAATACAAGAA+GGG 0.630634 2.1:+74375873 MS.gene01133:CDS
GTTCTGAGGTTGCAATGCCA+GGG 0.630775 2.1:+74376674 MS.gene01133:CDS
GGTGGTGATAAGAAGGGCAA+GGG 0.630826 2.1:+74376867 MS.gene01133:CDS
GTAACGACGCTTACCTTGAG+CGG 0.638526 2.1:-74375910 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGATTTTTTTTTTAATTGAA+TGG + chr2.1:74376587-74376606 MS.gene01133:intron 10.0%
!!! TGTATTTGATTTTATTGTAT+AGG + chr2.1:74376631-74376650 MS.gene01133:intron 15.0%
!! AAATGTATAAAAGTAATGAG+GGG - chr2.1:74376007-74376026 None:intergenic 20.0%
!! CTTACAATCAACTAAAAAAA+TGG - chr2.1:74376051-74376070 None:intergenic 20.0%
!! GAAATGTATAAAAGTAATGA+GGG - chr2.1:74376008-74376027 None:intergenic 20.0%
!! TGAAATGTATAAAAGTAATG+AGG - chr2.1:74376009-74376028 None:intergenic 20.0%
!!! CAGAAATTTTATTTTGTAGA+TGG + chr2.1:74376769-74376788 MS.gene01133:intron 20.0%
!!! TTTTATTTTGTAGATGGATA+TGG + chr2.1:74376775-74376794 MS.gene01133:intron 20.0%
! AATGTATAAAAGTAATGAGG+GGG - chr2.1:74376006-74376025 None:intergenic 25.0%
! ATATGGTTGTTTGTATCTAA+TGG + chr2.1:74376792-74376811 MS.gene01133:intron 25.0%
! GAAAATCCAACATCAAAAAA+GGG - chr2.1:74375785-74375804 None:intergenic 25.0%
! TGAAAATCCAACATCAAAAA+AGG - chr2.1:74375786-74375805 None:intergenic 25.0%
! TGATATAATTACGATTACGT+AGG - chr2.1:74375754-74375773 None:intergenic 25.0%
!!! TAGCTTTATGCAAATGATTA+GGG + chr2.1:74376133-74376152 MS.gene01133:intron 25.0%
!!! TCAAGGTTAGTTTGTTTATT+TGG + chr2.1:74376723-74376742 MS.gene01133:intron 25.0%
!!! TTAGCTTTATGCAAATGATT+AGG + chr2.1:74376132-74376151 MS.gene01133:intron 25.0%
!!! TTTTTTGATGTTGGATTTTC+AGG + chr2.1:74375785-74375804 MS.gene01133:intron 25.0%
AATTAAATTACTACACCCTC+CGG - chr2.1:74376346-74376365 None:intergenic 30.0%
AGGGAAGATTTAGAGATTAA+TGG + chr2.1:74376152-74376171 MS.gene01133:intron 30.0%
ATCTTTACCCTTCTTGTATT+GGG - chr2.1:74375883-74375902 None:intergenic 30.0%
GGGAAGATTTAGAGATTAAT+GGG + chr2.1:74376153-74376172 MS.gene01133:intron 30.0%
TATCTTTACCCTTCTTGTAT+TGG - chr2.1:74375884-74375903 None:intergenic 30.0%
! AGATTTAGAGATTAATGGGT+TGG + chr2.1:74376157-74376176 MS.gene01133:intron 30.0%
! CTTTTGCTTATATTAGTGAC+CGG + chr2.1:74376324-74376343 MS.gene01133:intron 30.0%
! CTTTTGCTTATATTAGTGAC+CGG - chr2.1:74376343-74376324 None:intergenic 30.0%
! TTTTGAACTGAATGCGAAAT+TGG + chr2.1:74376424-74376443 MS.gene01133:intron 30.0%
AAGGTTACCCAATACAAGAA+GGG + chr2.1:74375873-74375892 MS.gene01133:CDS 35.0%
AGTTACCTTCTTGTGAAAGA+CGG - chr2.1:74375973-74375992 None:intergenic 35.0%
CCACTAAGAAAATTGTTCTG+AGG + chr2.1:74376660-74376679 MS.gene01133:CDS 35.0%
TGTTTCTCAACATGCAATCA+AGG + chr2.1:74376706-74376725 MS.gene01133:CDS 35.0%
! CAGTAGGTTTTCTTTGTCTT+TGG - chr2.1:74375819-74375838 None:intergenic 35.0%
! CCTCAGAACAATTTTCTTAG+TGG - chr2.1:74376663-74376682 None:intergenic 35.0%
! TGGGTTGGATTCATCAAATA+TGG + chr2.1:74376172-74376191 MS.gene01133:intron 35.0%
!!! GCTAAACCCTTTTTTGATGT+TGG + chr2.1:74375776-74375795 MS.gene01133:intron 35.0%
CAAGGTTACCCAATACAAGA+AGG + chr2.1:74375872-74375891 MS.gene01133:CDS 40.0%
GTTACCTTCTTGTGAAAGAC+GGG - chr2.1:74375972-74375991 None:intergenic 40.0%
TGCTTATATTAGTGACCGGA+GGG + chr2.1:74376328-74376347 MS.gene01133:intron 40.0%
TGCTTATATTAGTGACCGGA+GGG - chr2.1:74376347-74376328 None:intergenic 40.0%
TTGCTTATATTAGTGACCGG+AGG + chr2.1:74376327-74376346 MS.gene01133:intron 40.0%
TTGCTTATATTAGTGACCGG+AGG - chr2.1:74376346-74376327 None:intergenic 40.0%
! AAGAAGCCTTATACCACTGT+GGG - chr2.1:74376381-74376400 None:intergenic 40.0%
! CAAGAAGCATACACTTCACA+AGG + chr2.1:74375854-74375873 MS.gene01133:CDS 40.0%
! GTTGTGTTTCTGTTATGCAG+AGG + chr2.1:74376826-74376845 MS.gene01133:intron 40.0%
!! GAGATTGGTGGTGATAAGAA+GGG + chr2.1:74376861-74376880 MS.gene01133:CDS 40.0%
!! TGAGATTGGTGGTGATAAGA+AGG + chr2.1:74376860-74376879 MS.gene01133:CDS 40.0%
!!! AGGTGCAAGCATTTTGAGAT+TGG + chr2.1:74376846-74376865 MS.gene01133:CDS 40.0%
!!! TGCAAGCATTTTGAGATTGG+TGG + chr2.1:74376849-74376868 MS.gene01133:CDS 40.0%
AAAGTAATGAGGGGGTGAAG+TGG - chr2.1:74375998-74376017 None:intergenic 45.0%
AAGTAATGAGGGGGTGAAGT+GGG - chr2.1:74375997-74376016 None:intergenic 45.0%
CGATTACGTAGGAACAGACA+CGG - chr2.1:74375743-74375762 None:intergenic 45.0%
GAAAACCTACTGCAAGAGCA+AGG + chr2.1:74375827-74375846 MS.gene01133:CDS 45.0%
GATCGCAAACAGTCTGGTTA+TGG + chr2.1:74375933-74375952 MS.gene01133:CDS 45.0%
GGTTTATGACATACACCCTC+CGG + chr2.1:74376193-74376212 MS.gene01133:intron 45.0%
TAAGCCCGTCTTTCACAAGA+AGG + chr2.1:74375965-74375984 MS.gene01133:CDS 45.0%
! CAAGAAGCCTTATACCACTG+TGG - chr2.1:74376382-74376401 None:intergenic 45.0%
AAAGATAGCATCGCCGCTCA+AGG + chr2.1:74375897-74375916 MS.gene01133:CDS 50.0%
CGCAAACAGTCTGGTTATGG+TGG + chr2.1:74375936-74375955 MS.gene01133:CDS 50.0%
CGTTACGATCGCAAACAGTC+TGG + chr2.1:74375927-74375946 MS.gene01133:CDS 50.0%
GCATTCCTTGCTCTTGCAGT+AGG - chr2.1:74375835-74375854 None:intergenic 50.0%
GCCAAACCCACAGTGGTATA+AGG + chr2.1:74376372-74376391 MS.gene01133:intron 50.0%
GCCTTATACCACTGTGGGTT+TGG - chr2.1:74376376-74376395 None:intergenic 50.0%
GGTGGTGATAAGAAGGGCAA+GGG + chr2.1:74376867-74376886 MS.gene01133:CDS 50.0%
GTAACGACGCTTACCTTGAG+CGG - chr2.1:74375913-74375932 None:intergenic 50.0%
TCATGTAGCCAAACCCACAG+TGG + chr2.1:74376365-74376384 MS.gene01133:intron 50.0%
TTACGTAGGAACAGACACGG+TGG - chr2.1:74375740-74375759 None:intergenic 50.0%
! TGGTGGTGATAAGAAGGGCA+AGG + chr2.1:74376866-74376885 MS.gene01133:CDS 50.0%
!! GTTCTGAGGTTGCAATGCCA+GGG + chr2.1:74376674-74376693 MS.gene01133:CDS 50.0%
!! TGTTCTGAGGTTGCAATGCC+AGG + chr2.1:74376673-74376692 MS.gene01133:CDS 50.0%
GAGAAACATGCTTGCAGCCC+TGG - chr2.1:74376694-74376713 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 74375724 74376905 74375724 ID=MS.gene01133
chr2.1 mRNA 74375724 74376905 74375724 ID=MS.gene01133.t1;Parent=MS.gene01133
chr2.1 exon 74375724 74375726 74375724 ID=MS.gene01133.t1.exon1;Parent=MS.gene01133.t1
chr2.1 CDS 74375724 74375726 74375724 ID=cds.MS.gene01133.t1;Parent=MS.gene01133.t1
chr2.1 exon 74375807 74375986 74375807 ID=MS.gene01133.t1.exon2;Parent=MS.gene01133.t1
chr2.1 CDS 74375807 74375986 74375807 ID=cds.MS.gene01133.t1;Parent=MS.gene01133.t1
chr2.1 exon 74376653 74376727 74376653 ID=MS.gene01133.t1.exon3;Parent=MS.gene01133.t1
chr2.1 CDS 74376653 74376727 74376653 ID=cds.MS.gene01133.t1;Parent=MS.gene01133.t1
chr2.1 exon 74376846 74376905 74376846 ID=MS.gene01133.t1.exon4;Parent=MS.gene01133.t1
chr2.1 CDS 74376846 74376905 74376846 ID=cds.MS.gene01133.t1;Parent=MS.gene01133.t1
Gene Sequence

>MS.gene01133

ATGGTAATCATCTCCACCGTGTCTGTTCCTACGTAATCGTAATTATATCAGCGCTAAACCCTTTTTTGATGTTGGATTTTCAGGTGAACGTTCCAAAGACAAAGAAAACCTACTGCAAGAGCAAGGAATGCAAGAAGCATACACTTCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCATCGCCGCTCAAGGTAAGCGTCGTTACGATCGCAAACAGTCTGGTTATGGTGGTCAGACTAAGCCCGTCTTTCACAAGAAGGTAACTACCCACTTCACCCCCTCATTACTTTTATACATTTCATCATTTGATTTTGTAAATTCCATTTTTTTAGTTGATTGTAAGAAATAAGTAGTTGTATGTAAATTTGATTTTTTTTTTTAGCTGAATATAATTATGATTATTGTTAGCTTTATGCAAATGATTAGGGAAGATTTAGAGATTAATGGGTTGGATTCATCAAATATGGTTTATGACATACACCCTCCGGTCACTAATATAAGCAAAAGTTTGATTTTTAGATTCATTCATTAAATGACGTATGTAGTCTATAATAAAGACTACATACATCATTTAATGAATGAATCTAAAAATCAAACTTTTGCTTATATTAGTGACCGGAGGGTGTAGTAATTTAATTCATGTAGCCAAACCCACAGTGGTATAAGGCTTCTTGTTGTTGTTGAATGCTAATGTGATTTTGAACTGAATGCGAAATTGGTTTTTTTTAATAGAAAGTAAATTCGATTTTATTTAGTTGAATGTGAATTTGAATTTTTTAAGCTGAATGCAAAAAATTCAAATTTGTTTTTTATTTTATGATTTTGTATGTTTGATTTTTTGTTTAGTTTAATGTACATTTGATTTTTTTTTTAATTGAATGGAAATTTGATTTAATTTTTGTTTGTATTTGATTTTATTGTATAGGCAAAAACCACTAAGAAAATTGTTCTGAGGTTGCAATGCCAGGGCTGCAAGCATGTTTCTCAACATGCAATCAAGGTTAGTTTGTTTATTTGGTTGAAAGAAAGAAAGAACAGCTTCAGAAATTTTATTTTGTAGATGGATATGGTTGTTTGTATCTAATGGTAGTTATTTGTGTTGTGTTTCTGTTATGCAGAGGTGCAAGCATTTTGAGATTGGTGGTGATAAGAAGGGCAAGGGAACTTCTCTCTTCTAG
Protein sequence

>MS.gene01133.t1

MVNVPKTKKTYCKSKECKKHTLHKVTQYKKGKDSIAAQGKRRYDRKQSGYGGQTKPVFHKKAKTTKKIVLRLQCQGCKHVSQHAIKRCKHFEIGGDKKGKGTSLF