AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene41820

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41820.t1 MTR_7g086940 96.154 78 3 0 5 82 49 126 2.51e-36 124
MS.gene41820.t1 MTR_7g025010 51.852 54 26 0 5 58 68 121 3.42e-13 63.9
MS.gene41820.t1 MTR_6g027390 84.444 45 7 0 6 50 54 98 9.44e-13 62.0
MS.gene41820.t1 MTR_2g015000 58.140 43 18 0 5 47 76 118 7.78e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene41820.t1 AT3G03660 80.000 30 6 0 6 35 55 84 6.41e-12 59.7
MS.gene41820.t1 AT3G03660 77.419 31 7 0 5 35 54 84 6.93e-12 60.1
MS.gene41820.t1 AT3G03660 77.419 31 7 0 5 35 54 84 7.23e-12 59.7
MS.gene41820.t1 AT3G03660 77.419 31 7 0 5 35 54 84 1.69e-11 58.9
MS.gene41820.t1 AT5G17810 76.744 43 10 0 5 47 42 84 2.23e-11 58.2
MS.gene41820.t1 AT5G17810 76.744 43 10 0 5 47 42 84 2.29e-11 58.2
MS.gene41820.t1 AT5G17810 76.744 43 10 0 5 47 42 84 2.29e-11 58.2
MS.gene41820.t1 AT2G33880 51.064 47 23 0 5 51 76 122 5.53e-11 57.4
MS.gene41820.t1 AT2G33880 51.064 47 23 0 5 51 76 122 6.06e-11 57.4

Find 24 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAAACTTCTTGAGAAATT+CGG 0.326558 7.3:-21889860 MS.gene41820:CDS
GAGATCTAGACCGGCGGTTT+TGG 0.333606 7.3:+21889804 None:intergenic
CAAGTGTGGCCTGCTGCATC+TGG 0.348372 7.3:+21889768 None:intergenic
TGATAGTTTCTTCTTCTTGT+GGG 0.355719 7.3:+21889888 None:intergenic
CCTGCTGCATCTGGCGTTGT+CGG 0.413984 7.3:+21889777 None:intergenic
TTGATAGTTTCTTCTTCTTG+TGG 0.415013 7.3:+21889887 None:intergenic
CCGACAACGCCAGATGCAGC+AGG 0.426272 7.3:-21889777 MS.gene41820:CDS
AAGTGCAATTCCTTGTGATA+TGG 0.444028 7.3:-21889687 MS.gene41820:CDS
GATAGTTTCTTCTTCTTGTG+GGG 0.508851 7.3:+21889889 None:intergenic
GTGATGCTAACGTCTTCTAC+TGG 0.530664 7.3:-21889829 MS.gene41820:CDS
CTTGAGAAATTCGGCAACGT+CGG 0.555714 7.3:-21889851 MS.gene41820:CDS
ATTTCTTTGCTGATCAAGTG+TGG 0.555910 7.3:+21889754 None:intergenic
GCTGCATCTGGCGTTGTCGG+CGG 0.572272 7.3:+21889780 None:intergenic
AGAAGAATCATTTAAACAAG+AGG 0.579493 7.3:+21889629 None:intergenic
GTCGGCGGCGAGATCTAGAC+CGG 0.586191 7.3:+21889795 None:intergenic
TGATCAGCAAAGAAATCAGA+TGG 0.591537 7.3:-21889747 MS.gene41820:CDS
AGAATCATTTAAACAAGAGG+AGG 0.602089 7.3:+21889632 None:intergenic
GTCCATCTTCAACAGTGGCA+TGG 0.623516 7.3:-21889917 None:intergenic
TCTACTGGTTCCAAAACCGC+CGG 0.624539 7.3:-21889814 MS.gene41820:CDS
TGGTTCAAACCACCCAACCA+TGG 0.633526 7.3:-21889667 MS.gene41820:CDS
CCTCAGCAAGTTGTTAACGA+TGG 0.634528 7.3:-21889713 MS.gene41820:CDS
CCATCGTTAACAACTTGCTG+AGG 0.647740 7.3:+21889713 None:intergenic
GTGGTTTGAACCATATCACA+AGG 0.665238 7.3:+21889677 None:intergenic
GGCGGCGAGATCTAGACCGG+CGG 0.697708 7.3:+21889798 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGAAAACTTCTTGAGAAATT+CGG - chr7.3:21889682-21889701 MS.gene41820:CDS 25.0%
TGATAGTTTCTTCTTCTTGT+GGG + chr7.3:21889657-21889676 None:intergenic 30.0%
! TTGATAGTTTCTTCTTCTTG+TGG + chr7.3:21889658-21889677 None:intergenic 30.0%
AAGTGCAATTCCTTGTGATA+TGG - chr7.3:21889855-21889874 MS.gene41820:CDS 35.0%
ATTTCTTTGCTGATCAAGTG+TGG + chr7.3:21889791-21889810 None:intergenic 35.0%
GATAGTTTCTTCTTCTTGTG+GGG + chr7.3:21889656-21889675 None:intergenic 35.0%
TGATCAGCAAAGAAATCAGA+TGG - chr7.3:21889795-21889814 MS.gene41820:CDS 35.0%
AACCACCAAAAACCATGGTT+GGG + chr7.3:21889890-21889909 None:intergenic 40.0%
GTGGTTTGAACCATATCACA+AGG + chr7.3:21889868-21889887 None:intergenic 40.0%
! TGGTTCCTCCTCTTGTTTAA+TGG - chr7.3:21889905-21889924 MS.gene41820:CDS 40.0%
CCTCAGCAAGTTGTTAACGA+TGG - chr7.3:21889829-21889848 MS.gene41820:CDS 45.0%
CTTGAGAAATTCGGCAACGT+CGG - chr7.3:21889691-21889710 MS.gene41820:CDS 45.0%
GAACCACCAAAAACCATGGT+TGG + chr7.3:21889891-21889910 None:intergenic 45.0%
GTGATGCTAACGTCTTCTAC+TGG - chr7.3:21889713-21889732 MS.gene41820:CDS 45.0%
! AACCACCCAACCATGGTTTT+TGG - chr7.3:21889882-21889901 MS.gene41820:CDS 45.0%
!! CCATCGTTAACAACTTGCTG+AGG + chr7.3:21889832-21889851 None:intergenic 45.0%
CACCAAAAACCATGGTTGGG+TGG + chr7.3:21889887-21889906 None:intergenic 50.0%
GGAGGAACCACCAAAAACCA+TGG + chr7.3:21889895-21889914 None:intergenic 50.0%
TGGTTCAAACCACCCAACCA+TGG - chr7.3:21889875-21889894 MS.gene41820:CDS 50.0%
!! CACCCAACCATGGTTTTTGG+TGG - chr7.3:21889885-21889904 MS.gene41820:CDS 50.0%
!! TCTACTGGTTCCAAAACCGC+CGG - chr7.3:21889728-21889747 MS.gene41820:CDS 50.0%
! GAGATCTAGACCGGCGGTTT+TGG + chr7.3:21889741-21889760 None:intergenic 55.0%
CAAGTGTGGCCTGCTGCATC+TGG + chr7.3:21889777-21889796 None:intergenic 60.0%
CCTGCTGCATCTGGCGTTGT+CGG + chr7.3:21889768-21889787 None:intergenic 60.0%
CCGACAACGCCAGATGCAGC+AGG - chr7.3:21889765-21889784 MS.gene41820:CDS 65.0%
GCTGCATCTGGCGTTGTCGG+CGG + chr7.3:21889765-21889784 None:intergenic 65.0%
GTCGGCGGCGAGATCTAGAC+CGG + chr7.3:21889750-21889769 None:intergenic 65.0%
GGCGGCGAGATCTAGACCGG+CGG + chr7.3:21889747-21889766 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 21889640 21889924 21889640 ID=MS.gene41820
chr7.3 mRNA 21889640 21889924 21889640 ID=MS.gene41820.t1;Parent=MS.gene41820
chr7.3 exon 21889640 21889924 21889640 ID=MS.gene41820.t1.exon1;Parent=MS.gene41820.t1
chr7.3 CDS 21889640 21889924 21889640 ID=cds.MS.gene41820.t1;Parent=MS.gene41820.t1
Gene Sequence

>MS.gene41820

TGGCATGGTGAATCCCCACAAGAAGAAGAAACTATCAAAATAAGAAAACTTCTTGAGAAATTCGGCAACGTCGGTGATGCTAACGTCTTCTACTGGTTCCAAAACCGCCGGTCTAGATCTCGCCGCCGACAACGCCAGATGCAGCAGGCCACACTTGATCAGCAAAGAAATCAGATGGCTATGATGCAGCCTCAGCAAGTTGTTAACGATGGTGCAAGTGCAATTCCTTGTGATATGGTTCAAACCACCCAACCATGGTTTTTGGTGGTTCCTCCTCTTGTTTAA
Protein sequence

>MS.gene41820.t1

WHGESPQEEETIKIRKLLEKFGNVGDANVFYWFQNRRSRSRRRQRQMQQATLDQQRNQMAMMQPQQVVNDGASAIPCDMVQTTQPWFLVVPPLV