AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0772150


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0772150 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
Msa0772150 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_2:+46305289 Msa0772150:CDS
GAATCAGGATTTCCACCTTT+TGG 0.277176 5_2:-46305230 None:intergenic
CTGATAAGTGTGTTTGAATC+AGG 0.321702 5_2:-46305245 None:intergenic
ATTGAGATGTTTGTTCTTAG+AGG 0.359760 5_2:-46304975 None:intergenic
ATTGGTCTAGCAGCTGATTC+AGG 0.370444 5_2:+46305146 Msa0772150:CDS
CACAACCACTGTGATATGTT+TGG 0.440482 5_2:+46305271 Msa0772150:CDS
AGTTAAAGCTATTAAAGCTT+AGG 0.446558 5_2:+46305388 Msa0772150:CDS
TACCATTCTTTGGATAGAAC+TGG 0.449333 5_2:+46305299 Msa0772150:CDS
TACCAGTTCTATCCAAAGAA+TGG 0.458109 5_2:-46305301 None:intergenic
AGATCAAAATCATTAGCTCT+TGG 0.471925 5_2:-46305353 None:intergenic
CTAGCAGCTGATTCAGGATG+TGG 0.497361 5_2:+46305152 Msa0772150:CDS
TACTTGATAACATGTGGAGC+AGG 0.532032 5_2:+46305104 Msa0772150:CDS
GACTCACAGACAATTGTGAT+TGG 0.537034 5_2:+46305128 Msa0772150:CDS
GGTGCAGCAGAGCCACCAAA+AGG 0.546897 5_2:+46305215 Msa0772150:CDS
AGAACTGGTAGAAAAGAGAA+AGG 0.567928 5_2:+46305314 Msa0772150:CDS
GCAGCAGAGCCACCAAAAGG+TGG 0.593621 5_2:+46305218 Msa0772150:CDS
AGAAGATACTTGATAACATG+TGG 0.629598 5_2:+46305098 Msa0772150:CDS
ATCATCCAAACATATCACAG+TGG 0.763501 5_2:-46305276 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTGGTTTTAATCAAAAAC+AGG + chr5_2:46305019-46305038 Msa0772150:CDS 25.0%
ATTGAGATGTTTGTTCTTAG+AGG - chr5_2:46304978-46304997 None:intergenic 30.0%
!!! ACATGTGTTTTTGATGATGT+TGG - chr5_2:46305002-46305021 None:intergenic 30.0%
ACATCATCAAAAACACATGT+TGG + chr5_2:46305002-46305021 Msa0772150:CDS 30.0%
! AGAAGATACTTGATAACATG+TGG + chr5_2:46305098-46305117 Msa0772150:CDS 30.0%
TTTGGATGATTACCATTCTT+TGG + chr5_2:46305289-46305308 Msa0772150:CDS 30.0%
! AGATCAAAATCATTAGCTCT+TGG - chr5_2:46305356-46305375 None:intergenic 30.0%
! TCTTCTGTTGTTGCTCTTTT+TGG - chr5_2:46305063-46305082 None:intergenic 35.0%
! AGAAGACTCACAAGTGTTTT+TGG + chr5_2:46305191-46305210 Msa0772150:CDS 35.0%
CTGATAAGTGTGTTTGAATC+AGG - chr5_2:46305248-46305267 None:intergenic 35.0%
ATCATCCAAACATATCACAG+TGG - chr5_2:46305279-46305298 None:intergenic 35.0%
TACCATTCTTTGGATAGAAC+TGG + chr5_2:46305299-46305318 Msa0772150:CDS 35.0%
TACCAGTTCTATCCAAAGAA+TGG - chr5_2:46305304-46305323 None:intergenic 35.0%
AGAACTGGTAGAAAAGAGAA+AGG + chr5_2:46305314-46305333 Msa0772150:CDS 35.0%
! TACTTGATAACATGTGGAGC+AGG + chr5_2:46305104-46305123 Msa0772150:CDS 40.0%
GACTCACAGACAATTGTGAT+TGG + chr5_2:46305128-46305147 Msa0772150:CDS 40.0%
!!! AGACTCACAAGTGTTTTTGG+AGG + chr5_2:46305194-46305213 Msa0772150:CDS 40.0%
! GAATCAGGATTTCCACCTTT+TGG - chr5_2:46305233-46305252 None:intergenic 40.0%
CACAACCACTGTGATATGTT+TGG + chr5_2:46305271-46305290 Msa0772150:CDS 40.0%
! ATTGGTCTAGCAGCTGATTC+AGG + chr5_2:46305146-46305165 Msa0772150:CDS 45.0%
! TCAGGATTTCCACCTTTTGG+TGG - chr5_2:46305230-46305249 None:intergenic 45.0%
! CTAGCAGCTGATTCAGGATG+TGG + chr5_2:46305152-46305171 Msa0772150:CDS 50.0%
GGTGCAGCAGAGCCACCAAA+AGG + chr5_2:46305215-46305234 Msa0772150:CDS 60.0%
GCAGCAGAGCCACCAAAAGG+TGG + chr5_2:46305218-46305237 Msa0772150:CDS 60.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 46304945 46305409 46304945 ID=Msa0772150;Name=Msa0772150
chr5_2 mRNA 46304945 46305409 46304945 ID=Msa0772150-mRNA-1;Parent=Msa0772150;Name=Msa0772150-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|-1|0|1|-1|1|1|0|154
chr5_2 exon 46304945 46305409 46304945 ID=Msa0772150-mRNA-1:exon:13880;Parent=Msa0772150-mRNA-1
chr5_2 CDS 46304945 46305409 46304945 ID=Msa0772150-mRNA-1:cds;Parent=Msa0772150-mRNA-1
Gene Sequence

>Msa0772150

ATGGCAGCATGTACTGTCTACTCAACACAACCTCTAAGAACAAACATCTCAATTCCAACATCATCAAAAACACATGTTGGTTTTAATCAAAAACAGGTAGTGTTCTACACAACAACCAAAAAGAGCAACAACAGAAGAACTAACAGTAACAGCAGAAGATACTTGATAACATGTGGAGCAGGTGACTCACAGACAATTGTGATTGGTCTAGCAGCTGATTCAGGATGTGGAAAAAGTACTTTCATGAGAAGACTCACAAGTGTTTTTGGAGGTGCAGCAGAGCCACCAAAAGGTGGAAATCCTGATTCAAACACACTTATCAGTGACACAACCACTGTGATATGTTTGGATGATTACCATTCTTTGGATAGAACTGGTAGAAAAGAGAAAGGTGTTACTGCACTTGATCCAAGAGCTAATGATTTTGATCTTATGTATGAACAAGTTAAAGCTATTAAAGCTTAG

Protein sequence

>Msa0772150

MAACTVYSTQPLRTNISIPTSSKTHVGFNQKQVVFYTTTKKSNNRRTNSNSRRYLITCGAGDSQTIVIGLAADSGCGKSTFMRRLTSVFGGAAEPPKGGNPDSNTLISDTTTVICLDDYHSLDRTGRKEKGVTALDPRANDFDLMYEQVKAIKA*