AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049346


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049346.t1 MTR_3g095180 98.824 85 1 0 1 85 1 85 6.75e-59 174
MS.gene049346.t1 MTR_8g092340 52.941 85 32 4 1 85 1 77 5.49e-21 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 16 sgRNAs with CRISPR-Local

Find 20 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCATCCATATTCAAGTTAA+AGG 0.155938 3.1:+75911300 MS.gene049346:CDS
AGGTACCTTTAACTTGAATA+TGG 0.246398 3.1:-75911305 None:intergenic
TGCACTATTTAATTGTGAAT+TGG 0.396593 3.1:-75911600 None:intergenic
ATTGGTGGTTTCCTTGATGC+TGG 0.439868 3.1:-75911582 None:intergenic
TGTTGACATCCTCACTACTT+TGG 0.458998 3.1:-75911464 None:intergenic
CAACAAAGCTCAACAACATA+AGG 0.461599 3.1:+75911482 MS.gene049346:CDS
ACCTTTAACTTGAATATGGA+TGG 0.490545 3.1:-75911301 None:intergenic
ACTATTTAATTGTGAATTGG+TGG 0.515565 3.1:-75911597 None:intergenic
GACATGTTTAAGCTAAAAGA+AGG 0.527331 3.1:+75911516 MS.gene049346:CDS
TATGGATGGAGAAGAAGCAA+AGG 0.568511 3.1:-75911287 None:intergenic
TGGATTATACTCCAGCATCA+AGG 0.596772 3.1:+75911571 MS.gene049346:CDS
AATAAACAACCAAAGTAGTG+AGG 0.645718 3.1:+75911455 MS.gene049346:CDS
CAAAGCTCAACAACATAAGG+AGG 0.647677 3.1:+75911485 MS.gene049346:CDS
ATGTTTAAGCTAAAAGAAGG+AGG 0.667536 3.1:+75911519 MS.gene049346:CDS
AAAGAAGGAGGAGATAACGT+TGG 0.669136 3.1:+75911531 MS.gene049346:CDS
TGATGCTGGAGTATAATCCA+TGG 0.719915 3.1:-75911568 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAAACAGAAAATAAAAA+TGG - chr3.1:75911388-75911407 None:intergenic 10.0%
!! TAAAAAAAATATTACAACAT+TGG + chr3.1:75911349-75911368 MS.gene049346:intron 10.0%
!!! AATTTTTCTTACATTTTTTT+TGG + chr3.1:75911408-75911427 MS.gene049346:intron 10.0%
!!! TGTAATATTTTTTTTAGCTA+TGG - chr3.1:75911345-75911364 None:intergenic 15.0%
AATAAACAACCAAAGTAGTG+AGG + chr3.1:75911455-75911474 MS.gene049346:CDS 30.0%
ATGTTTAAGCTAAAAGAAGG+AGG + chr3.1:75911519-75911538 MS.gene049346:CDS 30.0%
GACATGTTTAAGCTAAAAGA+AGG + chr3.1:75911516-75911535 MS.gene049346:CDS 30.0%
! CTATGGATATTTGAAGCAAA+AGG - chr3.1:75911328-75911347 None:intergenic 30.0%
! TCCATCCATATTCAAGTTAA+AGG + chr3.1:75911300-75911319 MS.gene049346:CDS 30.0%
!! ACCTTTAACTTGAATATGGA+TGG - chr3.1:75911304-75911323 None:intergenic 30.0%
!! AGGTACCTTTAACTTGAATA+TGG - chr3.1:75911308-75911327 None:intergenic 30.0%
CAACAAAGCTCAACAACATA+AGG + chr3.1:75911482-75911501 MS.gene049346:CDS 35.0%
AAAGAAGGAGGAGATAACGT+TGG + chr3.1:75911531-75911550 MS.gene049346:CDS 40.0%
CAAAGCTCAACAACATAAGG+AGG + chr3.1:75911485-75911504 MS.gene049346:CDS 40.0%
TATGGATGGAGAAGAAGCAA+AGG - chr3.1:75911290-75911309 None:intergenic 40.0%
TGATGCTGGAGTATAATCCA+TGG - chr3.1:75911571-75911590 None:intergenic 40.0%
TGGATTATACTCCAGCATCA+AGG + chr3.1:75911571-75911590 MS.gene049346:CDS 40.0%
TGTTGACATCCTCACTACTT+TGG - chr3.1:75911467-75911486 None:intergenic 40.0%
!!! TGGTTCTGATGTTTTCACCA+TGG + chr3.1:75911551-75911570 MS.gene049346:CDS 40.0%
! ATTGGTGGTTTCCTTGATGC+TGG - chr3.1:75911585-75911604 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 75911240 75911614 75911240 ID=MS.gene049346
chr3.1 mRNA 75911240 75911614 75911240 ID=MS.gene049346.t1;Parent=MS.gene049346
chr3.1 exon 75911240 75911321 75911240 ID=MS.gene049346.t1.exon1;Parent=MS.gene049346.t1
chr3.1 CDS 75911240 75911321 75911240 ID=cds.MS.gene049346.t1;Parent=MS.gene049346.t1
chr3.1 exon 75911439 75911614 75911439 ID=MS.gene049346.t1.exon2;Parent=MS.gene049346.t1
chr3.1 CDS 75911439 75911614 75911439 ID=cds.MS.gene049346.t1;Parent=MS.gene049346.t1
Gene Sequence

>MS.gene049346

ATGGTTGCTTCACAAAACAAACGCATTCTACAAGTGATTTTTGTTCTCCTTTGCTTCTTCTCCATCCATATTCAAGTTAAAGGTACCTTTTGCTTCAAATATCCATAGCTAAAAAAAATATTACAACATTGGATTTAGAATATTTCCATTTTTATTTTCTGTTTAATTAATTTTTCTTACATTTTTTTTGGTTATGCAGCAAGAGTATTGAAAGAAATAAACAACCAAAGTAGTGAGGATGTCAACAAAGCTCAACAACATAAGGAGGTACATGCTGACATGTTTAAGCTAAAAGAAGGAGGAGATAACGTTGGTTCTGATGTTTTCACCATGGATTATACTCCAGCATCAAGGAAACCACCAATTCACAATTAA

Protein sequence

>MS.gene049346.t1

MVASQNKRILQVIFVLLCFFSIHIQVKARVLKEINNQSSEDVNKAQQHKEVHADMFKLKEGGDNVGSDVFTMDYTPASRKPPIHN