AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0719340


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0719340 MtrunA17_Chr5g0409821 98.693 153 2 0 1 153 1 153 1.27e-108 315
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0719340 AT1G32060.1 69.281 153 32 4 1 153 1 138 1.61e-63 199

Find 18 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGGATGATTACCATTCTT+TGG 0.234705 5_1:-14413181 Msa0719340:CDS
GAATCAGGATTTCCACCTTT+TGG 0.277176 5_1:+14413240 None:intergenic
CTGATAAGTGTGTTTGAATC+AGG 0.321702 5_1:+14413225 None:intergenic
ATTGAGATGTTTGTTCTTAG+AGG 0.359760 5_1:+14413495 None:intergenic
ATTGGTCTAGCAGCTGATTC+AGG 0.370444 5_1:-14413324 Msa0719340:CDS
CACAACCACTGTGATATGTT+TGG 0.440482 5_1:-14413199 Msa0719340:CDS
AGTTAAAGCTATTAAAGCTT+AGG 0.446558 5_1:-14413082 None:intergenic
TACCATTCTTTGGATAGAAC+TGG 0.449333 5_1:-14413171 Msa0719340:CDS
TACCAGTTCTATCCAAAGAA+TGG 0.458109 5_1:+14413169 None:intergenic
AGATCAAAATCATTAGCTCT+TGG 0.471925 5_1:+14413117 None:intergenic
CTAGCAGCTGATTCAGGATG+TGG 0.497361 5_1:-14413318 Msa0719340:CDS
TACTTGATAACATGTGGAGC+AGG 0.532032 5_1:-14413366 Msa0719340:CDS
GACTCACAGACAATTGTGAT+TGG 0.537034 5_1:-14413342 Msa0719340:CDS
GGTGCAGCAGAGCCACCAAA+AGG 0.546897 5_1:-14413255 Msa0719340:CDS
AGAACTGGTAGAAAAGAGAA+AGG 0.567928 5_1:-14413156 Msa0719340:CDS
GCAGCAGAGCCACCAAAAGG+TGG 0.593621 5_1:-14413252 Msa0719340:CDS
AGAAGATACTTGATAACATG+TGG 0.629598 5_1:-14413372 Msa0719340:CDS
ATCATCCAAACATATCACAG+TGG 0.763501 5_1:+14413194 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTGGTTTTAATCAAAAAC+AGG - chr5_1:14413157-14413176 Msa0719340:CDS 25.0%
ATTGAGATGTTTGTTCTTAG+AGG + chr5_1:14413116-14413135 None:intergenic 30.0%
!!! ACATGTGTTTTTGATGATGT+TGG + chr5_1:14413140-14413159 None:intergenic 30.0%
ACATCATCAAAAACACATGT+TGG - chr5_1:14413140-14413159 Msa0719340:CDS 30.0%
! AGAAGATACTTGATAACATG+TGG - chr5_1:14413236-14413255 Msa0719340:CDS 30.0%
TTTGGATGATTACCATTCTT+TGG - chr5_1:14413427-14413446 Msa0719340:CDS 30.0%
! AGATCAAAATCATTAGCTCT+TGG + chr5_1:14413494-14413513 None:intergenic 30.0%
! TCTTCTGTTGTTGCTCTTTT+TGG + chr5_1:14413201-14413220 None:intergenic 35.0%
! AGAAGACTCACAAGTGTTTT+TGG - chr5_1:14413329-14413348 Msa0719340:CDS 35.0%
CTGATAAGTGTGTTTGAATC+AGG + chr5_1:14413386-14413405 None:intergenic 35.0%
ATCATCCAAACATATCACAG+TGG + chr5_1:14413417-14413436 None:intergenic 35.0%
TACCATTCTTTGGATAGAAC+TGG - chr5_1:14413437-14413456 Msa0719340:CDS 35.0%
TACCAGTTCTATCCAAAGAA+TGG + chr5_1:14413442-14413461 None:intergenic 35.0%
AGAACTGGTAGAAAAGAGAA+AGG - chr5_1:14413452-14413471 Msa0719340:CDS 35.0%
! TACTTGATAACATGTGGAGC+AGG - chr5_1:14413242-14413261 Msa0719340:CDS 40.0%
GACTCACAGACAATTGTGAT+TGG - chr5_1:14413266-14413285 Msa0719340:CDS 40.0%
!!! AGACTCACAAGTGTTTTTGG+AGG - chr5_1:14413332-14413351 Msa0719340:CDS 40.0%
! GAATCAGGATTTCCACCTTT+TGG + chr5_1:14413371-14413390 None:intergenic 40.0%
CACAACCACTGTGATATGTT+TGG - chr5_1:14413409-14413428 Msa0719340:CDS 40.0%
! ATTGGTCTAGCAGCTGATTC+AGG - chr5_1:14413284-14413303 Msa0719340:CDS 45.0%
! TCAGGATTTCCACCTTTTGG+TGG + chr5_1:14413368-14413387 None:intergenic 45.0%
! CTAGCAGCTGATTCAGGATG+TGG - chr5_1:14413290-14413309 Msa0719340:CDS 50.0%
GGTGCAGCAGAGCCACCAAA+AGG - chr5_1:14413353-14413372 Msa0719340:CDS 60.0%
GCAGCAGAGCCACCAAAAGG+TGG - chr5_1:14413356-14413375 Msa0719340:CDS 60.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 14413083 14413547 14413083 ID=Msa0719340;Name=Msa0719340
chr5_1 mRNA 14413083 14413547 14413083 ID=Msa0719340-mRNA-1;Parent=Msa0719340;Name=Msa0719340-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|-1|0|1|-1|1|1|0|154
chr5_1 exon 14413083 14413547 14413083 ID=Msa0719340-mRNA-1:exon:5675;Parent=Msa0719340-mRNA-1
chr5_1 CDS 14413083 14413547 14413083 ID=Msa0719340-mRNA-1:cds;Parent=Msa0719340-mRNA-1
Gene Sequence

>Msa0719340

ATGGCAGCATGTACTGTCTACTCAACACAACCTCTAAGAACAAACATCTCAATTCCAACATCATCAAAAACACATGTTGGTTTTAATCAAAAACAGGTAGTGTTCTACACAACAACCAAAAAGAGCAACAACAGAAGAACTAACAGTAACAGCAGAAGATACTTGATAACATGTGGAGCAGGTGACTCACAGACAATTGTGATTGGTCTAGCAGCTGATTCAGGATGTGGAAAAAGTACTTTCATGAGAAGACTCACAAGTGTTTTTGGAGGTGCAGCAGAGCCACCAAAAGGTGGAAATCCTGATTCAAACACACTTATCAGTGACACAACCACTGTGATATGTTTGGATGATTACCATTCTTTGGATAGAACTGGTAGAAAAGAGAAAGGTGTTACTGCACTTGATCCAAGAGCTAATGATTTTGATCTTATGTATGAACAAGTTAAAGCTATTAAAGCTTAG

Protein sequence

>Msa0719340

MAACTVYSTQPLRTNISIPTSSKTHVGFNQKQVVFYTTTKKSNNRRTNSNSRRYLITCGAGDSQTIVIGLAADSGCGKSTFMRRLTSVFGGAAEPPKGGNPDSNTLISDTTTVICLDDYHSLDRTGRKEKGVTALDPRANDFDLMYEQVKAIKA*