AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene062177

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062177.t1 MTR_1g077700 54.839 186 22 3 1 124 1 186 2.62e-46 148
MS.gene062177.t1 MTR_1g077730 89.474 76 6 2 1 75 1 75 4.19e-40 132
MS.gene062177.t1 MTR_1g077730 64.634 82 12 1 43 124 130 194 2.96e-30 107
MS.gene062177.t1 MTR_1g077120 85.185 27 4 0 37 63 40 66 3.39e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062177.t1 AT2G28200 60.526 38 15 0 37 74 108 145 5.73e-11 58.5

Find 28 sgRNAs with CRISPR-Local

Find 51 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATGAATGTCTCTTTGGATT+TGG 0.240224 1.1:+58237201 MS.gene062177:CDS
AAAGAAAATGAATGTCTCTT+TGG 0.298164 1.1:+58237195 MS.gene062177:CDS
CATGAACAACAACTCTCTTT+AGG 0.379285 1.1:+58236680 MS.gene062177:CDS
CTCGATGAGGTTGCCTCCAC+CGG 0.381070 1.1:-58237127 None:intergenic
GGTTCTTCATCTTCTTCGTC+TGG 0.399717 1.1:-58237166 None:intergenic
CTTTGATCTGCTTAAGCTGC+AGG 0.401494 1.1:-58237235 None:intergenic
TTCACTTCATTTCAAGCACT+TGG 0.418538 1.1:+58236824 MS.gene062177:CDS
GAATAAGCAATGATGGAGAA+AGG 0.461472 1.1:-58236728 None:intergenic
TCGTCTGGTTTCAAAGCCAT+TGG 0.468001 1.1:-58237151 None:intergenic
GTGCATGGTGGAAGGTCATA+TGG 0.468572 1.1:-58237105 None:intergenic
TTCACATCTGGCCAGGCACT+TGG 0.470440 1.1:+58237079 MS.gene062177:intron
TGTAGAAGAATAAGCAATGA+TGG 0.477070 1.1:-58236735 None:intergenic
TATTCTTCTACAAGAGAAGA+AGG 0.493297 1.1:+58236746 MS.gene062177:CDS
AATAAGCAATGATGGAGAAA+GGG 0.497448 1.1:-58236727 None:intergenic
CTTCCACCATGCACCGGTGG+AGG 0.506143 1.1:+58237114 MS.gene062177:CDS
TGAACCTGACTATCATCTCT+AGG 0.517943 1.1:-58236872 None:intergenic
ACTTCATTTCAAGCACTTGG+AGG 0.520190 1.1:+58236827 MS.gene062177:CDS
GAAACCTAGAGATGATAGTC+AGG 0.521179 1.1:+58236868 MS.gene062177:CDS
ACATCTGGCCAGGCACTTGG+TGG 0.529943 1.1:+58237082 MS.gene062177:intron
CTCCACCGGTGCATGGTGGA+AGG 0.537215 1.1:-58237113 None:intergenic
GCAATGATGGAGAAAGGGGT+AGG 0.559315 1.1:-58236722 None:intergenic
ATAAGCAATGATGGAGAAAG+GGG 0.560403 1.1:-58236726 None:intergenic
AGGTTGCCTCCACCGGTGCA+TGG 0.568155 1.1:-58237120 None:intergenic
TATGACCTTCCACCATGCAC+CGG 0.585865 1.1:+58237108 MS.gene062177:CDS
CAAAGCCATTGGTCTCGATG+AGG 0.605389 1.1:-58237140 None:intergenic
GGCAACCTCATCGAGACCAA+TGG 0.607582 1.1:+58237135 MS.gene062177:CDS
GACCTTCCACCATGCACCGG+TGG 0.615351 1.1:+58237111 MS.gene062177:CDS
TTGCCTCCACCGGTGCATGG+TGG 0.647313 1.1:-58237117 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTGATACTATTCAATTTAA+GGG - chr1.1:58236933-58236952 None:intergenic 15.0%
!! CATTGATACTATTCAATTTA+AGG - chr1.1:58236934-58236953 None:intergenic 20.0%
!! CTTAAATTGAATAGTATCAA+TGG + chr1.1:58236932-58236951 MS.gene062177:intron 20.0%
! AAAGAAAATGAATGTCTCTT+TGG + chr1.1:58237195-58237214 MS.gene062177:CDS 25.0%
! ATTGAATAGTATCAATGGTA+TGG + chr1.1:58236937-58236956 MS.gene062177:intron 25.0%
! TTGAATAGTATCAATGGTAT+GGG + chr1.1:58236938-58236957 MS.gene062177:intron 25.0%
AACAACAAAACCAAGGTTTA+TGG + chr1.1:58237034-58237053 MS.gene062177:intron 30.0%
AATGAATGTCTCTTTGGATT+TGG + chr1.1:58237201-58237220 MS.gene062177:CDS 30.0%
ACAACAAAACCAAGGTTTAT+GGG + chr1.1:58237035-58237054 MS.gene062177:intron 30.0%
TATTCTTCTACAAGAGAAGA+AGG + chr1.1:58236746-58236765 MS.gene062177:CDS 30.0%
TGTAGAAGAATAAGCAATGA+TGG - chr1.1:58236738-58236757 None:intergenic 30.0%
! AATAAGCAATGATGGAGAAA+GGG - chr1.1:58236730-58236749 None:intergenic 30.0%
! AGAGACATTCATTTTCTTTG+TGG - chr1.1:58237194-58237213 None:intergenic 30.0%
! GAGACATTCATTTTCTTTGT+GGG - chr1.1:58237193-58237212 None:intergenic 30.0%
! GTTTCTTGTGAACTTTTCTA+TGG - chr1.1:58236853-58236872 None:intergenic 30.0%
! TGTGAATTTAGAACCACAAA+TGG - chr1.1:58237065-58237084 None:intergenic 30.0%
CAACAACAACAACAAAACCA+AGG + chr1.1:58237027-58237046 MS.gene062177:intron 35.0%
CATGAACAACAACTCTCTTT+AGG + chr1.1:58236680-58236699 MS.gene062177:CDS 35.0%
TTCACTTCATTTCAAGCACT+TGG + chr1.1:58236824-58236843 MS.gene062177:CDS 35.0%
! ACATTCATTTTCTTTGTGGG+TGG - chr1.1:58237190-58237209 None:intergenic 35.0%
! ATAAGCAATGATGGAGAAAG+GGG - chr1.1:58236729-58236748 None:intergenic 35.0%
! GAATAAGCAATGATGGAGAA+AGG - chr1.1:58236731-58236750 None:intergenic 35.0%
! GTTATTGTTGTTGTTGGTAG+TGG - chr1.1:58237002-58237021 None:intergenic 35.0%
!! TGTGGTTCTAAATTCACATC+TGG + chr1.1:58237067-58237086 MS.gene062177:intron 35.0%
!!! CTTGGTTTTGTTGTTGTTGT+TGG - chr1.1:58237029-58237048 None:intergenic 35.0%
ACTTCATTTCAAGCACTTGG+AGG + chr1.1:58236827-58236846 MS.gene062177:CDS 40.0%
GAAACCTAGAGATGATAGTC+AGG + chr1.1:58236868-58236887 MS.gene062177:CDS 40.0%
TGAACCTGACTATCATCTCT+AGG - chr1.1:58236875-58236894 None:intergenic 40.0%
TTCTAAATTCACATCTGGCC+AGG + chr1.1:58237072-58237091 MS.gene062177:intron 40.0%
!! ATTGTTGTTGTTGGTAGTGG+TGG - chr1.1:58236999-58237018 None:intergenic 40.0%
!! GGTGGTGTTATTGTTGTTGT+TGG - chr1.1:58237008-58237027 None:intergenic 40.0%
!!! GGTTTTGTTGTTGTTGTTGG+TGG - chr1.1:58237026-58237045 None:intergenic 40.0%
AATGGTGCACCCATAAACCT+TGG - chr1.1:58237047-58237066 None:intergenic 45.0%
GGTTCTTCATCTTCTTCGTC+TGG - chr1.1:58237169-58237188 None:intergenic 45.0%
GTTTATGGGTGCACCATTTG+TGG + chr1.1:58237049-58237068 MS.gene062177:intron 45.0%
! TCGTCTGGTTTCAAAGCCAT+TGG - chr1.1:58237154-58237173 None:intergenic 45.0%
TATGACCTTCCACCATGCAC+CGG + chr1.1:58237108-58237127 MS.gene062177:CDS 50.0%
! CAAAGCCATTGGTCTCGATG+AGG - chr1.1:58237143-58237162 None:intergenic 50.0%
! GCAATGATGGAGAAAGGGGT+AGG - chr1.1:58236725-58236744 None:intergenic 50.0%
! GTGCATGGTGGAAGGTCATA+TGG - chr1.1:58237108-58237127 None:intergenic 50.0%
!! GTTGTTGTTGGTAGTGGTGG+TGG - chr1.1:58236996-58237015 None:intergenic 50.0%
GGCAACCTCATCGAGACCAA+TGG + chr1.1:58237135-58237154 MS.gene062177:CDS 55.0%
TCATATGGCCACCAAGTGCC+TGG - chr1.1:58237093-58237112 None:intergenic 55.0%
TTCACATCTGGCCAGGCACT+TGG + chr1.1:58237079-58237098 MS.gene062177:intron 55.0%
ACATCTGGCCAGGCACTTGG+TGG + chr1.1:58237082-58237101 MS.gene062177:intron 60.0%
CTCGATGAGGTTGCCTCCAC+CGG - chr1.1:58237130-58237149 None:intergenic 60.0%
AGGTTGCCTCCACCGGTGCA+TGG - chr1.1:58237123-58237142 None:intergenic 65.0%
GACCTTCCACCATGCACCGG+TGG + chr1.1:58237111-58237130 MS.gene062177:CDS 65.0%
TTGCCTCCACCGGTGCATGG+TGG - chr1.1:58237120-58237139 None:intergenic 65.0%
! CTCCACCGGTGCATGGTGGA+AGG - chr1.1:58237116-58237135 None:intergenic 65.0%
! CTTCCACCATGCACCGGTGG+AGG + chr1.1:58237114-58237133 MS.gene062177:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 58236668 58237246 58236668 ID=MS.gene062177
chr1.1 mRNA 58236668 58237246 58236668 ID=MS.gene062177.t1;Parent=MS.gene062177
chr1.1 exon 58236668 58236889 58236668 ID=MS.gene062177.t1.exon1;Parent=MS.gene062177.t1
chr1.1 CDS 58236668 58236889 58236668 ID=cds.MS.gene062177.t1;Parent=MS.gene062177.t1
chr1.1 exon 58237094 58237246 58237094 ID=MS.gene062177.t1.exon2;Parent=MS.gene062177.t1
chr1.1 CDS 58237094 58237246 58237094 ID=cds.MS.gene062177.t1;Parent=MS.gene062177.t1
Gene Sequence

>MS.gene062177

ATGGAAGCATCTCATGAACAACAACTCTCTTTAGGCTCTATAGAACAACAATCTCCTACCCCTTTCTCCATCATTGCTTATTCTTCTACAAGAGAAGAAGGAACAAGAGAAAGTGCACGTTACAATGTGTATGCATGCAAAACATGCAAGAAAACTTTCACTTCATTTCAAGCACTTGGAGGCCATAGAAAAGTTCACAAGAAACCTAGAGATGATAGTCAGGTTCAAGAGTTTCAATTCAAAATCAATAATAAATCAATTTCCCTTAAATTGAATAGTATCAATGGTATGGGAAATATATATGCTAGTAGCAACAACAACAACACCACCACCACTACCAACAACAACAATAACACCACCAACAACAACAACAAAACCAAGGTTTATGGGTGCACCATTTGTGGTTCTAAATTCACATCTGGCCAGGCACTTGGTGGCCATATGACCTTCCACCATGCACCGGTGGAGGCAACCTCATCGAGACCAATGGCTTTGAAACCAGACGAAGAAGATGAAGAACCACCCACAAAGAAAATGAATGTCTCTTTGGATTTGGATCTCAACGTTCCTGCAGCTTAA
Protein sequence

>MS.gene062177.t1

MEASHEQQLSLGSIEQQSPTPFSIIAYSSTREEGTRESARYNVYACKTCKKTFTSFQALGGHRKVHKKPRDDSQALGGHMTFHHAPVEATSSRPMALKPDEEDEEPPTKKMNVSLDLDLNVPAA