AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene030919

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene030919.t1 MTR_8g089170 90.385 156 15 0 1 156 1 156 8.14e-97 276
MS.gene030919.t1 MTR_8g089130 82.278 158 26 2 1 156 1 158 7.35e-88 253
MS.gene030919.t1 MTR_8g089145 87.671 73 9 0 1 73 1 73 1.25e-42 136
MS.gene030919.t1 MTR_1g089830 37.415 147 63 4 4 150 3 120 2.42e-21 84.3
MS.gene030919.t1 MTR_4g028990 53.425 73 32 1 81 151 20 92 5.77e-18 74.3
MS.gene030919.t1 MTR_1g045040 38.621 145 63 4 7 150 6 125 5.49e-17 72.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATAAAACTGGCTTGTCTTT+TGG 0.254968 4.3:+11238167 None:intergenic
CTTTGAGGTTTCCCCAGTTT+TGG 0.256311 4.3:+11238123 None:intergenic
TTTATACCTTCAAATGAAAT+TGG 0.266437 4.3:-11237673 MS.gene030919:CDS
TGGCGCCATGCTGGAGTTGC+TGG 0.314815 4.3:+11238194 None:intergenic
GATGTTTCTGATTCAGATAA+TGG 0.318368 4.3:-11238008 MS.gene030919:intron
ATCCTCAAACTACGTCTCTT+TGG 0.326261 4.3:+11237820 None:intergenic
CTGTTCGTAACAAGTTCTTT+TGG 0.340372 4.3:+11238077 None:intergenic
TTTGGTCCCTGGCGCCATGC+TGG 0.374123 4.3:+11238185 None:intergenic
CCAAGACCAATTTCATTTGA+AGG 0.378872 4.3:+11237667 None:intergenic
CCTTCAAATGAAATTGGTCT+TGG 0.383519 4.3:-11237667 MS.gene030919:CDS
GAAAACAACGTTTGAGAGAA+TGG 0.387976 4.3:+11238099 None:intergenic
GTGGACTAAGATACCAAAAC+TGG 0.405891 4.3:-11238136 MS.gene030919:CDS
CCACATGCATTGCATAAAAC+TGG 0.410323 4.3:+11238155 None:intergenic
CTCCAAAGAGACGTAGTTTG+AGG 0.422942 4.3:-11237822 MS.gene030919:CDS
AGCAACTCCAGCATGGCGCC+AGG 0.436034 4.3:-11238192 MS.gene030919:CDS
TCCCTTCTACATAGAAGAAC+CGG 0.461538 4.3:+11237624 None:intergenic
GTTTGAGAGAATGGTCTTTG+AGG 0.475222 4.3:+11238108 None:intergenic
TCTTCTGAGGATGACTCATC+TGG 0.485391 4.3:+11237724 None:intergenic
ATCTGAATCAGAAACATCAA+TGG 0.539843 4.3:+11238013 None:intergenic
GCAGTTCTTCTTAAACCAGC+CGG 0.561335 4.3:-11237643 MS.gene030919:CDS
GAACAATAAGGCCTCTTCTG+AGG 0.569819 4.3:+11237711 None:intergenic
GCAACTCCAGCATGGCGCCA+GGG 0.585142 4.3:-11238191 MS.gene030919:CDS
AGATGAGTCATCCTCAGAAG+AGG 0.600054 4.3:-11237722 MS.gene030919:CDS
TTCTACATAGAAGAACCGGC+TGG 0.612139 4.3:+11237628 None:intergenic
CAATCAGAAGATGACACCGA+TGG 0.614691 4.3:-11237794 MS.gene030919:CDS
TGGACTAAGATACCAAAACT+GGG 0.618651 4.3:-11238135 MS.gene030919:CDS
AAAGAACTTGTTACGAACAG+TGG 0.644687 4.3:-11238074 MS.gene030919:CDS
CATCACCAGCAACTCCAGCA+TGG 0.651498 4.3:-11238199 MS.gene030919:CDS
GGACTAAGATACCAAAACTG+GGG 0.731002 4.3:-11238134 MS.gene030919:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTATACCTTCAAATGAAAT+TGG - chr4.3:11238163-11238182 MS.gene030919:CDS 20.0%
! TGTAAAGAAAAGAGTGAAAA+TGG + chr4.3:11237876-11237895 None:intergenic 25.0%
!! GTTCACATTTTTGAACAATA+AGG + chr4.3:11238140-11238159 None:intergenic 25.0%
!!! GATATATACTACTTTTGTGA+GGG - chr4.3:11237898-11237917 MS.gene030919:intron 25.0%
!!! TGATATATACTACTTTTGTG+AGG - chr4.3:11237897-11237916 MS.gene030919:intron 25.0%
ATCTGAATCAGAAACATCAA+TGG + chr4.3:11237826-11237845 None:intergenic 30.0%
! GATGTTTCTGATTCAGATAA+TGG - chr4.3:11237828-11237847 MS.gene030919:CDS 30.0%
! TCTTGTTGAAACTTTTCCAT+CGG + chr4.3:11238061-11238080 None:intergenic 30.0%
CCAAGACCAATTTCATTTGA+AGG + chr4.3:11238172-11238191 None:intergenic 35.0%
GAAAACAACGTTTGAGAGAA+TGG + chr4.3:11237740-11237759 None:intergenic 35.0%
TGGACTAAGATACCAAAACT+GGG - chr4.3:11237701-11237720 MS.gene030919:CDS 35.0%
! CCTTCAAATGAAATTGGTCT+TGG - chr4.3:11238169-11238188 MS.gene030919:CDS 35.0%
! CTGTTCGTAACAAGTTCTTT+TGG + chr4.3:11237762-11237781 None:intergenic 35.0%
!! AAAGAACTTGTTACGAACAG+TGG - chr4.3:11237762-11237781 MS.gene030919:CDS 35.0%
!! ATATACTACTTTTGTGAGGG+TGG - chr4.3:11237901-11237920 MS.gene030919:intron 35.0%
!! TATACTACTTTTGTGAGGGT+GGG - chr4.3:11237902-11237921 MS.gene030919:intron 35.0%
!!! CATAAAACTGGCTTGTCTTT+TGG + chr4.3:11237672-11237691 None:intergenic 35.0%
ATCCTCAAACTACGTCTCTT+TGG + chr4.3:11238019-11238038 None:intergenic 40.0%
CCACATGCATTGCATAAAAC+TGG + chr4.3:11237684-11237703 None:intergenic 40.0%
GGACTAAGATACCAAAACTG+GGG - chr4.3:11237702-11237721 MS.gene030919:CDS 40.0%
GTTTGAGAGAATGGTCTTTG+AGG + chr4.3:11237731-11237750 None:intergenic 40.0%
! GTGGACTAAGATACCAAAAC+TGG - chr4.3:11237700-11237719 MS.gene030919:CDS 40.0%
!! CCAGTTTTATGCAATGCATG+TGG - chr4.3:11237681-11237700 MS.gene030919:CDS 40.0%
AGATGAGTCATCCTCAGAAG+AGG - chr4.3:11238114-11238133 MS.gene030919:CDS 45.0%
CAATCAGAAGATGACACCGA+TGG - chr4.3:11238042-11238061 MS.gene030919:CDS 45.0%
CTCCAAAGAGACGTAGTTTG+AGG - chr4.3:11238014-11238033 MS.gene030919:CDS 45.0%
GAACAATAAGGCCTCTTCTG+AGG + chr4.3:11238128-11238147 None:intergenic 45.0%
GCAGTTCTTCTTAAACCAGC+CGG - chr4.3:11238193-11238212 MS.gene030919:CDS 45.0%
! TCTTCTGAGGATGACTCATC+TGG + chr4.3:11238115-11238134 None:intergenic 45.0%
!!! CTTTGAGGTTTCCCCAGTTT+TGG + chr4.3:11237716-11237735 None:intergenic 45.0%
CATCACCAGCAACTCCAGCA+TGG - chr4.3:11237637-11237656 MS.gene030919:CDS 55.0%
!! CTGGCTTGTCTTTTGGTCCC+TGG + chr4.3:11237665-11237684 None:intergenic 55.0%
AGCAACTCCAGCATGGCGCC+AGG - chr4.3:11237644-11237663 MS.gene030919:CDS 65.0%
GCAACTCCAGCATGGCGCCA+GGG - chr4.3:11237645-11237664 MS.gene030919:CDS 65.0%
TGGCGCCATGCTGGAGTTGC+TGG + chr4.3:11237645-11237664 None:intergenic 65.0%
TTTGGTCCCTGGCGCCATGC+TGG + chr4.3:11237654-11237673 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 11237630 11238228 11237630 ID=MS.gene030919
chr4.3 mRNA 11237630 11238228 11237630 ID=MS.gene030919.t1;Parent=MS.gene030919
chr4.3 exon 11238009 11238228 11238009 ID=MS.gene030919.t1.exon1;Parent=MS.gene030919.t1
chr4.3 CDS 11238009 11238228 11238009 ID=cds.MS.gene030919.t1;Parent=MS.gene030919.t1
chr4.3 exon 11237630 11237880 11237630 ID=MS.gene030919.t1.exon2;Parent=MS.gene030919.t1
chr4.3 CDS 11237630 11237880 11237630 ID=cds.MS.gene030919.t1;Parent=MS.gene030919.t1
Gene Sequence

>MS.gene030919

ATGGATTCATCACCAGCAACTCCAGCATGGCGCCAGGGACCAAAAGACAAGCCAGTTTTATGCAATGCATGTGGACTAAGATACCAAAACTGGGGAAACCTCAAAGACCATTCTCTCAAACGTTGTTTTCCAAAAGAACTTGTTACGAACAGTGGCAACAGTAGCAACAACAGTCTCAAAGAAAGTTCATCAACCATTGATGTTTCTGATTCAGATAATGGTATGTGTTTATACTAGTACTAGCCATTTTCACTCTTTTCTTTACAATGATATATACTACTTTTGTGAGGGTGGGCGTGCGTGAATACTTCTTTTAAATTGTCAATAAATAAGAGAATTTTTACTCAGATGAAAAAGATTCAGATTCATGCAAGTCTGCAGTCTCTCCAAAGAGACGTAGTTTGAGGATTATCAATCAGAAGATGACACCGATGGAAAAGTTTCAACAAGAACTTCTCGATGAGTTGAAAAATCACGAGATACCAGATGAGTCATCCTCAGAAGAGGCCTTATTGTTCAAAAATGTGAACAACTTTATACCTTCAAATGAAATTGGTCTTGGAGCAGTTCTTCTTAAACCAGCCGGTTCTTCTATGTAG
Protein sequence

>MS.gene030919.t1

MDSSPATPAWRQGPKDKPVLCNACGLRYQNWGNLKDHSLKRCFPKELVTNSGNSSNNSLKESSSTIDVSDSDNDEKDSDSCKSAVSPKRRSLRIINQKMTPMEKFQQELLDELKNHEIPDESSSEEALLFKNVNNFIPSNEIGLGAVLLKPAGSSM