AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene76063

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76063.t1 MTR_6g042060 87.500 80 10 0 1 80 1 80 3.82e-47 144
MS.gene76063.t1 MTR_7g111710 92.754 69 5 0 1 69 602 670 7.04e-40 139
MS.gene76063.t1 MTR_1g068945 89.552 67 7 0 14 80 1 67 7.69e-40 125
MS.gene76063.t1 MTR_8g096550 77.586 58 13 0 23 80 5 62 3.15e-28 96.7
MS.gene76063.t1 MTR_1g112310 37.681 69 43 0 1 69 699 767 2.04e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene76063.t1 AT3G07100 78.261 69 15 0 1 69 620 688 2.18e-33 120

Find 15 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAATTGAGTCATGAATTA+AGG 0.308061 5.2:-70777261 MS.gene76063:CDS
CATACACATTTACTGAGATT+TGG 0.310882 5.2:+70777779 None:intergenic
TCCTGTCTGTGTAGGAACTC+TGG 0.429146 5.2:-70777344 MS.gene76063:intron
TCTCCCCATGAGTAGCTGAT+TGG 0.442822 5.2:+70777281 None:intergenic
TGAGTAGCTGATTGGAAAGC+TGG 0.469035 5.2:+70777289 None:intergenic
GAGAGACTGCATGGGAAGCA+TGG 0.524555 5.2:-70777225 MS.gene76063:CDS
GCTTTCCAATCAGCTACTCA+TGG 0.528786 5.2:-70777286 MS.gene76063:CDS
TACACTGACATAGCCTCCTT+AGG 0.536987 5.2:-70777742 MS.gene76063:intron
CTTTCCAATCAGCTACTCAT+GGG 0.542155 5.2:-70777285 MS.gene76063:CDS
GGAAAATAAAACACCTAAGG+AGG 0.554451 5.2:+70777729 None:intergenic
ACCTCACAAGAGAGACTGCA+TGG 0.560035 5.2:-70777234 MS.gene76063:CDS
ACTCTGGCAAAGTACACTGC+TGG 0.591069 5.2:-70777328 MS.gene76063:CDS
CCCATGCAGTCTCTCTTGTG+AGG 0.598716 5.2:+70777233 None:intergenic
TTTCCAATCAGCTACTCATG+GGG 0.686768 5.2:-70777284 MS.gene76063:CDS
CCTCACAAGAGAGACTGCAT+GGG 0.693489 5.2:-70777233 MS.gene76063:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAACAGGTTTAAAAATAGAA+TGG + chr5.2:70777316-70777335 None:intergenic 20.0%
! ACGAAATACATAGAAATTGA+AGG + chr5.2:70777289-70777308 None:intergenic 25.0%
! AGAAATTGAGTCATGAATTA+AGG - chr5.2:70777733-70777752 MS.gene76063:intron 25.0%
! ATCAATTAATCAAGAGTAAC+AGG + chr5.2:70777332-70777351 None:intergenic 25.0%
AAATGCTGACAGAATTACAT+CGG + chr5.2:70777565-70777584 None:intergenic 30.0%
CATACACATTTACTGAGATT+TGG + chr5.2:70777218-70777237 None:intergenic 30.0%
GAAGGAAAATAAAACACCTA+AGG + chr5.2:70777271-70777290 None:intergenic 30.0%
TAAACTGATACTCTAACTCA+TGG - chr5.2:70777435-70777454 MS.gene76063:intron 30.0%
! ACTTGATGACATGAGTTTAT+GGG - chr5.2:70777392-70777411 MS.gene76063:intron 30.0%
! ATTTGATGATTCTTCAGTTG+TGG - chr5.2:70777354-70777373 MS.gene76063:intron 30.0%
AATGCTGACAGAATTACATC+GGG + chr5.2:70777564-70777583 None:intergenic 35.0%
GGAAAATAAAACACCTAAGG+AGG + chr5.2:70777268-70777287 None:intergenic 35.0%
GGATCTATTTGACTATGAAC+TGG - chr5.2:70777456-70777475 MS.gene76063:intron 35.0%
TGTAATTCTGTCAGCATTTG+CGG - chr5.2:70777566-70777585 MS.gene76063:intron 35.0%
! GACTTGATGACATGAGTTTA+TGG - chr5.2:70777391-70777410 MS.gene76063:intron 35.0%
!!! TGTTTTTTTCCTGTCTGTGT+AGG - chr5.2:70777642-70777661 MS.gene76063:intron 35.0%
CTTTCCAATCAGCTACTCAT+GGG - chr5.2:70777709-70777728 MS.gene76063:intron 40.0%
TTTCCAATCAGCTACTCATG+GGG - chr5.2:70777710-70777729 MS.gene76063:intron 40.0%
ACAGAATTACATCGGGACAC+GGG + chr5.2:70777557-70777576 None:intergenic 45.0%
CATCAGCACGCAAGACTATA+TGG + chr5.2:70777600-70777619 None:intergenic 45.0%
GACAGAATTACATCGGGACA+CGG + chr5.2:70777558-70777577 None:intergenic 45.0%
GCTTTCCAATCAGCTACTCA+TGG - chr5.2:70777708-70777727 MS.gene76063:intron 45.0%
TACACTGACATAGCCTCCTT+AGG - chr5.2:70777252-70777271 MS.gene76063:CDS 45.0%
TGAGTAGCTGATTGGAAAGC+TGG + chr5.2:70777708-70777727 None:intergenic 45.0%
ACCTCACAAGAGAGACTGCA+TGG - chr5.2:70777760-70777779 MS.gene76063:CDS 50.0%
ACTCTGGCAAAGTACACTGC+TGG - chr5.2:70777666-70777685 MS.gene76063:intron 50.0%
CAGAATTACATCGGGACACG+GGG + chr5.2:70777556-70777575 None:intergenic 50.0%
CCTCACAAGAGAGACTGCAT+GGG - chr5.2:70777761-70777780 MS.gene76063:CDS 50.0%
TCCTGTCTGTGTAGGAACTC+TGG - chr5.2:70777650-70777669 MS.gene76063:intron 50.0%
TCTCCCCATGAGTAGCTGAT+TGG + chr5.2:70777716-70777735 None:intergenic 50.0%
CCCATGCAGTCTCTCTTGTG+AGG + chr5.2:70777764-70777783 None:intergenic 55.0%
GAGAGACTGCATGGGAAGCA+TGG - chr5.2:70777769-70777788 MS.gene76063:CDS 55.0%
GCCAGAGTTCCTACACAGAC+AGG + chr5.2:70777654-70777673 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 70777192 70777824 70777192 ID=MS.gene76063
chr5.2 mRNA 70777192 70777824 70777192 ID=MS.gene76063.t1;Parent=MS.gene76063
chr5.2 exon 70777743 70777824 70777743 ID=MS.gene76063.t1.exon1;Parent=MS.gene76063.t1
chr5.2 CDS 70777743 70777824 70777743 ID=cds.MS.gene76063.t1;Parent=MS.gene76063.t1
chr5.2 exon 70777192 70777352 70777192 ID=MS.gene76063.t1.exon2;Parent=MS.gene76063.t1
chr5.2 CDS 70777192 70777352 70777192 ID=cds.MS.gene76063.t1;Parent=MS.gene76063.t1
Gene Sequence

>MS.gene76063

ATGGCTGCTGAGTTTTTCAAGTACCAAATCTCAGTAAATGTGTATGCATTCAGTGATAAGTACACTGACATAGCCTCCTTAGGTGTTTTATTTTCCTTCAATTTCTATGTATTTCGTTATGCCATTCTATTTTTAAACCTGTTACTCTTGATTAATTGATATATTTGATGATTCTTCAGTTGTGGCAGTGTTTTATGATGACTTGATGACATGAGTTTATGGGCTTCAACTATGATTTGATTATAAACTGATACTCTAACTCATGGATCTATTTGACTATGAACTGGTATGTAGATGCTCAAAAAGAATTCACAAGTTATGTGTTGATTGTTGTAGTTATATCTGTAAACAATCAATGTATCCCCGTGTCCCGATGTAATTCTGTCAGCATTTGCGGTCTTCTAACCATATAGTCTTGCGTGCTGATGATCTTATACTTGAAGTAAATTATGTTTTTTTCCTGTCTGTGTAGGAACTCTGGCAAAGTACACTGCTGGTCAAGTGTATTACTTTCCAGCTTTCCAATCAGCTACTCATGGGGAGAAATTGAGTCATGAATTAAGGAGATACCTCACAAGAGAGACTGCATGGGAAGCATGGATCATATGCATTGCAGAGATACTTAGTAACTAG
Protein sequence

>MS.gene76063.t1

MAAEFFKYQISVNVYAFSDKYTDIASLGTLAKYTAGQVYYFPAFQSATHGEKLSHELRRYLTRETAWEAWIICIAEILSN