AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene054308

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054308.t1 MTR_1g101810 67.769 121 39 0 14 134 54 174 4.92e-50 162
MS.gene054308.t1 MTR_1g101810 67.769 121 39 0 14 134 84 204 1.05e-49 162
MS.gene054308.t1 MTR_8g033070 53.782 119 45 4 24 134 80 196 8.56e-33 117
MS.gene054308.t1 MTR_7g028160 54.545 88 40 0 21 108 47 134 1.76e-27 103
MS.gene054308.t1 MTR_1g038650 51.579 95 44 1 7 99 15 109 1.20e-25 97.1
MS.gene054308.t1 MTR_2g006150 52.747 91 43 0 21 111 127 217 2.11e-25 99.8
MS.gene054308.t1 MTR_4g108370 60.759 79 25 1 14 86 81 159 3.91e-25 99.0
MS.gene054308.t1 MTR_1g114380 65.152 66 23 0 21 86 30 95 1.19e-24 95.1
MS.gene054308.t1 MTR_5g039600 60.870 69 27 0 18 86 61 129 4.00e-24 95.9
MS.gene054308.t1 MTR_2g006150 46.296 108 58 0 4 111 110 217 3.65e-23 93.6
MS.gene054308.t1 MTR_1g063870 58.442 77 31 1 13 89 39 114 5.79e-23 89.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene054308.t1 AT2G45680 53.390 118 52 2 18 134 69 184 4.12e-35 124
MS.gene054308.t1 AT5G51910 55.200 125 48 3 16 134 48 170 1.98e-33 118
MS.gene054308.t1 AT5G51910 55.200 125 48 3 16 134 48 170 1.98e-33 118
MS.gene054308.t1 AT1G72010 66.176 68 23 0 19 86 58 125 8.09e-26 100
MS.gene054308.t1 AT5G23280 58.228 79 31 1 8 86 25 101 3.28e-25 96.3
MS.gene054308.t1 AT5G08330 66.667 66 22 0 21 86 28 93 4.84e-25 95.9
MS.gene054308.t1 AT1G69690 62.319 69 26 0 18 86 46 114 1.72e-24 95.9
MS.gene054308.t1 AT3G47620 61.842 76 23 1 17 86 104 179 2.41e-24 97.1
MS.gene054308.t1 AT1G35560 66.667 66 22 0 21 86 52 117 4.61e-24 95.1
MS.gene054308.t1 AT1G58100 63.636 66 24 0 21 86 57 122 9.30e-24 94.7
MS.gene054308.t1 AT3G27010 64.615 65 23 0 21 85 75 139 1.61e-23 93.2
MS.gene054308.t1 AT3G27010 64.615 65 23 0 21 85 75 139 1.61e-23 93.2
MS.gene054308.t1 AT5G41030 62.319 69 26 0 21 89 65 133 2.43e-23 91.3
MS.gene054308.t1 AT2G37000 67.797 59 19 0 24 82 43 101 1.46e-21 85.5
MS.gene054308.t1 AT3G45150 47.692 65 34 0 20 84 13 77 2.78e-16 71.2

Find 43 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATGGTGAATTTGAATATT+TGG 0.164281 6.1:-24680463 MS.gene054308:CDS
TTCTCTTGCTTCTCTTCCTT+GGG 0.199687 6.1:+24680490 None:intergenic
ATATTCAAATTCACCATTTC+CGG 0.203311 6.1:+24680467 None:intergenic
GTTCTCTTGCTTCTCTTCCT+TGG 0.258930 6.1:+24680489 None:intergenic
GTCAGAGGAAGGAAGGTTTA+AGG 0.282964 6.1:-24680553 MS.gene054308:CDS
TTCTTGCGACGGTCTCTTGA+TGG 0.302619 6.1:+24680753 None:intergenic
ATCCTCTCTGCGCATGTTGC+CGG 0.377821 6.1:+24680699 None:intergenic
CTTGGGGCGTCTTGGCAGTC+TGG 0.382512 6.1:+24680507 None:intergenic
TTCTCTTCCTTGGGGCGTCT+TGG 0.415275 6.1:+24680499 None:intergenic
AGGAAGAGAAGCAAGAGAAC+CGG 0.427388 6.1:-24680486 MS.gene054308:CDS
CTTGATGGTTTCTTCGCTGC+CGG 0.454854 6.1:+24680768 None:intergenic
ATTATTAAAGCCACCGGCAC+AGG 0.466222 6.1:-24680597 MS.gene054308:CDS
TCCTCTGACACGGCTATGGC+CGG 0.473917 6.1:+24680567 None:intergenic
AGAGACAATAAAGTGGTTGT+TGG 0.483172 6.1:-24680637 MS.gene054308:CDS
GAGCTTGGTCACAAGTCTGC+TGG 0.487994 6.1:-24680660 MS.gene054308:CDS
CCGGTGGCTTTAATAATCTC+AGG 0.489828 6.1:+24680603 None:intergenic
GGCCGGAGTTATTCCTGTGC+CGG 0.490368 6.1:+24680584 None:intergenic
GGTCTAGCCGCCGATGATGT+TGG 0.499400 6.1:+24680528 None:intergenic
AGAAGCAAGAGAACCGGAAA+TGG 0.499819 6.1:-24680480 MS.gene054308:CDS
TTTCAGTTGACAATGGAGCT+TGG 0.532527 6.1:-24680675 MS.gene054308:CDS
TCCTTCCTCTGACACGGCTA+TGG 0.539656 6.1:+24680563 None:intergenic
AGACCGTCGCAAGAAGGTGG+AGG 0.548236 6.1:-24680745 MS.gene054308:CDS
CGGAGTTATTCCTGTGCCGG+TGG 0.551737 6.1:+24680587 None:intergenic
AAGAGACCGTCGCAAGAAGG+TGG 0.572157 6.1:-24680748 MS.gene054308:CDS
ATCAAGAGACCGTCGCAAGA+AGG 0.573809 6.1:-24680751 MS.gene054308:CDS
GTTTAAGGTTCCAACATCAT+CGG 0.575076 6.1:-24680538 MS.gene054308:CDS
GCCATAGCCGTGTCAGAGGA+AGG 0.578070 6.1:-24680564 MS.gene054308:CDS
AGATATGACAATGACAGTGC+CGG 0.584868 6.1:-24680787 MS.gene054308:CDS
GTCCCTCCACCTTCTTGCGA+CGG 0.586255 6.1:+24680742 None:intergenic
GTTGCCGGCAGTGTGACTCT+CGG 0.586671 6.1:+24680714 None:intergenic
TCCGGCCATAGCCGTGTCAG+AGG 0.592138 6.1:-24680568 MS.gene054308:CDS
CAGACTGCCAAGACGCCCCA+AGG 0.592901 6.1:-24680506 MS.gene054308:CDS
TCTCTTGCTTCTCTTCCTTG+GGG 0.595692 6.1:+24680491 None:intergenic
CACCGGCACAGGAATAACTC+CGG 0.602275 6.1:-24680586 MS.gene054308:CDS
GAGGATCTTTCAGTTGACAA+TGG 0.606295 6.1:-24680682 MS.gene054308:CDS
TAGCCGTGTCAGAGGAAGGA+AGG 0.607914 6.1:-24680560 MS.gene054308:CDS
AAACCTTCCTTCCTCTGACA+CGG 0.608846 6.1:+24680557 None:intergenic
GACCGTCGCAAGAAGGTGGA+GGG 0.609162 6.1:-24680744 MS.gene054308:CDS
CCTGAGATTATTAAAGCCAC+CGG 0.619985 6.1:-24680603 MS.gene054308:CDS
TGTTCCGAGAGTCACACTGC+CGG 0.623038 6.1:-24680718 MS.gene054308:CDS
TGCCGGCAACATGCGCAGAG+AGG 0.645605 6.1:-24680701 MS.gene054308:CDS
TAAGGTTCCAACATCATCGG+CGG 0.648326 6.1:-24680535 MS.gene054308:CDS
CTGCTGGAGAGACAATAAAG+TGG 0.658576 6.1:-24680644 MS.gene054308:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATGGTGAATTTGAATATT+TGG - chr6.1:24680793-24680812 MS.gene054308:CDS 20.0%
! ATATTCAAATTCACCATTTC+CGG + chr6.1:24680792-24680811 None:intergenic 25.0%
AGAGACAATAAAGTGGTTGT+TGG - chr6.1:24680619-24680638 MS.gene054308:CDS 35.0%
! GTTTAAGGTTCCAACATCAT+CGG - chr6.1:24680718-24680737 MS.gene054308:CDS 35.0%
AGATATGACAATGACAGTGC+CGG - chr6.1:24680469-24680488 MS.gene054308:CDS 40.0%
CCTGAGATTATTAAAGCCAC+CGG - chr6.1:24680653-24680672 MS.gene054308:CDS 40.0%
GAGGATCTTTCAGTTGACAA+TGG - chr6.1:24680574-24680593 MS.gene054308:CDS 40.0%
TTCTCTTGCTTCTCTTCCTT+GGG + chr6.1:24680769-24680788 None:intergenic 40.0%
TTTCAGTTGACAATGGAGCT+TGG - chr6.1:24680581-24680600 MS.gene054308:CDS 40.0%
AAACCTTCCTTCCTCTGACA+CGG + chr6.1:24680702-24680721 None:intergenic 45.0%
AGAAGCAAGAGAACCGGAAA+TGG - chr6.1:24680776-24680795 MS.gene054308:CDS 45.0%
AGGAAGAGAAGCAAGAGAAC+CGG - chr6.1:24680770-24680789 MS.gene054308:CDS 45.0%
ATTATTAAAGCCACCGGCAC+AGG - chr6.1:24680659-24680678 MS.gene054308:CDS 45.0%
CTGCTGGAGAGACAATAAAG+TGG - chr6.1:24680612-24680631 MS.gene054308:CDS 45.0%
GTCAGAGGAAGGAAGGTTTA+AGG - chr6.1:24680703-24680722 MS.gene054308:CDS 45.0%
GTTCTCTTGCTTCTCTTCCT+TGG + chr6.1:24680770-24680789 None:intergenic 45.0%
TAAGGTTCCAACATCATCGG+CGG - chr6.1:24680721-24680740 MS.gene054308:CDS 45.0%
TCTCTTGCTTCTCTTCCTTG+GGG + chr6.1:24680768-24680787 None:intergenic 45.0%
!! CCGGTGGCTTTAATAATCTC+AGG + chr6.1:24680656-24680675 None:intergenic 45.0%
ATCAAGAGACCGTCGCAAGA+AGG - chr6.1:24680505-24680524 MS.gene054308:CDS 50.0%
TTCTTGCGACGGTCTCTTGA+TGG + chr6.1:24680506-24680525 None:intergenic 50.0%
! CTTGATGGTTTCTTCGCTGC+CGG + chr6.1:24680491-24680510 None:intergenic 50.0%
AAGAGACCGTCGCAAGAAGG+TGG - chr6.1:24680508-24680527 MS.gene054308:CDS 55.0%
ATCCTCTCTGCGCATGTTGC+CGG + chr6.1:24680560-24680579 None:intergenic 55.0%
CACCGGCACAGGAATAACTC+CGG - chr6.1:24680670-24680689 MS.gene054308:CDS 55.0%
GAGCTTGGTCACAAGTCTGC+TGG - chr6.1:24680596-24680615 MS.gene054308:CDS 55.0%
TAGCCGTGTCAGAGGAAGGA+AGG - chr6.1:24680696-24680715 MS.gene054308:CDS 55.0%
TCCTTCCTCTGACACGGCTA+TGG + chr6.1:24680696-24680715 None:intergenic 55.0%
TGTTCCGAGAGTCACACTGC+CGG - chr6.1:24680538-24680557 MS.gene054308:CDS 55.0%
! TTCTCTTCCTTGGGGCGTCT+TGG + chr6.1:24680760-24680779 None:intergenic 55.0%
AGACCGTCGCAAGAAGGTGG+AGG - chr6.1:24680511-24680530 MS.gene054308:CDS 60.0%
CGGAGTTATTCCTGTGCCGG+TGG + chr6.1:24680672-24680691 None:intergenic 60.0%
GACCGTCGCAAGAAGGTGGA+GGG - chr6.1:24680512-24680531 MS.gene054308:CDS 60.0%
GCCATAGCCGTGTCAGAGGA+AGG - chr6.1:24680692-24680711 MS.gene054308:CDS 60.0%
GGCCGGAGTTATTCCTGTGC+CGG + chr6.1:24680675-24680694 None:intergenic 60.0%
GGTCTAGCCGCCGATGATGT+TGG + chr6.1:24680731-24680750 None:intergenic 60.0%
GTCCCTCCACCTTCTTGCGA+CGG + chr6.1:24680517-24680536 None:intergenic 60.0%
GTTGCCGGCAGTGTGACTCT+CGG + chr6.1:24680545-24680564 None:intergenic 60.0%
TCCTCTGACACGGCTATGGC+CGG + chr6.1:24680692-24680711 None:intergenic 60.0%
CAGACTGCCAAGACGCCCCA+AGG - chr6.1:24680750-24680769 MS.gene054308:CDS 65.0%
TCCGGCCATAGCCGTGTCAG+AGG - chr6.1:24680688-24680707 MS.gene054308:CDS 65.0%
TGCCGGCAACATGCGCAGAG+AGG - chr6.1:24680555-24680574 MS.gene054308:CDS 65.0%
! CTTGGGGCGTCTTGGCAGTC+TGG + chr6.1:24680752-24680771 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr6.1 gene 24680437 24680841 24680437 ID=MS.gene054308
chr6.1 mRNA 24680437 24680841 24680437 ID=MS.gene054308.t1;Parent=MS.gene054308
chr6.1 exon 24680437 24680841 24680437 ID=MS.gene054308.t1.exon1;Parent=MS.gene054308.t1
chr6.1 CDS 24680437 24680841 24680437 ID=cds.MS.gene054308.t1;Parent=MS.gene054308.t1
Gene Sequence

>MS.gene054308

ATGGAACAACAAACGTTGAACATGCTAGAGCAAGATATGACAATGACAGTGCCGGCAGCGAAGAAACCATCAAGAGACCGTCGCAAGAAGGTGGAGGGACGTGTTCCGAGAGTCACACTGCCGGCAACATGCGCAGAGAGGATCTTTCAGTTGACAATGGAGCTTGGTCACAAGTCTGCTGGAGAGACAATAAAGTGGTTGTTGGAACAAGCTGAACCTGAGATTATTAAAGCCACCGGCACAGGAATAACTCCGGCCATAGCCGTGTCAGAGGAAGGAAGGTTTAAGGTTCCAACATCATCGGCGGCTAGACCAGACTGCCAAGACGCCCCAAGGAAGAGAAGCAAGAGAACCGGAAATGGTGAATTTGAATATTTGGATGATCAAGATTCAATTGCTTCTTGA
Protein sequence

>MS.gene054308.t1

MEQQTLNMLEQDMTMTVPAAKKPSRDRRKKVEGRVPRVTLPATCAERIFQLTMELGHKSAGETIKWLLEQAEPEIIKATGTGITPAIAVSEEGRFKVPTSSAARPDCQDAPRKRSKRTGNGEFEYLDDQDSIAS