AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene71781

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71781.t1 MTR_1g109660 98.000 100 2 0 1 100 1 100 4.27e-66 197
MS.gene71781.t1 MTR_8g027455 90.164 61 6 0 32 92 319 379 4.35e-34 121
MS.gene71781.t1 MTR_7g114270 76.712 73 12 1 25 97 2 69 7.10e-34 112
MS.gene71781.t1 MTR_1g109700 55.000 100 43 1 1 100 1 98 7.85e-34 115
MS.gene71781.t1 MTR_1g109690 52.000 100 46 1 1 100 1 98 1.44e-28 99.4
MS.gene71781.t1 MTR_2g079830 44.330 97 54 0 4 100 3 99 5.31e-27 98.2
MS.gene71781.t1 MTR_5g057670 40.206 97 58 0 4 100 7 103 1.82e-20 81.3
MS.gene71781.t1 MTR_5g057335 40.206 97 58 0 4 100 7 103 1.82e-20 81.3
MS.gene71781.t1 MTR_4g089100 37.000 100 61 2 1 100 1 98 6.05e-17 72.0
MS.gene71781.t1 MTR_8g098920 91.429 35 3 0 46 80 100 134 1.69e-15 67.4
MS.gene71781.t1 MTR_4g094850 71.429 49 10 1 32 80 79 123 1.60e-14 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71781.t1 AT1G68220 63.366 101 36 1 1 100 1 101 1.54e-42 138
MS.gene71781.t1 AT3G15480 46.000 100 53 1 1 100 1 99 1.76e-23 88.6
MS.gene71781.t1 AT1G52910 44.000 100 55 1 1 100 1 99 2.21e-23 88.6
MS.gene71781.t1 AT4G27435 45.833 96 50 1 5 100 6 99 1.80e-21 83.6
MS.gene71781.t1 AT1G13380 45.361 97 53 0 4 100 7 103 1.09e-20 82.0
MS.gene71781.t1 AT1G61065 39.286 84 50 1 17 100 16 98 1.17e-14 66.2

Find 16 sgRNAs with CRISPR-Local

Find 20 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAACAGTTTGACTAAGAAGC+AGG 0.481436 1.3:+74723674 None:intergenic
TCATCTTCTTCATTCTCTCA+TGG 0.481945 1.3:-74723582 MS.gene71781:CDS
AGAGATGAAGAGAAATGATA+AGG 0.482501 1.3:+74723909 None:intergenic
GTTCGGTCATCGTACTCATC+AGG 0.486965 1.3:+74723754 None:intergenic
AGATGTCTTTGCTGTGGTAA+AGG 0.489539 1.3:-74723637 MS.gene71781:CDS
TGTGGTAAAGGTCTCATCTC+TGG 0.498793 1.3:-74723625 MS.gene71781:CDS
TGGTGTAAACACAGAAAGTT+CGG 0.520390 1.3:+74723737 None:intergenic
GAAGAAGATGACAGCGCAAG+TGG 0.562935 1.3:+74723594 None:intergenic
ACCGACGCTTCCACTGTCTA+CGG 0.578522 1.3:-74723715 MS.gene71781:CDS
CGCTGAACGACGTCGTAGTG+AGG 0.588172 1.3:-74723864 MS.gene71781:intron
AGCAGCAACACCGTAGACAG+TGG 0.594874 1.3:+74723705 None:intergenic
GTACTCATCAGGAACCACTT+TGG 0.600621 1.3:+74723765 None:intergenic
ACCGTAGACAGTGGAAGCGT+CGG 0.606731 1.3:+74723714 None:intergenic
GTCACTAGATGTCTTTGCTG+TGG 0.617569 1.3:-74723643 MS.gene71781:CDS
GTAGACAGTGGAAGCGTCGG+TGG 0.627400 1.3:+74723717 None:intergenic
ACAGCAAAGACATCTAGTGA+CGG 0.697347 1.3:+74723645 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAGTGTTGAAATTAAAGAA+AGG + chr1.3:74723686-74723705 None:intergenic 20.0%
!! AATCTGATTAATCTCTTTTC+AGG - chr1.3:74723726-74723745 MS.gene71781:CDS 25.0%
AGAGATGAAGAGAAATGATA+AGG + chr1.3:74723608-74723627 None:intergenic 30.0%
!! TTAGCTTTCGTTTTTGCTAT+AGG - chr1.3:74723627-74723646 MS.gene71781:CDS 30.0%
TCATCTTCTTCATTCTCTCA+TGG - chr1.3:74723932-74723951 MS.gene71781:CDS 35.0%
TGGTGTAAACACAGAAAGTT+CGG + chr1.3:74723780-74723799 None:intergenic 35.0%
ACAGCAAAGACATCTAGTGA+CGG + chr1.3:74723872-74723891 None:intergenic 40.0%
GAACAGTTTGACTAAGAAGC+AGG + chr1.3:74723843-74723862 None:intergenic 40.0%
! AGATGTCTTTGCTGTGGTAA+AGG - chr1.3:74723877-74723896 MS.gene71781:CDS 40.0%
!! AATCTCTTTTCAGGCCAAAG+TGG - chr1.3:74723735-74723754 MS.gene71781:CDS 40.0%
GTACTCATCAGGAACCACTT+TGG + chr1.3:74723752-74723771 None:intergenic 45.0%
GTCACTAGATGTCTTTGCTG+TGG - chr1.3:74723871-74723890 MS.gene71781:CDS 45.0%
TGTGGTAAAGGTCTCATCTC+TGG - chr1.3:74723889-74723908 MS.gene71781:CDS 45.0%
GAAGAAGATGACAGCGCAAG+TGG + chr1.3:74723923-74723942 None:intergenic 50.0%
GTTCGGTCATCGTACTCATC+AGG + chr1.3:74723763-74723782 None:intergenic 50.0%
ACCGACGCTTCCACTGTCTA+CGG - chr1.3:74723799-74723818 MS.gene71781:intron 55.0%
AGCAGCAACACCGTAGACAG+TGG + chr1.3:74723812-74723831 None:intergenic 55.0%
! ACCGTAGACAGTGGAAGCGT+CGG + chr1.3:74723803-74723822 None:intergenic 55.0%
CGCTGAACGACGTCGTAGTG+AGG - chr1.3:74723650-74723669 MS.gene71781:CDS 60.0%
!! GTAGACAGTGGAAGCGTCGG+TGG + chr1.3:74723800-74723819 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 74723579 74723957 74723579 ID=MS.gene71781
chr1.3 mRNA 74723579 74723957 74723579 ID=MS.gene71781.t1;Parent=MS.gene71781
chr1.3 exon 74723865 74723957 74723865 ID=MS.gene71781.t1.exon1;Parent=MS.gene71781.t1
chr1.3 CDS 74723865 74723957 74723865 ID=cds.MS.gene71781.t1;Parent=MS.gene71781.t1
chr1.3 exon 74723579 74723788 74723579 ID=MS.gene71781.t1.exon2;Parent=MS.gene71781.t1
chr1.3 CDS 74723579 74723788 74723579 ID=cds.MS.gene71781.t1;Parent=MS.gene71781.t1
Gene Sequence

>MS.gene71781

ATGGCTGTGTCTGTAACAATTATAGTCCTTATCATTTCTCTTCATCTCTTAGCTTTCGTTTTTGCTATAGGCGCTGAACGACGTCGTAGTGAGGTAATCTTTATCCTTTCTTTAATTTCAACACTAATCTTGCTTTTTTGTTTCTTAAATCTGATTAATCTCTTTTCAGGCCAAAGTGGTTCCTGATGAGTACGATGACCGAACTTTCTGTGTTTACACCACCGACGCTTCCACTGTCTACGGTGTTGCTGCTTTCTCTCTCCTGCTTCTTAGTCAAACTGTTCTTAACGCCGTCACTAGATGTCTTTGCTGTGGTAAAGGTCTCATCTCTGGTTGTTCTACCACTTGCGCTGTCATCTTCTTCATTCTCTCATGGTAA
Protein sequence

>MS.gene71781.t1

MAVSVTIIVLIISLHLLAFVFAIGAERRRSEAKVVPDEYDDRTFCVYTTDASTVYGVAAFSLLLLSQTVLNAVTRCLCCGKGLISGCSTTCAVIFFILSW