AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene40425

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40425.t1 MTR_6g048860 82.692 52 9 0 39 90 266 317 3.42e-24 94.0
MS.gene40425.t1 MTR_3g037670 80.952 42 8 0 39 80 224 265 8.42e-18 76.3
MS.gene40425.t1 MTR_4g007610 78.947 57 12 0 39 95 294 350 1.07e-17 76.6
MS.gene40425.t1 MTR_8g107350 76.190 42 10 0 39 80 192 233 1.10e-16 73.2
MS.gene40425.t1 MTR_5g038770 50.847 59 28 1 11 68 6 64 9.00e-12 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAGGATAAACAACATTATT+TGG 0.112137 6.3:+70871270 MS.gene40425:intron
AAATTATGATGTTAATAAAA+TGG 0.232813 6.3:+70871132 MS.gene40425:CDS
TCTATCTGCAACTGTGAAAT+TGG 0.248781 6.3:-70870698 None:intergenic
TTATATTTCAGGGATAAGTT+TGG 0.382899 6.3:+70871085 MS.gene40425:intron
GTGTTACCTGTGAGCGAAAG+AGG 0.447507 6.3:-70870735 None:intergenic
GTGAAGCATTCCACCATTCT+CGG 0.464051 6.3:-70871450 None:intergenic
AGGATGAAGTTCAATAGATC+CGG 0.465533 6.3:-70870675 None:intergenic
AACATGAGAAACTTAAGAAA+AGG 0.495000 6.3:+70871317 MS.gene40425:CDS
AGGACTTACTTCATTACTCA+TGG 0.496503 6.3:-70871173 None:intergenic
ATAAAATGGTTGTTAAAGCA+TGG 0.505549 6.3:+70871146 MS.gene40425:CDS
CCGGGACTGTGAAGCTCGAT+CGG 0.546676 6.3:-70870656 None:intergenic
GAATAGGGTGACTCCGAGAA+TGG 0.550110 6.3:+70871437 MS.gene40425:intron
CCGATCGAGCTTCACAGTCC+CGG 0.552827 6.3:+70870656 MS.gene40425:CDS
CGGTGAAGTGTGAAGCTCCA+TGG 0.558822 6.3:-70870636 None:intergenic
ATCTGCAACTGTGAAATTGG+AGG 0.566506 6.3:-70870695 None:intergenic
GGATGAAGTTCAATAGATCC+GGG 0.594180 6.3:-70870674 None:intergenic
GGATAAAGCATCTAAGCGCA+AGG 0.626619 6.3:+70871291 MS.gene40425:CDS
TAGGGTGACTCCGAGAATGG+TGG 0.628698 6.3:+70871440 MS.gene40425:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATTATGATGTTAATAAAA+TGG + chr6.3:70871132-70871151 MS.gene40425:CDS 10.0%
!! AAGTATAAAATTTATATTTC+AGG + chr6.3:70871074-70871093 MS.gene40425:intron 10.0%
!! AGTATAAAATTTATATTTCA+GGG + chr6.3:70871075-70871094 MS.gene40425:intron 10.0%
!! ATTGATTATATTATTTAATC+AGG + chr6.3:70871252-70871271 MS.gene40425:intron 10.0%
!! AACACAAAATCAATTAAATT+TGG - chr6.3:70871356-70871375 None:intergenic 15.0%
!! ACACAAAATCAATTAAATTT+GGG - chr6.3:70871355-70871374 None:intergenic 15.0%
!! AAAGAAGATTTCTTATTCTT+TGG - chr6.3:70871017-70871036 None:intergenic 20.0%
! AACATGAGAAACTTAAGAAA+AGG + chr6.3:70871317-70871336 MS.gene40425:CDS 25.0%
! ATAAAATGGTTGTTAAAGCA+TGG + chr6.3:70871146-70871165 MS.gene40425:CDS 25.0%
! TCAGGATAAACAACATTATT+TGG + chr6.3:70871270-70871289 MS.gene40425:intron 25.0%
! TTATATTTCAGGGATAAGTT+TGG + chr6.3:70871085-70871104 MS.gene40425:intron 25.0%
! TTTGTGTGTTTGATTGAATA+GGG + chr6.3:70871422-70871441 MS.gene40425:intron 25.0%
CATGTGTTGTAATATACTAG+AGG - chr6.3:70871196-70871215 None:intergenic 30.0%
CTTTGTGTGTTTGATTGAAT+AGG + chr6.3:70871421-70871440 MS.gene40425:intron 30.0%
AGGACTTACTTCATTACTCA+TGG - chr6.3:70871176-70871195 None:intergenic 35.0%
AGGATGAAGTTCAATAGATC+CGG - chr6.3:70870678-70870697 None:intergenic 35.0%
TCTATCTGCAACTGTGAAAT+TGG - chr6.3:70870701-70870720 None:intergenic 35.0%
ATCTGCAACTGTGAAATTGG+AGG - chr6.3:70870698-70870717 None:intergenic 40.0%
CTTTGGCAACATCAAACACA+TGG - chr6.3:70871000-70871019 None:intergenic 40.0%
GGATGAAGTTCAATAGATCC+GGG - chr6.3:70870677-70870696 None:intergenic 40.0%
!!! TTTTTTCCTCTTTCGCTCAC+AGG + chr6.3:70870729-70870748 MS.gene40425:CDS 40.0%
! GGATAAAGCATCTAAGCGCA+AGG + chr6.3:70871291-70871310 MS.gene40425:CDS 45.0%
! GTGAAGCATTCCACCATTCT+CGG - chr6.3:70871453-70871472 None:intergenic 45.0%
GAATAGGGTGACTCCGAGAA+TGG + chr6.3:70871437-70871456 MS.gene40425:intron 50.0%
GTGTTACCTGTGAGCGAAAG+AGG - chr6.3:70870738-70870757 None:intergenic 50.0%
TAGGGTGACTCCGAGAATGG+TGG + chr6.3:70871440-70871459 MS.gene40425:intron 55.0%
CCGATCGAGCTTCACAGTCC+CGG + chr6.3:70870656-70870675 MS.gene40425:CDS 60.0%
CCGGGACTGTGAAGCTCGAT+CGG - chr6.3:70870659-70870678 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 70870638 70871479 70870638 ID=MS.gene40425
chr6.3 mRNA 70870638 70871479 70870638 ID=MS.gene40425.t1;Parent=MS.gene40425
chr6.3 exon 70870638 70870750 70870638 ID=MS.gene40425.t1.exon1;Parent=MS.gene40425.t1
chr6.3 CDS 70870638 70870750 70870638 ID=cds.MS.gene40425.t1;Parent=MS.gene40425.t1
chr6.3 exon 70871096 70871186 70871096 ID=MS.gene40425.t1.exon2;Parent=MS.gene40425.t1
chr6.3 CDS 70871096 70871186 70871096 ID=cds.MS.gene40425.t1;Parent=MS.gene40425.t1
chr6.3 exon 70871274 70871338 70871274 ID=MS.gene40425.t1.exon3;Parent=MS.gene40425.t1
chr6.3 CDS 70871274 70871338 70871274 ID=cds.MS.gene40425.t1;Parent=MS.gene40425.t1
chr6.3 exon 70871443 70871479 70871443 ID=MS.gene40425.t1.exon4;Parent=MS.gene40425.t1
chr6.3 CDS 70871443 70871479 70871443 ID=cds.MS.gene40425.t1;Parent=MS.gene40425.t1
Gene Sequence

>MS.gene40425

ATGGAGCTTCACACTTCACCGATCGAGCTTCACAGTCCCGGATCTATTGAACTTCATCCTCCAATTTCACAGTTGCAGATAGAAACAAATCTTTTTTCCTCTTTCGCTCACAGGTAACACTTCTCGAATTCTTCTTATGTTTTGCATTTTTCGCGCTTTCAATTTTGATTTCTCTTAGATTTCAGCGCAATTATCTTCGATTCATGCTTTTTCTATATTATGAATCACAATTTTGATCTATTTCGCTCACATTGTTTAATTTTCGTTTTGAAATTCTATGTGTTTAATTTTCGTTTCACAATTTAACTCAAATTCTTCTTGTTCTGTTTCACATTTGTGATTTATGTTTTCTTTGAAATCCATGTGTTTGATGTTGCCAAAGAATAAGAAATCTTCTTTGTTTAATATATTTTTTAATTTTGCGTTATTTATTAATAAGTATAAAATTTATATTTCAGGGATAAGTTTGGCAATTTTTTTAAAGAATTAGATCAAAATTATGATGTTAATAAAATGGTTGTTAAAGCATGGAACTCCATGAGTAATGAAGTAAGTCCTCTAGTATATTACAACACATGCAATTTGATGAACATAAATAATGTTTGTCTTTTAAAATTGATTATATTATTTAATCAGGATAAACAACATTATTTGGATAAAGCATCTAAGCGCAAGGCAAAACATGAGAAACTTAAGAAAAGGTACTATGTTTATCCCAAATTTAATTGATTTTGTGTTACTGAACTCAATTTCTAATAATATTCTTATAATTGTGTGAATTATCTTTGTGTGTTTGATTGAATAGGGTGACTCCGAGAATGGTGGAATGCTTCACAATTTGA
Protein sequence

>MS.gene40425.t1

MELHTSPIELHSPGSIELHPPISQLQIETNLFSSFAHRDKFGNFFKELDQNYDVNKMVVKAWNSMSNEDKQHYLDKASKRKAKHEKLKKRVTPRMVECFTI