AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene33002

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene33002.t1 MTR_1g016170 70.000 50 12 1 26 72 185 234 1.10e-19 80.9
MS.gene33002.t1 MTR_7g112330 42.857 63 36 0 24 86 18 80 1.53e-15 66.6
MS.gene33002.t1 MTR_1g016200 52.459 61 26 1 12 72 47 104 1.20e-14 63.9
MS.gene33002.t1 MTR_4g126350 78.788 33 7 0 25 57 183 215 2.82e-14 66.2
MS.gene33002.t1 MTR_4g121110 54.717 53 19 2 28 80 30 77 5.68e-14 63.2
MS.gene33002.t1 MTR_2g038720 78.125 32 7 0 26 57 162 193 6.82e-14 65.1
MS.gene33002.t1 MTR_5g020230 65.714 35 12 0 28 62 122 156 4.27e-12 59.7
MS.gene33002.t1 MTR_8g077510 62.857 35 13 0 28 62 125 159 1.63e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene33002.t1 AT3G16870 53.226 62 28 1 26 87 40 100 4.65e-16 69.7
MS.gene33002.t1 AT5G56860 55.738 61 24 1 4 61 203 263 4.85e-16 71.6
MS.gene33002.t1 AT5G26930 43.836 73 32 1 26 89 24 96 7.20e-15 64.7
MS.gene33002.t1 AT5G49300 51.852 54 21 1 14 62 17 70 1.34e-14 64.7
MS.gene33002.t1 AT4G26150 73.529 34 9 0 26 59 197 230 1.71e-14 67.0
MS.gene33002.t1 AT4G16141 62.222 45 16 1 26 70 35 78 1.44e-13 63.2
MS.gene33002.t1 AT2G18380 48.276 58 25 1 9 66 78 130 1.61e-13 63.2
MS.gene33002.t1 AT4G36620 50.000 50 25 0 28 77 75 124 6.21e-13 61.6
MS.gene33002.t1 AT3G06740 66.667 33 11 0 30 62 43 75 3.10e-12 58.9
MS.gene33002.t1 AT3G50870 65.714 35 12 0 28 62 152 186 5.46e-12 60.1

Find 23 sgRNAs with CRISPR-Local

Find 58 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTCCTCCAAAGGGGAGTC+TGG 0.241417 1.1:-5951757 None:intergenic
TGCAAAAGCTGCTAAAGGTT+TGG 0.372433 1.1:+5952717 MS.gene33002:CDS
GTGTTAAATGCTCTAGCCTT+TGG 0.380174 1.1:-5951686 None:intergenic
CCTTTGGAGGAATGGACCTA+TGG 0.408130 1.1:+5951766 MS.gene33002:CDS
CAGACTCCCCTTTGGAGGAA+TGG 0.484698 1.1:+5951758 MS.gene33002:CDS
AAACAACCCAGACTCCCCTT+TGG 0.489759 1.1:+5951750 MS.gene33002:CDS
TGCTCTAGCCTTTGGATATG+TGG 0.489809 1.1:-5951678 None:intergenic
CAACCCAGACTCCCCTTTGG+AGG 0.510000 1.1:+5951753 MS.gene33002:CDS
ATTCCTCCAAAGGGGAGTCT+GGG 0.513653 1.1:-5951756 None:intergenic
AAAGTTGCAAAAGCTGCTAA+AGG 0.521958 1.1:+5952712 MS.gene33002:CDS
CTTTGGAGGAATGGACCTAT+GGG 0.526288 1.1:+5951767 MS.gene33002:CDS
CATAGGTCCATTCCTCCAAA+GGG 0.526859 1.1:-5951765 None:intergenic
ACTCTAGTAGTTGTAGCAGC+TGG 0.535951 1.1:-5951713 None:intergenic
GAATGGACCTATGGGTCCTA+AGG 0.540865 1.1:+5951775 MS.gene33002:CDS
AGTAGTTGTAGCAGCTGGAA+TGG 0.562471 1.1:-5951708 None:intergenic
CCATAGGTCCATTCCTCCAA+AGG 0.569794 1.1:-5951766 None:intergenic
CTAATTACCTTAGGACCCAT+AGG 0.580046 1.1:-5951782 None:intergenic
CGATGAAAGCTCATCATCTG+AGG 0.597007 1.1:+5952762 MS.gene33002:CDS
CATGTGGCCTAAAACAGAGA+AGG 0.633100 1.1:+5952689 MS.gene33002:CDS
CAGTCGTTGTGCAACGCATG+TGG 0.634101 1.1:+5952673 MS.gene33002:intron
TGCTACCACCACATATCCAA+AGG 0.634178 1.1:+5951670 MS.gene33002:CDS
TCTAGCCTTTGGATATGTGG+TGG 0.675688 1.1:-5951675 None:intergenic
ATAGGTCCATTCCTCCAAAG+GGG 0.737737 1.1:-5951764 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATTTGAATATATATCT+AGG + chr1.1:5952164-5952183 MS.gene33002:intron 10.0%
!!! AAAAATATAATTGATTTGTA+AGG - chr1.1:5952424-5952443 None:intergenic 10.0%
!!! TACTTTTAATATTATCTTAA+GGG + chr1.1:5952525-5952544 MS.gene33002:intron 10.0%
!!! TTACTTTTAATATTATCTTA+AGG + chr1.1:5952524-5952543 MS.gene33002:intron 10.0%
!!! TTTGAATATTTTTTTTTTGA+AGG + chr1.1:5952139-5952158 MS.gene33002:intron 10.0%
!! ATATTTATTGATCCAAAATA+TGG - chr1.1:5952501-5952520 None:intergenic 15.0%
!! TATTATCTTAAGGGTTAAAT+TGG + chr1.1:5952534-5952553 MS.gene33002:intron 20.0%
!! TATTGTTTCATTTACTTTCA+TGG + chr1.1:5952022-5952041 MS.gene33002:intron 20.0%
! ATAGTTAACATGAAACATGT+TGG + chr1.1:5952648-5952667 MS.gene33002:intron 25.0%
! TTGGACACTAAAAAAGAAAA+GGG + chr1.1:5952736-5952755 MS.gene33002:CDS 25.0%
! TTTGGACACTAAAAAAGAAA+AGG + chr1.1:5952735-5952754 MS.gene33002:CDS 25.0%
!! ACAAGATTTTCTCATAAGTT+GGG - chr1.1:5951823-5951842 None:intergenic 25.0%
ACTTATGAGAAAATCTTGTG+TGG + chr1.1:5951824-5951843 MS.gene33002:intron 30.0%
AGAGACTAACTAATTACCTT+AGG - chr1.1:5951794-5951813 None:intergenic 30.0%
CAAATACAGAGGTAAAATAG+AGG - chr1.1:5952451-5952470 None:intergenic 30.0%
TTACTTTCATGGTACACTTT+AGG + chr1.1:5952033-5952052 MS.gene33002:intron 30.0%
! CAAGATTTTCTCATAAGTTG+GGG - chr1.1:5951822-5951841 None:intergenic 30.0%
! CACAAGATTTTCTCATAAGT+TGG - chr1.1:5951824-5951843 None:intergenic 30.0%
!!! ATATGTTGGTAGCCATATTT+TGG + chr1.1:5952486-5952505 MS.gene33002:intron 30.0%
AAAACCAAAATTCTTGGTCC+TGG + chr1.1:5951974-5951993 MS.gene33002:intron 35.0%
AAAGTTGCAAAAGCTGCTAA+AGG + chr1.1:5952712-5952731 MS.gene33002:CDS 35.0%
GTGACCAAAACCAAAATTCT+TGG + chr1.1:5951968-5951987 MS.gene33002:intron 35.0%
TGAAATGAGAAACACTTGTG+TGG - chr1.1:5952001-5952020 None:intergenic 35.0%
! CAACTTTCCTTCTCTGTTTT+AGG - chr1.1:5952699-5952718 None:intergenic 35.0%
!!! AGGACCAAGAATTTTGGTTT+TGG - chr1.1:5951975-5951994 None:intergenic 35.0%
ACTCTTGTCGAGCTATATGT+TGG + chr1.1:5952472-5952491 MS.gene33002:intron 40.0%
CTAATTACCTTAGGACCCAT+AGG - chr1.1:5951785-5951804 None:intergenic 40.0%
TGCAAAAGCTGCTAAAGGTT+TGG + chr1.1:5952717-5952736 MS.gene33002:CDS 40.0%
! GTGTTAAATGCTCTAGCCTT+TGG - chr1.1:5951689-5951708 None:intergenic 40.0%
ACTCTAGTAGTTGTAGCAGC+TGG - chr1.1:5951716-5951735 None:intergenic 45.0%
AGTAGTTGTAGCAGCTGGAA+TGG - chr1.1:5951711-5951730 None:intergenic 45.0%
ATAGGTCCATTCCTCCAAAG+GGG - chr1.1:5951767-5951786 None:intergenic 45.0%
CATAGGTCCATTCCTCCAAA+GGG - chr1.1:5951768-5951787 None:intergenic 45.0%
CATGTGGCCTAAAACAGAGA+AGG + chr1.1:5952689-5952708 MS.gene33002:CDS 45.0%
CGATGAAAGCTCATCATCTG+AGG + chr1.1:5952762-5952781 MS.gene33002:CDS 45.0%
GAGAAAATCTTGTGTGGTCC+TGG + chr1.1:5951830-5951849 MS.gene33002:intron 45.0%
GAGAGAAGAGAAGAGAGAGA+AGG + chr1.1:5951930-5951949 MS.gene33002:intron 45.0%
TGCTACCACCACATATCCAA+AGG + chr1.1:5951670-5951689 MS.gene33002:CDS 45.0%
! CGACAAGAGTGCAAATACAG+AGG - chr1.1:5952462-5952481 None:intergenic 45.0%
! CTTTGGAGGAATGGACCTAT+GGG + chr1.1:5951767-5951786 MS.gene33002:CDS 45.0%
! TCTAGCCTTTGGATATGTGG+TGG - chr1.1:5951678-5951697 None:intergenic 45.0%
! TGCTCTAGCCTTTGGATATG+TGG - chr1.1:5951681-5951700 None:intergenic 45.0%
! TGGACCAGGACCAAGAATTT+TGG - chr1.1:5951981-5952000 None:intergenic 45.0%
!!! AAAAAAGTTTTAAATATTTA+TGG + chr1.1:5952242-5952261 MS.gene33002:intron 5.0%
AAACAACCCAGACTCCCCTT+TGG + chr1.1:5951750-5951769 MS.gene33002:CDS 50.0%
AAAGACCACTTGTGTGGACC+AGG - chr1.1:5951851-5951870 None:intergenic 50.0%
ATTCCTCCAAAGGGGAGTCT+GGG - chr1.1:5951759-5951778 None:intergenic 50.0%
CCATAGGTCCATTCCTCCAA+AGG - chr1.1:5951769-5951788 None:intergenic 50.0%
GAATGGACCTATGGGTCCTA+AGG + chr1.1:5951775-5951794 MS.gene33002:CDS 50.0%
GAGAAACACTTGTGTGGACC+AGG - chr1.1:5951995-5952014 None:intergenic 50.0%
GTGACCAAAGACCACTTGTG+TGG - chr1.1:5951857-5951876 None:intergenic 50.0%
TGGTCCACACAAGTGGTCTT+TGG + chr1.1:5951850-5951869 MS.gene33002:intron 50.0%
! CCTTTGGAGGAATGGACCTA+TGG + chr1.1:5951766-5951785 MS.gene33002:CDS 50.0%
CAGTCGTTGTGCAACGCATG+TGG + chr1.1:5952673-5952692 MS.gene33002:intron 55.0%
CATTCCTCCAAAGGGGAGTC+TGG - chr1.1:5951760-5951779 None:intergenic 55.0%
! CAGACTCCCCTTTGGAGGAA+TGG + chr1.1:5951758-5951777 MS.gene33002:CDS 55.0%
CAACCCAGACTCCCCTTTGG+AGG + chr1.1:5951753-5951772 MS.gene33002:CDS 60.0%
GTGGTCCTGGTCCACACAAG+TGG + chr1.1:5951843-5951862 MS.gene33002:intron 60.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 5951650 5952801 5951650 ID=MS.gene33002
chr1.1 mRNA 5951650 5952801 5951650 ID=MS.gene33002.t1;Parent=MS.gene33002
chr1.1 exon 5951650 5951796 5951650 ID=MS.gene33002.t1.exon1;Parent=MS.gene33002.t1
chr1.1 CDS 5951650 5951796 5951650 ID=cds.MS.gene33002.t1;Parent=MS.gene33002.t1
chr1.1 exon 5952676 5952801 5952676 ID=MS.gene33002.t1.exon2;Parent=MS.gene33002.t1
chr1.1 CDS 5952676 5952801 5952676 ID=cds.MS.gene33002.t1;Parent=MS.gene33002.t1
Gene Sequence

>MS.gene33002

ATGAGAATGAAGAAAACAACTGCTACCACCACATATCCAAAGGCTAGAGCATTTAACACCATTCCAGCTGCTACAACTACTAGAGTTTGTTCAGATTGTCAAACAACCCAGACTCCCCTTTGGAGGAATGGACCTATGGGTCCTAAGGTAATTAGTTAGTCTCTCTACTCCCCAACTTATGAGAAAATCTTGTGTGGTCCTGGTCCACACAAGTGGTCTTTGGTCACACAAAGAGAAAAAAGAGAAGAGAGAGAAGAGAGAAGAGAGAGAAAATGAAGAAGAGAGAAGAGAAGAGAGAGAAGGAAAAAACTTGTGTGTGTGACCAAAACCAAAATTCTTGGTCCTGGTCCACACAAGTGTTTCTCATTTCACTATTGTTTCATTTACTTTCATGGTACACTTTAGGTTTTAATGTCATGATCAATTTAAATTCAACAATTTCATTTCAATTCTTGCAAGTGTTATTTCAACTTATGTATTGATAAATAATTTGAATATTTTTTTTTTGAAGGAAAATAATTTGAATATATATCTAGGTTTTAATGTCATGATCAACTTAAATTCAACAATTTCATTTCGATTCGTGCATTATAAAAAAGTTTTAAATATTTATGGTTTATATATAAGATTTTTTTATCGAAGAAAATAAAAAATTCTCACACAAACACACACTTGTCTTCAATAAATTTCGTTTATAAAAAAGATATAGTAAAAAGTTGAACAAGTGATAAAATAACATGACATTCATCATGAATGTTAGAAACATCAAAACCTTACAAATCAATTATATTTTTTCTGCCTCTATTTTACCTCTGTATTTGCACTCTTGTCGAGCTATATGTTGGTAGCCATATTTTGGATCAATAAATATTTATTACTTTTAATATTATCTTAAGGGTTAAATTGGTTTAATACTTCAATAGATCACACTATAGACTCATGCAAGTGTTATTTCATACTTATACATTGATAAATAATTTGAATATCTAGTTATGTATATAGTTAACATGAAACATGTTGGTGCAGTCGTTGTGCAACGCATGTGGCCTAAAACAGAGAAGGAAAGTTGCAAAAGCTGCTAAAGGTTTGGACACTAAAAAAGAAAAGGGCAACGATGAAAGCTCATCATCTGAGGATGTGAAGAAGCTTTAA
Protein sequence

>MS.gene33002.t1

MRMKKTTATTTYPKARAFNTIPAATTTRVCSDCQTTQTPLWRNGPMGPKSLCNACGLKQRRKVAKAAKGLDTKKEKGNDESSSSEDVKKL