AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene002165

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002165.t1 MTR_7g100280 100.000 105 0 0 1 105 1 105 1.57e-71 208
MS.gene002165.t1 MTR_4g094308 100.000 105 0 0 1 105 1 105 1.57e-71 208
MS.gene002165.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.gene002165.t1 AT4G14320 92.381 105 8 0 1 105 1 105 1.00e-66 196
MS.gene002165.t1 AT3G23390 92.381 105 8 0 1 105 1 105 1.00e-66 196
MS.gene002165.t1 AT4G14320 91.398 93 8 0 1 93 1 93 3.30e-57 174

Find 25 sgRNAs with CRISPR-Local

Find 62 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTTTACCCTTCTTGTATT+GGG 0.247979 2.2:-71887920 None:intergenic
TATCTTTACCCTTCTTGTAT+TGG 0.312780 2.2:-71887921 None:intergenic
CAAGGGAACTTCTCTCTTCT+AGG 0.380957 2.2:+71888783 MS.gene002165:CDS
GATCGCAAACAGTCTGGTTA+TGG 0.387570 2.2:+71887973 MS.gene002165:CDS
TGTTCTGAGGTTGCAATGCC+AGG 0.411690 2.2:+71888572 MS.gene002165:CDS
GCATTCCTTGCTCTTGCAGT+AGG 0.441918 2.2:-71887872 None:intergenic
TGAGATTGGTGGTGATAAGA+AGG 0.451732 2.2:+71888759 MS.gene002165:CDS
GAGAAACATGCTTGCAGCCC+TGG 0.453437 2.2:-71888590 None:intergenic
CGTTACGATCGCAAACAGTC+TGG 0.464861 2.2:+71887967 MS.gene002165:CDS
TGTTTCTCAACATGCAATCA+AGG 0.468902 2.2:+71888605 MS.gene002165:CDS
GTTACCTTCTTGTGAAAGAC+GGG 0.495280 2.2:-71888009 None:intergenic
GAGATTGGTGGTGATAAGAA+GGG 0.526133 2.2:+71888760 MS.gene002165:CDS
CAAGGTTACCCAATACAAGA+AGG 0.553515 2.2:+71887912 MS.gene002165:CDS
CGCAAACAGTCTGGTTATGG+TGG 0.554816 2.2:+71887976 MS.gene002165:CDS
TGGTGGTGATAAGAAGGGCA+AGG 0.556388 2.2:+71888765 MS.gene002165:CDS
AAAGATAGCATCGCCGCTCA+AGG 0.571046 2.2:+71887937 MS.gene002165:CDS
AGTTACCTTCTTGTGAAAGA+CGG 0.572609 2.2:-71888010 None:intergenic
CAAGAAGCATACACTTCACA+AGG 0.596444 2.2:+71887894 MS.gene002165:CDS
GAAAACCTACTGCAAGAGCA+AGG 0.601503 2.2:+71887867 MS.gene002165:CDS
CCACTAAGAAAATTGTTCTG+AGG 0.602363 2.2:+71888559 MS.gene002165:CDS
TAAGCCCGTCTTTCACAAGA+AGG 0.606865 2.2:+71888005 MS.gene002165:CDS
AAGGTTACCCAATACAAGAA+GGG 0.630634 2.2:+71887913 MS.gene002165:CDS
GTTCTGAGGTTGCAATGCCA+GGG 0.630775 2.2:+71888573 MS.gene002165:CDS
GGTGGTGATAAGAAGGGCAA+GGG 0.630826 2.2:+71888766 MS.gene002165:CDS
GTAACGACGCTTACCTTGAG+CGG 0.638526 2.2:-71887950 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGATTTTTTTTTAGTTGAA+TGG + chr2.2:71888486-71888505 MS.gene002165:intron 15.0%
!! AAATGTATAAAAGTAATGAG+GGG - chr2.2:71888047-71888066 None:intergenic 20.0%
!! CTTACAATCAACTAAAAAAA+TGG - chr2.2:71888091-71888110 None:intergenic 20.0%
!! GAAATGTATAAAAGTAATGA+GGG - chr2.2:71888048-71888067 None:intergenic 20.0%
!! GAATGCAAAAAATTCAAATT+TGG + chr2.2:71888411-71888430 MS.gene002165:intron 20.0%
!! TAATATAATTACGATTACGT+AGG - chr2.2:71887794-71887813 None:intergenic 20.0%
!! TGAAATGTATAAAAGTAATG+AGG - chr2.2:71888049-71888068 None:intergenic 20.0%
!!! CAGAAATTTTATTTTGTAGA+TGG + chr2.2:71888668-71888687 MS.gene002165:intron 20.0%
!!! TGTGTTTGATTTTATTGTAT+AGG + chr2.2:71888530-71888549 MS.gene002165:intron 20.0%
!!! TTTTATTTTGTAGATGGATA+TGG + chr2.2:71888674-71888693 MS.gene002165:intron 20.0%
! AATGTATAAAAGTAATGAGG+GGG - chr2.2:71888046-71888065 None:intergenic 25.0%
! ATATGGTTGTTTGTATCTAA+TGG + chr2.2:71888691-71888710 MS.gene002165:intron 25.0%
! GAAAATCCAACATCAAAAAA+GGG - chr2.2:71887825-71887844 None:intergenic 25.0%
! TGAAAATCCAACATCAAAAA+AGG - chr2.2:71887826-71887845 None:intergenic 25.0%
! TGGATTCAAATATGGTTAAT+AGG + chr2.2:71888214-71888233 MS.gene002165:intron 25.0%
!!! TAGCTTTATGCAAATGATTA+GGG + chr2.2:71888171-71888190 MS.gene002165:intron 25.0%
!!! TCAAGGTTAGTTTGTTTATT+TGG + chr2.2:71888622-71888641 MS.gene002165:intron 25.0%
!!! TTAGCTTTATGCAAATGATT+AGG + chr2.2:71888170-71888189 MS.gene002165:intron 25.0%
!!! TTTTTTGATGTTGGATTTTC+AGG + chr2.2:71887825-71887844 MS.gene002165:intron 25.0%
ATCTTTACCCTTCTTGTATT+GGG - chr2.2:71887923-71887942 None:intergenic 30.0%
GGTTAATAGGAAGAACATTA+TGG + chr2.2:71888227-71888246 MS.gene002165:intron 30.0%
TATCTTTACCCTTCTTGTAT+TGG - chr2.2:71887924-71887943 None:intergenic 30.0%
! AAAAGCCTTATATCACTAAG+TGG - chr2.2:71888278-71888297 None:intergenic 30.0%
! AAAGCCTTATATCACTAAGT+GGG - chr2.2:71888277-71888296 None:intergenic 30.0%
! TTTTGAGCTGAATGTGAAAT+TGG + chr2.2:71888324-71888343 MS.gene002165:intron 30.0%
AAGGTTACCCAATACAAGAA+GGG + chr2.2:71887913-71887932 MS.gene002165:CDS 35.0%
AGGGAAGATTTAGAGATTGA+TGG + chr2.2:71888190-71888209 MS.gene002165:intron 35.0%
AGTTACCTTCTTGTGAAAGA+CGG - chr2.2:71888013-71888032 None:intergenic 35.0%
CAAACCCACTTAGTGATATA+AGG + chr2.2:71888270-71888289 MS.gene002165:intron 35.0%
CCACTAAGAAAATTGTTCTG+AGG + chr2.2:71888559-71888578 MS.gene002165:CDS 35.0%
TGTTTCTCAACATGCAATCA+AGG + chr2.2:71888605-71888624 MS.gene002165:CDS 35.0%
! AAGATTTAGAGATTGATGGC+TGG + chr2.2:71888194-71888213 MS.gene002165:intron 35.0%
! CAGTAGGTTTTCTTTGTCTT+TGG - chr2.2:71887859-71887878 None:intergenic 35.0%
! CCTCAGAACAATTTTCTTAG+TGG - chr2.2:71888562-71888581 None:intergenic 35.0%
! CTTATATCACTAAGTGGGTT+TGG - chr2.2:71888272-71888291 None:intergenic 35.0%
! TTGATGGCTGGATTCAAATA+TGG + chr2.2:71888206-71888225 MS.gene002165:intron 35.0%
!!! GCTAAACCCTTTTTTGATGT+TGG + chr2.2:71887816-71887835 MS.gene002165:intron 35.0%
AAAGTAATGAGGGGGTGAAA+TGG - chr2.2:71888038-71888057 None:intergenic 40.0%
AAGTAATGAGGGGGTGAAAT+GGG - chr2.2:71888037-71888056 None:intergenic 40.0%
CAAGGTTACCCAATACAAGA+AGG + chr2.2:71887912-71887931 MS.gene002165:CDS 40.0%
GTTACCTTCTTGTGAAAGAC+GGG - chr2.2:71888012-71888031 None:intergenic 40.0%
! CAAGAAGCATACACTTCACA+AGG + chr2.2:71887894-71887913 MS.gene002165:CDS 40.0%
! GTTGTGTTTCTGTTATGCAG+AGG + chr2.2:71888725-71888744 MS.gene002165:intron 40.0%
!! GAGATTGGTGGTGATAAGAA+GGG + chr2.2:71888760-71888779 MS.gene002165:CDS 40.0%
!! TGAGATTGGTGGTGATAAGA+AGG + chr2.2:71888759-71888778 MS.gene002165:CDS 40.0%
!!! AGGTGCAAGCATTTTGAGAT+TGG + chr2.2:71888745-71888764 MS.gene002165:CDS 40.0%
!!! TGCAAGCATTTTGAGATTGG+TGG + chr2.2:71888748-71888767 MS.gene002165:CDS 40.0%
CGATTACGTAGGAACAGACA+CGG - chr2.2:71887783-71887802 None:intergenic 45.0%
GAAAACCTACTGCAAGAGCA+AGG + chr2.2:71887867-71887886 MS.gene002165:CDS 45.0%
GATCGCAAACAGTCTGGTTA+TGG + chr2.2:71887973-71887992 MS.gene002165:CDS 45.0%
TAAGCCCGTCTTTCACAAGA+AGG + chr2.2:71888005-71888024 MS.gene002165:CDS 45.0%
AAAGATAGCATCGCCGCTCA+AGG + chr2.2:71887937-71887956 MS.gene002165:CDS 50.0%
CGCAAACAGTCTGGTTATGG+TGG + chr2.2:71887976-71887995 MS.gene002165:CDS 50.0%
CGTTACGATCGCAAACAGTC+TGG + chr2.2:71887967-71887986 MS.gene002165:CDS 50.0%
GCATTCCTTGCTCTTGCAGT+AGG - chr2.2:71887875-71887894 None:intergenic 50.0%
GGTGGTGATAAGAAGGGCAA+GGG + chr2.2:71888766-71888785 MS.gene002165:CDS 50.0%
GTAACGACGCTTACCTTGAG+CGG - chr2.2:71887953-71887972 None:intergenic 50.0%
TTACGTAGGAACAGACACGG+TGG - chr2.2:71887780-71887799 None:intergenic 50.0%
! TGGTGGTGATAAGAAGGGCA+AGG + chr2.2:71888765-71888784 MS.gene002165:CDS 50.0%
!! GTTCTGAGGTTGCAATGCCA+GGG + chr2.2:71888573-71888592 MS.gene002165:CDS 50.0%
!! TGTTCTGAGGTTGCAATGCC+AGG + chr2.2:71888572-71888591 MS.gene002165:CDS 50.0%
GAGAAACATGCTTGCAGCCC+TGG - chr2.2:71888593-71888612 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 71887764 71888804 71887764 ID=MS.gene002165
chr2.2 mRNA 71887764 71888804 71887764 ID=MS.gene002165.t1;Parent=MS.gene002165
chr2.2 exon 71887764 71887766 71887764 ID=MS.gene002165.t1.exon1;Parent=MS.gene002165.t1
chr2.2 CDS 71887764 71887766 71887764 ID=cds.MS.gene002165.t1;Parent=MS.gene002165.t1
chr2.2 exon 71887847 71888026 71887847 ID=MS.gene002165.t1.exon2;Parent=MS.gene002165.t1
chr2.2 CDS 71887847 71888026 71887847 ID=cds.MS.gene002165.t1;Parent=MS.gene002165.t1
chr2.2 exon 71888552 71888626 71888552 ID=MS.gene002165.t1.exon3;Parent=MS.gene002165.t1
chr2.2 CDS 71888552 71888626 71888552 ID=cds.MS.gene002165.t1;Parent=MS.gene002165.t1
chr2.2 exon 71888745 71888804 71888745 ID=MS.gene002165.t1.exon4;Parent=MS.gene002165.t1
chr2.2 CDS 71888745 71888804 71888745 ID=cds.MS.gene002165.t1;Parent=MS.gene002165.t1
Gene Sequence

>MS.gene002165

ATGGTAATCATCTCCACCGTGTCTGTTCCTACGTAATCGTAATTATATTAGCGCTAAACCCTTTTTTGATGTTGGATTTTCAGGTGAACGTTCCAAAGACAAAGAAAACCTACTGCAAGAGCAAGGAATGCAAGAAGCATACACTTCACAAGGTTACCCAATACAAGAAGGGTAAAGATAGCATCGCCGCTCAAGGTAAGCGTCGTTACGATCGCAAACAGTCTGGTTATGGTGGTCAGACTAAGCCCGTCTTTCACAAGAAGGTAACTACCCATTTCACCCCCTCATTACTTTTATACATTTCATCATTTGATTTTGTAAATTCCATTTTTTTAGTTGATTGTAAGAAATAAGTAGTTGTATGTAAATTTGATTTTTTTTTAGCTGAATATAATTATGATTTTTGTTAGCTTTATGCAAATGATTAGGGAAGATTTAGAGATTGATGGCTGGATTCAAATATGGTTAATAGGAAGAACATTATGGCGTAATTTGATTCATGTAGCCAAACCCACTTAGTGATATAAGGCTTTTGTTGTTGTTGTTGAATGCTAATGTGATTTTGAGCTGAATGTGAAATTGGTTTTTTTCAATAGAAAGTAAATTCGATTTTTTTTAGTTGAATGTGAATTTGAATTTTTTAAGCTGAATGCAAAAAATTCAAATTTGGTTTTTATTTCTTGATTTTGTATGTTTGATTTTTTGTTTAGTTTAATGTAAATTTGATTTTTTTTTAGTTGAATGGAAATTTGATTTAATTTTTGTTTGTGTTTGATTTTATTGTATAGGCAAAAACCACTAAGAAAATTGTTCTGAGGTTGCAATGCCAGGGCTGCAAGCATGTTTCTCAACATGCAATCAAGGTTAGTTTGTTTATTTGGTTGAAAGAAAGAAAGAACAGCTTCAGAAATTTTATTTTGTAGATGGATATGGTTGTTTGTATCTAATGGTAGTTATTTGTGTTGTGTTTCTGTTATGCAGAGGTGCAAGCATTTTGAGATTGGTGGTGATAAGAAGGGCAAGGGAACTTCTCTCTTCTAG
Protein sequence

>MS.gene002165.t1

MVNVPKTKKTYCKSKECKKHTLHKVTQYKKGKDSIAAQGKRRYDRKQSGYGGQTKPVFHKKAKTTKKIVLRLQCQGCKHVSQHAIKRCKHFEIGGDKKGKGTSLF